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ARID1A.md
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# [ARID1A]
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+ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes a subunit of the SWI/SNF chromatin remodeling complex, which is involved in regulating DNA accessibility. Mutations in ARID1A are implicated in various cancers, including B-cell lymphomas. They are the most abundant in Burkitt lymphoma but also occur in FL and, to a lesser extent, DLBCL.
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+
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## Mutation tier
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|Entity|Tier|Description |
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+<h1 id="arid1a">[ARID1A]</h1>
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+<p>ARID1A (AT-rich interactive domain-containing protein 1A) is a gene that encodes a subunit of the SWI/SNF chromatin remodeling complex, which is involved in regulating DNA accessibility. Mutations in ARID1A are implicated in various cancers, including B-cell lymphomas. They are the most abundant in Burkitt lymphoma but also occur in FL and, to a lesser extent, DLBCL.</p>
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+<h2 id="mutation-tier">Mutation tier</h2>
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+<table>
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+<thead>
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+<tr>
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+<th style="text-align:center">Entity</th>
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+<th style="text-align:center">Tier</th>
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+<th>Description</th>
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+</tr>
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+</thead>
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+<tbody>
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+<tr>
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+<td style="text-align:center">BL</td>
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+<td style="text-align:center">1</td>
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+<td>high-confidence BL gene</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">1</td>
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+<td>high-confidence DLBCL gene</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">FL</td>
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+<td style="text-align:center">1</td>
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+<td>high-confidence FL gene</td>
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+</tr>
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+</tbody>
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+</table>
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+<h2 id="mutation-incidence">Mutation incidence</h2>
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+<table>
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+<thead>
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+<tr>
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+<th style="text-align:center">Entity</th>
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+<th style="text-align:center">source</th>
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+<th style="text-align:center">frequency (%)</th>
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+</tr>
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+</thead>
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+<tbody>
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+<tr>
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+<td style="text-align:center">BL</td>
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+<td style="text-align:center">GAMBL genomes+capture</td>
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+<td style="text-align:center">28.64</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">BL</td>
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+<td style="text-align:center">Thomas cohort</td>
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+<td style="text-align:center">36.00</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">BL</td>
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+<td style="text-align:center">Panea cohort</td>
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+<td style="text-align:center">19.80</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">GAMBL genomes</td>
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+<td style="text-align:center">8.80</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">Schmitz cohort</td>
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+<td style="text-align:center">8.94</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">Reddy cohort</td>
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+<td style="text-align:center">4.40</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">Chapuy cohort</td>
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+<td style="text-align:center">4.27</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">FL</td>
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+<td style="text-align:center">GAMBL genomes</td>
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+<td style="text-align:center">12.47</td>
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+</tr>
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+</tbody>
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+</table>
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+<h2 id="mutation-pattern">Mutation pattern</h2>
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+<table>
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+<thead>
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+<tr>
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+<th style="text-align:center">Entity</th>
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+<th style="text-align:center">aSHM</th>
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+<th style="text-align:center">Significant selection</th>
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+<th style="text-align:center">dN/dS (missense)</th>
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+<th style="text-align:center">dN/dS (nonsense)</th>
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+</tr>
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+</thead>
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+<tbody>
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+<tr>
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+<td style="text-align:center">BL</td>
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+<td style="text-align:center">No</td>
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+<td style="text-align:center">Yes</td>
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+<td style="text-align:center">3.218</td>
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+<td style="text-align:center">130.201</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">DLBCL</td>
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+<td style="text-align:center">No</td>
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+<td style="text-align:center">Yes</td>
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+<td style="text-align:center">2.364</td>
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+<td style="text-align:center">38.689</td>
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+</tr>
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+<tr>
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+<td style="text-align:center">FL</td>
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+<td style="text-align:center">No</td>
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+<td style="text-align:center">Yes</td>
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+<td style="text-align:center">3.794</td>
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+<td style="text-align:center">248.722</td>
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+</tr>
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+</tbody>
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+</table>
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+<blockquote>
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+<p>[!NOTE]
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+First described in BL in 2012 by <a href="https://pubmed.ncbi.nlm.nih.gov/23143597">Love C</a>. First described in DLBCL in 2013 by <a href="https://pubmed.ncbi.nlm.nih.gov/23292937">Zhang J</a></p>
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+</blockquote>
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+<p>View coding variants in ProteinPaint <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein.html">hg19</a> or <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_protein_hg38.html">hg38</a></p>
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+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARID1A_NM_006015.svg" alt="image"></p>
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+<p>View all variants in GenomePaint <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A.html">hg19</a> or <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ARID1A_hg38.html">hg38</a></p>
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+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARID1A.svg" alt="image"></p>
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+
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+</body>
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+</html>
ARID1B.md
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|Entity|Tier|Description |
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|:------:|:----:|-----------------------------------------|
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|DLBCL |2 |relevance in DLBCL not firmly established|
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+|MCL |2 |relevance in MCL not firmly established |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |5.16 |
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-|DLBCL |Schmitz cohort|6.00 |
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+|DLBCL |Schmitz cohort|5.96 |
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|DLBCL |Reddy cohort |3.30 |
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-|DLBCL |Chapuy cohort |2.10 |
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+|DLBCL |Chapuy cohort |2.14 |
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+|MCL |GAMBL genomes |1.90 |
16 18
17 19
## Mutation pattern
18 20
ATM.md
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|Entity|Tier|Description |
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|:------:|:----:|--------------------------|
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|DLBCL |1 |high-confidence DLBCL gene|
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+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |6.88 |
13
-|DLBCL |Schmitz cohort|5.50 |
14
-|DLBCL |Reddy cohort |5.90 |
15
-|DLBCL |Chapuy cohort |4.70 |
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+|DLBCL |GAMBL genomes | 6.88 |
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+|DLBCL |Schmitz cohort| 5.53 |
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+|DLBCL |Reddy cohort | 5.91 |
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+|DLBCL |Chapuy cohort | 4.70 |
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+|MCL |GAMBL genomes |45.02 |
16 18
17 19
## Mutation pattern
18 20
... ...
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> [!NOTE]
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-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
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+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
28 30
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30 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATM_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATM_protein_hg38.html)
ATP11C.md
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+# [ATP11C]
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+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
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+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |4.946 |0 |
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+|DLBCL |No |No |0.894 |0 |
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+|FL |No |No |0.000 |0 |
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+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
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+
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+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP11C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP11C_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/ATP11C_NM_173694.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP11C.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP11C_hg38.html)
32
+
33
+![image](images/proteinpaint/ATP11C.svg)
ATP6AP1.md
... ...
@@ -21,7 +21,6 @@
21 21
22 22
23 23
24
-
25 24
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6AP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ATP6AP1_protein_hg38.html)
26 25
27 26
![image](images/proteinpaint/ATP6AP1_NM_001183.svg)
ATR.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.68 |
13
-|DLBCL |Schmitz cohort|4.90 |
13
+|DLBCL |Schmitz cohort|4.89 |
14 14
|DLBCL |Reddy cohort |2.80 |
15
-|DLBCL |Chapuy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |3.85 |
16 16
17 17
## Mutation pattern
18 18
B2M.md
... ...
@@ -3,11 +3,12 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
3 3
4 4
## Mutation tier
5 5
6
-|Entity|Tier|Description |
7
-|:------:|:----:|--------------------------------------|
8
-|BL |2 |relevance in BL not firmly established|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
6
+|Entity|Tier|Description |
7
+|:------:|:----:|---------------------------------------|
8
+|BL |2 |relevance in BL not firmly established |
9
+|DLBCL |1 |high-confidence DLBCL gene |
10
+|FL |1 |high-confidence FL gene |
11
+|MCL |2 |relevance in MCL not firmly established|
11 12
## Mutation incidence
12 13
13 14
|Entity|source |frequency (%)|
... ...
@@ -16,10 +17,11 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
16 17
|BL |Thomas cohort | 2.50 |
17 18
|BL |Panea cohort | 3.00 |
18 19
|DLBCL |GAMBL genomes |15.11 |
19
-|DLBCL |Schmitz cohort |15.50 |
20
-|DLBCL |Reddy cohort |12.10 |
21
-|DLBCL |Chapuy cohort |12.00 |
20
+|DLBCL |Schmitz cohort |15.53 |
21
+|DLBCL |Reddy cohort |12.11 |
22
+|DLBCL |Chapuy cohort |11.97 |
22 23
|FL |GAMBL genomes | 8.55 |
24
+|MCL |GAMBL genomes | 1.42 |
23 25
24 26
## Mutation pattern
25 27
... ...
@@ -30,7 +32,8 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
30 32
|FL |No |Yes |54.190 |326.834 |
31 33
32 34
33
-
35
+> [!NOTE]
36
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
34 37
35 38
## B2M Hotspots
36 39
BACH2.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
BCL10.md
... ...
@@ -15,9 +15,9 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an
15 15
|BL |Thomas cohort |0.40 |
16 16
|BL |Panea cohort | NA |
17 17
|DLBCL |GAMBL genomes |3.82 |
18
-|DLBCL |Schmitz cohort |7.70 |
18
+|DLBCL |Schmitz cohort |7.66 |
19 19
|DLBCL |Reddy cohort |3.10 |
20
-|DLBCL |Chapuy cohort |6.40 |
20
+|DLBCL |Chapuy cohort |6.41 |
21 21
|FL |GAMBL genomes |2.31 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an
29 29
|FL |No |Yes | 0.000 |223.832 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
33 34
34 35
## BCL10 Hotspots
35 36
BCL11A.md
... ...
@@ -4,8 +4,8 @@ BCL11A (B-cell lymphoma/leukemia 11A) is a transcription factor involved in the
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a |relevance in BL not firmly established, hypermutated|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 9
## Mutation incidence
10 10
11 11
|Entity|source |frequency (%)|
... ...
@@ -14,9 +14,9 @@ BCL11A (B-cell lymphoma/leukemia 11A) is a transcription factor involved in the
14 14
|BL |Thomas cohort |1.70 |
15 15
|BL |Panea cohort |5.90 |
16 16
|DLBCL |GAMBL genomes |4.02 |
17
-|DLBCL |Schmitz cohort |4.50 |
17
+|DLBCL |Schmitz cohort |4.47 |
18 18
|DLBCL |Reddy cohort |1.60 |
19
-|DLBCL |Chapuy cohort |3.40 |
19
+|DLBCL |Chapuy cohort |3.42 |
20 20
21 21
## Mutation pattern
22 22
BCL2.md
... ...
@@ -36,6 +36,8 @@ BCL2 mutations are frequently found in DLBCL, particularly in the germinal cente
36 36
|chr18 |60982728 |60988342|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr18%3A60982728%2D60988342) |active_promoter |
37 37
38 38
39
+> [!NOTE]
40
+> First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
39 41
40 42
## BCL2 Hotspots
41 43
BCL2L11.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
... ...
@@ -28,7 +28,6 @@
28 28
|chr2 |111874854 |111882174|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A111874854%2D111882174)|active_promoter |
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2L11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BCL2L11_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/BCL2L11_NM_138621.svg)
BCL6.md
... ...
@@ -5,9 +5,9 @@ BCL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
5 5
6 6
|Entity|Tier|Description |
7 7
|:------:|:----:|--------------------------------------|
8
-|BL |2-a |relevance in BL not firmly established, hypermutated|
9
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
10
-|FL |1-a |high-confidence FL gene, hypermutated |
8
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10
+|FL |1-a | aSHM target and high-confidence FL gene |
11 11
## Mutation incidence
12 12
13 13
|Entity|source |frequency (%)|
... ...
@@ -16,9 +16,9 @@ BCL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 16
|BL |Thomas cohort | 3.40 |
17 17
|BL |Panea cohort | 7.90 |
18 18
|DLBCL |GAMBL genomes |11.66 |
19
-|DLBCL |Schmitz cohort | 9.80 |
20
-|DLBCL |Reddy cohort | 6.40 |
21
-|DLBCL |Chapuy cohort | 5.10 |
19
+|DLBCL |Schmitz cohort |10.85 |
20
+|DLBCL |Reddy cohort | 6.41 |
21
+|DLBCL |Chapuy cohort | 5.13 |
22 22
|FL |GAMBL genomes | 5.77 |
23 23
24 24
## Mutation pattern
BCL7A.md
... ...
@@ -4,9 +4,9 @@ BCL7A protein interacts with components of the SWI/SNF chromatin remodeling comp
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a |relevance in BL not firmly established, hypermutated|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@ BCL7A protein interacts with components of the SWI/SNF chromatin remodeling comp
15 15
|BL |Thomas cohort | 5.50 |
16 16
|BL |Panea cohort | 5.00 |
17 17
|DLBCL |GAMBL genomes | 7.65 |
18
-|DLBCL |Schmitz cohort |10.60 |
19
-|DLBCL |Reddy cohort | 8.40 |
20
-|DLBCL |Chapuy cohort | 6.40 |
18
+|DLBCL |Schmitz cohort |10.64 |
19
+|DLBCL |Reddy cohort | 8.41 |
20
+|DLBCL |Chapuy cohort | 6.41 |
21 21
|FL |GAMBL genomes |13.86 |
22 22
23 23
## Mutation pattern
BCOR.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|7.70 |
14
+|DLBCL |Schmitz cohort|7.66 |
14 15
|DLBCL |Reddy cohort |2.50 |
15
-|DLBCL |Chapuy cohort |2.60 |
16
+|DLBCL |Chapuy cohort |2.56 |
17
+|MCL |GAMBL genomes |3.79 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -23,6 +25,8 @@
23 25
|FL |No |No |1.743 |0 |
24 26
25 27
28
+> [!NOTE]
29
+> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970)
26 30
27 31
28 32
## BCOR Hotspots
BCR.md
... ...
@@ -4,8 +4,8 @@ BCR (Breakpoint Cluster Region Protein) is one of [a number of genes](https://gi
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2-a |relevance in BL not firmly established, hypermutated|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 9
## Mutation incidence
10 10
11 11
|Entity|source |frequency (%)|
... ...
@@ -14,9 +14,9 @@ BCR (Breakpoint Cluster Region Protein) is one of [a number of genes](https://gi
14 14
|BL |Thomas cohort | 6.40 |
15 15
|BL |Panea cohort |10.90 |
16 16
|DLBCL |GAMBL genomes | 4.97 |
17
-|DLBCL |Schmitz cohort | 6.40 |
17
+|DLBCL |Schmitz cohort | 6.38 |
18 18
|DLBCL |Reddy cohort | 3.90 |
19
-|DLBCL |Chapuy cohort | 4.30 |
19
+|DLBCL |Chapuy cohort | 4.27 |
20 20
21 21
## Mutation pattern
22 22
BIRC3.md
... ...
@@ -0,0 +1,43 @@
1
+# [BIRC3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+|MCL |1-a | aSHM target and high-confidence MCL gene |
9
+## Mutation incidence
10
+
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |1.53 |
14
+|DLBCL |Schmitz cohort|1.91 |
15
+|DLBCL |Reddy cohort |1.30 |
16
+|DLBCL |Chapuy cohort |1.71 |
17
+|MCL |GAMBL genomes |7.11 |
18
+
19
+## Mutation pattern
20
+
21
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23
+|BL |Yes |No |0.000 |0 |
24
+|DLBCL |Yes |No |1.404 |0 |
25
+|FL |Yes |No |2.427 |0 |
26
+
27
+## aSHM regions
28
+
29
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
30
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
31
+|chr11 |102188170 |102190077|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A102188170%2D102190077)|active_promoter |
32
+
33
+> [!NOTE]
34
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
35
+
36
+
37
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC3_protein_hg38.html)
38
+
39
+![image](images/proteinpaint/BIRC3_NM_001165.svg)
40
+
41
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BIRC3_hg38.html)
42
+
43
+![image](images/proteinpaint/BIRC3.svg)
BIRC6.md
... ...
@@ -16,7 +16,7 @@
16 16
|BL |Panea cohort |14.90 |
17 17
|DLBCL |GAMBL genomes | 7.27 |
18 18
|DLBCL |Schmitz cohort |10.00 |
19
-|DLBCL |Reddy cohort | 6.40 |
19
+|DLBCL |Reddy cohort | 6.41 |
20 20
|DLBCL |Chapuy cohort | 4.70 |
21 21
|FL |GAMBL genomes | 3.70 |
22 22
... ...
@@ -29,6 +29,8 @@
29 29
|FL |No |No |2.997 |7.132 |
30 30
31 31
32
+> [!NOTE]
33
+> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
32 34
33 35
34 36
## BIRC6 Hotspots
BLK.md
... ...
@@ -0,0 +1,38 @@
1
+# [BLK]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0.528 |0 |
22
+|DLBCL |Yes |No |1.614 |0 |
23
+|FL |Yes |No |3.528 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr8 |11347723 |11355318|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr8%3A11347723%2D11355318)|strong_enhancer |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BLK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BLK_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/BLK_NM_001715.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BLK.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BLK_hg38.html)
37
+
38
+![image](images/proteinpaint/BLK.svg)
BRAF.md
... ...
@@ -16,7 +16,7 @@
16 16
|DLBCL |GAMBL genomes |2.29 |
17 17
|DLBCL |Schmitz cohort |3.40 |
18 18
|DLBCL |Reddy cohort |2.00 |
19
-|DLBCL |Chapuy cohort |5.60 |
19
+|DLBCL |Chapuy cohort |5.56 |
20 20
21 21
## Mutation pattern
22 22
BRINP3.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |2.68 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |3.30 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
BTBD3.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort |1.80 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
BTG1.md
... ...
@@ -4,9 +4,9 @@ BTG1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@ BTG1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 15
|BL |Thomas cohort | NA |
16 16
|BL |Panea cohort | NA |
17 17
|DLBCL |GAMBL genomes |10.13 |
18
-|DLBCL |Schmitz cohort |14.50 |
19
-|DLBCL |Reddy cohort | 7.50 |
20
-|DLBCL |Chapuy cohort |14.50 |
18
+|DLBCL |Schmitz cohort |14.47 |
19
+|DLBCL |Reddy cohort | 7.51 |
20
+|DLBCL |Chapuy cohort |14.53 |
21 21
|FL |GAMBL genomes | 6.47 |
22 22
23 23
## Mutation pattern
BTG2.md
... ...
@@ -4,9 +4,9 @@ BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@ BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 15
|BL |Thomas cohort | 4.20 |
16 16
|BL |Panea cohort | 9.90 |
17 17
|DLBCL |GAMBL genomes |13.38 |
18
-|DLBCL |Schmitz cohort |17.20 |
19
-|DLBCL |Reddy cohort | 9.20 |
20
-|DLBCL |Chapuy cohort | 6.00 |
18
+|DLBCL |Schmitz cohort |17.23 |
19
+|DLBCL |Reddy cohort | 9.21 |
20
+|DLBCL |Chapuy cohort | 5.98 |
21 21
|FL |GAMBL genomes | 4.39 |
22 22
23 23
## Mutation pattern
BTK.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |6.88 |
14
-|DLBCL |Schmitz cohort|3.60 |
14
+|DLBCL |Schmitz cohort|3.40 |
15 15
|DLBCL |Reddy cohort |3.10 |
16
-|DLBCL |Chapuy cohort |2.10 |
16
+|DLBCL |Chapuy cohort |2.14 |
17 17
|FL |GAMBL genomes |6.93 |
18 18
19 19
## Mutation pattern
... ...
@@ -26,7 +26,6 @@
26 26
27 27
28 28
29
-
30 29
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/BTK_protein_hg38.html)
31 30
32 31
![image](images/proteinpaint/BTK_NM_000061.svg)
C10orf12.md
... ...
@@ -26,6 +26,9 @@
26 26
27 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_protein_hg38.html)
28 28
29
+![image](images/proteinpaint/C10orf12_NM_001346516.svg
30
+images/proteinpaint/C10orf12_NM_032440.svg)
31
+
29 32
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/C10orf12_hg38.html)
30 33
31 34
![image](images/proteinpaint/C10orf12.svg)
C6orf27.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
CADPS2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.63 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|6.38 |
14
+|DLBCL |Reddy cohort |4.30 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CADPS2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CADPS2_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/CADPS2_NM_017954.svg)
CARD11.md
... ...
@@ -7,6 +7,7 @@
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |1 |high-confidence FL gene |
10
+|MCL |1 |high-confidence MCL gene |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,10 +16,11 @@
15 16
|BL |Thomas cohort | 1.70 |
16 17
|BL |Panea cohort |10.90 |
17 18
|DLBCL |GAMBL genomes |11.28 |
18
-|DLBCL |Schmitz cohort |15.30 |
19
-|DLBCL |Reddy cohort | 7.80 |
20
-|DLBCL |Chapuy cohort | 8.10 |
19
+|DLBCL |Schmitz cohort |15.32 |
20
+|DLBCL |Reddy cohort | 7.81 |
21
+|DLBCL |Chapuy cohort | 8.12 |
21 22
|FL |GAMBL genomes |14.78 |
23
+|MCL |GAMBL genomes | 1.42 |
22 24
23 25
## Mutation pattern
24 26
... ...
@@ -29,7 +31,8 @@
29 31
|FL |No |Yes |28.329 |27.096 |
30 32
31 33
32
-
34
+> [!NOTE]
35
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2016 by [Wu C](https://pubmed.ncbi.nlm.nih.gov/27224912)
33 36
34 37
## CARD11 Hotspots
35 38
CARD4.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
CASP8.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.68 |
13
-|DLBCL |Schmitz cohort|1.10 |
13
+|DLBCL |Schmitz cohort|1.06 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
CBLB.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.72 |
13
-|DLBCL |Schmitz cohort|2.80 |
13
+|DLBCL |Schmitz cohort|2.77 |
14 14
|DLBCL |Reddy cohort |1.60 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
CCDC42BPB.md
... ...
@@ -13,11 +13,13 @@
13 13
14 14
## Mutation pattern
15 15
16
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
16
+|
18 17
19 18
20 19
> [!NOTE]
20
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
21
+
22
+
21 23
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCDC42BPB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCDC42BPB_protein_hg38.html)
22 24
23 25
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCDC42BPB.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCDC42BPB_hg38.html)
CCL4.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.19 |
13
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |0.60 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
CCND1.md
... ...
@@ -0,0 +1,33 @@
1
+# [CCND1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|14.69 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.909 |0 |
19
+|DLBCL |No |No |0.000 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/CCND1_NM_053056.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CCND1_hg38.html)
32
+
33
+![image](images/proteinpaint/CCND1.svg)
CCND3.md
... ...
@@ -1,6 +1,6 @@
1 1
# [CCND3]
2 2
3
-CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of the cell cycle. Mutations in CCND3 are implicated in various types of B-cell lymphomas, including Burkitt lymphoma and diffuse large B-cell lymphoma (DLBCL). Somatic mutations in CCND3 often stabilize the Cyclin D3 protein by altering the phosphorylation motif, which is crucial for proteasomal degradation. These mutations are associated with an increase in Cyclin D3 protein stability and oncogenic potential.
3
+CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of the cell cycle. Mutations in CCND3 are implicated in various types of B-cell lymphomas, including Burkitt lymphoma and diffuse large B-cell lymphoma (DLBCL).<sup>1</sup> Somatic mutations in CCND3 often stabilize the Cyclin D3 protein by altering the phosphorylation motif, which is crucial for proteasomal degradation. These mutations are associated with an increase in Cyclin D3 protein stability and oncogenic potential.
4 4
5 5
## Mutation tier
6 6
... ...
@@ -17,7 +17,7 @@ CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of
17 17
|BL |Thomas cohort |28.00 |
18 18
|BL |Panea cohort |17.80 |
19 19
|DLBCL |GAMBL genomes | 7.46 |
20
-|DLBCL |Schmitz cohort | 9.80 |
20
+|DLBCL |Schmitz cohort | 9.79 |
21 21
|DLBCL |Reddy cohort | 3.80 |
22 22
|DLBCL |Chapuy cohort | 4.70 |
23 23
|FL |GAMBL genomes | 3.23 |
... ...
@@ -86,4 +86,4 @@ View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/
86 86
87 87
## References
88 88
89
-*Schmitz, R., et al. (2012). "Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics." Nature, 490(7418), 116-120.*
... ...
\ No newline at end of file
0
+1. *Schmitz, R., et al. (2012). "Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics." Nature, 490(7418), 116-120.*
... ...
\ No newline at end of file
CD22.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |1.15 |
13 13
|DLBCL |Schmitz cohort|1.70 |
14 14
|DLBCL |Reddy cohort |2.80 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
CD274.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |1.30 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
CD36.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.29 |
13
-|DLBCL |Schmitz cohort|4.90 |
13
+|DLBCL |Schmitz cohort|4.89 |
14 14
|DLBCL |Reddy cohort |2.80 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -23,6 +23,8 @@
23 23
|FL |No |No |1.559 |0.000 |
24 24
25 25
26
+> [!NOTE]
27
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
26 28
27 29
28 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD36_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD36_protein_hg38.html)
CD44.md
... ...
@@ -0,0 +1,41 @@
1
+# [CD44]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|1.49 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |2.14 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0.00 |0 |
22
+|DLBCL |Yes |No |2.09 |0 |
23
+|FL |Yes |No |0.00 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr11 |35156769 |35164248|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A35156769%2D35164248)|active_promoter |
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD44_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD44_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/CD44_NM_000610.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD44.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD44_hg38.html)
40
+
41
+![image](images/proteinpaint/CD44.svg)
CD58.md
... ...
@@ -16,7 +16,7 @@
16 16
|DLBCL |GAMBL genomes | 7.84 |
17 17
|DLBCL |Schmitz cohort |10.00 |
18 18
|DLBCL |Reddy cohort | 2.80 |
19
-|DLBCL |Chapuy cohort | 6.80 |
19
+|DLBCL |Chapuy cohort | 6.84 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -27,6 +27,8 @@
27 27
|FL |No |Yes |0.00 |107.458 |
28 28
29 29
30
+> [!NOTE]
31
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
30 32
31 33
32 34
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD58_protein_hg38.html)
CD70.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |0.40 |
16 16
|BL |Panea cohort |3.00 |
17 17
|DLBCL |GAMBL genomes |5.54 |
18
-|DLBCL |Schmitz cohort |9.40 |
19
-|DLBCL |Reddy cohort |6.90 |
20
-|DLBCL |Chapuy cohort |7.70 |
18
+|DLBCL |Schmitz cohort |9.36 |
19
+|DLBCL |Reddy cohort |6.91 |
20
+|DLBCL |Chapuy cohort |7.69 |
21 21
|FL |GAMBL genomes |1.15 |
22 22
23 23
## Mutation pattern
CD74.md
... ...
@@ -0,0 +1,41 @@
1
+# [CD74]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|2.55 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No | 0.000 | 0.000 |
22
+|DLBCL |Yes |No | 7.870 |13.428 |
23
+|FL |Yes |No |15.844 |34.375 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr5 |149790977 |149792349|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A149790977%2D149792349)|active_promoter |
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD74_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD74_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/CD74_NM_001025159.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD74.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD74_hg38.html)
40
+
41
+![image](images/proteinpaint/CD74.svg)
CD79B.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 0.00 |
16 16
|BL |Panea cohort | 4.00 |
17 17
|DLBCL |GAMBL genomes | 9.94 |
18
-|DLBCL |Schmitz cohort |14.90 |
19
-|DLBCL |Reddy cohort | 8.30 |
20
-|DLBCL |Chapuy cohort |15.40 |
18
+|DLBCL |Schmitz cohort |14.89 |
19
+|DLBCL |Reddy cohort | 8.31 |
20
+|DLBCL |Chapuy cohort |15.38 |
21 21
|FL |GAMBL genomes | 2.77 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@
29 29
|FL |No |No |10.310 | 0.000 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33 34
34 35
## CD79B Hotspots
35 36
CD83.md
... ...
@@ -1,12 +1,14 @@
1
+# CD83
2
+
1 3
CD83 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3 5
## Mutation tier
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
9
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
10
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
11
+|FL |1-a | aSHM target and high-confidence FL gene |
10 12
## Mutation incidence
11 13
12 14
|Entity|source |frequency (%)|
... ...
@@ -15,9 +17,9 @@ CD83 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 17
|BL |Thomas cohort |1.70 |
16 18
|BL |Panea cohort | NA |
17 19
|DLBCL |GAMBL genomes |4.40 |
18
-|DLBCL |Schmitz cohort |5.70 |
19
-|DLBCL |Reddy cohort |5.80 |
20
-|DLBCL |Chapuy cohort |7.30 |
20
+|DLBCL |Schmitz cohort |5.74 |
21
+|DLBCL |Reddy cohort |5.81 |
22
+|DLBCL |Chapuy cohort |7.26 |
21 23
|FL |GAMBL genomes |1.85 |
22 24
23 25
## Mutation pattern
... ...
@@ -35,7 +37,7 @@ CD83 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 37
|chr6 |14118026 |14120025|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A14118026%2D14120025)|active_promoter-strong_enhancer|
36 38
37 39
> [!NOTE]
38
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
40
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
39 41
40 42
41 43
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD83_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CD83_protein_hg38.html)
CDC73.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | NA |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |0.57 |
17
-|DLBCL |Schmitz cohort |0.60 |
17
+|DLBCL |Schmitz cohort |0.64 |
18 18
|DLBCL |Reddy cohort |0.70 |
19
-|DLBCL |Chapuy cohort |1.30 |
19
+|DLBCL |Chapuy cohort |1.28 |
20 20
21 21
## Mutation pattern
22 22
CDH8.md
... ...
@@ -0,0 +1,33 @@
1
+# [CDH8]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |2.176 |0.00 |
19
+|DLBCL |No |No |0.926 |3.68 |
20
+|FL |No |No |0.000 |0.00 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH8_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/CDH8_NM_001796.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH8.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH8_hg38.html)
32
+
33
+![image](images/proteinpaint/CDH8.svg)
CDH9.md
... ...
@@ -0,0 +1,36 @@
1
+# [CDH9]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.63 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.920 |0 |
22
+|DLBCL |No |No |2.641 |0 |
23
+|FL |No |No |0.774 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH9_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH9_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/CDH9_NM_016279.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH9.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDH9_hg38.html)
35
+
36
+![image](images/proteinpaint/CDH9.svg)
CDKN2A.md
... ...
@@ -14,24 +14,26 @@
14 14
|BL |Thomas cohort |3.00 |
15 15
|BL |Panea cohort |3.00 |
16 16
|DLBCL |GAMBL genomes |3.25 |
17
-|DLBCL |Schmitz cohort |6.00 |
17
+|DLBCL |Schmitz cohort |4.89 |
18 18
|DLBCL |Reddy cohort |1.00 |
19
-|DLBCL |Chapuy cohort |1.70 |
19
+|DLBCL |Chapuy cohort |1.71 |
20 20
21 21
## Mutation pattern
22 22
23
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23
+|Entity|Isoform |aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24
+|:------:|:---------------:|:----:|:---------------------:|:----------------:|:----------------:|
25
+|BL |CDKN2A.p14arf |No |No |10.947 | 72.708 |
26
+|DLBCL |CDKN2A.p14arf |No |Yes |19.055 |102.121 |
27
+|FL |CDKN2A.p14arf |No |No | 0.000 |117.964 |
28
+|BL |CDKN2A.p16INK4a|No |No | 2.931 |104.823 |
29
+|DLBCL |CDKN2A.p16INK4a|No |Yes | 5.631 |442.466 |
30
+|FL |CDKN2A.p16INK4a|No |No | 0.000 |159.196 |
25 31
26 32
33
+> [!NOTE]
34
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
27 35
28 36
29
- ## CDKN2A Hotspots
30
-
31
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
32
- | :---:| :---: | :--: | :---: |
33
-| chr9 | 21971120 | G>A | R80* |
34
-
35 37
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CDKN2A_protein_hg38.html)
36 38
37 39
![image](images/proteinpaint/CDKN2A_NM_000077.svg)
CHD1.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|3.0 |
14
-|DLBCL |Reddy cohort |2.9 |
15
-|DLBCL |Chapuy cohort |2.1 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
CHD8.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 8.50 |
15 15
|BL |Panea cohort |16.80 |
16 16
|DLBCL |GAMBL genomes | 1.91 |
17
-|DLBCL |Schmitz cohort | 3.60 |
17
+|DLBCL |Schmitz cohort | 3.62 |
18 18
|DLBCL |Reddy cohort | 2.90 |
19
-|DLBCL |Chapuy cohort | 3.00 |
19
+|DLBCL |Chapuy cohort | 2.99 |
20 20
21 21
## Mutation pattern
22 22
CHST2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |0.70 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
CIITA.md
... ...
@@ -1,11 +1,12 @@
1
+# CIITA
2
+
1 3
CIITA is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 4
3 5
## Mutation tier
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-
9
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -13,7 +14,7 @@ CIITA is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
13 14
|DLBCL |GAMBL genomes |2.87 |
14 15
|DLBCL |Schmitz cohort|6.60 |
15 16
|DLBCL |Reddy cohort |4.30 |
16
-|DLBCL |Chapuy cohort |4.30 |
17
+|DLBCL |Chapuy cohort |4.27 |
17 18
18 19
## Mutation pattern
19 20
CNOT2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|0.64 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNOT2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNOT2_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/CNOT2_NM_014515.svg)
CNTNAP5.md
... ...
@@ -0,0 +1,36 @@
1
+# [CNTNAP5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |5.16 |
13
+|DLBCL |Schmitz cohort|8.72 |
14
+|DLBCL |Reddy cohort |4.00 |
15
+|DLBCL |Chapuy cohort |4.27 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.357 |0.000 |
22
+|DLBCL |No |No |1.375 |2.662 |
23
+|FL |No |No |2.893 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNTNAP5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNTNAP5_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/CNTNAP5_NM_130773.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNTNAP5.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CNTNAP5_hg38.html)
35
+
36
+![image](images/proteinpaint/CNTNAP5.svg)
COL11A1.md
... ...
@@ -0,0 +1,33 @@
1
+# [COL11A1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.881 |2.674 |
19
+|DLBCL |No |No |4.904 |2.190 |
20
+|FL |No |No |0.628 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL11A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL11A1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/COL11A1_NM_001854.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL11A1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL11A1_hg38.html)
32
+
33
+![image](images/proteinpaint/COL11A1.svg)
COL16A1.md
... ...
@@ -0,0 +1,33 @@
1
+# [COL16A1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.95 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.703 |0.000 |
19
+|DLBCL |No |No |1.319 |2.178 |
20
+|FL |No |No |0.000 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL16A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL16A1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/COL16A1_NM_001856.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL16A1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/COL16A1_hg38.html)
32
+
33
+![image](images/proteinpaint/COL16A1.svg)
COQ7.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort|0.60 |
13
+|DLBCL |Schmitz cohort|0.64 |
14 14
|DLBCL |Reddy cohort |0.50 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
CPNE8.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CPNE8_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CPNE8_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/CPNE8_NM_153634.svg)
CREBBP.md
... ...
@@ -1,4 +1,4 @@
1
-# [CREBBP]
1
+# CREBBP
2 2
3 3
## Mutation tier
4 4
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 3.00 |
16 16
|BL |Panea cohort |12.90 |
17 17
|DLBCL |GAMBL genomes |25.81 |
18
-|DLBCL |Schmitz cohort |17.90 |
19
-|DLBCL |Reddy cohort |12.10 |
20
-|DLBCL |Chapuy cohort |16.70 |
18
+|DLBCL |Schmitz cohort |17.87 |
19
+|DLBCL |Reddy cohort |12.11 |
20
+|DLBCL |Chapuy cohort |16.67 |
21 21
|FL |GAMBL genomes |65.13 |
22 22
23 23
## Mutation pattern
... ...
@@ -30,7 +30,7 @@
30 30
31 31
32 32
> [!NOTE]
33
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21390126). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
34 34
35 35
36 36
## CREBBP Hotspots
CRIP1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.19 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort |0.70 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
CTNNA2.md
... ...
@@ -0,0 +1,33 @@
1
+# [CTNNA2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.458 |0.000 |
19
+|DLBCL |No |No |1.173 |2.351 |
20
+|FL |No |No |2.047 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTNNA2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTNNA2_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/CTNNA2_NM_004389.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTNNA2.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/CTNNA2_hg38.html)
32
+
33
+![image](images/proteinpaint/CTNNA2.svg)
CXCR4.md
... ...
@@ -1,12 +1,13 @@
1
+# CXCR4
1 2
CXCR4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 3
3 4
## Mutation tier
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|--------------------------------------|
7
-|BL |2-a |relevance in BL not firmly established, hypermutated|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |2-a |relevance in FL not firmly established, hypermutated|
8
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,9 +16,9 @@ CXCR4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 16
|BL |Thomas cohort |2.10 |
16 17
|BL |Panea cohort |2.00 |
17 18
|DLBCL |GAMBL genomes |2.87 |
18
-|DLBCL |Schmitz cohort |2.60 |
19
+|DLBCL |Schmitz cohort |2.55 |
19 20
|DLBCL |Reddy cohort |1.50 |
20
-|DLBCL |Chapuy cohort |2.60 |
21
+|DLBCL |Chapuy cohort |2.56 |
21 22
|FL |GAMBL genomes |3.46 |
22 23
23 24
## Mutation pattern
CXCR5.md
... ...
@@ -1,18 +1,19 @@
1
+# CXCR5
1 2
CXCR5 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 3
3 4
## Mutation tier
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort|4.00 |
14
+|DLBCL |Schmitz cohort|4.04 |
14 15
|DLBCL |Reddy cohort |2.10 |
15
-|DLBCL |Chapuy cohort |1.70 |
16
+|DLBCL |Chapuy cohort |1.71 |
16 17
17 18
## Mutation pattern
18 19
DAZAP1.md
... ...
@@ -1,18 +1,20 @@
1
-# [DAZAP1]
1
+# DAZAP1
2 2
3 3
## Mutation tier
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort|5.30 |
14
+|DLBCL |Schmitz cohort|5.32 |
14 15
|DLBCL |Reddy cohort |1.60 |
15
-|DLBCL |Chapuy cohort |0.40 |
16
+|DLBCL |Chapuy cohort |0.43 |
17
+|MCL |GAMBL genomes |4.27 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -23,6 +25,8 @@
23 25
|FL |No |No |0 |53.351 |
24 26
25 27
28
+> [!NOTE]
29
+> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
26 30
27 31
28 32
## DAZAP1 Hotspots
DCAF6.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.15 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |1.30 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
DDX10.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |0.80 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
DDX3X.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene |
9
-|FL |2 |relevance in FL not firmly established|
7
+|BL |1-a | aSHM target and high-confidence BL gene |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |48.70 |
16 16
|BL |Panea cohort |39.60 |
17 17
|DLBCL |GAMBL genomes | 8.80 |
18
-|DLBCL |Schmitz cohort | 4.70 |
18
+|DLBCL |Schmitz cohort | 4.68 |
19 19
|DLBCL |Reddy cohort | 4.50 |
20
-|DLBCL |Chapuy cohort | 5.60 |
20
+|DLBCL |Chapuy cohort | 5.56 |
21 21
|FL |GAMBL genomes | 2.54 |
22 22
23 23
## Mutation pattern
DHDH.md
... ...
@@ -0,0 +1,33 @@
1
+# [DHDH]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0 |0 |
19
+|DLBCL |No |No |0 |0 |
20
+|FL |No |No |0 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHDH_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHDH_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/DHDH_NM_014475.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHDH.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHDH_hg38.html)
32
+
33
+![image](images/proteinpaint/DHDH.svg)
DHX15.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHX15_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHX15_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/DHX15_NM_001358.svg)
DHX16.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort| NA |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHX16_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DHX16_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/DHX16_NM_003587.svg)
DICER1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |1.10 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
DLC1.md
... ...
@@ -0,0 +1,33 @@
1
+# [DLC1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|1.42 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.482 |2.481 |
19
+|DLBCL |No |No |2.068 |0.000 |
20
+|FL |No |No |1.697 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLC1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLC1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/DLC1_NM_182643.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLC1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DLC1_hg38.html)
32
+
33
+![image](images/proteinpaint/DLC1.svg)
DNAH5.md
... ...
@@ -0,0 +1,36 @@
1
+# [DNAH5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 9.18 |
13
+|DLBCL |Schmitz cohort|14.04 |
14
+|DLBCL |Reddy cohort | 6.91 |
15
+|DLBCL |Chapuy cohort |11.54 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.484 |1.096 |
22
+|DLBCL |No |No |1.720 |0.000 |
23
+|FL |No |No |1.327 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNAH5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNAH5_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/DNAH5_NM_001369.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNAH5.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DNAH5_hg38.html)
35
+
36
+![image](images/proteinpaint/DNAH5.svg)
DNM2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.29 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |1.80 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+
28
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
29
+
27 30
## DNM2 Hotspots
28 31
29 32
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
DNMT3A.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.76 |
13
-|DLBCL |Schmitz cohort|2.10 |
13
+|DLBCL |Schmitz cohort|2.13 |
14 14
|DLBCL |Reddy cohort |1.40 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
DOCK1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 3.82 |
13
-|DLBCL |Schmitz cohort|10.20 |
13
+|DLBCL |Schmitz cohort|10.21 |
14 14
|DLBCL |Reddy cohort | 4.90 |
15
-|DLBCL |Chapuy cohort | 6.00 |
15
+|DLBCL |Chapuy cohort | 5.98 |
16 16
17 17
## Mutation pattern
18 18
DSG4.md
... ...
@@ -0,0 +1,36 @@
1
+# [DSG4]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.06 |
13
+|DLBCL |Schmitz cohort|5.32 |
14
+|DLBCL |Reddy cohort |2.40 |
15
+|DLBCL |Chapuy cohort |5.13 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.456 |4.388 |
22
+|DLBCL |No |No |1.561 |3.392 |
23
+|FL |No |No |1.374 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DSG4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DSG4_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/DSG4_NM_001134453.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DSG4.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/DSG4_hg38.html)
35
+
36
+![image](images/proteinpaint/DSG4.svg)
DTX1.md
... ...
@@ -1,12 +1,13 @@
1
+# DTX1
1 2
DTX1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 3
3 4
## Mutation tier
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
8
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10
+|FL |1-a | aSHM target and high-confidence FL gene |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,9 +16,9 @@ DTX1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 16
|BL |Thomas cohort | 5.90 |
16 17
|BL |Panea cohort | 8.90 |
17 18
|DLBCL |GAMBL genomes |10.71 |
18
-|DLBCL |Schmitz cohort |13.60 |
19
-|DLBCL |Reddy cohort | 5.90 |
20
-|DLBCL |Chapuy cohort |11.50 |
19
+|DLBCL |Schmitz cohort |13.62 |
20
+|DLBCL |Reddy cohort | 5.91 |
21
+|DLBCL |Chapuy cohort |11.54 |
21 22
|FL |GAMBL genomes | 5.54 |
22 23
23 24
## Mutation pattern
DUSP2.md
... ...
@@ -1,19 +1,20 @@
1
+# DUSP2
1 2
DUSP2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
2 3
3 4
## Mutation tier
4 5
5 6
|Entity|Tier|Description |
6 7
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |2-a |relevance in FL not firmly established, hypermutated|
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
13 14
|DLBCL |GAMBL genomes |10.13 |
14
-|DLBCL |Schmitz cohort|12.60 |
15
-|DLBCL |Reddy cohort | 9.70 |
16
-|DLBCL |Chapuy cohort | 4.30 |
15
+|DLBCL |Schmitz cohort|12.55 |
16
+|DLBCL |Reddy cohort | 9.71 |
17
+|DLBCL |Chapuy cohort | 4.27 |
17 18
|FL |GAMBL genomes | 2.31 |
18 19
19 20
## Mutation pattern
EBF1.md
... ...
@@ -4,9 +4,9 @@ EBF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9
-|FL |1-a |high-confidence FL gene, hypermutated |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@ EBF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 15
|BL |Thomas cohort | 1.30 |
16 16
|BL |Panea cohort | 5.90 |
17 17
|DLBCL |GAMBL genomes | 8.99 |
18
-|DLBCL |Schmitz cohort |10.90 |
19
-|DLBCL |Reddy cohort | 8.80 |
20
-|DLBCL |Chapuy cohort |12.80 |
18
+|DLBCL |Schmitz cohort |10.85 |
19
+|DLBCL |Reddy cohort | 8.81 |
20
+|DLBCL |Chapuy cohort |12.82 |
21 21
|FL |GAMBL genomes | 8.55 |
22 22
23 23
## Mutation pattern
EEF1A1.md
... ...
@@ -11,7 +11,7 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes | 4.78 |
14
-|DLBCL |Schmitz cohort| 3.00 |
14
+|DLBCL |Schmitz cohort| 2.98 |
15 15
|DLBCL |Reddy cohort | 2.50 |
16 16
|DLBCL |Chapuy cohort | 4.70 |
17 17
|FL |GAMBL genomes |11.32 |
EHD1.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EHD1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EHD1_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/EHD1_NM_006795.svg)
EIF2AK3.md
... ...
@@ -0,0 +1,33 @@
1
+# [EIF2AK3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.44 |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |2.99 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.775 |12.366 |
22
+|DLBCL |No |No |1.884 |18.647 |
23
+|FL |No |No |9.265 |22.931 |
24
+
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK3_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/EIF2AK3_NM_004836.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK3_hg38.html)
32
+
33
+![image](images/proteinpaint/EIF2AK3.svg)
EIF2AK4.md
... ...
@@ -0,0 +1,33 @@
1
+# [EIF2AK4]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.923 |0 |
19
+|DLBCL |No |No |2.632 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK4_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/EIF2AK4_NM_001013703.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK4.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EIF2AK4_hg38.html)
32
+
33
+![image](images/proteinpaint/EIF2AK4.svg)
EIF2C4.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
EP300.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 4.20 |
16 16
|BL |Panea cohort | 7.90 |
17 17
|DLBCL |GAMBL genomes |11.85 |
18
-|DLBCL |Schmitz cohort | 9.80 |
19
-|DLBCL |Reddy cohort | 7.10 |
20
-|DLBCL |Chapuy cohort | 8.10 |
18
+|DLBCL |Schmitz cohort | 9.79 |
19
+|DLBCL |Reddy cohort | 7.11 |
20
+|DLBCL |Chapuy cohort | 8.12 |
21 21
|FL |GAMBL genomes |12.47 |
22 22
23 23
## Mutation pattern
... ...
@@ -30,6 +30,8 @@
30 30
31 31
32 32
33
+> [!NOTE]
34
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21390126). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33 35
34 36
## EP300 Hotspots
35 37
ESX1.md
... ...
@@ -0,0 +1,33 @@
1
+# [ESX1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.967 |0 |
19
+|DLBCL |No |No |0.000 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ESX1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ESX1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/ESX1_NM_153448.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ESX1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ESX1_hg38.html)
32
+
33
+![image](images/proteinpaint/ESX1.svg)
ETS1.md
... ...
@@ -4,9 +4,8 @@ ETS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|BL |2 |relevance in BL not firmly established|
9
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
... ...
@@ -15,9 +14,9 @@ ETS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 14
|BL |Thomas cohort | 7.60 |
16 15
|BL |Panea cohort |11.90 |
17 16
|DLBCL |GAMBL genomes | 4.59 |
18
-|DLBCL |Schmitz cohort | 7.90 |
17
+|DLBCL |Schmitz cohort | 7.87 |
19 18
|DLBCL |Reddy cohort | 4.40 |
20
-|DLBCL |Chapuy cohort | 5.60 |
19
+|DLBCL |Chapuy cohort | 5.56 |
21 20
22 21
## Mutation pattern
23 22
ETV6.md
... ...
@@ -4,15 +4,15 @@ ETV6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 4.97 |
13
-|DLBCL |Schmitz cohort|10.40 |
14
-|DLBCL |Reddy cohort | 5.80 |
15
-|DLBCL |Chapuy cohort |10.30 |
13
+|DLBCL |Schmitz cohort|10.43 |
14
+|DLBCL |Reddy cohort | 5.81 |
15
+|DLBCL |Chapuy cohort |10.26 |
16 16
17 17
## Mutation pattern
18 18
EWSR1.md
... ...
@@ -0,0 +1,33 @@
1
+# [EWSR1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|3.32 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.000 |9.89 |
19
+|DLBCL |No |No |0.000 |0.00 |
20
+|FL |No |No |3.052 |0.00 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EWSR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EWSR1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/EWSR1_NM_013986.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EWSR1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EWSR1_hg38.html)
32
+
33
+![image](images/proteinpaint/EWSR1.svg)
EZH2.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 1.30 |
16 16
|BL |Panea cohort |10.90 |
17 17
|DLBCL |GAMBL genomes |13.77 |
18
-|DLBCL |Schmitz cohort | 9.10 |
19
-|DLBCL |Reddy cohort | 8.90 |
20
-|DLBCL |Chapuy cohort | 5.60 |
18
+|DLBCL |Schmitz cohort | 9.15 |
19
+|DLBCL |Reddy cohort | 8.91 |
20
+|DLBCL |Chapuy cohort | 5.56 |
21 21
|FL |GAMBL genomes |24.94 |
22 22
23 23
## Mutation pattern
EZR.md
... ...
@@ -0,0 +1,38 @@
1
+# [EZR]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|2.13 |
14
+|DLBCL |Reddy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |1.425 |16.138 |
22
+|DLBCL |Yes |No |2.869 |14.423 |
23
+|FL |Yes |No |3.576 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr6 |159237903 |159240216|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A159237903%2D159240216)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZR_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/EZR_NM_003379.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZR.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/EZR_hg38.html)
37
+
38
+![image](images/proteinpaint/EZR.svg)
FAM102A.md
... ...
@@ -0,0 +1,38 @@
1
+# [FAM102A]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|3.83 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |2.14 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No | 3.842 |13.756 |
22
+|DLBCL |Yes |No | 3.475 | 8.506 |
23
+|FL |Yes |No |10.512 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr9 |130740362 |130744800|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A130740362%2D130744800)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM102A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM102A_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/FAM102A_NM_001035254.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM102A.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAM102A_hg38.html)
37
+
38
+![image](images/proteinpaint/FAM102A.svg)
FAM38B.md
... ...
@@ -0,0 +1,23 @@
1
+# [FAM38B]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+
22
+> [!NOTE]
23
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
FANK1.md
... ...
@@ -0,0 +1,38 @@
1
+# [FANK1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|0.64 |
14
+|DLBCL |Reddy cohort |1.00 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |1.665 |0 |
22
+|DLBCL |Yes |No |1.593 |0 |
23
+|FL |Yes |No |2.933 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:--------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr10 |127578912 |127591133|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr10%3A127578912%2D127591133)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FANK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FANK1_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/FANK1_NM_145235.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FANK1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FANK1_hg38.html)
37
+
38
+![image](images/proteinpaint/FANK1.svg)
FAS.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 1.70 |
16 16
|BL |Panea cohort | 4.00 |
17 17
|DLBCL |GAMBL genomes | 9.18 |
18
-|DLBCL |Schmitz cohort |10.90 |
18
+|DLBCL |Schmitz cohort |10.85 |
19 19
|DLBCL |Reddy cohort | 4.70 |
20
-|DLBCL |Chapuy cohort | 9.00 |
20
+|DLBCL |Chapuy cohort | 8.97 |
21 21
|FL |GAMBL genomes | 5.08 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,6 +29,8 @@
29 29
|FL |No |Yes | 0.000 |176.866 |
30 30
31 31
32
+> [!NOTE]
33
+> First described in DLBCL in 2007 by [Scholl V](https://pubmed.ncbi.nlm.nih.gov/17487740). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
32 34
33 35
34 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAS_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAS_protein_hg38.html)
FAT4.md
... ...
@@ -0,0 +1,38 @@
1
+# [FAT4]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|MCL |2 |relevance in MCL not firmly established |
9
+## Mutation incidence
10
+
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |12.81 |
14
+|DLBCL |Schmitz cohort|20.43 |
15
+|DLBCL |Reddy cohort |14.91 |
16
+|DLBCL |Chapuy cohort |16.67 |
17
+|MCL |GAMBL genomes | 3.79 |
18
+
19
+## Mutation pattern
20
+
21
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
23
+|BL |No |No |0.000 |0.000 |
24
+|DLBCL |No |No |1.682 |4.189 |
25
+|FL |No |No |0.000 |0.000 |
26
+
27
+
28
+> [!NOTE]
29
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAT4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAT4_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/FAT4_NM_024582.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAT4.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FAT4_hg38.html)
37
+
38
+![image](images/proteinpaint/FAT4.svg)
FBXO11.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |21.60 |
15 15
|BL |Panea cohort |15.80 |
16 16
|DLBCL |GAMBL genomes | 3.82 |
17
-|DLBCL |Schmitz cohort | 2.10 |
17
+|DLBCL |Schmitz cohort | 2.13 |
18 18
|DLBCL |Reddy cohort | 2.10 |
19
-|DLBCL |Chapuy cohort | 2.60 |
19
+|DLBCL |Chapuy cohort | 2.56 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -28,7 +28,7 @@
28 28
29 29
30 30
> [!NOTE]
31
-> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743)
31
+> First described in BL in 2023 by [Thomas N](https://pubmed.ncbi.nlm.nih.gov/36201743). First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
32 32
33 33
34 34
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXO11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXO11_protein_hg38.html)
FBXW7.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|3.0 |
14
-|DLBCL |Reddy cohort |1.3 |
15
-|DLBCL |Chapuy cohort |1.7 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,13 +24,6 @@
24 24
25 25
26 26
27
-
28
- ## FBXW7 Hotspots
29
-
30
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
31
- | :---:| :---: | :--: | :---: |
32
-| chr4 | 153250907 | T>G | T385P |
33
-
34 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXW7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FBXW7_protein_hg38.html)
35 28
36 29
![image](images/proteinpaint/FBXW7_NM_033632.svg)
FCRL3.md
... ...
@@ -0,0 +1,38 @@
1
+# [FCRL3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|3.40 |
14
+|DLBCL |Reddy cohort |2.70 |
15
+|DLBCL |Chapuy cohort |3.42 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |3.558 |0.000 |
22
+|DLBCL |Yes |No |2.408 |7.608 |
23
+|FL |Yes |No |0.000 |0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr2 |157669490 |157671299|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A157669490%2D157671299)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FCRL3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FCRL3_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/FCRL3_NM_052939.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FCRL3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FCRL3_hg38.html)
37
+
38
+![image](images/proteinpaint/FCRL3.svg)
FIP1L1.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FIP1L1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FIP1L1_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/FIP1L1_NM_030917.svg)
FNBP1.md
... ...
@@ -0,0 +1,38 @@
1
+# [FNBP1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |2.768 |0 |
22
+|DLBCL |Yes |No |0.000 |0 |
23
+|FL |Yes |No |0.000 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr9 |132800698 |132805491|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A132800698%2D132805491)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNBP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNBP1_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/FNBP1_NM_015033.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNBP1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNBP1_hg38.html)
37
+
38
+![image](images/proteinpaint/FNBP1.svg)
FNDC1.md
... ...
@@ -0,0 +1,36 @@
1
+# [FNDC1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|5.32 |
14
+|DLBCL |Reddy cohort |2.80 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.313 |4.152 |
22
+|DLBCL |No |No |0.315 |0.000 |
23
+|FL |No |No |0.000 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNDC1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNDC1_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/FNDC1_NM_032532.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNDC1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FNDC1_hg38.html)
35
+
36
+![image](images/proteinpaint/FNDC1.svg)
FOXC1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|4.50 |
13
+|DLBCL |Schmitz cohort|4.47 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXC1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FOXC1_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/FOXC1_NM_001453.svg)
FOXO1.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |28.00 |
16 16
|BL |Panea cohort |21.80 |
17 17
|DLBCL |GAMBL genomes |10.13 |
18
-|DLBCL |Schmitz cohort | 7.20 |
18
+|DLBCL |Schmitz cohort | 7.23 |
19 19
|DLBCL |Reddy cohort | 2.40 |
20
-|DLBCL |Chapuy cohort | 2.10 |
20
+|DLBCL |Chapuy cohort | 2.14 |
21 21
|FL |GAMBL genomes |12.93 |
22 22
23 23
## Mutation pattern
FOXP1.md
... ...
@@ -4,15 +4,15 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|3.62 |
14 14
|DLBCL |Reddy cohort |2.10 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
FUBP1.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|1.5 |
14
-|DLBCL |Reddy cohort |1.5 |
15
-|DLBCL |Chapuy cohort |0.9 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|1.49 |
14
+|DLBCL |Reddy cohort |1.50 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
FUT5.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort |0.30 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
FZR1.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FZR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/FZR1_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/FZR1_NM_001136198.svg)
GABRA2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.15 |
13
-|DLBCL |Schmitz cohort|2.60 |
13
+|DLBCL |Schmitz cohort|2.55 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
GAK.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|3.62 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GAK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GAK_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/GAK_NM_005255.svg)
GGTLA4.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
GNA13.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |21.60 |
16 16
|BL |Panea cohort |20.80 |
17 17
|DLBCL |GAMBL genomes |11.66 |
18
-|DLBCL |Schmitz cohort | 8.50 |
19
-|DLBCL |Reddy cohort |11.90 |
20
-|DLBCL |Chapuy cohort |10.30 |
18
+|DLBCL |Schmitz cohort | 8.51 |
19
+|DLBCL |Reddy cohort |11.91 |
20
+|DLBCL |Chapuy cohort |10.26 |
21 21
|FL |GAMBL genomes |10.16 |
22 22
23 23
## Mutation pattern
GNAI2.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 9.70 |
16 16
|BL |Panea cohort | 8.90 |
17 17
|DLBCL |GAMBL genomes | 5.35 |
18
-|DLBCL |Schmitz cohort | 6.40 |
18
+|DLBCL |Schmitz cohort | 6.38 |
19 19
|DLBCL |Reddy cohort | 1.90 |
20
-|DLBCL |Chapuy cohort | 3.80 |
20
+|DLBCL |Chapuy cohort | 3.85 |
21 21
|FL |GAMBL genomes | 4.16 |
22 22
23 23
## Mutation pattern
... ...
@@ -30,7 +30,7 @@
30 30
31 31
32 32
> [!NOTE]
33
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
33
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
34 34
35 35
36 36
## GNAI2 Hotspots
GNAS.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.29 |
13
-|DLBCL |Schmitz cohort|3.20 |
13
+|DLBCL |Schmitz cohort|3.19 |
14 14
|DLBCL |Reddy cohort |1.90 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
GOLGA5.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|0.90 |
13
+|DLBCL |Schmitz cohort|0.85 |
14 14
|DLBCL |Reddy cohort |1.90 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
GPC5.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort |2.20 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
GRB2.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |0.40 |
15 15
|BL |Panea cohort |1.00 |
16 16
|DLBCL |GAMBL genomes |3.25 |
17
-|DLBCL |Schmitz cohort |2.80 |
17
+|DLBCL |Schmitz cohort |2.77 |
18 18
|DLBCL |Reddy cohort |1.50 |
19
-|DLBCL |Chapuy cohort |3.00 |
19
+|DLBCL |Chapuy cohort |2.99 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -28,7 +28,7 @@
28 28
29 29
30 30
> [!NOTE]
31
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
31
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
32 32
33 33
34 34
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRB2_protein_hg38.html)
GRHPR.md
... ...
@@ -4,13 +4,13 @@ GRHPR is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.68 |
13
-|DLBCL |Schmitz cohort|4.50 |
13
+|DLBCL |Schmitz cohort|4.47 |
14 14
|DLBCL |Reddy cohort |3.60 |
15 15
|DLBCL |Chapuy cohort |4.70 |
16 16
... ...
@@ -28,6 +28,8 @@ GRHPR is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
28 28
|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29 29
|chr9 |37423010 |37425279|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37423010%2D37425279)|active_promoter |
30 30
31
+> [!NOTE]
32
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
31 33
32 34
33 35
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRHPR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRHPR_protein_hg38.html)
GRIN2A.md
... ...
@@ -0,0 +1,33 @@
1
+# [GRIN2A]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.437 |4.209 |
19
+|DLBCL |No |No |0.961 |0.000 |
20
+|FL |No |No |0.618 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIN2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIN2A_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/GRIN2A_NM_001134407.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIN2A.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/GRIN2A_hg38.html)
32
+
33
+![image](images/proteinpaint/GRIN2A.svg)
GSG2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|4.00 |
13
+|DLBCL |Schmitz cohort|4.04 |
14 14
|DLBCL |Reddy cohort |1.50 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
HDAC7.md
... ...
@@ -0,0 +1,36 @@
1
+# [HDAC7]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|4.68 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.610 |0 |
22
+|DLBCL |No |No |1.696 |0 |
23
+|FL |No |No |6.314 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HDAC7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HDAC7_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/HDAC7_NM_015401.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HDAC7.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HDAC7_hg38.html)
35
+
36
+![image](images/proteinpaint/HDAC7.svg)
HEPH.md
... ...
@@ -0,0 +1,33 @@
1
+# [HEPH]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.95 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.000 |0 |
19
+|DLBCL |No |No |0.876 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HEPH_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HEPH_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/HEPH_NM_138737.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HEPH.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HEPH_hg38.html)
32
+
33
+![image](images/proteinpaint/HEPH.svg)
HIST1H1B.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |5.50 |
16 16
|BL |Panea cohort |4.00 |
17 17
|DLBCL |GAMBL genomes |8.41 |
18
-|DLBCL |Schmitz cohort |8.50 |
19
-|DLBCL |Reddy cohort |7.30 |
20
-|DLBCL |Chapuy cohort |9.80 |
18
+|DLBCL |Schmitz cohort |8.51 |
19
+|DLBCL |Reddy cohort |7.31 |
20
+|DLBCL |Chapuy cohort |9.83 |
21 21
|FL |GAMBL genomes |5.54 |
22 22
23 23
## Mutation pattern
... ...
@@ -30,7 +30,6 @@
30 30
31 31
32 32
33
-
34 33
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1B_protein_hg38.html)
35 34
36 35
![image](images/proteinpaint/HIST1H1B_NM_005322.svg)
HIST1H1C.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 3.80 |
16 16
|BL |Panea cohort | 9.90 |
17 17
|DLBCL |GAMBL genomes | 9.94 |
18
-|DLBCL |Schmitz cohort | 9.80 |
19
-|DLBCL |Reddy cohort | 9.40 |
20
-|DLBCL |Chapuy cohort |12.40 |
18
+|DLBCL |Schmitz cohort | 9.79 |
19
+|DLBCL |Reddy cohort | 9.41 |
20
+|DLBCL |Chapuy cohort |12.39 |
21 21
|FL |GAMBL genomes | 5.08 |
22 22
23 23
## Mutation pattern
HIST1H1D.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |4.70 |
16 16
|BL |Panea cohort |4.00 |
17 17
|DLBCL |GAMBL genomes |6.12 |
18
-|DLBCL |Schmitz cohort |5.70 |
19
-|DLBCL |Reddy cohort |6.10 |
20
-|DLBCL |Chapuy cohort |7.70 |
18
+|DLBCL |Schmitz cohort |5.74 |
19
+|DLBCL |Reddy cohort |6.11 |
20
+|DLBCL |Chapuy cohort |7.69 |
21 21
|FL |GAMBL genomes |3.23 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,6 +29,8 @@
29 29
|FL |No |No |0.857 |0 |
30 30
31 31
32
+> [!NOTE]
33
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
32 34
33 35
34 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H1D_protein_hg38.html)
HIST1H1E.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 7.60 |
16 16
|BL |Panea cohort |19.80 |
17 17
|DLBCL |GAMBL genomes |18.55 |
18
-|DLBCL |Schmitz cohort |17.90 |
19
-|DLBCL |Reddy cohort |14.50 |
20
-|DLBCL |Chapuy cohort |11.50 |
18
+|DLBCL |Schmitz cohort |17.87 |
19
+|DLBCL |Reddy cohort |14.51 |
20
+|DLBCL |Chapuy cohort |11.54 |
21 21
|FL |GAMBL genomes |12.93 |
22 22
23 23
## Mutation pattern
HIST1H2AC.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |5.16 |
14
-|DLBCL |Schmitz cohort|6.20 |
14
+|DLBCL |Schmitz cohort|6.17 |
15 15
|DLBCL |Reddy cohort |3.40 |
16
-|DLBCL |Chapuy cohort |6.40 |
16
+|DLBCL |Chapuy cohort |6.41 |
17 17
|FL |GAMBL genomes |2.31 |
18 18
19 19
## Mutation pattern
... ...
@@ -26,6 +26,8 @@
26 26
27 27
28 28
29
+> [!NOTE]
30
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
29 31
30 32
## HIST1H2AC Hotspots
31 33
HIST1H2AG.md
... ...
@@ -2,10 +2,11 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|FL |1 |high-confidence FL gene |
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9
+|FL |1 |high-confidence FL gene |
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -13,6 +14,10 @@
13 14
|BL |GAMBL genomes+capture|1.39 |
14 15
|BL |Thomas cohort |2.50 |
15 16
|BL |Panea cohort |1.00 |
17
+|DLBCL |GAMBL genomes |3.44 |
18
+|DLBCL |Schmitz cohort |3.62 |
19
+|DLBCL |Reddy cohort |1.90 |
20
+|DLBCL |Chapuy cohort |2.99 |
16 21
|FL |GAMBL genomes |2.08 |
17 22
18 23
## Mutation pattern
... ...
@@ -25,8 +30,7 @@
25 30
26 31
27 32
> [!NOTE]
28
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468)
29
-
33
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
30 34
31 35
## HIST1H2AG Hotspots
32 36
HIST1H2AM.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |1.70 |
16 16
|BL |Panea cohort |3.00 |
17 17
|DLBCL |GAMBL genomes |5.93 |
18
-|DLBCL |Schmitz cohort |5.70 |
18
+|DLBCL |Schmitz cohort |5.74 |
19 19
|DLBCL |Reddy cohort |4.80 |
20
-|DLBCL |Chapuy cohort |6.00 |
20
+|DLBCL |Chapuy cohort |5.98 |
21 21
|FL |GAMBL genomes |3.70 |
22 22
23 23
## Mutation pattern
HIST1H2BC.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |4.59 |
14
-|DLBCL |Schmitz cohort|5.50 |
14
+|DLBCL |Schmitz cohort|5.53 |
15 15
|DLBCL |Reddy cohort |4.30 |
16
-|DLBCL |Chapuy cohort |5.60 |
16
+|DLBCL |Chapuy cohort |5.56 |
17 17
|FL |GAMBL genomes |3.46 |
18 18
19 19
## Mutation pattern
HIST1H2BD.md
... ...
@@ -21,7 +21,6 @@
21 21
22 22
23 23
24
-
25 24
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD_protein_hg38.html)
26 25
27 26
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BD_hg38.html)
HIST1H2BG.md
... ...
@@ -21,7 +21,6 @@
21 21
22 22
23 23
24
-
25 24
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG_protein_hg38.html)
26 25
27 26
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H2BG_hg38.html)
HIST1H2BK.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |4.70 |
15 15
|BL |Panea cohort |7.90 |
16 16
|DLBCL |GAMBL genomes |4.59 |
17
-|DLBCL |Schmitz cohort |4.90 |
17
+|DLBCL |Schmitz cohort |5.32 |
18 18
|DLBCL |Reddy cohort |4.20 |
19
-|DLBCL |Chapuy cohort |5.60 |
19
+|DLBCL |Chapuy cohort |5.56 |
20 20
21 21
## Mutation pattern
22 22
HIST1H3B.md
... ...
@@ -13,7 +13,7 @@
13 13
|DLBCL |GAMBL genomes |2.10 |
14 14
|DLBCL |Schmitz cohort|1.70 |
15 15
|DLBCL |Reddy cohort |2.00 |
16
-|DLBCL |Chapuy cohort |2.10 |
16
+|DLBCL |Chapuy cohort |2.14 |
17 17
|FL |GAMBL genomes |1.62 |
18 18
19 19
## Mutation pattern
HIST1H3G.md
... ...
@@ -21,7 +21,6 @@
21 21
22 22
23 23
24
-
25 24
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3G_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST1H3G_protein_hg38.html)
26 25
27 26
![image](images/proteinpaint/HIST1H3G_NM_003534.svg)
HIST2H2BE.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.49 |
13
-|DLBCL |Schmitz cohort|3.20 |
13
+|DLBCL |Schmitz cohort|3.19 |
14 14
|DLBCL |Reddy cohort |2.60 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE_protein_hg38.html)
29 28
30 29
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HIST2H2BE_hg38.html)
HLA-A.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 1.30 |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes | 7.46 |
17
-|DLBCL |Schmitz cohort |11.10 |
17
+|DLBCL |Schmitz cohort |11.06 |
18 18
|DLBCL |Reddy cohort | 0.20 |
19
-|DLBCL |Chapuy cohort | 9.00 |
19
+|DLBCL |Chapuy cohort | 8.97 |
20 20
21 21
## Mutation pattern
22 22
HLA-B.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 3.80 |
16 16
|BL |Panea cohort | 5.00 |
17 17
|DLBCL |GAMBL genomes | 9.18 |
18
-|DLBCL |Schmitz cohort |16.40 |
18
+|DLBCL |Schmitz cohort |16.38 |
19 19
|DLBCL |Reddy cohort | 1.20 |
20
-|DLBCL |Chapuy cohort |10.70 |
20
+|DLBCL |Chapuy cohort |10.68 |
21 21
|FL |GAMBL genomes | 3.46 |
22 22
23 23
## Mutation pattern
HLA-C.md
... ...
@@ -10,7 +10,7 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.63 |
13
-|DLBCL |Schmitz cohort|5.50 |
13
+|DLBCL |Schmitz cohort|5.53 |
14 14
|DLBCL |Reddy cohort | NA |
15 15
|DLBCL |Chapuy cohort |4.70 |
16 16
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-C_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/HLA-C_NM_002117.svg)
HLA-DMA.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMA_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/HLA-DMA_NM_006120.svg)
HLA-DMB.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |0.00 |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |3.82 |
17
-|DLBCL |Schmitz cohort |5.10 |
17
+|DLBCL |Schmitz cohort |5.11 |
18 18
|DLBCL |Reddy cohort | NA |
19
-|DLBCL |Chapuy cohort |1.70 |
19
+|DLBCL |Chapuy cohort |1.71 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -28,7 +28,6 @@
28 28
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HLA-DMB_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/HLA-DMB_NM_002118.svg)
HLA-DQA1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|0.64 |
14
+|DLBCL |Reddy cohort |0.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,4 +24,4 @@
24 24
25 25
26 26
> [!NOTE]
27
-> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
... ...
\ No newline at end of file
0
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
HNF1B.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.19 |
13
-|DLBCL |Schmitz cohort|2.60 |
13
+|DLBCL |Schmitz cohort|2.55 |
14 14
|DLBCL |Reddy cohort |0.30 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,7 @@
24 24
25 25
26 26
> [!NOTE]
27
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
27
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
28 28
29 29
30 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNF1B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNF1B_protein_hg38.html)
HNRNPD.md
... ...
@@ -10,11 +10,11 @@
10 10
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13
-|DLBCL |GAMBL genomes |2.1 |
14
-|DLBCL |Schmitz cohort|2.1 |
15
-|DLBCL |Reddy cohort |1.8 |
16
-|DLBCL |Chapuy cohort |0.9 |
17
-|FL |GAMBL genomes | NA |
13
+|DLBCL |GAMBL genomes |2.10 |
14
+|DLBCL |Schmitz cohort|2.13 |
15
+|DLBCL |Reddy cohort |1.80 |
16
+|DLBCL |Chapuy cohort |0.85 |
17
+|FL |GAMBL genomes | NA |
18 18
19 19
## Mutation pattern
20 20
... ...
@@ -26,7 +26,6 @@
26 26
27 27
28 28
29
-
30 29
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/HNRNPD_protein_hg38.html)
31 30
32 31
![image](images/proteinpaint/HNRNPD_NM_031370.svg)
HNRNPH1.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|3.2 |
14
-|DLBCL |Reddy cohort |1.4 |
15
-|DLBCL |Chapuy cohort |3.4 |
13
+|DLBCL |GAMBL genomes |2.10 |
14
+|DLBCL |Schmitz cohort|3.19 |
15
+|DLBCL |Reddy cohort |1.40 |
16
+|DLBCL |Chapuy cohort |3.42 |
17
+|MCL |GAMBL genomes |3.79 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -23,7 +25,8 @@
23 25
|FL |No |No |0.000 | 0.000 |
24 26
25 27
26
-
28
+> [!NOTE]
29
+> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
27 30
28 31
## HNRNPH1 Hotspots
29 32
HNRNPU.md
... ...
@@ -4,8 +4,8 @@ HNRNPU is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|BL |1-a |high-confidence BL gene, hypermutated |
8
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
7
+|BL |1-a | aSHM target and high-confidence BL gene |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 9
## Mutation incidence
10 10
11 11
|Entity|source |frequency (%)|
... ...
@@ -16,7 +16,7 @@ HNRNPU is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
16 16
|DLBCL |GAMBL genomes |2.49 |
17 17
|DLBCL |Schmitz cohort |3.40 |
18 18
|DLBCL |Reddy cohort |2.40 |
19
-|DLBCL |Chapuy cohort |3.40 |
19
+|DLBCL |Chapuy cohort |3.42 |
20 20
21 21
## Mutation pattern
22 22
HRAS.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes | NA |
13
-|DLBCL |Schmitz cohort|0.2 |
14
-|DLBCL |Reddy cohort |0.7 |
15
-|DLBCL |Chapuy cohort |0.4 |
12
+|DLBCL |GAMBL genomes | NA |
13
+|DLBCL |Schmitz cohort|0.21 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
HVCN1.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |0.80 |
16 16
|BL |Panea cohort |2.00 |
17 17
|DLBCL |GAMBL genomes |3.06 |
18
-|DLBCL |Schmitz cohort |1.90 |
18
+|DLBCL |Schmitz cohort |1.91 |
19 19
|DLBCL |Reddy cohort |2.30 |
20
-|DLBCL |Chapuy cohort |3.40 |
20
+|DLBCL |Chapuy cohort |3.42 |
21 21
|FL |GAMBL genomes |6.47 |
22 22
23 23
## Mutation pattern
ID3.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
-|FL |2 |relevance in FL not firmly established |
7
+|BL |1-a | aSHM target and high-confidence BL gene |
8
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |47.00 |
16 16
|BL |Panea cohort |31.70 |
17 17
|DLBCL |GAMBL genomes | 1.53 |
18
-|DLBCL |Schmitz cohort | 4.70 |
18
+|DLBCL |Schmitz cohort | 4.68 |
19 19
|DLBCL |Reddy cohort | 3.50 |
20
-|DLBCL |Chapuy cohort | 0.90 |
20
+|DLBCL |Chapuy cohort | 0.85 |
21 21
|FL |GAMBL genomes | 0.92 |
22 22
23 23
## Mutation pattern
... ...
@@ -38,57 +38,6 @@
38 38
> First described in BL in 2012 by [Richter J](https://pubmed.ncbi.nlm.nih.gov/23143595). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
39 39
40 40
41
- ## ID3 Hotspots
42
-
43
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
44
- | :---:| :---: | :--: | :---: |
45
-| chr1 | 23885787 | ATGTCGTCCAGCA>- | L40* |
46
-| chr1 | 23885787 | A>T | M44K |
47
-| chr1 | 23885782 | G>A | H46Y |
48
-| chr1 | 23885778 | C>T | C47Y |
49
-| chr1 | 23885777 | G>T | C47* |
50
-| chr1 | 23885776 | A>G | Y48H |
51
-| chr1 | 23885775 | T>G | Y48S |
52
-| chr1 | 23885774 | G>T | Y48* |
53
-| chr1 | 23885774 | G>C | Y48* |
54
-| chr1 | 23885761 | C>A | E53* |
55
-| chr1 | 23885758 | G>C | L54V |
56
-| chr1 | 23885754 | A>T | V55E |
57
-| chr1 | 23885754 | A>G | V55A |
58
-| chr1 | 23885752 | G>T | P56T |
59
-| chr1 | 23885752 | G>C | P56A |
60
-| chr1 | 23885752 | G>A | P56S |
61
-| chr1 | 23885751 | G>T | P56H |
62
-| chr1 | 23885751 | G>A | P56L |
63
-| chr1 | 23885748 | C>G | G57A |
64
-| chr1 | 23885748 | C>A | G57V |
65
-| chr1 | 23885740 | T>C | R60G |
66
-| chr1 | 23885740 | T>A | R60* |
67
-| chr1 | 23885737 | C>A | G61C |
68
-| chr1 | 23885733 | G>A | T62I |
69
-| chr1 | 23885731 | G>A | Q63* |
70
-| chr1 | 23885728 | GC>AT | L64F |
71
-| chr1 | 23885728 | G>T | L64I |
72
-| chr1 | 23885728 | G>C | L64V |
73
-| chr1 | 23885728 | G>A | L64F |
74
-| chr1 | 23885727 | A>T | L64H |
75
-| chr1 | 23885727 | A>G | L64P |
76
-| chr1 | 23885723 | G>C | S65R |
77
-| chr1 | 23885718 | A>T | V67E |
78
-| chr1 | 23885718 | A>G | V67A |
79
-| chr1 | 23885716 | C>T | E68K |
80
-| chr1 | 23885716 | C>A | E68* |
81
-| chr1 | 23885715 | T>A | E68V |
82
-| chr1 | 23885712 | A>G | I69T |
83
-| chr1 | 23885712 | A>C | I69S |
84
-| chr1 | 23885711 | G>C | I69M |
85
-| chr1 | 23885710 | G>C | L70V |
86
-| chr1 | 23885709 | A>T | L70Q |
87
-| chr1 | 23885709 | A>G | L70P |
88
-| chr1 | 23885709 | A>C | L70R |
89
-| chr1 | 23885707 | G>A | Q71* |
90
-| chr1 | 23885706 | T>C | Q71R |
91
-
92 41
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ID3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ID3_protein_hg38.html)
93 42
94 43
![image](images/proteinpaint/ID3_NM_002167.svg)
IER2.md
... ...
@@ -0,0 +1,27 @@
1
+# [IER2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |0.60 |
15
+|DLBCL |Chapuy cohort |1.28 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.695 |0 |
22
+|DLBCL |No |No |0.319 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
IFNGR1.md
... ...
@@ -0,0 +1,36 @@
1
+# [IFNGR1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.008 |0 |
22
+|DLBCL |No |No |0.000 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IFNGR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IFNGR1_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/IFNGR1_NM_000416.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IFNGR1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IFNGR1_hg38.html)
35
+
36
+![image](images/proteinpaint/IFNGR1.svg)
IGLL5.md
... ...
@@ -4,9 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |2 |relevance in BL not firmly established |
8
-|DLBCL |2 |relevance in DLBCL not firmly established|
9
-|FL |2 |relevance in FL not firmly established |
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
10 10
## Mutation incidence
11 11
12 12
|Entity|source |frequency (%)|
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |25.00 |
16 16
|BL |Panea cohort |23.80 |
17 17
|DLBCL |GAMBL genomes |41.49 |
18
-|DLBCL |Schmitz cohort |36.00 |
19
-|DLBCL |Reddy cohort |16.10 |
20
-|DLBCL |Chapuy cohort | 9.00 |
18
+|DLBCL |Schmitz cohort |35.96 |
19
+|DLBCL |Reddy cohort |16.12 |
20
+|DLBCL |Chapuy cohort | 8.97 |
21 21
|FL |GAMBL genomes |35.33 |
22 22
23 23
## Mutation pattern
... ...
@@ -34,133 +34,10 @@
34 34
|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
35 35
|chr22 |23229554 |23232042|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A23229554%2D23232042)|NA |
36 36
37
+> [!NOTE]
38
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
37 39
38 40
39
- ## IGLL5 Hotspots
40
-
41
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
42
- | :---:| :---: | :--: | :---: |
43
-| chr22 | 23230340 | A>T | H36L |
44
-| chr22 | 23230341 | T>A | H36Q |
45
-| chr22 | 23230343 | G>A | G37D |
46
-| chr22 | 23230346 | T>C | L38P |
47
-| chr22 | 23230346 | T>G | L38R |
48
-| chr22 | 23230348 | C>A | L39M |
49
-| chr22 | 23230348 | C>G | L39V |
50
-| chr22 | 23230348 | CT>GC | L39A |
51
-| chr22 | 23230349 | T>A | L39Q |
52
-| chr22 | 23230349 | T>C | L39P |
53
-| chr22 | 23230351 | C>T | R40C |
54
-| chr22 | 23230357 | A>C | M42L |
55
-| chr22 | 23230357 | A>G | M42V |
56
-| chr22 | 23230357 | A>T | M42L |
57
-| chr22 | 23230358 | T>A | M42K |
58
-| chr22 | 23230358 | T>C | M42T |
59
-| chr22 | 23230359 | G>A | M42I |
60
-| chr22 | 23230359 | G>C | M42I |
61
-| chr22 | 23230359 | GG>AC | MV42IL |
62
-| chr22 | 23230360 | G>A | V43I |
63
-| chr22 | 23230360 | G>C | V43L |
64
-| chr22 | 23230360 | G>T | V43F |
65
-| chr22 | 23230361 | T>C | V43A |
66
-| chr22 | 23230361 | T>G | V43G |
67
-| chr22 | 23230361 | TT>AG | V43E |
68
-| chr22 | 23230361 | TT>CC | V43A |
69
-| chr22 | 23230363 | G>A | A44T |
70
-| chr22 | 23230363 | G>T | A44S |
71
-| chr22 | 23230363 | GC>AT | A44I |
72
-| chr22 | 23230364 | C>A | A44E |
73
-| chr22 | 23230364 | C>G | A44G |
74
-| chr22 | 23230364 | C>T | A44V |
75
-| chr22 | 23230365 | AC>GT | P45S |
76
-| chr22 | 23230366 | C>A | P45T |
77
-| chr22 | 23230366 | C>G | P45A |
78
-| chr22 | 23230366 | C>T | P45S |
79
-| chr22 | 23230367 | C>T | P45L |
80
-| chr22 | 23230369 | C>G | Q46E |
81
-| chr22 | 23230370 | A>G | Q46R |
82
-| chr22 | 23230370 | A>T | Q46L |
83
-| chr22 | 23230372 | A>C | S47R |
84
-| chr22 | 23230372 | A>T | S47C |
85
-| chr22 | 23230373 | G>A | S47N |
86
-| chr22 | 23230373 | G>C | S47T |
87
-| chr22 | 23230374 | C>G | S47R |
88
-| chr22 | 23230376 | G>A | G48E |
89
-| chr22 | 23230379 | A>C | D49A |
90
-| chr22 | 23230379 | A>G | D49G |
91
-| chr22 | 23230381 | C>A | P50T |
92
-| chr22 | 23230381 | C>G | P50A |
93
-| chr22 | 23230381 | C>T | P50S |
94
-| chr22 | 23230382 | C>G | P50R |
95
-| chr22 | 23230382 | C>T | P50L |
96
-| chr22 | 23230385 | A>C | D51A |
97
-| chr22 | 23230386 | C>A | D51E |
98
-| chr22 | 23230386 | CC>AA | DP51ET |
99
-| chr22 | 23230387 | C>A | P52T |
100
-| chr22 | 23230387 | C>T | P52S |
101
-| chr22 | 23230388 | C>T | P52L |
102
-| chr22 | 23230390 | G>A | G53R |
103
-| chr22 | 23230391 | G>A | G53E |
104
-| chr22 | 23230393 | G>A | A54T |
105
-| chr22 | 23230393 | G>C | A54P |
106
-| chr22 | 23230394 | C>A | A54D |
107
-| chr22 | 23230394 | C>G | A54G |
108
-| chr22 | 23230394 | C>T | A54V |
109
-| chr22 | 23230396 | T>C | S55P |
110
-| chr22 | 23230397 | C>A | S55* |
111
-| chr22 | 23230399 | G>A | V56I |
112
-| chr22 | 23230399 | G>C | V56L |
113
-| chr22 | 23230399 | G>T | V56F |
114
-| chr22 | 23230399 | GT>CC | V56P |
115
-| chr22 | 23230400 | T>C | V56A |
116
-| chr22 | 23230400 | T>G | V56G |
117
-| chr22 | 23230402 | G>A | G57R |
118
-| chr22 | 23230402 | G>T | G57* |
119
-| chr22 | 23230403 | G>A | G57E |
120
-| chr22 | 23230403 | G>C | G57A |
121
-| chr22 | 23230405 | A>G | S58G |
122
-| chr22 | 23230405 | A>T | S58C |
123
-| chr22 | 23230405 | AG>GA | S58D |
124
-| chr22 | 23230406 | G>A | S58N |
125
-| chr22 | 23230407 | C>G | S58R |
126
-| chr22 | 23230408 | A>C | S59R |
127
-| chr22 | 23230408 | A>G | S59G |
128
-| chr22 | 23230409 | G>C | S59T |
129
-| chr22 | 23230409 | G>T | S59I |
130
-| chr22 | 23230410 | C>G | S59R |
131
-| chr22 | 23230414 | T>C | S61P |
132
-| chr22 | 23230414 | T>G | S61A |
133
-| chr22 | 23230415 | C>G | S61C |
134
-| chr22 | 23230415 | C>T | S61F |
135
-| chr22 | 23230418 | G>A | S62N |
136
-| chr22 | 23230418 | G>C | S62T |
137
-| chr22 | 23230419 | C>A | S62R |
138
-| chr22 | 23230419 | C>G | S62R |
139
-| chr22 | 23230420 | C>G | L63V |
140
-| chr22 | 23230421 | T>A | L63Q |
141
-| chr22 | 23230426 | A>G | S65G |
142
-| chr22 | 23230427 | G>A | S65N |
143
-| chr22 | 23230427 | G>C | S65T |
144
-| chr22 | 23230428 | C>A | S65R |
145
-| chr22 | 23230428 | C>G | S65R |
146
-| chr22 | 23230430 | T>A | L66Q |
147
-| chr22 | 23230430 | T>G | L66R |
148
-| chr22 | 23230432 | T>C | W67R |
149
-| chr22 | 23230432 | T>G | W67G |
150
-| chr22 | 23230434 | G>A | W67* |
151
-| chr22 | 23230435 | GGC>AAT | G68N |
152
-| chr22 | 23230436 | G>A | G68D |
153
-| chr22 | 23230436 | G>C | G68A |
154
-| chr22 | 23230436 | G>T | G68V |
155
-| chr22 | 23230437 | C>T | G68= |
156
-| chr22 | 23230438 | A>C | R69= |
157
-| chr22 | 23230438 | A>G | R69G |
158
-| chr22 | 23230439 | G>A | R69K |
159
-| chr22 | 23230439 | G>C | R69T |
160
-| chr22 | 23235887 | C>T | L72F |
161
-| chr22 | 23235906 | G>C | R78T |
162
-| chr22 | 23235921 | G>A | C83Y |
163
-
164 41
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IGLL5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IGLL5_protein_hg38.html)
165 42
166 43
![image](images/proteinpaint/IGLL5_NM_001178126.svg)
IKBKB.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|3.00 |
13
+|DLBCL |Schmitz cohort|2.98 |
14 14
|DLBCL |Reddy cohort |1.10 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
IKBKE.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.76 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|1.06 |
14
+|DLBCL |Reddy cohort |1.00 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKBKE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IKBKE_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/IKBKE_NM_014002.svg)
IKZF3.md
... ...
@@ -4,9 +4,8 @@ IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|BL |2 |relevance in BL not firmly established|
9
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
... ...
@@ -15,9 +14,9 @@ IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 14
|BL |Thomas cohort |0.80 |
16 15
|BL |Panea cohort |3.00 |
17 16
|DLBCL |GAMBL genomes |4.78 |
18
-|DLBCL |Schmitz cohort |4.50 |
17
+|DLBCL |Schmitz cohort |4.47 |
19 18
|DLBCL |Reddy cohort |3.90 |
20
-|DLBCL |Chapuy cohort |4.30 |
19
+|DLBCL |Chapuy cohort |4.27 |
21 20
22 21
## Mutation pattern
23 22
... ...
@@ -35,8 +34,7 @@ IKZF3 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 34
|chr17 |38015776 |38024832|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A38015776%2D38024832)|NA |
36 35
37 36
> [!NOTE]
38
-> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2017 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/28479318)
39
-
37
+> First described in BL in 2019 by [Panea RI](https://pubmed.ncbi.nlm.nih.gov/31558468). First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
40 38
41 39
## IKZF3 Hotspots
42 40
IL16.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.29 |
13
-|DLBCL |Schmitz cohort|3.80 |
13
+|DLBCL |Schmitz cohort|3.83 |
14 14
|DLBCL |Reddy cohort |2.80 |
15
-|DLBCL |Chapuy cohort |5.10 |
15
+|DLBCL |Chapuy cohort |5.13 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL16_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IL16_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/IL16_NM_004513.svg)
IL4R.md
... ...
@@ -4,16 +4,15 @@ IL4R is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11 10
|Entity|source |frequency (%)|
12 11
|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes |2.68 |
14
-|DLBCL |Schmitz cohort|2.10 |
13
+|DLBCL |Schmitz cohort|2.13 |
15 14
|DLBCL |Reddy cohort |2.50 |
16
-|DLBCL |Chapuy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |3.85 |
17 16
18 17
## Mutation pattern
19 18
IL6.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort|2.80 |
13
+|DLBCL |Schmitz cohort|2.77 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
INO80.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|4.30 |
13
+|DLBCL |Schmitz cohort|4.26 |
14 14
|DLBCL |Reddy cohort |2.50 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
IRAG2.md
... ...
@@ -0,0 +1,20 @@
1
+# [IRAG2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
IRF1.md
... ...
@@ -4,15 +4,15 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.29 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -29,6 +29,9 @@
29 29
|chr5 |131823933 |131826458|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A131823933%2D131826458)|active_promoter |
30 30
31 31
> [!NOTE]
32
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
33
+
34
+
32 35
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/IRF1_protein_hg38.html)
33 36
34 37
![image](images/proteinpaint/IRF1_NM_002198.svg)
IRF4.md
... ...
@@ -4,17 +4,16 @@ IRF4 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
+|FL |1-a | aSHM target and high-confidence FL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:--------------:|:-------------:|
14 13
|DLBCL |GAMBL genomes |4.40 |
15
-|DLBCL |Schmitz cohort|7.00 |
14
+|DLBCL |Schmitz cohort|7.02 |
16 15
|DLBCL |Reddy cohort |4.40 |
17
-|DLBCL |Chapuy cohort |2.10 |
16
+|DLBCL |Chapuy cohort |2.14 |
18 17
|FL |GAMBL genomes |1.15 |
19 18
20 19
## Mutation pattern
IRF8.md
... ...
@@ -4,10 +4,9 @@ IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort | 1.30 |
17 16
|BL |Panea cohort | 6.90 |
18 17
|DLBCL |GAMBL genomes | 8.03 |
19
-|DLBCL |Schmitz cohort |10.40 |
20
-|DLBCL |Reddy cohort | 7.60 |
21
-|DLBCL |Chapuy cohort |10.30 |
18
+|DLBCL |Schmitz cohort |10.43 |
19
+|DLBCL |Reddy cohort | 7.61 |
20
+|DLBCL |Chapuy cohort |10.26 |
22 21
|FL |GAMBL genomes |12.01 |
23 22
24 23
## Mutation pattern
... ...
@@ -36,6 +35,8 @@ IRF8 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
36 35
|chr16 |85931918 |85933977|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A85931918%2D85933977)|active_promoter |
37 36
38 37
38
+> [!NOTE]
39
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
39 40
40 41
## IRF8 Hotspots
41 42
ITPKB.md
... ...
@@ -4,15 +4,15 @@ ITPKB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-|FL |1-a |high-confidence FL gene, hypermutated |
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
+|FL |1-a | aSHM target and high-confidence FL gene |
9 9
## Mutation incidence
10 10
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |6.69 |
14
-|DLBCL |Schmitz cohort|6.80 |
15
-|DLBCL |Reddy cohort |6.70 |
14
+|DLBCL |Schmitz cohort|6.81 |
15
+|DLBCL |Reddy cohort |6.71 |
16 16
|DLBCL |Chapuy cohort |9.40 |
17 17
|FL |GAMBL genomes |3.23 |
18 18
JAK1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.49 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort |2.20 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
JAK3.md
... ...
@@ -10,7 +10,7 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort |1.00 |
15 15
|DLBCL |Chapuy cohort | NA |
16 16
JUNB.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.25 |
13
-|DLBCL |Schmitz cohort|3.20 |
13
+|DLBCL |Schmitz cohort|3.19 |
14 14
|DLBCL |Reddy cohort |3.50 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
JUP.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JUP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/JUP_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/JUP_NM_002230.svg)
KCMF1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |1.00 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
KIR3DL1.md
... ...
@@ -24,13 +24,6 @@
24 24
> First described in FL in 2023 by [Kalmbach S](https://pubmed.ncbi.nlm.nih.gov/37563306)
25 25
26 26
27
- ## KIR3DL1 Hotspots
28
-
29
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
30
- | :---:| :---: | :--: | :---: |
31
-| chr19 | 55331362 | C>T | P184S |
32
-| chr19 | 55331372 | T>G | L187R |
33
-
34 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIR3DL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KIR3DL1_protein_hg38.html)
35 28
36 29
![image](images/proteinpaint/KIR3DL1_NM_013289.svg)
KLF2.md
... ...
@@ -4,17 +4,16 @@ KLF2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
+|FL |1-a | aSHM target and high-confidence FL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:--------------:|:-------------:|
14 13
|DLBCL |GAMBL genomes |8.60 |
15
-|DLBCL |Schmitz cohort|7.00 |
14
+|DLBCL |Schmitz cohort|7.02 |
16 15
|DLBCL |Reddy cohort |2.10 |
17
-|DLBCL |Chapuy cohort |3.00 |
16
+|DLBCL |Chapuy cohort |2.99 |
18 17
|FL |GAMBL genomes |2.31 |
19 18
20 19
## Mutation pattern
... ...
@@ -32,7 +31,7 @@ KLF2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
32 31
|chr19 |16434978 |16439011|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A16434978%2D16439011)|intron |
33 32
34 33
> [!NOTE]
35
-> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
34
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
36 35
37 36
38 37
## KLF2 Hotspots
KLHL14.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |4.59 |
13 13
|DLBCL |Schmitz cohort|6.60 |
14 14
|DLBCL |Reddy cohort |4.60 |
15
-|DLBCL |Chapuy cohort |7.30 |
15
+|DLBCL |Chapuy cohort |7.26 |
16 16
17 17
## Mutation pattern
18 18
KLHL21.md
... ...
@@ -4,15 +4,15 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|4.70 |
13
+|DLBCL |Schmitz cohort|4.68 |
14 14
|DLBCL |Reddy cohort |2.50 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -32,14 +32,6 @@
32 32
> First described in DLBCL in 2018 by [Schmitz R](https://pubmed.ncbi.nlm.nih.gov/29641966)
33 33
34 34
35
- ## KLHL21 Hotspots
36
-
37
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
38
- | :---:| :---: | :--: | :---: |
39
-| chr1 | 6662199 | G>T | P227T |
40
-| chr1 | 6662178 | G>C | L234V |
41
-| chr1 | 6662172 | C>T | A236T |
42
-
43 35
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL21_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KLHL21_protein_hg38.html)
44 36
45 37
![image](images/proteinpaint/KLHL21_NM_014851.svg)
KLHL6.md
... ...
@@ -4,10 +4,9 @@ KLHL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ KLHL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort |3.00 |
17 16
|BL |Panea cohort |6.90 |
18 17
|DLBCL |GAMBL genomes |5.35 |
19
-|DLBCL |Schmitz cohort |9.10 |
20
-|DLBCL |Reddy cohort |6.40 |
21
-|DLBCL |Chapuy cohort |9.00 |
18
+|DLBCL |Schmitz cohort |9.15 |
19
+|DLBCL |Reddy cohort |6.41 |
20
+|DLBCL |Chapuy cohort |8.97 |
22 21
|FL |GAMBL genomes |7.16 |
23 22
24 23
## Mutation pattern
... ...
@@ -35,7 +34,8 @@ KLHL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 34
|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:-------------------------------:|
36 35
|chr3 |183269360 |183274139|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A183269360%2D183274139)|active_promoter-strong_enhancer|
37 36
38
-
37
+> [!NOTE]
38
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
39 39
40 40
## KLHL6 Hotspots
41 41
KMT2C.md
... ...
@@ -2,10 +2,11 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
8
-|DLBCL |1 |high-confidence DLBCL gene |
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |1 |high-confidence DLBCL gene |
9
+|MCL |2 |relevance in MCL not firmly established|
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -15,8 +16,9 @@
15 16
|BL |Panea cohort | NA |
16 17
|DLBCL |GAMBL genomes |3.25 |
17 18
|DLBCL |Schmitz cohort |8.30 |
18
-|DLBCL |Reddy cohort |7.30 |
19
-|DLBCL |Chapuy cohort |6.40 |
19
+|DLBCL |Reddy cohort |7.31 |
20
+|DLBCL |Chapuy cohort |6.41 |
21
+|MCL |GAMBL genomes |0.47 |
20 22
21 23
## Mutation pattern
22 24
... ...
@@ -28,7 +30,7 @@
28 30
29 31
30 32
> [!NOTE]
31
-> First described in BL in 2019 by [Zhou P](https://pubmed.ncbi.nlm.nih.gov/31300419). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
33
+> First described in BL in 2019 by [Zhou P](https://pubmed.ncbi.nlm.nih.gov/31300419). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
32 34
33 35
34 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2C_protein_hg38.html)
KMT2D.md
... ...
@@ -7,6 +7,7 @@
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9 9
|FL |1 |high-confidence FL gene |
10
+|MCL |1 |high-confidence MCL gene |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,10 +16,11 @@
15 16
|BL |Thomas cohort |14.00 |
16 17
|BL |Panea cohort |15.80 |
17 18
|DLBCL |GAMBL genomes |33.46 |
18
-|DLBCL |Schmitz cohort |34.50 |
19
-|DLBCL |Reddy cohort |22.30 |
20
-|DLBCL |Chapuy cohort |26.10 |
19
+|DLBCL |Schmitz cohort |34.47 |
20
+|DLBCL |Reddy cohort |22.32 |
21
+|DLBCL |Chapuy cohort |26.07 |
21 22
|FL |GAMBL genomes |67.67 |
23
+|MCL |GAMBL genomes |16.59 |
22 24
23 25
## Mutation pattern
24 26
... ...
@@ -30,29 +32,8 @@
30 32
31 33
32 34
> [!NOTE]
33
-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
34
-
35
-
36
- ## KMT2D Hotspots
37
-
38
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
39
- | :---:| :---: | :--: | :---: |
40
-| chr12 | 49433521 | C>A | E2678* |
41
-| chr12 | 49433397 | G>A | Q2684* |
42
-| chr12 | 49433394 | G>A | R2685* |
43
-| chr12 | 49433388 | G>A | R2687* |
44
-| chr12 | 49432710 | A>T | L2810* |
45
-| chr12 | 49432699 | G>A | Q2814* |
46
-| chr12 | 49432684 | G>A | Q2819* |
47
-| chr12 | 49432681 | G>A | Q2820* |
48
-| chr12 | 49424741 | G>A | R4536* |
49
-| chr12 | 49420607 | G>A | R5048C |
50
-| chr12 | 49420606 | C>T | R5048H |
51
-| chr12 | 49420493 | G>A | R5086* |
52
-| chr12 | 49420214 | G>A | R5179C |
53
-| chr12 | 49420213 | C>T | R5179H |
54
-| chr12 | 49420115 | C>G | A5212P |
55
-| chr12 | 49420108 | C>T | R5214H |
35
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
36
+
56 37
57 38
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/KMT2D_protein_hg38.html)
58 39
KRAS.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort|3.60 |
13
+|DLBCL |Schmitz cohort|3.62 |
14 14
|DLBCL |Reddy cohort |1.70 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
LAMA5.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 3.44 |
13
-|DLBCL |Schmitz cohort|12.10 |
13
+|DLBCL |Schmitz cohort|12.13 |
14 14
|DLBCL |Reddy cohort | 4.70 |
15
-|DLBCL |Chapuy cohort | 5.60 |
15
+|DLBCL |Chapuy cohort | 5.56 |
16 16
17 17
## Mutation pattern
18 18
LAPTM5.md
... ...
@@ -2,14 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
8 9
## Mutation incidence
9 10
10
-|Entity|source |frequency (%)|
11
-|:------:|:-------------:|:-------------:|
12
-|FL |GAMBL genomes|5.77 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |3.06 |
14
+|DLBCL |Schmitz cohort|3.40 |
15
+|DLBCL |Reddy cohort |2.20 |
16
+|DLBCL |Chapuy cohort |2.56 |
17
+|FL |GAMBL genomes |5.77 |
13 18
14 19
## Mutation pattern
15 20
... ...
@@ -26,6 +31,9 @@
26 31
|chr1 |31229012 |31232011|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A31229012%2D31232011)|NA |
27 32
28 33
> [!NOTE]
34
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
35
+
36
+
29 37
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LAPTM5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LAPTM5_protein_hg38.html)
30 38
31 39
![image](images/proteinpaint/LAPTM5_NM_006762.svg)
LCOR.md
... ...
@@ -2,17 +2,21 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|--------------------------------------|
7
+|BL |2 |relevance in BL not firmly established|
8
+|DLBCL |1 |high-confidence DLBCL gene |
8 9
## Mutation incidence
9 10
10
-|Entity|source |frequency (%)|
11
-|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |6.31 |
13
-|DLBCL |Schmitz cohort|3.40 |
14
-|DLBCL |Reddy cohort |0.50 |
15
-|DLBCL |Chapuy cohort |0.40 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture|3.46 |
14
+|BL |Thomas cohort |0.00 |
15
+|BL |Panea cohort | NA |
16
+|DLBCL |GAMBL genomes |6.31 |
17
+|DLBCL |Schmitz cohort |0.43 |
18
+|DLBCL |Reddy cohort |0.50 |
19
+|DLBCL |Chapuy cohort |0.43 |
16 20
17 21
## Mutation pattern
18 22
... ...
@@ -24,7 +28,6 @@
24 28
25 29
26 30
27
-
28 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LCOR_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LCOR_protein_hg38.html)
29 32
30 33
![image](images/proteinpaint/LCOR_NM_001346516.svg
LIN54.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|2.10 |
13
+|DLBCL |Schmitz cohort|2.13 |
14 14
|DLBCL |Reddy cohort |0.90 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
LPP.md
... ...
@@ -0,0 +1,49 @@
1
+# [LPP]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|1.28 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0 |0 |
22
+|DLBCL |Yes |No |0 |0 |
23
+|FL |Yes |No |0 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:------------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr3 |187771678 |187801626|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187771678%2D187801626) |NA |
30
+|chr3 |187801627 |187813568|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187801627%2D187813568) |NA |
31
+|chr3 |187813569 |187955254|[TSS-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187813569%2D187955254) |NA |
32
+|chr3 |187955255 |187969220|[TSS-4](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A187955255%2D187969220) |NA |
33
+|chr3 |188261523 |188327097|[TSS-5](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A188261523%2D188327097) |NA |
34
+|chr3 |188377178 |188401951|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A188377178%2D188401951)|NA |
35
+|chr3 |188401952 |188461879|[intron-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A188401952%2D188461879)|NA |
36
+|chr3 |188461880 |188474683|[intron-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A188461880%2D188474683)|NA |
37
+|chr3 |188474684 |188491248|[intron-4](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A188474684%2D188491248)|NA |
38
+
39
+> [!NOTE]
40
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
41
+
42
+
43
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LPP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LPP_protein_hg38.html)
44
+
45
+![image](images/proteinpaint/LPP_NM_005578.svg)
46
+
47
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LPP.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LPP_hg38.html)
48
+
49
+![image](images/proteinpaint/LPP.svg)
LRP12.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.49 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |2.40 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRP12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRP12_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/LRP12_NM_013437.svg)
LRRN3.md
... ...
@@ -0,0 +1,36 @@
1
+# [LRRN3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |8.22 |
13
+|DLBCL |Schmitz cohort|8.09 |
14
+|DLBCL |Reddy cohort |6.51 |
15
+|DLBCL |Chapuy cohort |6.84 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.141 |0 |
22
+|DLBCL |No |No |2.591 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRRN3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRRN3_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/LRRN3_NM_001099660.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRRN3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LRRN3_hg38.html)
35
+
36
+![image](images/proteinpaint/LRRN3.svg)
LTB.md
... ...
@@ -4,10 +4,9 @@ LTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene |
8
-|FL |1-a |high-confidence FL gene |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ LTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
16 15
|BL |Thomas cohort |3.00 |
17 16
|BL |Panea cohort |5.90 |
18 17
|DLBCL |GAMBL genomes |9.37 |
19
-|DLBCL |Schmitz cohort |8.50 |
18
+|DLBCL |Schmitz cohort |8.51 |
20 19
|DLBCL |Reddy cohort | NA |
21
-|DLBCL |Chapuy cohort |9.80 |
20
+|DLBCL |Chapuy cohort |9.83 |
22 21
|FL |GAMBL genomes |8.78 |
23 22
24 23
## Mutation pattern
... ...
@@ -36,7 +35,6 @@ LTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
36 35
|chr6 |31548325 |31550717|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A31548325%2D31550717)|enhancer |
37 36
38 37
39
-
40 38
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LTB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LTB_protein_hg38.html)
41 39
42 40
![image](images/proteinpaint/LTB_NM_002341.svg)
LYN.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |2.29 |
13 13
|DLBCL |Schmitz cohort|1.70 |
14 14
|DLBCL |Reddy cohort |1.30 |
15
-|DLBCL |Chapuy cohort |5.60 |
15
+|DLBCL |Chapuy cohort |5.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LYN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/LYN_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/LYN_ENST00000519728.svg)
MAGT1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.53 |
13
-|DLBCL |Schmitz cohort|3.00 |
13
+|DLBCL |Schmitz cohort|2.98 |
14 14
|DLBCL |Reddy cohort |1.90 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
MALAT1.md
... ...
@@ -0,0 +1,34 @@
1
+# [MALAT1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+## aSHM regions
22
+
23
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
24
+|:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:|
25
+|chr11 |65265237 |65268359|[ncRNA](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A65265237%2D65268359)|enhancer |
26
+
27
+
28
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MALAT1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MALAT1_protein_hg38.html)
29
+
30
+![image](images/proteinpaint/MALAT1_NR_002819.svg)
31
+
32
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MALAT1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MALAT1_hg38.html)
33
+
34
+![image](images/proteinpaint/MALAT1.svg)
MAP2K1.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |1.34 |
14
-|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Schmitz cohort|3.19 |
15 15
|DLBCL |Reddy cohort |2.20 |
16
-|DLBCL |Chapuy cohort |2.10 |
16
+|DLBCL |Chapuy cohort |2.14 |
17 17
|FL |GAMBL genomes |1.39 |
18 18
19 19
## Mutation pattern
... ...
@@ -25,7 +25,8 @@
25 25
|FL |No |No | 5.696 |0 |
26 26
27 27
28
-
28
+> [!NOTE]
29
+> First described in FL in 2016 by [Louissaint A Jr](https://pubmed.ncbi.nlm.nih.gov/27325104)
29 30
30 31
## MAP2K1 Hotspots
31 32
MAP4K4.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.15 |
13
-|DLBCL |Schmitz cohort|2.10 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |2.10 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
MARK1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|1.90 |
13
+|DLBCL |Schmitz cohort|1.91 |
14 14
|DLBCL |Reddy cohort |1.30 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
MCL1.md
... ...
@@ -4,9 +4,8 @@ MCL1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|BL |2 |relevance in BL not firmly established|
9
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
... ...
@@ -15,9 +14,9 @@ MCL1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
15 14
|BL |Thomas cohort |2.10 |
16 15
|BL |Panea cohort |2.00 |
17 16
|DLBCL |GAMBL genomes |2.49 |
18
-|DLBCL |Schmitz cohort |3.60 |
17
+|DLBCL |Schmitz cohort |3.62 |
19 18
|DLBCL |Reddy cohort |4.70 |
20
-|DLBCL |Chapuy cohort |3.40 |
19
+|DLBCL |Chapuy cohort |3.42 |
21 20
22 21
## Mutation pattern
23 22
MECOM.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|4.0 |
14
-|DLBCL |Reddy cohort |2.1 |
15
-|DLBCL |Chapuy cohort |3.4 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|4.04 |
14
+|DLBCL |Reddy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
MEF2B.md
... ...
@@ -4,9 +4,9 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established and seems unlikely|
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
10 10
11 11
## Mutation incidence
12 12
... ...
@@ -16,10 +16,11 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 16
|BL |Thomas cohort | 0.80 |
17 17
|BL |Panea cohort | 3.00 |
18 18
|DLBCL |GAMBL genomes |11.28 |
19
-|DLBCL |Schmitz cohort | 9.10 |
20
-|DLBCL |Reddy cohort | 5.90 |
21
-|DLBCL |Chapuy cohort | 5.60 |
19
+|DLBCL |Schmitz cohort | 9.79 |
20
+|DLBCL |Reddy cohort | 5.91 |
21
+|DLBCL |Chapuy cohort | 5.56 |
22 22
|FL |GAMBL genomes |12.93 |
23
+|MCL |GAMBL genomes | 5.69 |
23 24
24 25
## Mutation pattern
25 26
... ...
@@ -35,6 +36,8 @@ MEF2B is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 36
|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
36 37
|chr19 |19279635 |19281441|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr19%3A19279635%2D19281441)|active_promoter |
37 38
39
+> [!NOTE]
40
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
38 41
39 42
## MEF2B Hotspots
40 43
MEF2C.md
... ...
@@ -4,17 +4,16 @@ MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
8
+|FL |1-a | aSHM target and high-confidence FL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
13 12
|:------:|:--------------:|:-------------:|
14 13
|DLBCL |GAMBL genomes |3.44 |
15
-|DLBCL |Schmitz cohort|1.90 |
14
+|DLBCL |Schmitz cohort|1.91 |
16 15
|DLBCL |Reddy cohort |1.70 |
17
-|DLBCL |Chapuy cohort |3.00 |
16
+|DLBCL |Chapuy cohort |2.99 |
18 17
|FL |GAMBL genomes |6.24 |
19 18
20 19
## Mutation pattern
... ...
@@ -34,7 +33,6 @@ MEF2C is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
34 33
|chr5 |88182244 |88206620|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr5%3A88182244%2D88206620)|active_promoter |
35 34
36 35
37
-
38 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MEF2C_protein_hg38.html)
39 37
40 38
![image](images/proteinpaint/MEF2C_NM_002397.svg)
MET.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.76 |
13
-|DLBCL |Schmitz cohort|3.80 |
13
+|DLBCL |Schmitz cohort|3.83 |
14 14
|DLBCL |Reddy cohort |1.70 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
MGA.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.02 |
13
-|DLBCL |Schmitz cohort|7.20 |
13
+|DLBCL |Schmitz cohort|7.23 |
14 14
|DLBCL |Reddy cohort |4.70 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
MGEA5.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MGEA5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MGEA5_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/MGEA5_NM_012215.svg)
MIR142.md
... ...
@@ -0,0 +1,27 @@
1
+# [MIR142]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|DLBCL |2 |relevance in DLBCL not firmly established|
9
+## Mutation incidence
10
+
11
+|Entity|source |frequency (%)|
12
+|:------:|:---------------------:|:-------------:|
13
+|BL |GAMBL genomes+capture|NA |
14
+|BL |Thomas cohort |NA |
15
+|BL |Panea cohort |NA |
16
+|DLBCL |GAMBL genomes |NA |
17
+|DLBCL |Schmitz cohort |NA |
18
+|DLBCL |Reddy cohort |NA |
19
+|DLBCL |Chapuy cohort |NA |
20
+
21
+## Mutation pattern
22
+
23
+|
24
+
25
+
26
+> [!NOTE]
27
+> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194). First described in DLBCL in 2012 by [Kwanhian W](https://pubmed.ncbi.nlm.nih.gov/23342264)
MIR155HG.md
... ...
@@ -0,0 +1,34 @@
1
+# [MIR155HG]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+## aSHM regions
22
+
23
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
24
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
25
+|chr21 |26934372 |26937651|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr21%3A26934372%2D26937651)|active_promoter |
26
+
27
+
28
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MIR155HG_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MIR155HG_protein_hg38.html)
29
+
30
+![image](images/proteinpaint/MIR155HG_NR_001458.svg)
31
+
32
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MIR155HG.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MIR155HG_hg38.html)
33
+
34
+![image](images/proteinpaint/MIR155HG.svg)
MPDZ.md
... ...
@@ -0,0 +1,36 @@
1
+# [MPDZ]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes | 6.31 |
13
+|DLBCL |Schmitz cohort|11.70 |
14
+|DLBCL |Reddy cohort | 5.61 |
15
+|DLBCL |Chapuy cohort | 2.99 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.932 |8.789 |
22
+|DLBCL |No |No |0.632 |1.772 |
23
+|FL |No |No |2.769 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPDZ_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPDZ_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/MPDZ_NM_003829.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPDZ.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPDZ_hg38.html)
35
+
36
+![image](images/proteinpaint/MPDZ.svg)
MPEG1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 4.78 |
13
-|DLBCL |Schmitz cohort| 9.10 |
14
-|DLBCL |Reddy cohort | 5.80 |
15
-|DLBCL |Chapuy cohort |10.70 |
13
+|DLBCL |Schmitz cohort| 9.15 |
14
+|DLBCL |Reddy cohort | 5.81 |
15
+|DLBCL |Chapuy cohort |10.68 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -23,6 +23,8 @@
23 23
|FL |No |No |4.371 |0.000 |
24 24
25 25
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
26 28
27 29
28 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPEG1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MPEG1_protein_hg38.html)
MRGPRF.md
... ...
@@ -0,0 +1,33 @@
1
+# [MRGPRF]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.899 | 0.000 |
19
+|DLBCL |No |No |0.000 |150.717 |
20
+|FL |No |No |0.000 | 0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MRGPRF_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MRGPRF_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/MRGPRF_NM_001098515.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MRGPRF.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MRGPRF_hg38.html)
32
+
33
+![image](images/proteinpaint/MRGPRF.svg)
MS4A1.md
... ...
@@ -4,16 +4,15 @@ MS4A1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene|
8
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11 10
|Entity|source |frequency (%)|
12 11
|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes |1.53 |
14
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
15 14
|DLBCL |Reddy cohort |1.30 |
16
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
17 16
18 17
## Mutation pattern
19 18
... ...
@@ -30,7 +29,6 @@ MS4A1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
30 29
|chr11 |60223385 |60225310|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A60223385%2D60225310)|active_promoter |
31 30
32 31
33
-
34 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1_protein_hg38.html)
35 33
36 34
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MS4A1_hg38.html)
MSH2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.72 |
13
-|DLBCL |Schmitz cohort|0.90 |
13
+|DLBCL |Schmitz cohort|0.85 |
14 14
|DLBCL |Reddy cohort |1.50 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
MSH6.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.91 |
13
-|DLBCL |Schmitz cohort|2.60 |
13
+|DLBCL |Schmitz cohort|2.55 |
14 14
|DLBCL |Reddy cohort |2.60 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
MTOR.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 3.40 |
15 15
|BL |Panea cohort |10.90 |
16 16
|DLBCL |GAMBL genomes | 4.02 |
17
-|DLBCL |Schmitz cohort | 4.00 |
17
+|DLBCL |Schmitz cohort | 4.04 |
18 18
|DLBCL |Reddy cohort | 2.40 |
19
-|DLBCL |Chapuy cohort | 2.10 |
19
+|DLBCL |Chapuy cohort | 2.14 |
20 20
21 21
## Mutation pattern
22 22
MYB.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|2.10 |
13
+|DLBCL |Schmitz cohort|2.13 |
14 14
|DLBCL |Reddy cohort |1.10 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
MYBPC2.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |0.57 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |2.80 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
MYC.md
... ...
@@ -4,10 +4,9 @@ MYC is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |1-a |high-confidence BL gene |
8
-|DLBCL |1-a |high-confidence DLBCL gene |
9
-|FL |2 |relevance of missense mutations in FL not firmly established|
10
-
7
+|BL |1-a | aSHM target and high-confidence BL gene |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ MYC is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) a
16 15
|BL |Thomas cohort |60.20 |
17 16
|BL |Panea cohort |49.50 |
18 17
|DLBCL |GAMBL genomes |10.90 |
19
-|DLBCL |Schmitz cohort | 5.30 |
20
-|DLBCL |Reddy cohort | 6.20 |
21
-|DLBCL |Chapuy cohort | 6.40 |
18
+|DLBCL |Schmitz cohort | 5.32 |
19
+|DLBCL |Reddy cohort | 6.21 |
20
+|DLBCL |Chapuy cohort | 6.41 |
22 21
|FL |GAMBL genomes | 0.92 |
23 22
24 23
## Mutation pattern
MYCBP2.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYCBP2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYCBP2_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/MYCBP2_NM_015057.svg)
MYD88.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 0.40 |
16 16
|BL |Panea cohort | 1.00 |
17 17
|DLBCL |GAMBL genomes |13.38 |
18
-|DLBCL |Schmitz cohort |26.40 |
19
-|DLBCL |Reddy cohort |15.20 |
20
-|DLBCL |Chapuy cohort |21.40 |
18
+|DLBCL |Schmitz cohort |26.38 |
19
+|DLBCL |Reddy cohort |15.12 |
20
+|DLBCL |Chapuy cohort |21.37 |
21 21
|FL |GAMBL genomes | 1.85 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@
29 29
|FL |No |No |17.159 |0 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2011 by [Ngo VN](https://pubmed.ncbi.nlm.nih.gov/21179087)
33 34
34 35
## MYD88 Hotspots
35 36
MYO1E.md
... ...
@@ -2,9 +2,10 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
... ...
@@ -12,6 +13,10 @@
12 13
|BL |GAMBL genomes+capture|2.08 |
13 14
|BL |Thomas cohort |1.30 |
14 15
|BL |Panea cohort |4.00 |
16
+|DLBCL |GAMBL genomes |2.49 |
17
+|DLBCL |Schmitz cohort |3.40 |
18
+|DLBCL |Reddy cohort |3.00 |
19
+|DLBCL |Chapuy cohort |1.28 |
15 20
16 21
## Mutation pattern
17 22
... ...
@@ -28,14 +33,6 @@
28 33
|chr15 |59658991 |59671152|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr15%3A59658991%2D59671152)|NA |
29 34
30 35
31
-
32
- ## MYO1E Hotspots
33
-
34
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
35
- | :---:| :---: | :--: | :---: |
36
-| chr15 | 59664698 | A>G | M1? |
37
-| chr15 | 59664699 | T>A | M1? |
38
-
39 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO1E_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYO1E_protein_hg38.html)
40 37
41 38
![image](images/proteinpaint/MYO1E_NM_004998.svg)
MYOM2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.25 |
13
-|DLBCL |Schmitz cohort|8.10 |
13
+|DLBCL |Schmitz cohort|8.09 |
14 14
|DLBCL |Reddy cohort |3.20 |
15
-|DLBCL |Chapuy cohort |4.30 |
15
+|DLBCL |Chapuy cohort |4.27 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -23,6 +23,8 @@
23 23
|FL |No |No |0.649 |12.057 |
24 24
25 25
26
+> [!NOTE]
27
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
26 28
27 29
28 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYOM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/MYOM2_protein_hg38.html)
N2RF2.md
... ...
@@ -16,11 +16,13 @@
16 16
17 17
## Mutation pattern
18 18
19
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
19
+|
21 20
22 21
23 22
> [!NOTE]
23
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
24
+
25
+
24 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/N2RF2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/N2RF2_protein_hg38.html)
25 27
26 28
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/N2RF2.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/N2RF2_hg38.html)
NANOG.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes | NA |
13
-|DLBCL |Schmitz cohort|0.2 |
14
-|DLBCL |Reddy cohort |0.4 |
15
-|DLBCL |Chapuy cohort |0.4 |
12
+|DLBCL |GAMBL genomes | NA |
13
+|DLBCL |Schmitz cohort|0.21 |
14
+|DLBCL |Reddy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
NAV1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.49 |
13
-|DLBCL |Schmitz cohort|2.80 |
13
+|DLBCL |Schmitz cohort|2.77 |
14 14
|DLBCL |Reddy cohort |2.00 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
NCOA3.md
... ...
@@ -0,0 +1,38 @@
1
+# [NCOA3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |2.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |1.087 |0.000 |
22
+|DLBCL |Yes |No |0.000 |6.508 |
23
+|FL |Yes |No |5.600 |0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr20 |46128611 |46138099|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr20%3A46128611%2D46138099)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOA3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOA3_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/NCOA3_NM_181659.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOA3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NCOA3_hg38.html)
37
+
38
+![image](images/proteinpaint/NCOA3.svg)
NCOR1.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|4.5 |
14
-|DLBCL |Reddy cohort |2.7 |
15
-|DLBCL |Chapuy cohort |2.1 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|4.47 |
14
+|DLBCL |Reddy cohort |2.70 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
NCOR2.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | NA |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |2.10 |
17
-|DLBCL |Schmitz cohort |5.70 |
17
+|DLBCL |Schmitz cohort |5.74 |
18 18
|DLBCL |Reddy cohort |3.60 |
19
-|DLBCL |Chapuy cohort |4.30 |
19
+|DLBCL |Chapuy cohort |4.27 |
20 20
21 21
## Mutation pattern
22 22
NEAT1.md
... ...
@@ -0,0 +1,34 @@
1
+# [NEAT1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+## aSHM regions
22
+
23
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
24
+|:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:|
25
+|chr11 |65190369 |65192380|[ncRNA](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A65190369%2D65192380)|enhancer |
26
+
27
+
28
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NEAT1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NEAT1_protein_hg38.html)
29
+
30
+![image](images/proteinpaint/NEAT1_NR_028272.svg)
31
+
32
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NEAT1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NEAT1_hg38.html)
33
+
34
+![image](images/proteinpaint/NEAT1.svg)
NF1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.87 |
13
-|DLBCL |Schmitz cohort|4.00 |
13
+|DLBCL |Schmitz cohort|4.04 |
14 14
|DLBCL |Reddy cohort |2.50 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
NFKB1.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|1.3 |
14
-|DLBCL |Reddy cohort |1.6 |
15
-|DLBCL |Chapuy cohort |3.4 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|1.28 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
NFKB2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.53 |
13
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |1.40 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
NFKBIA.md
... ...
@@ -15,7 +15,7 @@
15 15
|BL |Thomas cohort |1.70 |
16 16
|BL |Panea cohort |2.00 |
17 17
|DLBCL |GAMBL genomes |4.40 |
18
-|DLBCL |Schmitz cohort |3.80 |
18
+|DLBCL |Schmitz cohort |3.83 |
19 19
|DLBCL |Reddy cohort |3.60 |
20 20
|DLBCL |Chapuy cohort |4.70 |
21 21
|FL |GAMBL genomes |0.69 |
... ...
@@ -29,6 +29,8 @@
29 29
|FL |No |No |0.000 |28.519 |
30 30
31 31
32
+> [!NOTE]
33
+> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
32 34
33 35
34 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIA_protein_hg38.html)
NFKBIE.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|5.70 |
14
+|DLBCL |Schmitz cohort|5.74 |
14 15
|DLBCL |Reddy cohort |2.90 |
15
-|DLBCL |Chapuy cohort |3.40 |
16
+|DLBCL |Chapuy cohort |3.42 |
17
+|MCL |GAMBL genomes |2.84 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -24,7 +26,7 @@
24 26
25 27
26 28
> [!NOTE]
27
-> First described in DLBCL in 2016 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/26647218)
29
+> First described in DLBCL in 2016 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/26647218). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
28 30
29 31
30 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIE_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIE_protein_hg38.html)
NFKBIZ.md
... ...
@@ -4,16 +4,15 @@ NFKBIZ is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene|
8
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11 10
|Entity|source |frequency (%)|
12 11
|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes |1.53 |
14
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
15 14
|DLBCL |Reddy cohort |1.50 |
16
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
17 16
18 17
## Mutation pattern
19 18
... ...
@@ -31,7 +30,6 @@ NFKBIZ is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
31 30
|chr3 |101568239 |101569274|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A101568239%2D101569274)|active_promoter |
32 31
33 32
34
-
35 33
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIZ_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NFKBIZ_protein_hg38.html)
36 34
37 35
![image](images/proteinpaint/NFKBIZ_zoom.svg)
NIN.md
... ...
@@ -0,0 +1,33 @@
1
+# [NIN]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |6.284 |0.000 |
19
+|DLBCL |No |No |0.964 |0.000 |
20
+|FL |No |No |4.145 |8.842 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NIN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NIN_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/NIN_NM_182944.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NIN.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NIN_hg38.html)
32
+
33
+![image](images/proteinpaint/NIN.svg)
NLRC5.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |3.06 |
13 13
|DLBCL |Schmitz cohort|8.30 |
14 14
|DLBCL |Reddy cohort |3.70 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRC5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRC5_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/NLRC5_NM_032206.svg)
NLRP5.md
... ...
@@ -0,0 +1,36 @@
1
+# [NLRP5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.72 |
13
+|DLBCL |Schmitz cohort|4.04 |
14
+|DLBCL |Reddy cohort |2.20 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |1.110 |2.507 |
22
+|DLBCL |No |No |1.256 |0.000 |
23
+|FL |No |No |3.057 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP5_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/NLRP5_NM_153447.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP5.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NLRP5_hg38.html)
35
+
36
+![image](images/proteinpaint/NLRP5.svg)
NLRP8.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |0.38 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |2.10 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
NOL9.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.97 |
13
-|DLBCL |Schmitz cohort|6.80 |
13
+|DLBCL |Schmitz cohort|6.81 |
14 14
|DLBCL |Reddy cohort |1.30 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
NOTCH1.md
... ...
@@ -6,6 +6,7 @@
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
+|MCL |1 |high-confidence MCL gene |
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -14,9 +15,10 @@
14 15
|BL |Thomas cohort | NA |
15 16
|BL |Panea cohort | NA |
16 17
|DLBCL |GAMBL genomes |3.44 |
17
-|DLBCL |Schmitz cohort |8.90 |
18
+|DLBCL |Schmitz cohort |8.94 |
18 19
|DLBCL |Reddy cohort |3.40 |
19
-|DLBCL |Chapuy cohort |3.00 |
20
+|DLBCL |Chapuy cohort |2.99 |
21
+|MCL |GAMBL genomes |5.21 |
20 22
21 23
## Mutation pattern
22 24
... ...
@@ -28,8 +30,7 @@
28 30
29 31
30 32
> [!NOTE]
31
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2012 by [Lohr JG](https://pubmed.ncbi.nlm.nih.gov/22343534)
32
-
33
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
33 34
34 35
## NOTCH1 Hotspots
35 36
NOTCH2.md
... ...
@@ -6,6 +6,7 @@
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
+|MCL |1 |high-confidence MCL gene |
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -14,9 +15,10 @@
14 15
|BL |Thomas cohort | 0.00 |
15 16
|BL |Panea cohort | 5.00 |
16 17
|DLBCL |GAMBL genomes | 5.74 |
17
-|DLBCL |Schmitz cohort |11.30 |
18
+|DLBCL |Schmitz cohort |11.28 |
18 19
|DLBCL |Reddy cohort | 3.70 |
19
-|DLBCL |Chapuy cohort | 7.30 |
20
+|DLBCL |Chapuy cohort | 7.26 |
21
+|MCL |GAMBL genomes | 2.84 |
20 22
21 23
## Mutation pattern
22 24
... ...
@@ -27,7 +29,8 @@
27 29
|FL |No |No |0.000 | 0.000 |
28 30
29 31
30
-
32
+> [!NOTE]
33
+> First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
31 34
32 35
## NOTCH2 Hotspots
33 36
NSD2.md
... ...
@@ -0,0 +1,29 @@
1
+# [NSD2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|7.11 |
13
+
14
+## Mutation pattern
15
+
16
+|
17
+
18
+
19
+> [!NOTE]
20
+> First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
21
+
22
+
23
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NSD2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NSD2_protein_hg38.html)
24
+
25
+![image](images/proteinpaint/NSD2_NM_133330.svg)
26
+
27
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NSD2.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/NSD2_hg38.html)
28
+
29
+![image](images/proteinpaint/NSD2.svg)
ODZ3.md
... ...
@@ -0,0 +1,23 @@
1
+# [ODZ3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+
22
+> [!NOTE]
23
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
OGDHL.md
... ...
@@ -0,0 +1,33 @@
1
+# [OGDHL]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|1.42 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.674 |0 |
19
+|DLBCL |No |No |0.000 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OGDHL_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OGDHL_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/OGDHL_NM_018245.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OGDHL.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OGDHL_hg38.html)
32
+
33
+![image](images/proteinpaint/OGDHL.svg)
OSBPL10.md
... ...
@@ -4,9 +4,8 @@ OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|BL |2 |relevance in BL not firmly established|
9
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
... ...
@@ -15,9 +14,9 @@ OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
15 14
|BL |Thomas cohort | 2.10 |
16 15
|BL |Panea cohort | 3.00 |
17 16
|DLBCL |GAMBL genomes | 8.80 |
18
-|DLBCL |Schmitz cohort |14.30 |
17
+|DLBCL |Schmitz cohort |14.26 |
19 18
|DLBCL |Reddy cohort | 2.30 |
20
-|DLBCL |Chapuy cohort | 2.60 |
19
+|DLBCL |Chapuy cohort | 2.56 |
21 20
22 21
## Mutation pattern
23 22
... ...
@@ -34,7 +33,6 @@ OSBPL10 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
34 33
|chr3 |32020518 |32024930|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A32020518%2D32024930)|active_promoter |
35 34
36 35
37
-
38 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OSBPL10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/OSBPL10_protein_hg38.html)
39 37
40 38
![image](images/proteinpaint/OSBPL10_NM_017784.svg)
P2RX5.md
... ...
@@ -0,0 +1,41 @@
1
+# [P2RX5]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |1.60 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |2.368 |12.182 |
22
+|DLBCL |Yes |No |4.647 |21.997 |
23
+|FL |Yes |No |0.000 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr17 |3597616 |3599572 |[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A3597616%2D3599572)|active_promoter |
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RX5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RX5_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/P2RX5_NM_002561.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RX5.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/P2RX5_hg38.html)
40
+
41
+![image](images/proteinpaint/P2RX5.svg)
P2RY8.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |11.00 |
16 16
|BL |Panea cohort | NA |
17 17
|DLBCL |GAMBL genomes | 6.88 |
18
-|DLBCL |Schmitz cohort | 7.20 |
18
+|DLBCL |Schmitz cohort | 7.23 |
19 19
|DLBCL |Reddy cohort | NA |
20
-|DLBCL |Chapuy cohort | 6.00 |
20
+|DLBCL |Chapuy cohort | 5.98 |
21 21
|FL |GAMBL genomes | 2.31 |
22 22
23 23
## Mutation pattern
PAPOLG.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort|0.90 |
13
+|DLBCL |Schmitz cohort|0.85 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
PASK.md
... ...
@@ -0,0 +1,36 @@
1
+# [PASK]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.91 |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |2.00 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |3.029 |0 |
22
+|DLBCL |No |No |0.681 |0 |
23
+|FL |No |No |1.504 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PASK_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PASK_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/PASK_NM_015148.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PASK.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PASK_hg38.html)
35
+
36
+![image](images/proteinpaint/PASK.svg)
PAX5.md
... ...
@@ -4,15 +4,15 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.63 |
13
-|DLBCL |Schmitz cohort|3.20 |
13
+|DLBCL |Schmitz cohort|3.19 |
14 14
|DLBCL |Reddy cohort |1.90 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
PCBP1.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |12.30 |
15 15
|BL |Panea cohort |11.90 |
16 16
|DLBCL |GAMBL genomes | 1.34 |
17
-|DLBCL |Schmitz cohort | 2.30 |
17
+|DLBCL |Schmitz cohort | 2.34 |
18 18
|DLBCL |Reddy cohort | 2.40 |
19
-|DLBCL |Chapuy cohort | 1.70 |
19
+|DLBCL |Chapuy cohort | 1.71 |
20 20
21 21
## Mutation pattern
22 22
PCDHB11.md
... ...
@@ -0,0 +1,36 @@
1
+# [PCDHB11]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.53 |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |1.20 |
15
+|DLBCL |Chapuy cohort |1.28 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.106 | 0.000 |
22
+|DLBCL |No |No |0.848 |11.264 |
23
+|FL |No |No |1.816 | 0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB11_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB11_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/PCDHB11_NM_018931.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB11.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB11_hg38.html)
35
+
36
+![image](images/proteinpaint/PCDHB11.svg)
PCDHB2.md
... ...
@@ -0,0 +1,33 @@
1
+# [PCDHB2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0.47 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.502 |0 |
19
+|DLBCL |No |No |5.792 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB2_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/PCDHB2_NM_018936.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB2.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PCDHB2_hg38.html)
32
+
33
+![image](images/proteinpaint/PCDHB2.svg)
PCLO.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |16.44 |
14
-|DLBCL |Schmitz cohort|21.30 |
15
-|DLBCL |Reddy cohort |15.10 |
16
-|DLBCL |Chapuy cohort |23.10 |
14
+|DLBCL |Schmitz cohort|21.28 |
15
+|DLBCL |Reddy cohort |15.12 |
16
+|DLBCL |Chapuy cohort |23.08 |
17 17
|FL |GAMBL genomes | 9.24 |
18 18
19 19
## Mutation pattern
PDE4DIP.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes | NA |
13
-|DLBCL |Schmitz cohort|2.3 |
14
-|DLBCL |Reddy cohort |5.3 |
15
-|DLBCL |Chapuy cohort |8.5 |
12
+|DLBCL |GAMBL genomes | NA |
13
+|DLBCL |Schmitz cohort|3.83 |
14
+|DLBCL |Reddy cohort |5.31 |
15
+|DLBCL |Chapuy cohort |8.55 |
16 16
17 17
## Mutation pattern
18 18
PDS5B.md
... ...
@@ -2,14 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|FL |2 |relevance in FL not firmly established |
8 9
## Mutation incidence
9 10
10
-|Entity|source |frequency (%)|
11
-|:------:|:-------------:|:-------------:|
12
-|FL |GAMBL genomes|1.62 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |3.25 |
14
+|DLBCL |Schmitz cohort|4.47 |
15
+|DLBCL |Reddy cohort |1.80 |
16
+|DLBCL |Chapuy cohort |2.14 |
17
+|FL |GAMBL genomes |1.62 |
13 18
14 19
## Mutation pattern
15 20
... ...
@@ -21,6 +26,9 @@
21 26
22 27
23 28
> [!NOTE]
29
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
30
+
31
+
24 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDS5B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PDS5B_protein_hg38.html)
25 33
26 34
![image](images/proteinpaint/PDS5B_NM_015032.svg)
PHF6.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |5.50 |
15 15
|BL |Panea cohort |5.90 |
16 16
|DLBCL |GAMBL genomes |2.49 |
17
-|DLBCL |Schmitz cohort |1.50 |
17
+|DLBCL |Schmitz cohort |1.49 |
18 18
|DLBCL |Reddy cohort |1.40 |
19
-|DLBCL |Chapuy cohort |0.90 |
19
+|DLBCL |Chapuy cohort |0.85 |
20 20
21 21
## Mutation pattern
22 22
PIK3CD.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|4.90 |
13
+|DLBCL |Schmitz cohort|4.89 |
14 14
|DLBCL |Reddy cohort |2.50 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
PIK3R1.md
... ...
@@ -14,7 +14,7 @@
14 14
|BL |Thomas cohort |2.50 |
15 15
|BL |Panea cohort |4.00 |
16 16
|DLBCL |GAMBL genomes |1.91 |
17
-|DLBCL |Schmitz cohort |2.10 |
17
+|DLBCL |Schmitz cohort |2.13 |
18 18
|DLBCL |Reddy cohort |2.00 |
19 19
|DLBCL |Chapuy cohort |4.70 |
20 20
PIM1.md
... ...
@@ -4,10 +4,9 @@ PIM1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established and appears unlikely|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ PIM1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort | NA |
17 16
|BL |Panea cohort | NA |
18 17
|DLBCL |GAMBL genomes |20.27 |
19
-|DLBCL |Schmitz cohort |27.70 |
20
-|DLBCL |Reddy cohort |19.10 |
21
-|DLBCL |Chapuy cohort |23.90 |
18
+|DLBCL |Schmitz cohort |27.66 |
19
+|DLBCL |Reddy cohort |19.12 |
20
+|DLBCL |Chapuy cohort |23.93 |
22 21
|FL |GAMBL genomes | 9.24 |
23 22
24 23
## Mutation pattern
PIM2.md
... ...
@@ -4,16 +4,15 @@ PIM2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11 10
|Entity|source |frequency (%)|
12 11
|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes |3.44 |
14
-|DLBCL |Schmitz cohort|6.40 |
13
+|DLBCL |Schmitz cohort|6.38 |
15 14
|DLBCL |Reddy cohort |4.00 |
16
-|DLBCL |Chapuy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |3.85 |
17 16
18 17
## Mutation pattern
19 18
... ...
@@ -30,7 +29,6 @@ PIM2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
30 29
|chrX |48774756 |48776255|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A48774756%2D48776255)|active_promoter |
31 30
32 31
33
-
34 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PIM2_protein_hg38.html)
35 33
36 34
![image](images/proteinpaint/PIM2_NM_006875.svg)
PKD1.md
... ...
@@ -0,0 +1,36 @@
1
+# [PKD1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |3.44 |
13
+|DLBCL |Schmitz cohort|7.02 |
14
+|DLBCL |Reddy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |6.41 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.596 |1.458 |
22
+|DLBCL |No |No |0.325 |0.000 |
23
+|FL |No |No |1.705 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PKD1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PKD1_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/PKD1_NM_001009944.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PKD1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PKD1_hg38.html)
35
+
36
+![image](images/proteinpaint/PKD1.svg)
PLXNB3.md
... ...
@@ -0,0 +1,33 @@
1
+# [PLXNB3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |2.316 |0 |
19
+|DLBCL |No |No |1.330 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLXNB3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLXNB3_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/PLXNB3_NM_005393.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLXNB3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PLXNB3_hg38.html)
32
+
33
+![image](images/proteinpaint/PLXNB3.svg)
PMAIP1.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PMAIP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PMAIP1_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/PMAIP1_NM_021127.svg)
PNPO.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.38 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|0.21 |
14
+|DLBCL |Reddy cohort |0.30 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PNPO_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PNPO_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/PNPO_NM_018129.svg)
POGZ.md
... ...
@@ -0,0 +1,36 @@
1
+# [POGZ]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|2.55 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0 |0 |
22
+|DLBCL |No |No |0 |0 |
23
+|FL |No |No |0 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POGZ_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POGZ_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/POGZ_NM_015100.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POGZ.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POGZ_hg38.html)
35
+
36
+![image](images/proteinpaint/POGZ.svg)
POT1.md
... ...
@@ -0,0 +1,33 @@
1
+# [POT1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|3.32 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.889 | 0.000 |
19
+|DLBCL |No |No |4.286 | 0.000 |
20
+|FL |No |No |0.000 |18.704 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POT1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POT1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/POT1_NM_015450.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POT1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/POT1_hg38.html)
32
+
33
+![image](images/proteinpaint/POT1.svg)
POU2AF1.md
... ...
@@ -12,9 +12,9 @@ POU2AF1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
12 12
|Entity|source |frequency (%)|
13 13
|:------:|:--------------:|:-------------:|
14 14
|DLBCL |GAMBL genomes | 5.16 |
15
-|DLBCL |Schmitz cohort| 2.30 |
15
+|DLBCL |Schmitz cohort| 2.34 |
16 16
|DLBCL |Reddy cohort | 3.30 |
17
-|DLBCL |Chapuy cohort | 5.60 |
17
+|DLBCL |Chapuy cohort | 5.56 |
18 18
|FL |GAMBL genomes |12.24 |
19 19
20 20
## Mutation pattern
POU2F2.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |5.93 |
14
-|DLBCL |Schmitz cohort|6.40 |
14
+|DLBCL |Schmitz cohort|6.38 |
15 15
|DLBCL |Reddy cohort |3.40 |
16
-|DLBCL |Chapuy cohort |6.40 |
16
+|DLBCL |Chapuy cohort |6.41 |
17 17
|FL |GAMBL genomes |6.24 |
18 18
19 19
## Mutation pattern
PPP1R9B.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |0.38 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |0.70 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B_protein_hg38.html)
29 28
30 29
View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PPP1R9B_hg38.html)
PPP4C.md
... ...
@@ -21,6 +21,8 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
24 26
## PPP4C Hotspots
25 27
26 28
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
PRDM1.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 0.80 |
15 15
|BL |Panea cohort | 5.90 |
16 16
|DLBCL |GAMBL genomes | 6.88 |
17
-|DLBCL |Schmitz cohort |10.20 |
18
-|DLBCL |Reddy cohort | 5.40 |
19
-|DLBCL |Chapuy cohort | 8.50 |
17
+|DLBCL |Schmitz cohort |10.21 |
18
+|DLBCL |Reddy cohort | 5.41 |
19
+|DLBCL |Chapuy cohort | 8.55 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -28,6 +28,8 @@
28 28
29 29
30 30
31
+> [!NOTE]
32
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
31 33
32 34
## PRDM1 Hotspots
33 35
PRKCB.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.97 |
13
-|DLBCL |Schmitz cohort|5.10 |
13
+|DLBCL |Schmitz cohort|5.11 |
14 14
|DLBCL |Reddy cohort |1.60 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -23,6 +23,8 @@
23 23
|FL |No |No |1.828 |0 |
24 24
25 25
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
26 28
27 29
28 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCB_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCB_protein_hg38.html)
PRKCD.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCD_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKCD_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/PRKCD_NM_006254.svg)
PRKDC.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |2.68 |
14
-|DLBCL |Schmitz cohort|7.70 |
15
-|DLBCL |Reddy cohort |6.60 |
16
-|DLBCL |Chapuy cohort |6.40 |
14
+|DLBCL |Schmitz cohort|7.66 |
15
+|DLBCL |Reddy cohort |6.61 |
16
+|DLBCL |Chapuy cohort |6.41 |
17 17
|FL |GAMBL genomes |3.00 |
18 18
19 19
## Mutation pattern
... ...
@@ -25,6 +25,8 @@
25 25
|FL |No |No |0.000 |7.794 |
26 26
27 27
28
+> [!NOTE]
29
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28 30
29 31
30 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKDC_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PRKDC_protein_hg38.html)
PRPS1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.76 |
13
-|DLBCL |Schmitz cohort|0.60 |
13
+|DLBCL |Schmitz cohort|0.64 |
14 14
|DLBCL |Reddy cohort |0.20 |
15
-|DLBCL |Chapuy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
PTEN.md
... ...
@@ -14,7 +14,7 @@
14 14
|BL |Thomas cohort |4.70 |
15 15
|BL |Panea cohort |4.00 |
16 16
|DLBCL |GAMBL genomes |3.82 |
17
-|DLBCL |Schmitz cohort |4.30 |
17
+|DLBCL |Schmitz cohort |4.26 |
18 18
|DLBCL |Reddy cohort |3.10 |
19 19
|DLBCL |Chapuy cohort |4.70 |
20 20
... ...
@@ -28,7 +28,6 @@
28 28
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTEN_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTEN_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/PTEN_NM_000314.svg)
PTMA.md
... ...
@@ -0,0 +1,38 @@
1
+# [PTMA]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.38 |
13
+|DLBCL |Schmitz cohort|0.21 |
14
+|DLBCL |Reddy cohort |0.20 |
15
+|DLBCL |Chapuy cohort |0.43 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |3.010 |0 |
22
+|DLBCL |Yes |No |3.468 |0 |
23
+|FL |Yes |No |0.000 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr2 |232572640 |232574297|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr2%3A232572640%2D232574297)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTMA_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTMA_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/PTMA_NM_001099285.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTMA.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTMA_hg38.html)
37
+
38
+![image](images/proteinpaint/PTMA.svg)
PTPN1.md
... ...
@@ -0,0 +1,38 @@
1
+# [PTPN1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.19 |
13
+|DLBCL |Schmitz cohort|1.06 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0 |0 |
22
+|DLBCL |Yes |No |0 |0 |
23
+|FL |Yes |No |0 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr20 |49120482 |49140477|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr20%3A49120482%2D49140477)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN1_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/PTPN1_NM_002827.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN1_hg38.html)
37
+
38
+![image](images/proteinpaint/PTPN1.svg)
PTPN23.md
... ...
@@ -0,0 +1,36 @@
1
+# [PTPN23]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.34 |
13
+|DLBCL |Schmitz cohort|4.68 |
14
+|DLBCL |Reddy cohort |2.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.502 |0 |
22
+|DLBCL |No |No |0.736 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN23_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN23_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/PTPN23_NM_015466.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN23.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/PTPN23_hg38.html)
35
+
36
+![image](images/proteinpaint/PTPN23.svg)
PTPN6.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.68 |
13
-|DLBCL |Schmitz cohort|4.50 |
13
+|DLBCL |Schmitz cohort|4.47 |
14 14
|DLBCL |Reddy cohort |2.90 |
15
-|DLBCL |Chapuy cohort |5.10 |
15
+|DLBCL |Chapuy cohort |5.13 |
16 16
17 17
## Mutation pattern
18 18
PTPRD.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |5.54 |
14
-|DLBCL |Schmitz cohort|7.70 |
15
-|DLBCL |Reddy cohort |5.20 |
16
-|DLBCL |Chapuy cohort |5.60 |
14
+|DLBCL |Schmitz cohort|7.66 |
15
+|DLBCL |Reddy cohort |5.21 |
16
+|DLBCL |Chapuy cohort |5.56 |
17 17
|FL |GAMBL genomes |3.70 |
18 18
19 19
## Mutation pattern
PTPRK.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.21 |
13
-|DLBCL |Schmitz cohort|3.60 |
13
+|DLBCL |Schmitz cohort|3.62 |
14 14
|DLBCL |Reddy cohort |3.30 |
15
-|DLBCL |Chapuy cohort |6.40 |
15
+|DLBCL |Chapuy cohort |6.41 |
16 16
17 17
## Mutation pattern
18 18
RAC2.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |0.40 |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |1.15 |
17
-|DLBCL |Schmitz cohort | NA |
18
-|DLBCL |Reddy cohort | NA |
19
-|DLBCL |Chapuy cohort | NA |
17
+|DLBCL |Schmitz cohort |1.70 |
18
+|DLBCL |Reddy cohort |1.20 |
19
+|DLBCL |Chapuy cohort |1.28 |
20 20
21 21
## Mutation pattern
22 22
RAD9A.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.19 |
13
-|DLBCL |Schmitz cohort|0.40 |
13
+|DLBCL |Schmitz cohort|0.43 |
14 14
|DLBCL |Reddy cohort |0.50 |
15
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
16 16
17 17
## Mutation pattern
18 18
RARA.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|4.00 |
13
+|DLBCL |Schmitz cohort|4.04 |
14 14
|DLBCL |Reddy cohort |0.70 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
RB1.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |4.78 |
13
-|DLBCL |Schmitz cohort|3.20 |
14
+|DLBCL |Schmitz cohort|3.19 |
14 15
|DLBCL |Reddy cohort |1.60 |
15
-|DLBCL |Chapuy cohort |3.80 |
16
+|DLBCL |Chapuy cohort |3.85 |
17
+|MCL |GAMBL genomes |0.47 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -23,6 +25,8 @@
23 25
|FL |No |No |1.890 | 0.000 |
24 26
25 27
28
+> [!NOTE]
29
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
26 30
27 31
28 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RB1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RB1_protein_hg38.html)
RBM6.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RBM6_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RBM6_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/RBM6_NM_005777.svg)
RCC.md
... ...
@@ -0,0 +1,20 @@
1
+# [RCC]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
RFTN1.md
... ...
@@ -0,0 +1,41 @@
1
+# [RFTN1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.59 |
13
+|DLBCL |Schmitz cohort|5.96 |
14
+|DLBCL |Reddy cohort |4.40 |
15
+|DLBCL |Chapuy cohort |4.70 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |1.080 |0.000 |
22
+|DLBCL |Yes |No |3.636 |3.809 |
23
+|FL |Yes |No |2.622 |0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment |
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:-------------------------------:|
29
+|chr3 |16546433 |16556786|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A16546433%2D16556786)|active_promoter-strong_enhancer|
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFTN1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFTN1_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/RFTN1_NM_015150.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFTN1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFTN1_hg38.html)
40
+
41
+![image](images/proteinpaint/RFTN1.svg)
RFX7.md
... ...
@@ -14,7 +14,7 @@
14 14
|BL |Thomas cohort |9.30 |
15 15
|BL |Panea cohort |4.00 |
16 16
|DLBCL |GAMBL genomes |4.02 |
17
-|DLBCL |Schmitz cohort |1.90 |
17
+|DLBCL |Schmitz cohort |2.13 |
18 18
|DLBCL |Reddy cohort |3.40 |
19 19
|DLBCL |Chapuy cohort |4.70 |
20 20
... ...
@@ -28,7 +28,6 @@
28 28
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFX7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFX7_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/RFX7_NM_022841.svg)
RFXAP.md
... ...
@@ -10,7 +10,7 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort |0.60 |
15 15
|DLBCL |Chapuy cohort | NA |
16 16
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFXAP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RFXAP_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/RFXAP_NM_000538.svg)
RHEX.md
... ...
@@ -0,0 +1,25 @@
1
+# [RHEX]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+## aSHM regions
22
+
23
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
24
+|:--------:|:----------:|:---------:|:-------------------------------------------------------------------------------------------:|:------------------:|
25
+|chr1 |206285239 |206288105|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A206285239%2D206288105)|NA |
RHOA.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 8.10 |
15 15
|BL |Panea cohort |12.90 |
16 16
|DLBCL |GAMBL genomes | 3.06 |
17
-|DLBCL |Schmitz cohort | 3.60 |
17
+|DLBCL |Schmitz cohort | 3.62 |
18 18
|DLBCL |Reddy cohort | 3.30 |
19
-|DLBCL |Chapuy cohort | 5.10 |
19
+|DLBCL |Chapuy cohort | 5.13 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -27,7 +27,8 @@
27 27
|FL |No |No |31.528 |0 |
28 28
29 29
30
-
30
+> [!NOTE]
31
+> First described in DLBCL in 2001 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/11460166)
31 32
32 33
## RHOA Hotspots
33 34
RHOH.md
... ...
@@ -0,0 +1,38 @@
1
+# [RHOH]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|0.43 |
14
+|DLBCL |Reddy cohort |0.10 |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0.000 |0 |
22
+|DLBCL |Yes |No |4.612 |0 |
23
+|FL |Yes |No |0.000 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr4 |40193105 |40204231|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr4%3A40193105%2D40204231)|active_promoter |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOH_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOH_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/RHOH_NM_004310.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOH.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RHOH_hg38.html)
37
+
38
+![image](images/proteinpaint/RHOH.svg)
RNF144B.md
... ...
@@ -4,7 +4,7 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
ROBO2.md
... ...
@@ -0,0 +1,24 @@
1
+# [ROBO2]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|1.9 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |3.941 |0.000 |
19
+|DLBCL |No |No |1.035 |3.094 |
20
+|FL |No |No |3.479 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
RPL22.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL22_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/RPL22_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/RPL22_NM_000983.svg)
RRAGC.md
... ...
@@ -11,9 +11,9 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes | 1.72 |
14
-|DLBCL |Schmitz cohort| 3.00 |
14
+|DLBCL |Schmitz cohort| 2.98 |
15 15
|DLBCL |Reddy cohort | 2.00 |
16
-|DLBCL |Chapuy cohort | 0.40 |
16
+|DLBCL |Chapuy cohort | 0.43 |
17 17
|FL |GAMBL genomes |10.85 |
18 18
19 19
## Mutation pattern
RUBCNL.md
... ...
@@ -0,0 +1,20 @@
1
+# [RUBCNL]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort| NA |
14
+|DLBCL |Reddy cohort | NA |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
RUNX1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|0.90 |
13
+|DLBCL |Schmitz cohort|0.85 |
14 14
|DLBCL |Reddy cohort |0.50 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
S1PR1.md
... ...
@@ -0,0 +1,33 @@
1
+# [S1PR1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|5.69 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.815 |0 |
19
+|DLBCL |No |No |2.579 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/S1PR1_NM_001400.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/S1PR1_hg38.html)
32
+
33
+![image](images/proteinpaint/S1PR1.svg)
S1PR2.md
... ...
@@ -4,10 +4,9 @@ S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ S1PR2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort |0.00 |
17 16
|BL |Panea cohort |4.00 |
18 17
|DLBCL |GAMBL genomes |4.78 |
19
-|DLBCL |Schmitz cohort |2.10 |
18
+|DLBCL |Schmitz cohort |2.13 |
20 19
|DLBCL |Reddy cohort |2.20 |
21
-|DLBCL |Chapuy cohort |2.60 |
20
+|DLBCL |Chapuy cohort |2.56 |
22 21
|FL |GAMBL genomes |6.24 |
23 22
24 23
## Mutation pattern
SAL3.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
SALL3.md
... ...
@@ -2,9 +2,10 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|BL |2 |relevance in BL not firmly established|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|BL |2 |relevance in BL not firmly established |
8
+|MCL |2 |relevance in MCL not firmly established|
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
... ...
@@ -12,6 +13,7 @@
12 13
|BL |GAMBL genomes+capture|4.16 |
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
16
+|MCL |GAMBL genomes |0.95 |
15 17
16 18
## Mutation pattern
17 19
... ...
@@ -23,15 +25,9 @@
23 25
24 26
25 27
> [!NOTE]
26
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597)
28
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
27 29
28 30
29
- ## SALL3 Hotspots
30
-
31
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
32
- | :---:| :---: | :--: | :---: |
33
-| chr18 | 76756928 | C>T | A1170V |
34
-
35 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SALL3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SALL3_protein_hg38.html)
36 32
37 33
![image](images/proteinpaint/SALL3_NM_171999.svg)
SAMD9L.md
... ...
@@ -0,0 +1,36 @@
1
+# [SAMD9L]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.49 |
13
+|DLBCL |Schmitz cohort|2.77 |
14
+|DLBCL |Reddy cohort |2.40 |
15
+|DLBCL |Chapuy cohort |1.71 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.289 |4.237 |
22
+|DLBCL |No |No |0.493 |0.000 |
23
+|FL |No |No |0.000 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAMD9L_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAMD9L_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/SAMD9L_NM_152703.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAMD9L.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SAMD9L_hg38.html)
35
+
36
+![image](images/proteinpaint/SAMD9L.svg)
SAPS2.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
SARM1.md
... ...
@@ -0,0 +1,36 @@
1
+# [SARM1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|1.28 |
14
+|DLBCL |Reddy cohort |0.70 |
15
+|DLBCL |Chapuy cohort |1.28 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.000 |0 |
22
+|DLBCL |No |No |1.098 |0 |
23
+|FL |No |No |0.000 |0 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SARM1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SARM1_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/SARM1_NM_015077.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SARM1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SARM1_hg38.html)
35
+
36
+![image](images/proteinpaint/SARM1.svg)
SEL1L3.md
... ...
@@ -0,0 +1,38 @@
1
+# [SEL1L3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |5.16 |
13
+|DLBCL |Schmitz cohort|4.04 |
14
+|DLBCL |Reddy cohort |2.20 |
15
+|DLBCL |Chapuy cohort | NA |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0.665 |3.278 |
22
+|DLBCL |Yes |No |1.724 |0.000 |
23
+|FL |Yes |No |2.299 |0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr4 |25861094 |25868788|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr4%3A25861094%2D25868788)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEL1L3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEL1L3_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/SEL1L3_NM_015187.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEL1L3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEL1L3_hg38.html)
37
+
38
+![image](images/proteinpaint/SEL1L3.svg)
SEPT10.md
... ...
@@ -23,7 +23,6 @@
23 23
24 24
25 25
26
-
27 26
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEPT10_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SEPT10_protein_hg38.html)
28 27
29 28
![image](images/proteinpaint/SEPT10_NM_144710.svg)
SEPTIN9.md
... ...
@@ -0,0 +1,27 @@
1
+# [SEPTIN9]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |NA |
13
+|DLBCL |Schmitz cohort|NA |
14
+|DLBCL |Reddy cohort |NA |
15
+|DLBCL |Chapuy cohort |NA |
16
+
17
+## Mutation pattern
18
+
19
+|
20
+
21
+## aSHM regions
22
+
23
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
24
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------------:|:------------------:|
25
+|chr17 |75424734 |75440956|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A75424734%2D75440956)|active_promoter |
26
+|chr17 |75443766 |75451177|[intron-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A75443766%2D75451177)|active_promoter |
27
+|chr17 |75453203 |75471471|[intron-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr17%3A75453203%2D75471471)|active_promoter |
SERPINA9.md
... ...
@@ -0,0 +1,41 @@
1
+# [SERPINA9]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|2.13 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |2.14 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |4.866 | 0.000 |
22
+|DLBCL |Yes |No |1.343 |39.076 |
23
+|FL |Yes |No |5.716 |42.861 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr14 |94940587 |94942549|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A94940587%2D94942549)|NA |
30
+
31
+> [!NOTE]
32
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SERPINA9_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SERPINA9_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/SERPINA9_NM_175739.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SERPINA9.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SERPINA9_hg38.html)
40
+
41
+![image](images/proteinpaint/SERPINA9.svg)
SETD1B.md
... ...
@@ -10,8 +10,8 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 5.16 |
13
-|DLBCL |Schmitz cohort|12.80 |
14
-|DLBCL |Reddy cohort | 5.80 |
13
+|DLBCL |Schmitz cohort|12.77 |
14
+|DLBCL |Reddy cohort | 5.81 |
15 15
|DLBCL |Chapuy cohort | NA |
16 16
17 17
## Mutation pattern
SETD1B.pdf
... ...
Binary files /dev/null and b/SETD1B.pdf differ
SETD2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.63 |
13
-|DLBCL |Schmitz cohort|6.40 |
13
+|DLBCL |Schmitz cohort|6.38 |
14 14
|DLBCL |Reddy cohort |4.60 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SETD2_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/SETD2_NM_014159.svg)
SETD5.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.49 |
13
-|DLBCL |Schmitz cohort|5.30 |
13
+|DLBCL |Schmitz cohort|5.32 |
14 14
|DLBCL |Reddy cohort |3.20 |
15
-|DLBCL |Chapuy cohort |2.10 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
SF3B1.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | NA |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |2.87 |
17
-|DLBCL |Schmitz cohort |2.10 |
17
+|DLBCL |Schmitz cohort |2.13 |
18 18
|DLBCL |Reddy cohort |2.00 |
19
-|DLBCL |Chapuy cohort |3.00 |
19
+|DLBCL |Chapuy cohort |2.99 |
20 20
21 21
## Mutation pattern
22 22
SGK1.md
... ...
@@ -1,13 +1,12 @@
1
-SGK1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
1
+# [SGK1]
2 2
3 3
## Mutation tier
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ SGK1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort | 2.50 |
17 16
|BL |Panea cohort | 4.00 |
18 17
|DLBCL |GAMBL genomes |11.09 |
19
-|DLBCL |Schmitz cohort |10.60 |
20
-|DLBCL |Reddy cohort |11.20 |
21
-|DLBCL |Chapuy cohort |12.80 |
18
+|DLBCL |Schmitz cohort |10.64 |
19
+|DLBCL |Reddy cohort |11.21 |
20
+|DLBCL |Chapuy cohort |12.82 |
22 21
|FL |GAMBL genomes | 6.00 |
23 22
24 23
## Mutation pattern
... ...
@@ -35,30 +34,10 @@ SGK1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
35 34
|:--------:|:----------:|:---------:|:---------------------------------------------------------------------------------------------:|:------------------:|
36 35
|chr6 |134487960 |134499859|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A134487960%2D134499859)|active_promoter |
37 36
37
+> [!NOTE]
38
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
38 39
39 40
40
- ## SGK1 Hotspots
41
-
42
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
43
- | :---:| :---: | :--: | :---: |
44
-| chr6 | 134495730 | G>T | NA |
45
-| chr6 | 134495730 | G>C | NA |
46
-| chr6 | 134495729 | G>C | NA |
47
-| chr6 | 134495729 | G>A | NA |
48
-| chr6 | 134495724 | G>C | A121G |
49
-| chr6 | 134495724 | G>A | A121V |
50
-| chr6 | 134495717 | C>A | M123I |
51
-| chr6 | 134495716 | T>C | K124E |
52
-| chr6 | 134495715 | T>A | K124M |
53
-| chr6 | 134495713 | G>A | Q125* |
54
-| chr6 | 134495712 | T>A | Q125L |
55
-| chr6 | 134495711 | C>G | Q125H |
56
-| chr6 | 134495706 | C>T | R127K |
57
-| chr6 | 134495706 | C>A | R127M |
58
-| chr6 | 134495703 | A>T | M128K |
59
-| chr6 | 134495700 | CC>TG | G129H |
60
-| chr6 | 134495700 | CC>TA | G129Y |
61
-
62 41
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SGK1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SGK1_protein_hg38.html)
63 42
64 43
![image](images/proteinpaint/SGK1_NM_005627.svg)
SI.md
... ...
@@ -0,0 +1,33 @@
1
+# [SI]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|1.42 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.870 |1.809 |
19
+|DLBCL |No |No |0.717 |2.002 |
20
+|FL |No |No |0.455 |1.135 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SI_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SI_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/SI_NM_001041.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SI.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SI_hg38.html)
32
+
33
+![image](images/proteinpaint/SI.svg)
SIAH2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.72 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|2.34 |
14
+|DLBCL |Reddy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SIAH2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SIAH2_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/SIAH2_NM_005067.svg)
SIN3A.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |10.60 |
15 15
|BL |Panea cohort |14.90 |
16 16
|DLBCL |GAMBL genomes | 3.06 |
17
-|DLBCL |Schmitz cohort | 2.80 |
17
+|DLBCL |Schmitz cohort | 2.77 |
18 18
|DLBCL |Reddy cohort | 3.00 |
19
-|DLBCL |Chapuy cohort | 3.80 |
19
+|DLBCL |Chapuy cohort | 3.85 |
20 20
21 21
## Mutation pattern
22 22
SLC34A2.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.76 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|1.70 |
14
+|DLBCL |Reddy cohort |1.40 |
15
+|DLBCL |Chapuy cohort |0.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SLC34A2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SLC34A2_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/SLC34A2_NM_006424.svg)
SMARCA4.md
... ...
@@ -7,6 +7,7 @@
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9 9
|FL |1 |high-confidence FL gene |
10
+|MCL |1 |high-confidence MCL gene |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,10 +16,11 @@
15 16
|BL |Thomas cohort |17.80 |
16 17
|BL |Panea cohort |18.80 |
17 18
|DLBCL |GAMBL genomes | 3.25 |
18
-|DLBCL |Schmitz cohort | 3.00 |
19
+|DLBCL |Schmitz cohort | 2.98 |
19 20
|DLBCL |Reddy cohort | 3.30 |
20
-|DLBCL |Chapuy cohort | 2.10 |
21
+|DLBCL |Chapuy cohort | 2.14 |
21 22
|FL |GAMBL genomes | 4.16 |
23
+|MCL |GAMBL genomes | 4.74 |
22 24
23 25
## Mutation pattern
24 26
... ...
@@ -30,22 +32,8 @@
30 32
31 33
32 34
> [!NOTE]
33
-> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
34
-
35
-
36
- ## SMARCA4 Hotspots
37
-
38
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
39
- | :---:| :---: | :--: | :---: |
40
-| chr19 | 11134241 | C>A | H969Q |
41
-| chr19 | 11134251 | C>T | R973W |
42
-| chr19 | 11134252 | G>A | R973Q |
43
-| chr19 | 11141562 | C>T | P1180L |
44
-| chr19 | 11143973 | A>T | Q1185L |
45
-| chr19 | 11143982 | A>T | D1188V |
46
-| chr19 | 11143985 | G>A | R1189Q |
47
-| chr19 | 11143993 | C>T | R1192C |
48
-| chr19 | 11143994 | G>A | R1192H |
35
+> First described in BL in 2012 by [Love C](https://pubmed.ncbi.nlm.nih.gov/23143597). First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986). First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970)
36
+
49 37
50 38
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCA4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCA4_protein_hg38.html)
51 39
SMARCB1.md
... ...
@@ -0,0 +1,33 @@
1
+# [SMARCB1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|1.9 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |10.709 |0 |
19
+|DLBCL |No |No | 0.000 |0 |
20
+|FL |No |No |15.559 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCB1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCB1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/SMARCB1_NM_003073.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCB1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMARCB1_hg38.html)
32
+
33
+![image](images/proteinpaint/SMARCB1.svg)
SMC1A.md
... ...
@@ -0,0 +1,33 @@
1
+# [SMC1A]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0 |0 |
19
+|DLBCL |No |No |0 |0 |
20
+|FL |No |No |0 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMC1A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMC1A_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/SMC1A_NM_006306.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMC1A.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SMC1A_hg38.html)
32
+
33
+![image](images/proteinpaint/SMC1A.svg)
SMEK1.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes | NA |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort |0.9 |
15
-|DLBCL |Chapuy cohort |3.0 |
12
+|DLBCL |GAMBL genomes | NA |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
SOCS1.md
... ...
@@ -1,13 +1,12 @@
1
-SOCS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
1
+# [SOCS1]
2 2
3 3
## Mutation tier
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,8 +15,8 @@ SOCS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
16 15
|BL |Thomas cohort | 1.70 |
17 16
|BL |Panea cohort | 3.00 |
18 17
|DLBCL |GAMBL genomes |15.30 |
19
-|DLBCL |Schmitz cohort |12.80 |
20
-|DLBCL |Reddy cohort |10.40 |
18
+|DLBCL |Schmitz cohort |12.77 |
19
+|DLBCL |Reddy cohort |10.41 |
21 20
|DLBCL |Chapuy cohort | 4.70 |
22 21
|FL |GAMBL genomes | 9.70 |
23 22
... ...
@@ -36,37 +35,6 @@ SOCS1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
36 35
|chr16 |11347512 |11350007|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr16%3A11347512%2D11350007)|enhancer |
37 36
38 37
39
-
40
- ## SOCS1 Hotspots
41
-
42
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
43
- | :---:| :---: | :--: | :---: |
44
-| chr16 | 11349022 | T>C | D105G |
45
-| chr16 | 11349019 | C>T | S106N |
46
-| chr16 | 11349018 | G>C | S106R |
47
-| chr16 | 11349006 | G>C | N110K |
48
-| chr16 | 11349004 | C>T | C111Y |
49
-| chr16 | 11349004 | C>G | C111S |
50
-| chr16 | 11349003 | G>C | C111W |
51
-| chr16 | 11349001 | A>T | F112Y |
52
-| chr16 | 11348989 | C>T | S116N |
53
-| chr16 | 11348988 | G>C | S116R |
54
-| chr16 | 11348987 | C>T | V117M |
55
-| chr16 | 11348981 | T>C | M119V |
56
-| chr16 | 11348980 | A>T | M119K |
57
-| chr16 | 11348977 | G>C | A120G |
58
-| chr16 | 11348972 | C>T | G122R |
59
-| chr16 | 11348972 | C>A | G122* |
60
-| chr16 | 11348969 | G>A | P123S |
61
-| chr16 | 11348962 | C>G | S125T |
62
-| chr16 | 11348956 | C>T | R127H |
63
-| chr16 | 11348951 | G>T | H129N |
64
-| chr16 | 11348951 | G>A | H129Y |
65
-| chr16 | 11348945 | G>A | Q131* |
66
-| chr16 | 11348936 | G>A | R134C |
67
-| chr16 | 11348933 | A>G | F135L |
68
-| chr16 | 11348932 | A>C | F135C |
69
-
70 38
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SOCS1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SOCS1_protein_hg38.html)
71 39
72 40
![image](images/proteinpaint/SOCS1_NM_003745.svg)
SP140.md
... ...
@@ -0,0 +1,33 @@
1
+# [SP140]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|5.21 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.000 | 0.000 |
19
+|DLBCL |No |No |0.803 |11.118 |
20
+|FL |No |No |0.000 | 0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP140_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP140_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/SP140_NM_007237.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP140.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SP140_hg38.html)
32
+
33
+![image](images/proteinpaint/SP140.svg)
SPEN.md
... ...
@@ -11,8 +11,8 @@
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes | 4.78 |
13 13
|DLBCL |Schmitz cohort|10.00 |
14
-|DLBCL |Reddy cohort | 7.40 |
15
-|DLBCL |Chapuy cohort | 9.80 |
14
+|DLBCL |Reddy cohort | 7.41 |
15
+|DLBCL |Chapuy cohort | 9.83 |
16 16
17 17
## Mutation pattern
18 18
SRRM2.md
... ...
@@ -2,14 +2,19 @@
2 2
3 3
## Mutation tier
4 4
5
-|Entity|Tier|Description |
6
-|:------:|:----:|--------------------------------------|
7
-|FL |2 |relevance in FL not firmly established|
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|FL |2 |relevance in FL not firmly established |
8 9
## Mutation incidence
9 10
10
-|Entity|source |frequency (%)|
11
-|:------:|:-------------:|:-------------:|
12
-|FL |GAMBL genomes|1.39 |
11
+|Entity|source |frequency (%)|
12
+|:------:|:--------------:|:-------------:|
13
+|DLBCL |GAMBL genomes |3.06 |
14
+|DLBCL |Schmitz cohort|6.38 |
15
+|DLBCL |Reddy cohort |6.61 |
16
+|DLBCL |Chapuy cohort |6.84 |
17
+|FL |GAMBL genomes |1.39 |
13 18
14 19
## Mutation pattern
15 20
... ...
@@ -21,15 +26,9 @@
21 26
22 27
23 28
> [!NOTE]
24
-> First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
29
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
25 30
26 31
27
- ## SRRM2 Hotspots
28
-
29
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
30
- | :---:| :---: | :--: | :---: |
31
-| chr16 | 2814100 | C>T | P1191S |
32
-
33 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SRRM2_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SRRM2_protein_hg38.html)
34 33
35 34
![image](images/proteinpaint/SRRM2_NM_016333.svg)
ST6GAL1.md
... ...
@@ -0,0 +1,41 @@
1
+# [ST6GAL1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |1.15 |
13
+|DLBCL |Schmitz cohort|1.49 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |4.123 | 0.000 |
22
+|DLBCL |Yes |Yes |2.511 |33.311 |
23
+|FL |Yes |No |0.000 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end |region |regulatory_comment|
28
+|:--------:|:----------:|:---------:|:------------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr3 |186647943 |186650177|[TSS-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A186647943%2D186650177) |NA |
30
+|chr3 |186739628 |186740875|[TSS-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A186739628%2D186740875) |active_promoter |
31
+|chr3 |186709494 |186721749|[intron-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A186709494%2D186721749)|NA |
32
+|chr3 |186782522 |186784438|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr3%3A186782522%2D186784438)|strong_enhancer |
33
+
34
+
35
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ST6GAL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ST6GAL1_protein_hg38.html)
36
+
37
+![image](images/proteinpaint/ST6GAL1_NM_173216.svg)
38
+
39
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ST6GAL1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ST6GAL1_hg38.html)
40
+
41
+![image](images/proteinpaint/ST6GAL1.svg)
STAT3.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |0.00 |
15 15
|BL |Panea cohort |1.00 |
16 16
|DLBCL |GAMBL genomes |7.07 |
17
-|DLBCL |Schmitz cohort |9.40 |
17
+|DLBCL |Schmitz cohort |9.36 |
18 18
|DLBCL |Reddy cohort |3.60 |
19
-|DLBCL |Chapuy cohort |7.30 |
19
+|DLBCL |Chapuy cohort |7.26 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -27,7 +27,8 @@
27 27
|FL |No |No |34.737 | 0.000 |
28 28
29 29
30
-
30
+> [!NOTE]
31
+> First described in DLBCL in 2014 by [Ohgami RS](https://pubmed.ncbi.nlm.nih.gov/24837465)
31 32
32 33
## STAT3 Hotspots
33 34
STAT5B.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|0.40 |
13
+|DLBCL |Schmitz cohort|0.43 |
14 14
|DLBCL |Reddy cohort |1.60 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
STAT6.md
... ...
@@ -1,4 +1,4 @@
1
-# [STAT6]
1
+# STAT6
2 2
3 3
The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT signaling pathway, plays a significant role in the pathogenesis of various lymphomas, including diffuse large B-cell lymphoma (DLBCL). Below is a summary of the common mutations in the STAT6 gene identified in DLBCL. Mutations in the DNA binding domain of STAT6 are common in PMBCL and more rare in DLBCL.
4 4
... ...
@@ -17,7 +17,7 @@ The STAT6 gene, which encodes a transcription factor involved in the JAK-STAT si
17 17
|BL |Thomas cohort | 1.70 |
18 18
|BL |Panea cohort | 2.00 |
19 19
|DLBCL |GAMBL genomes | 5.74 |
20
-|DLBCL |Schmitz cohort | 2.60 |
20
+|DLBCL |Schmitz cohort | 2.55 |
21 21
|DLBCL |Reddy cohort | 3.80 |
22 22
|DLBCL |Chapuy cohort | 4.70 |
23 23
|FL |GAMBL genomes |15.94 |
SYK.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.53 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |0.80 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
SYNE1.md
... ...
@@ -0,0 +1,33 @@
1
+# [SYNE1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|4.74 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.000 |0.000 |
19
+|DLBCL |No |No |0.927 |2.598 |
20
+|FL |No |No |0.000 |0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNE1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNE1_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/SYNE1_NM_182961.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNE1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYNE1_hg38.html)
32
+
33
+![image](images/proteinpaint/SYNE1.svg)
SYPL1.md
... ...
@@ -0,0 +1,36 @@
1
+# [SYPL1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.96 |
13
+|DLBCL |Schmitz cohort|1.28 |
14
+|DLBCL |Reddy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.85 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |0.00 | 0.000 |
22
+|DLBCL |No |No |2.65 |26.779 |
23
+|FL |No |No |0.00 | 0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYPL1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYPL1_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/SYPL1_NM_006754.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYPL1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/SYPL1_hg38.html)
35
+
36
+![image](images/proteinpaint/SYPL1.svg)
TAF1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.78 |
13
-|DLBCL |Schmitz cohort|4.90 |
13
+|DLBCL |Schmitz cohort|4.89 |
14 14
|DLBCL |Reddy cohort |4.00 |
15
-|DLBCL |Chapuy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |3.85 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,7 @@
24 24
25 25
26 26
> [!NOTE]
27
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28 28
29 29
30 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAF1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TAF1_protein_hg38.html)
TAP1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.57 |
13
-|DLBCL |Schmitz cohort|3.60 |
13
+|DLBCL |Schmitz cohort|3.62 |
14 14
|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
TBC1D26.md
... ...
@@ -0,0 +1,33 @@
1
+# [TBC1D26]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0 |0 |
19
+|DLBCL |No |No |0 |0 |
20
+|FL |No |No |0 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D26_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D26_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/TBC1D26_NM_178571.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D26.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D26_hg38.html)
32
+
33
+![image](images/proteinpaint/TBC1D26.svg)
TBC1D4.md
... ...
@@ -0,0 +1,38 @@
1
+# [TBC1D4]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |2.29 |
13
+|DLBCL |Schmitz cohort|5.11 |
14
+|DLBCL |Reddy cohort |2.70 |
15
+|DLBCL |Chapuy cohort |5.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |0.792 |0.000 |
22
+|DLBCL |Yes |No |1.783 |6.266 |
23
+|FL |Yes |No |0.860 |0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:---------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr13 |75982519 |75986015|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr13%3A75982519%2D75986015)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D4_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D4_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/TBC1D4_NM_014832.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D4.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TBC1D4_hg38.html)
37
+
38
+![image](images/proteinpaint/TBC1D4.svg)
TBL1XR1.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 4.70 |
16 16
|BL |Panea cohort | 7.90 |
17 17
|DLBCL |GAMBL genomes | 8.60 |
18
-|DLBCL |Schmitz cohort |12.80 |
19
-|DLBCL |Reddy cohort | 5.70 |
20
-|DLBCL |Chapuy cohort | 8.10 |
18
+|DLBCL |Schmitz cohort |12.77 |
19
+|DLBCL |Reddy cohort | 5.71 |
20
+|DLBCL |Chapuy cohort | 8.12 |
21 21
|FL |GAMBL genomes | 3.93 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,6 +29,8 @@
29 29
|FL |No |No |12.400 |18.940 |
30 30
31 31
32
+> [!NOTE]
33
+> First described in DLBCL in 2016 by [Mareschal S](https://pubmed.ncbi.nlm.nih.gov/26608593)
32 34
33 35
34 36
## TBL1XR1 Hotspots
TCL1A.md
... ...
@@ -4,8 +4,9 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|BL |1-a | aSHM target and high-confidence BL gene |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9
+
9 10
## Mutation incidence
10 11
11 12
|Entity|source |frequency (%)|
... ...
@@ -14,9 +15,9 @@
14 15
|BL |Thomas cohort |5.90 |
15 16
|BL |Panea cohort |4.00 |
16 17
|DLBCL |GAMBL genomes |2.10 |
17
-|DLBCL |Schmitz cohort |3.80 |
18
+|DLBCL |Schmitz cohort |3.83 |
18 19
|DLBCL |Reddy cohort |2.80 |
19
-|DLBCL |Chapuy cohort |3.00 |
20
+|DLBCL |Chapuy cohort |2.99 |
20 21
21 22
## Mutation pattern
22 23
TERT.md
... ...
@@ -0,0 +1,33 @@
1
+# [TERT]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|------------------------|
7
+|MCL |1 |high-confidence MCL gene|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0.000 |0 |
19
+|DLBCL |No |No |1.429 |0 |
20
+|FL |No |No |0.000 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2020 by [Nadeu F](https://pubmed.ncbi.nlm.nih.gov/32584970)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TERT_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TERT_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/TERT_NM_198253.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TERT.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TERT_hg38.html)
32
+
33
+![image](images/proteinpaint/TERT.svg)
TET2.md
... ...
@@ -15,8 +15,8 @@
15 15
|BL |Panea cohort |10.90 |
16 16
|DLBCL |GAMBL genomes | 5.54 |
17 17
|DLBCL |Schmitz cohort |11.70 |
18
-|DLBCL |Reddy cohort | 7.40 |
19
-|DLBCL |Chapuy cohort | 6.00 |
18
+|DLBCL |Reddy cohort | 7.41 |
19
+|DLBCL |Chapuy cohort | 5.98 |
20 20
21 21
## Mutation pattern
22 22
TGFBR2.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|1.9 |
14
-|DLBCL |Reddy cohort |1.9 |
15
-|DLBCL |Chapuy cohort |1.3 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |1.90 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
TIPARP.md
... ...
@@ -10,7 +10,7 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.19 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort |0.90 |
15 15
|DLBCL |Chapuy cohort | NA |
16 16
... ...
@@ -26,9 +26,6 @@
26 26
> [!NOTE]
27 27
> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
28 28
29
-> [!WARNING]
30
-> Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1)
31
-
32 29
33 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIPARP_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TIPARP_protein_hg38.html)
34 31
TLR2.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |2.87 |
13
-|DLBCL |Schmitz cohort|2.80 |
14
+|DLBCL |Schmitz cohort|2.77 |
14 15
|DLBCL |Reddy cohort |1.50 |
15
-|DLBCL |Chapuy cohort |3.00 |
16
+|DLBCL |Chapuy cohort |2.99 |
17
+|MCL |GAMBL genomes |0.00 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -24,7 +26,7 @@
24 26
25 27
26 28
> [!NOTE]
27
-> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087)
29
+> First described in DLBCL in 2018 by [Chapuy B](https://pubmed.ncbi.nlm.nih.gov/29713087). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
28 30
29 31
30 32
## TLR2 Hotspots
TMEM30A.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort |1.30 |
16 16
|BL |Panea cohort |5.00 |
17 17
|DLBCL |GAMBL genomes |4.78 |
18
-|DLBCL |Schmitz cohort |7.70 |
18
+|DLBCL |Schmitz cohort |7.66 |
19 19
|DLBCL |Reddy cohort |2.80 |
20
-|DLBCL |Chapuy cohort |5.60 |
20
+|DLBCL |Chapuy cohort |5.56 |
21 21
|FL |GAMBL genomes |0.92 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@
29 29
|FL |No |No |5.098 | 0.000 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33 34
34 35
## TMEM30A Hotspots
35 36
TMSB4X.md
... ...
@@ -4,10 +4,9 @@ TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|FL |1-a |high-confidence FL gene, hypermutated |
9
-|BL |2 |relevance in BL not firmly established|
10
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
+|FL |1-a | aSHM target and high-confidence FL gene |
11 10
## Mutation incidence
12 11
13 12
|Entity|source |frequency (%)|
... ...
@@ -16,9 +15,9 @@ TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
16 15
|BL |Thomas cohort | 0.00 |
17 16
|BL |Panea cohort | 2.00 |
18 17
|DLBCL |GAMBL genomes |12.43 |
19
-|DLBCL |Schmitz cohort |18.10 |
20
-|DLBCL |Reddy cohort |13.10 |
21
-|DLBCL |Chapuy cohort |18.40 |
18
+|DLBCL |Schmitz cohort |20.85 |
19
+|DLBCL |Reddy cohort |13.11 |
20
+|DLBCL |Chapuy cohort |18.38 |
22 21
|FL |GAMBL genomes | 4.39 |
23 22
24 23
## Mutation pattern
... ...
@@ -35,6 +34,8 @@ TMSB4X is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm
35 34
|:--------:|:----------:|:--------:|:--------------------------------------------------------------------------------------------:|:------------------:|
36 35
|chrX |12993308 |12994511|[intron](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chrX%3A12993308%2D12994511)|active_promoter |
37 36
37
+> [!NOTE]
38
+> First described in DLBCL in 2017 by [Albuquerque MA](https://pubmed.ncbi.nlm.nih.gov/28327945)
38 39
39 40
40 41
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMSB4X_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TMSB4X_protein_hg38.html)
TNFAIP3.md
... ...
@@ -16,8 +16,8 @@
16 16
|BL |Panea cohort | 2.00 |
17 17
|DLBCL |GAMBL genomes | 6.69 |
18 18
|DLBCL |Schmitz cohort |16.60 |
19
-|DLBCL |Reddy cohort | 8.10 |
20
-|DLBCL |Chapuy cohort |12.40 |
19
+|DLBCL |Reddy cohort | 8.11 |
20
+|DLBCL |Chapuy cohort |12.39 |
21 21
|FL |GAMBL genomes | 4.85 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@
29 29
|FL |No |No |5.686 |75.953 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2009 by [Compagno M](https://pubmed.ncbi.nlm.nih.gov/19412164). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33 34
34 35
## TNFAIP3 Hotspots
35 36
TNFRSF14.md
... ...
@@ -15,9 +15,9 @@
15 15
|BL |Thomas cohort | 0.80 |
16 16
|BL |Panea cohort | 3.00 |
17 17
|DLBCL |GAMBL genomes |14.34 |
18
-|DLBCL |Schmitz cohort |16.80 |
19
-|DLBCL |Reddy cohort | 9.70 |
20
-|DLBCL |Chapuy cohort |12.80 |
18
+|DLBCL |Schmitz cohort |16.81 |
19
+|DLBCL |Reddy cohort | 9.71 |
20
+|DLBCL |Chapuy cohort |12.82 |
21 21
|FL |GAMBL genomes |40.42 |
22 22
23 23
## Mutation pattern
... ...
@@ -29,7 +29,8 @@
29 29
|FL |No |Yes |96.380 |1034.281 |
30 30
31 31
32
-
32
+> [!NOTE]
33
+> First described in DLBCL in 2010 by [Cheung KJ](https://pubmed.ncbi.nlm.nih.gov/20884631). First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119)
33 34
34 35
## TNFRSF14 Hotspots
35 36
TOX.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |0.80 |
15 15
|BL |Panea cohort |5.90 |
16 16
|DLBCL |GAMBL genomes |4.21 |
17
-|DLBCL |Schmitz cohort |5.50 |
17
+|DLBCL |Schmitz cohort |5.53 |
18 18
|DLBCL |Reddy cohort |4.00 |
19
-|DLBCL |Chapuy cohort |5.10 |
19
+|DLBCL |Chapuy cohort |5.13 |
20 20
21 21
## Mutation pattern
22 22
TP53.md
... ...
@@ -7,6 +7,7 @@
7 7
|BL |1 |high-confidence BL gene |
8 8
|DLBCL |1 |high-confidence DLBCL gene|
9 9
|FL |1 |high-confidence FL gene |
10
+|MCL |1 |high-confidence MCL gene |
10 11
## Mutation incidence
11 12
12 13
|Entity|source |frequency (%)|
... ...
@@ -15,10 +16,11 @@
15 16
|BL |Thomas cohort |41.90 |
16 17
|BL |Panea cohort |43.60 |
17 18
|DLBCL |GAMBL genomes |27.53 |
18
-|DLBCL |Schmitz cohort |22.30 |
19
-|DLBCL |Reddy cohort |10.90 |
20
-|DLBCL |Chapuy cohort |21.40 |
19
+|DLBCL |Schmitz cohort |22.34 |
20
+|DLBCL |Reddy cohort |10.91 |
21
+|DLBCL |Chapuy cohort |21.37 |
21 22
|FL |GAMBL genomes | 6.93 |
23
+|MCL |GAMBL genomes | 9.00 |
22 24
23 25
## Mutation pattern
24 26
... ...
@@ -29,6 +31,8 @@
29 31
|FL |No |Yes | 63.211 |142.226 |
30 32
31 33
34
+> [!NOTE]
35
+> First described in FL in 2011 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/21796119). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
32 36
33 37
34 38
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TP53_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TP53_protein_hg38.html)
TPP1.md
... ...
@@ -21,6 +21,9 @@
21 21
22 22
23 23
> [!NOTE]
24
+> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25
+
26
+
24 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TPP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TPP1_protein_hg38.html)
25 28
26 29
![image](images/proteinpaint/TPP1_NM_000391.svg)
TRAF3.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |0.96 |
13
-|DLBCL |Schmitz cohort|1.50 |
13
+|DLBCL |Schmitz cohort|1.49 |
14 14
|DLBCL |Reddy cohort |0.90 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -23,6 +23,8 @@
23 23
|FL |No |No |0.000 |0 |
24 24
25 25
26
+> [!NOTE]
27
+> First described in DLBCL in 2011 by [Pasqualucci L](https://pubmed.ncbi.nlm.nih.gov/21804550)
26 28
27 29
28 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRAF3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRAF3_protein_hg38.html)
TRAF6.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|1.49 |
14
+|DLBCL |Reddy cohort |0.90 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,8 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
27 29
## TRAF6 Hotspots
28 30
29 31
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
TRIP12.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.25 |
13
-|DLBCL |Schmitz cohort|6.00 |
13
+|DLBCL |Schmitz cohort|5.96 |
14 14
|DLBCL |Reddy cohort |3.20 |
15
-|DLBCL |Chapuy cohort |3.00 |
15
+|DLBCL |Chapuy cohort |2.99 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRIP12_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/TRIP12_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/TRIP12_NM_004238.svg)
TRRAP.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |2.87 |
13
-|DLBCL |Schmitz cohort|8.90 |
13
+|DLBCL |Schmitz cohort|8.94 |
14 14
|DLBCL |Reddy cohort |3.50 |
15
-|DLBCL |Chapuy cohort |6.00 |
15
+|DLBCL |Chapuy cohort |5.98 |
16 16
17 17
## Mutation pattern
18 18
UBE2A.md
... ...
@@ -14,7 +14,7 @@
14 14
|BL |Thomas cohort |0.00 |
15 15
|BL |Panea cohort |3.00 |
16 16
|DLBCL |GAMBL genomes |4.21 |
17
-|DLBCL |Schmitz cohort |7.00 |
17
+|DLBCL |Schmitz cohort |7.02 |
18 18
|DLBCL |Reddy cohort |3.90 |
19 19
|DLBCL |Chapuy cohort |4.70 |
20 20
... ...
@@ -28,7 +28,6 @@
28 28
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2A_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/UBE2A_NM_003336.svg)
UBE2J1.md
... ...
@@ -0,0 +1,38 @@
1
+# [UBE2J1]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.76 |
13
+|DLBCL |Schmitz cohort|1.28 |
14
+|DLBCL |Reddy cohort |0.80 |
15
+|DLBCL |Chapuy cohort |0.43 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No | 0.000 |22.392 |
22
+|DLBCL |Yes |No | 0.000 |11.415 |
23
+|FL |Yes |No |12.947 | 0.000 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
29
+|chr6 |90059730 |90063703|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90059730%2D90063703)|NA |
30
+
31
+
32
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2J1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2J1_protein_hg38.html)
33
+
34
+![image](images/proteinpaint/UBE2J1_NM_016021.svg)
35
+
36
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2J1.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBE2J1_hg38.html)
37
+
38
+![image](images/proteinpaint/UBE2J1.svg)
UBR5.md
... ...
@@ -5,14 +5,16 @@
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
+|MCL |1 |high-confidence MCL gene |
8 9
## Mutation incidence
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
12 13
|DLBCL |GAMBL genomes |3.63 |
13
-|DLBCL |Schmitz cohort|5.50 |
14
+|DLBCL |Schmitz cohort|5.53 |
14 15
|DLBCL |Reddy cohort |3.20 |
15
-|DLBCL |Chapuy cohort |5.10 |
16
+|DLBCL |Chapuy cohort |5.13 |
17
+|MCL |GAMBL genomes |9.00 |
16 18
17 19
## Mutation pattern
18 20
... ...
@@ -24,7 +26,7 @@
24 26
25 27
26 28
> [!NOTE]
27
-> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937)
29
+> First described in DLBCL in 2013 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/23292937). First described in MCL in 2020 by [Pararajalingam P](https://pubmed.ncbi.nlm.nih.gov/32160292)
28 30
29 31
30 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBR5_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UBR5_protein_hg38.html)
UNC5B.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.53 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |1.80 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5B_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5B_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/UNC5B_NM_170744.svg)
UNC5C.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.44 |
13
-|DLBCL |Schmitz cohort|5.10 |
13
+|DLBCL |Schmitz cohort|5.11 |
14 14
|DLBCL |Reddy cohort |2.20 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5C_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5C_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/UNC5C_NM_003728.svg)
UNC5D.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort|1.9 |
14
-|DLBCL |Reddy cohort |1.8 |
15
-|DLBCL |Chapuy cohort |2.6 |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|1.91 |
14
+|DLBCL |Reddy cohort |1.80 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,7 +24,6 @@
24 24
25 25
26 26
27
-
28 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5D_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/UNC5D_protein_hg38.html)
29 28
30 29
![image](images/proteinpaint/UNC5D_NM_080872.svg)
USP7.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort |6.80 |
15 15
|BL |Panea cohort |5.90 |
16 16
|DLBCL |GAMBL genomes |1.34 |
17
-|DLBCL |Schmitz cohort |3.20 |
17
+|DLBCL |Schmitz cohort |3.19 |
18 18
|DLBCL |Reddy cohort |1.10 |
19
-|DLBCL |Chapuy cohort |3.80 |
19
+|DLBCL |Chapuy cohort |3.85 |
20 20
21 21
## Mutation pattern
22 22
... ...
@@ -28,7 +28,6 @@
28 28
29 29
30 30
31
-
32 31
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/USP7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/USP7_protein_hg38.html)
33 32
34 33
![image](images/proteinpaint/USP7_NM_003470.svg)
VMA21.md
... ...
@@ -24,14 +24,6 @@
24 24
> First described in FL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
25 25
26 26
27
- ## VMA21 Hotspots
28
-
29
-| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
30
- | :---:| :---: | :--: | :---: |
31
-| chrX | 150573501 | C>T | R93* |
32
-| chrX | 150573509 | G>T | W95C |
33
-| chrX | 150573519 | A>G | K99E |
34
-
35 27
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VMA21_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/VMA21_protein_hg38.html)
36 28
37 29
![image](images/proteinpaint/VMA21_NM_001017980.svg)
VPS13B.md
... ...
@@ -11,8 +11,8 @@
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |4.21 |
13 13
|DLBCL |Schmitz cohort|8.30 |
14
-|DLBCL |Reddy cohort |5.70 |
15
-|DLBCL |Chapuy cohort |4.30 |
14
+|DLBCL |Reddy cohort |5.71 |
15
+|DLBCL |Chapuy cohort |4.27 |
16 16
17 17
## Mutation pattern
18 18
WAC.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |2.68 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |1.20 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
WDFY3.md
... ...
@@ -0,0 +1,36 @@
1
+# [WDFY3]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |4.21 |
13
+|DLBCL |Schmitz cohort|8.30 |
14
+|DLBCL |Reddy cohort |4.70 |
15
+|DLBCL |Chapuy cohort |7.26 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |No |No |2.696 |0.000 |
22
+|DLBCL |No |No |1.207 |3.494 |
23
+|FL |No |No |2.069 |0.000 |
24
+
25
+
26
+> [!NOTE]
27
+> First described in DLBCL in 2013 by [Morin RD](https://pubmed.ncbi.nlm.nih.gov/23699601)
28
+
29
+
30
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDFY3_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDFY3_protein_hg38.html)
31
+
32
+![image](images/proteinpaint/WDFY3_NM_014991.svg)
33
+
34
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDFY3.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/WDFY3_hg38.html)
35
+
36
+![image](images/proteinpaint/WDFY3.svg)
WEE1.md
... ...
@@ -4,16 +4,15 @@ WEE1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8
-
7
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene|
9 8
## Mutation incidence
10 9
11 10
|Entity|source |frequency (%)|
12 11
|:------:|:--------------:|:-------------:|
13 12
|DLBCL |GAMBL genomes |4.02 |
14
-|DLBCL |Schmitz cohort|2.80 |
13
+|DLBCL |Schmitz cohort|2.77 |
15 14
|DLBCL |Reddy cohort |1.60 |
16
-|DLBCL |Chapuy cohort |1.70 |
15
+|DLBCL |Chapuy cohort |1.71 |
17 16
18 17
## Mutation pattern
19 18
WNK1.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | 6.80 |
15 15
|BL |Panea cohort |11.90 |
16 16
|DLBCL |GAMBL genomes | 4.59 |
17
-|DLBCL |Schmitz cohort | NA |
18
-|DLBCL |Reddy cohort | NA |
19
-|DLBCL |Chapuy cohort | NA |
17
+|DLBCL |Schmitz cohort | 5.11 |
18
+|DLBCL |Reddy cohort | 3.70 |
19
+|DLBCL |Chapuy cohort | 2.14 |
20 20
21 21
## Mutation pattern
22 22
XBP1.md
... ...
@@ -4,13 +4,13 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.15 |
13
-|DLBCL |Schmitz cohort|1.30 |
13
+|DLBCL |Schmitz cohort|1.28 |
14 14
|DLBCL |Reddy cohort |1.60 |
15 15
|DLBCL |Chapuy cohort | NA |
16 16
... ...
@@ -29,7 +29,6 @@
29 29
|chr22 |29194943 |29197461|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr22%3A29194943%2D29197461)|NA |
30 30
31 31
32
-
33 32
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XBP1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/XBP1_protein_hg38.html)
34 33
35 34
![image](images/proteinpaint/XBP1_NM_005080.svg)
XPO1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|2.30 |
13
+|DLBCL |Schmitz cohort|2.34 |
14 14
|DLBCL |Reddy cohort |1.40 |
15
-|DLBCL |Chapuy cohort |1.30 |
15
+|DLBCL |Chapuy cohort |1.28 |
16 16
17 17
## Mutation pattern
18 18
YY1.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.15 |
13
-|DLBCL |Schmitz cohort|4.30 |
13
+|DLBCL |Schmitz cohort|4.26 |
14 14
|DLBCL |Reddy cohort |1.10 |
15
-|DLBCL |Chapuy cohort |3.80 |
15
+|DLBCL |Chapuy cohort |3.85 |
16 16
17 17
## Mutation pattern
18 18
ZAN.md
... ...
@@ -15,8 +15,7 @@
15 15
16 16
## Mutation pattern
17 17
18
-|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19
-|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|
20 19
21 20
22 21
> [!NOTE]
ZBTB7A.md
... ...
@@ -14,9 +14,9 @@
14 14
|BL |Thomas cohort | NA |
15 15
|BL |Panea cohort | NA |
16 16
|DLBCL |GAMBL genomes |1.72 |
17
-|DLBCL |Schmitz cohort |1.50 |
17
+|DLBCL |Schmitz cohort |1.49 |
18 18
|DLBCL |Reddy cohort |1.30 |
19
-|DLBCL |Chapuy cohort |1.70 |
19
+|DLBCL |Chapuy cohort |1.71 |
20 20
21 21
## Mutation pattern
22 22
ZC3H12A.md
... ...
@@ -11,7 +11,7 @@
11 11
|Entity|source |frequency (%)|
12 12
|:------:|:--------------:|:-------------:|
13 13
|DLBCL |GAMBL genomes |2.68 |
14
-|DLBCL |Schmitz cohort|6.00 |
14
+|DLBCL |Schmitz cohort|5.96 |
15 15
|DLBCL |Reddy cohort |3.10 |
16 16
|DLBCL |Chapuy cohort |4.70 |
17 17
|FL |GAMBL genomes |0.46 |
... ...
@@ -26,7 +26,6 @@
26 26
27 27
28 28
29
-
30 29
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZC3H12A_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZC3H12A_protein_hg38.html)
31 30
32 31
![image](images/proteinpaint/ZC3H12A_NM_025079.svg)
ZCCHC7.md
... ...
@@ -0,0 +1,44 @@
1
+# [ZCCHC7]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|-----------------------------------------|
7
+|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:--------------:|:-------------:|
12
+|DLBCL |GAMBL genomes |0.57 |
13
+|DLBCL |Schmitz cohort|0.85 |
14
+|DLBCL |Reddy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |2.56 |
16
+
17
+## Mutation pattern
18
+
19
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
21
+|BL |Yes |No |2.124 |0 |
22
+|DLBCL |Yes |No |1.558 |0 |
23
+|FL |Yes |No |0.000 |0 |
24
+
25
+## aSHM regions
26
+
27
+|chr_name|hg19_start|hg19_end|region |regulatory_comment|
28
+|:--------:|:----------:|:--------:|:----------------------------------------------------------------------------------------------:|:------------------:|
29
+|chr9 |37192080 |37207549|[intron-4](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37192080%2D37207549)|intron |
30
+|chr9 |37275952 |37306152|[intron-2](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37275952%2D37306152)|intron |
31
+|chr9 |37312655 |37328260|[intron-3](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37312655%2D37328260)|intron |
32
+|chr9 |37329706 |37340398|[intron-1](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr9%3A37329706%2D37340398)|intron |
33
+
34
+> [!NOTE]
35
+> First described in DLBCL in 2018 by [Arthur SE](https://pubmed.ncbi.nlm.nih.gov/30275490)
36
+
37
+
38
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZCCHC7_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZCCHC7_protein_hg38.html)
39
+
40
+![image](images/proteinpaint/ZCCHC7_NM_032226.svg)
41
+
42
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZCCHC7.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZCCHC7_hg38.html)
43
+
44
+![image](images/proteinpaint/ZCCHC7.svg)
ZEB2.md
... ...
@@ -4,15 +4,15 @@
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
7
+|DLBCL |2 |relevance in DLBCL not firmly established|
8 8
## Mutation incidence
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |3.82 |
13
-|DLBCL |Schmitz cohort|6.80 |
13
+|DLBCL |Schmitz cohort|6.81 |
14 14
|DLBCL |Reddy cohort |3.70 |
15
-|DLBCL |Chapuy cohort |6.00 |
15
+|DLBCL |Chapuy cohort |5.98 |
16 16
17 17
## Mutation pattern
18 18
ZFAT.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |1.34 |
13
-|DLBCL |Schmitz cohort|2.80 |
13
+|DLBCL |Schmitz cohort|2.77 |
14 14
|DLBCL |Reddy cohort |2.70 |
15
-|DLBCL |Chapuy cohort |2.60 |
15
+|DLBCL |Chapuy cohort |2.56 |
16 16
17 17
## Mutation pattern
18 18
ZFP36L1.md
... ...
@@ -4,9 +4,8 @@ ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7
-|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
8
-|BL |2 |relevance in BL not firmly established|
9
-
7
+|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
+|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 9
## Mutation incidence
11 10
12 11
|Entity|source |frequency (%)|
... ...
@@ -15,9 +14,9 @@ ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
15 14
|BL |Thomas cohort |2.10 |
16 15
|BL |Panea cohort |3.00 |
17 16
|DLBCL |GAMBL genomes |6.69 |
18
-|DLBCL |Schmitz cohort |8.50 |
19
-|DLBCL |Reddy cohort |5.60 |
20
-|DLBCL |Chapuy cohort |8.10 |
17
+|DLBCL |Schmitz cohort |8.51 |
18
+|DLBCL |Reddy cohort |5.61 |
19
+|DLBCL |Chapuy cohort |8.12 |
21 20
22 21
## Mutation pattern
23 22
... ...
@@ -34,7 +33,6 @@ ZFP36L1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ash
34 33
|chr14 |69257848 |69259739|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr14%3A69257848%2D69259739)|active_promoter |
35 34
36 35
37
-
38 36
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFP36L1_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZFP36L1_protein_hg38.html)
39 37
40 38
![image](images/proteinpaint/ZFP36L1_NM_004926.svg)
ZFX.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |0.38 |
13 13
|DLBCL |Schmitz cohort|1.70 |
14 14
|DLBCL |Reddy cohort |1.40 |
15
-|DLBCL |Chapuy cohort |0.40 |
15
+|DLBCL |Chapuy cohort |0.43 |
16 16
17 17
## Mutation pattern
18 18
ZNF117.md
... ...
@@ -0,0 +1,33 @@
1
+# [ZNF117]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |0 |0 |
19
+|DLBCL |No |No |0 |0 |
20
+|FL |No |No |0 |0 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF117_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF117_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/ZNF117_NM_015852.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF117.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF117_hg38.html)
32
+
33
+![image](images/proteinpaint/ZNF117.svg)
ZNF217.md
... ...
@@ -9,10 +9,10 @@
9 9
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12
-|DLBCL |GAMBL genomes |2.1 |
13
-|DLBCL |Schmitz cohort| NA |
14
-|DLBCL |Reddy cohort | NA |
15
-|DLBCL |Chapuy cohort | NA |
12
+|DLBCL |GAMBL genomes |2.10 |
13
+|DLBCL |Schmitz cohort|2.98 |
14
+|DLBCL |Reddy cohort |2.90 |
15
+|DLBCL |Chapuy cohort |2.14 |
16 16
17 17
## Mutation pattern
18 18
... ...
@@ -24,6 +24,9 @@
24 24
25 25
26 26
> [!NOTE]
27
+> First described in DLBCL in 2021 by [Hübschmann D](https://pubmed.ncbi.nlm.nih.gov/33953289)
28
+
29
+
27 30
View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF217_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF217_protein_hg38.html)
28 31
29 32
![image](images/proteinpaint/ZNF217_NM_006526.svg)
ZNF292.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |5.35 |
13
-|DLBCL |Schmitz cohort|6.40 |
13
+|DLBCL |Schmitz cohort|6.38 |
14 14
|DLBCL |Reddy cohort |4.30 |
15
-|DLBCL |Chapuy cohort |6.00 |
15
+|DLBCL |Chapuy cohort |5.98 |
16 16
17 17
## Mutation pattern
18 18
ZNF296.md
... ...
@@ -0,0 +1,33 @@
1
+# [ZNF296]
2
+
3
+## Mutation tier
4
+
5
+|Entity|Tier|Description |
6
+|:------:|:----:|---------------------------------------|
7
+|MCL |2 |relevance in MCL not firmly established|
8
+## Mutation incidence
9
+
10
+|Entity|source |frequency (%)|
11
+|:------:|:-------------:|:-------------:|
12
+|MCL |GAMBL genomes|0 |
13
+
14
+## Mutation pattern
15
+
16
+|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17
+|:------:|:----:|:---------------------:|:----------------:|:----------------:|
18
+|BL |No |No |1.512 |35.625 |
19
+|DLBCL |No |No |0.000 | 0.000 |
20
+|FL |No |No |0.000 | 0.000 |
21
+
22
+
23
+> [!NOTE]
24
+> First described in MCL in 2014 by [Zhang J](https://pubmed.ncbi.nlm.nih.gov/24682267)
25
+
26
+
27
+View coding variants in ProteinPaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF296_protein.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF296_protein_hg38.html)
28
+
29
+![image](images/proteinpaint/ZNF296_NM_145288.svg)
30
+
31
+View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF296.html) or [hg38](https://www.bcgsc.ca/downloads/morinlab/GAMBL/test/genes/ZNF296_hg38.html)
32
+
33
+![image](images/proteinpaint/ZNF296.svg)
ZNF423.md
... ...
@@ -12,7 +12,7 @@
12 12
|DLBCL |GAMBL genomes |1.91 |
13 13
|DLBCL |Schmitz cohort|3.40 |
14 14
|DLBCL |Reddy cohort |2.10 |
15
-|DLBCL |Chapuy cohort |3.40 |
15
+|DLBCL |Chapuy cohort |3.42 |
16 16
17 17
## Mutation pattern
18 18
ZNF608.md
... ...
@@ -10,9 +10,9 @@
10 10
|Entity|source |frequency (%)|
11 11
|:------:|:--------------:|:-------------:|
12 12
|DLBCL |GAMBL genomes |6.12 |
13
-|DLBCL |Schmitz cohort|9.40 |
14
-|DLBCL |Reddy cohort |8.10 |
15
-|DLBCL |Chapuy cohort |7.70 |
13
+|DLBCL |Schmitz cohort|9.36 |
14
+|DLBCL |Reddy cohort |8.11 |
15
+|DLBCL |Chapuy cohort |7.69 |
16 16
17 17
## Mutation pattern
18 18
tier1_pmbl_hl_gz.md
... ...
@@ -0,0 +1,76 @@
1
+| Category | Gene | Details | Mutation frequency | Static view (Gene) | Static view (Protein) | Comment |
2
+| :---: | :----: | :---: | :---: | :---: |
3
+|:--:|[ACTB](ACTB)|:-:|:-:|
4
+|1|[ARID1A](ARID1A)||[view](images/proteinpaint/ARID1A.svg)|[view](images/proteinpaint/ARID1A_NM_006015.svg)|
5
+|1|[ARID5B](ARID5B)||[view](images/proteinpaint/ARID5B.svg)|[view](images/proteinpaint/ARID5B_NM_032199.svg)|
6
+|1|[B2M](B2M)||[view](images/proteinpaint/B2M.svg)|[view](images/proteinpaint/B2M_NM_004048.svg)|
7
+|1|[BIRC6](BIRC6)||[view](images/proteinpaint/BIRC6.svg)|[view](images/proteinpaint/BIRC6_NM_016252.svg)|
8
+|1-a|[BTG1](BTG1)||[view](images/proteinpaint/BTG1.svg)|[view](images/proteinpaint/BTG1_NM_001731.svg)|
9
+|1|[CARD11](CARD11)||[view](images/proteinpaint/CARD11.svg)|[view](images/proteinpaint/CARD11_NM_032415.svg)|
10
+|1|[CD58](CD58)||[view](images/proteinpaint/CD58.svg)|[view](images/proteinpaint/CD58_NM_001779.svg)|
11
+|1-a|[CD83](CD83)||[view](images/proteinpaint/CD83.svg)|[view](images/proteinpaint/CD83_NM_004233.svg)|
12
+|1|[CDKN2A](CDKN2A)||[view](images/proteinpaint/CDKN2A.svg)|[view](images/proteinpaint/CDKN2A_NM_000077.svg)|
13
+|1|[CHD8](CHD8)||[view](images/proteinpaint/CHD8.svg)|[view](images/proteinpaint/CHD8_NM_001170629.svg)|
14
+|1|[CREBBP](CREBBP)||[view](images/proteinpaint/CREBBP.svg)|[view](images/proteinpaint/CREBBP_NM_004380.svg)|
15
+|1|[CSF2RB](CSF2RB)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CSF2RB.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CSF2RB_protein.html)|
16
+|1|[DDX3X](DDX3X)||[view](images/proteinpaint/DDX3X.svg)|[view](images/proteinpaint/DDX3X_NM_001356.svg)|
17
+|1-a|[DTX1](DTX1)||[view](images/proteinpaint/DTX1.svg)|[view](images/proteinpaint/DTX1_NM_004416.svg)|
18
+|1-a|[DUSP2](DUSP2)||[view](images/proteinpaint/DUSP2.svg)|[view](images/proteinpaint/DUSP2_NM_004418.svg)|
19
+|1-a|[EBF1](EBF1)||[view](images/proteinpaint/EBF1.svg)|[view](images/proteinpaint/EBF1_NM_024007.svg)|
20
+|1|[EP300](EP300)||[view](images/proteinpaint/EP300.svg)|[view](images/proteinpaint/EP300_NM_001429.svg)|
21
+|1-a|[ETS1](ETS1)||[view](images/proteinpaint/ETS1.svg)|[view](images/proteinpaint/ETS1_NM_001143820.svg)|
22
+|1|[EWSR1](EWSR1)||[view](images/proteinpaint/EWSR1.svg)|[view](images/proteinpaint/EWSR1_NM_013986.svg)|
23
+|1|[EZH2](EZH2)||[view](images/proteinpaint/EZH2.svg)|[view](images/proteinpaint/EZH2_NM_001203247.svg)|
24
+|1|[FAS](FAS)||[view](images/proteinpaint/FAS.svg)|[view](images/proteinpaint/FAS_NM_000043.svg)|
25
+|1|[FAT1](FAT1)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/FAT1.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/FAT1_protein.html)|
26
+|1|[FAT4](FAT4)||[view](images/proteinpaint/FAT4.svg)|[view](images/proteinpaint/FAT4_NM_024582.svg)|
27
+|1|[GNA13](GNA13)||[view](images/proteinpaint/GNA13.svg)|[view](images/proteinpaint/GNA13_NM_006572.svg)|
28
+|1|[H1-2](H1-2)(HIST1H1C)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/H1-2.html)|[view](images/proteinpaint/HIST1H1C_NM_005319.svg)|
29
+|1|[H1-3](H1-3)(HIST1H1D)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/H1-3.html)|[view](images/proteinpaint/HIST1H1D_NM_005320.svg)|
30
+|1|[H1-4](H1-4)(HIST1H1E)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/H1-4.html)|[view](images/proteinpaint/HIST1H1E_NM_005321.svg)|
31
+|1|[H1-5](H1-5)(HIST1H1B)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/H1-5.html)|[view](images/proteinpaint/HIST1H1B_NM_005322.svg)|
32
+|1|[HLA-B](HLA-B)||[view](images/proteinpaint/HLA-B.svg)|[view](images/proteinpaint/HLA-B_NM_005514.svg)|
33
+|1-a|[IL4R](IL4R)||[view](images/proteinpaint/IL4R.svg)|[view](images/proteinpaint/IL4R_NM_000418.svg)|
34
+|1-a|[IRF8](IRF8)||[view](images/proteinpaint/IRF8.svg)|[view](images/proteinpaint/IRF8_NM_002163.svg)|
35
+|1-a|[ITPKB](ITPKB)||[view](images/proteinpaint/ITPKB.svg)|[view](images/proteinpaint/ITPKB_NM_002221.svg)|
36
+|1|[JAK1](JAK1)||[view](images/proteinpaint/JAK1.svg)|[view](images/proteinpaint/JAK1_NM_002227.svg)|
37
+|1|[KMT2C](KMT2C)||[view](images/proteinpaint/KMT2C.svg)|[view](images/proteinpaint/KMT2C_NM_170606.svg)|
38
+|1-a|[LTB](LTB)||[view](images/proteinpaint/LTB.svg)|[view](images/proteinpaint/LTB_NM_002341.svg)|
39
+|1-a|[MS4A1](MS4A1)||[view](images/proteinpaint/MS4A1.svg)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/MS4A1_protein.html)|
40
+|1|[NFKBIA](NFKBIA)||[view](images/proteinpaint/NFKBIA.svg)|[view](images/proteinpaint/NFKBIA_NM_020529.svg)|
41
+|1|[NFKBIE](NFKBIE)||[view](images/proteinpaint/NFKBIE.svg)|[view](images/proteinpaint/NFKBIE_NM_004556.svg)|
42
+|1-a|[OSBPL10](OSBPL10)||[view](images/proteinpaint/OSBPL10.svg)|[view](images/proteinpaint/OSBPL10_NM_017784.svg)|
43
+|1|[P2RY8](P2RY8)||[view](images/proteinpaint/P2RY8.svg)|[view](images/proteinpaint/P2RY8_NM_178129.svg)|
44
+|1|[PCLO](PCLO)||[view](images/proteinpaint/PCLO.svg)|[view](images/proteinpaint/PCLO_NM_033026.svg)|
45
+|1|[PHIP](PHIP)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PHIP.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PHIP_protein.html)|
46
+|1-a|[PIM1](PIM1)||[view](images/proteinpaint/PIM1.svg)|[view](images/proteinpaint/PIM1_NM_002648.svg)|
47
+|1-a|[PIM2](PIM2)||[view](images/proteinpaint/PIM2.svg)|[view](images/proteinpaint/PIM2_NM_006875.svg)|
48
+|1|[PRKDC](PRKDC)||[view](images/proteinpaint/PRKDC.svg)|[view](images/proteinpaint/PRKDC_NM_006904.svg)|
49
+|1-a|[PTPN1](PTPN1)||[view](images/proteinpaint/PTPN1.svg)|[view](images/proteinpaint/PTPN1_NM_002827.svg)|
50
+|1|[PTPRD](PTPRD)||[view](images/proteinpaint/PTPRD.svg)|[view](images/proteinpaint/PTPRD_NM_002839.svg)|
51
+|1|[RHOA](RHOA)||[view](images/proteinpaint/RHOA.svg)|[view](images/proteinpaint/RHOA_NM_001664.svg)|
52
+|1-a|[S1PR2](S1PR2)||[view](images/proteinpaint/S1PR2.svg)|[view](images/proteinpaint/S1PR2_NM_004230.svg)|
53
+|1-a|[SGK1](SGK1)||[view](images/proteinpaint/SGK1.svg)|[view](images/proteinpaint/SGK1_NM_005627.svg)|
54
+|1|[SIN3A](SIN3A)||[view](images/proteinpaint/SIN3A.svg)|[view](images/proteinpaint/SIN3A_NM_001145358.svg)|
55
+|1|[SMARCA2](SMARCA2)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SMARCA2.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SMARCA2_protein.html)|
56
+|1|[SMARCA4](SMARCA4)||[view](images/proteinpaint/SMARCA4.svg)|[view](images/proteinpaint/SMARCA4_NM_001128849.svg)|
57
+|1-a|[SOCS1](SOCS1)||[view](images/proteinpaint/SOCS1.svg)|[view](images/proteinpaint/SOCS1_NM_003745.svg)|
58
+|1|[SPEN](SPEN)||[view](images/proteinpaint/SPEN.svg)|[view](images/proteinpaint/SPEN_NM_015001.svg)|
59
+|1|[STAT3](STAT3)||[view](images/proteinpaint/STAT3.svg)|[view](images/proteinpaint/STAT3_NM_139276.svg)|
60
+|1|[STAT6](STAT6)||[view](images/proteinpaint/STAT6.svg)|[view](images/proteinpaint/STAT6_NM_003153.svg)|
61
+|1|[TAP1](TAP1)||[view](images/proteinpaint/TAP1.svg)|[view](images/proteinpaint/TAP1_NM_000593.svg)|
62
+|1|[TBL1XR1](TBL1XR1)||[view](images/proteinpaint/TBL1XR1.svg)|[view](images/proteinpaint/TBL1XR1_NM_024665.svg)|
63
+|1|[TCF3](TCF3)||[view](images/proteinpaint/TCF3.svg)|[view](images/proteinpaint/TCF3_NM_003200.svg)|
64
+|1|[TET3](TET3)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/TET3.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/TET3_protein.html)|
65
+|1-a|[TMSB4X](TMSB4X)||[view](images/proteinpaint/TMSB4X.svg)|[view](images/proteinpaint/TMSB4X_NM_021109.svg)|
66
+|1|[TNFAIP3](TNFAIP3)||[view](images/proteinpaint/TNFAIP3.svg)|[view](images/proteinpaint/TNFAIP3_NM_006290.svg)|
67
+|1|[TNFRSF1B](TNFRSF1B)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF1B.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/TNFRSF1B_protein.html)|
68
+|1|[TP53](TP53)||[view](images/proteinpaint/TP53.svg)|[view](images/proteinpaint/TP53_NM_000546.svg)|
69
+|1|[TRAF3](TRAF3)||[view](images/proteinpaint/TRAF3.svg)|[view](images/proteinpaint/TRAF3_NM_145725.svg)|
70
+|1|[UBE2A](UBE2A)||[view](images/proteinpaint/UBE2A.svg)|[view](images/proteinpaint/UBE2A_NM_003336.svg)|
71
+|1|[UBR5](UBR5)||[view](images/proteinpaint/UBR5.svg)|[view](images/proteinpaint/UBR5_NM_015902.svg)|
72
+|1|[UNC5C](UNC5C)||[view](images/proteinpaint/UNC5C.svg)|[view](images/proteinpaint/UNC5C_NM_003728.svg)|
73
+|1|[VPS13B](VPS13B)||[view](images/proteinpaint/VPS13B.svg)|[view](images/proteinpaint/VPS13B_NM_152564.svg)|
74
+|1-a|[WEE1](WEE1)||[view](images/proteinpaint/WEE1.svg)|[view](images/proteinpaint/WEE1_NM_003390.svg)|
75
+|1|[XPO1](XPO1)||[view](images/proteinpaint/XPO1.svg)|[view](images/proteinpaint/XPO1_NM_003400.svg)|
76
+|1-a|[ZFP36L1](ZFP36L1)||[view](images/proteinpaint/ZFP36L1.svg)|[view](images/proteinpaint/ZFP36L1_NM_004926.svg)|
tier2_pmbl_hl_gz.md
... ...
@@ -0,0 +1,35 @@
1
+| Category | Gene | Details | Mutation frequency | Static view (Gene) | Static view (Protein) | Comment |
2
+| :---: | :----: | :---: | :---: | :---: |
3
+|:--:|[ACTG1](ACTG1)|:-:|:-:|
4
+|2|[ADGRG6](ADGRG6)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ADGRG6.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ADGRG6_protein.html)|
5
+|2|[AXDND1](AXDND1)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/AXDND1.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/AXDND1_protein.html)|
6
+|2-a|[BCL7A](BCL7A)||[view](images/proteinpaint/BCL7A.svg)|[view](images/proteinpaint/BCL7A_NM_020993.svg)|
7
+|2|[CCND3](CCND3)||[view](images/proteinpaint/CCND3.svg)|[view](images/proteinpaint/CCND3_NM_001760.svg)|
8
+|2|[CDH5](CDH5)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CDH5.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CDH5_protein.html)|
9
+|2|[CHD2](CHD2)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CHD2.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CHD2_protein.html)|
10
+|2-a|[CIITA](CIITA)||[view](images/proteinpaint/CIITA.svg)|[view](images/proteinpaint/CIITA_NM_000246.svg)|
11
+|2|[CISH](CISH)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CISH.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/CISH_protein.html)|
12
+|2|[DNAH12](DNAH12)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/DNAH12.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/DNAH12_protein.html)|
13
+|2|[EEF1A1](EEF1A1)||[view](images/proteinpaint/EEF1A1.svg)|[view](images/proteinpaint/EEF1A1_NM_001402.svg)|
14
+|2|[EGR1](EGR1)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/EGR1.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/EGR1_protein.html)|
15
+|2|[HLA-A](HLA-A)||[view](images/proteinpaint/HLA-A.svg)|[view](images/proteinpaint/HLA-A_NM_002116.svg)|
16
+|2|[HLA-C](HLA-C)||[view](images/proteinpaint/HLA-C.svg)|[view](images/proteinpaint/HLA-C_NM_002117.svg)|
17
+|2-a|[IGLL5](IGLL5)||[view](images/proteinpaint/IGLL5.svg)|[view](images/proteinpaint/IGLL5_NM_001178126.svg)|
18
+|2-a|[IRF4](IRF4)||[view](images/proteinpaint/IRF4.svg)|[view](images/proteinpaint/IRF4_NM_002460.svg)|
19
+|2|[IKBKB](IKBKB)||[view](images/proteinpaint/IKBKB.svg)|[view](images/proteinpaint/IKBKB_NM_001556.svg)|
20
+|2|[ITGB2](ITGB2)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ITGB2.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/ITGB2_protein.html)|
21
+|2-a|[KLF2](KLF2)||[view](images/proteinpaint/KLF2.svg)|[view](images/proteinpaint/KLF2_NM_016270.svg)|
22
+|2|[KMT2D](KMT2D)||[view](images/proteinpaint/KMT2D.svg)|[view](images/proteinpaint/KMT2D_NM_003482.svg)|
23
+|2|[LIMD2](LIMD2)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/LIMD2.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/LIMD2_protein.html)|
24
+|2|[MYB](MYB)||[view](images/proteinpaint/MYB.svg)|[view](images/proteinpaint/MYB_NM_001130173.svg)|
25
+|2|[NFKB2](NFKB2)||[view](images/proteinpaint/NFKB2.svg)|[view](images/proteinpaint/NFKB2_NM_001077494.svg)|
26
+|2|[NSD2](NSD2)||[view](images/proteinpaint/NSD2.svg)|[view](images/proteinpaint/NSD2_NM_133330.svg)|
27
+|2|[OR13C2](OR13C2)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/OR13C2.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/OR13C2_protein.html)|
28
+|2|[PCDH7](PCDH7)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PCDH7.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/PCDH7_protein.html)|
29
+|2|[PCBP1](PCBP1)||[view](images/proteinpaint/PCBP1.svg)|[view](images/proteinpaint/PCBP1_NM_006196.svg)|
30
+|2|[RDH12](RDH12)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RDH12.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RDH12_protein.html)|
31
+|2|[RBM38](RBM38)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RBM38.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/RBM38_protein.html)|
32
+|2|[SCN9A](SCN9A)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SCN9A.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SCN9A_protein.html)|
33
+|2|[SMAD3](SMAD3)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SMAD3.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/SMAD3_protein.html)|
34
+|2|[STRAP](STRAP)||[LOAD](https://morinlab.github.io/LLMPP/GAMBL/STRAP.html)|[LOAD](https://morinlab.github.io/LLMPP/GAMBL/STRAP_protein.html)|
35
+|2|[ZNF217](ZNF217)||[view](images/proteinpaint/ZNF217.svg)|[view](images/proteinpaint/ZNF217_NM_006526.svg)|