ABL2.md
... ...
@@ -1,17 +1,18 @@
1
-# [ABL2]
1
+# ABL2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|0.69 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ACAD9.md
... ...
@@ -1,11 +1,12 @@
1
-# [ACAD9]
1
+# ACAD9
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ACE.md
... ...
@@ -1,11 +1,12 @@
1
-# [ACE]
1
+# ACE
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ACTB.md
... ...
@@ -1,13 +1,17 @@
1
+# ACTB
2
+## Overview
3
+
1 4
ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm) affected by aberrant somatic hypermutation in B-cell lymphomas.
2 5
3
-## Mutation tier
6
+## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
6 9
|:------:|:----:|--------------------------|
7 10
|DLBCL |1-a |high-confidence DLBCL gene, hypermutated|
8 11
|FL |1-a |high-confidence FL gene, hypermutated |
9 12
10
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 15
12 16
|Entity|source |frequency (%)|
13 17
|:------:|:--------------:|:-------------:|
... ...
@@ -17,7 +21,7 @@ ACTB is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
17 21
|DLBCL |Chapuy cohort |12.40 |
18 22
|FL |GAMBL genomes | 5.31 |
19 23
20
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
21 25
22 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
23 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ACTG1.md
... ...
@@ -1,12 +1,13 @@
1
-# [ACTG1]
1
+# ACTG1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
8 8
|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.99 |
17 18
|FL |GAMBL genomes |3.00 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ADAMTS1.md
... ...
@@ -1,11 +1,12 @@
1
-# [ADAMTS1]
1
+# ADAMTS1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.70 |
15 16
|DLBCL |Chapuy cohort |2.56 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ADAMTS5.md
... ...
@@ -1,11 +1,12 @@
1
-# [ADAMTS5]
1
+# ADAMTS5
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ADNP.md
... ...
@@ -1,11 +1,12 @@
1
-# [ADNP]
1
+# ADNP
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
AGO4.md
... ...
@@ -1,11 +1,12 @@
1
-# [AGO4]
1
+# AGO4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
AICDA.md
... ...
@@ -1,11 +1,12 @@
1
-# [AICDA]
1
+# AICDA
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.30 |
15 16
|DLBCL |Chapuy cohort |0.43 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ALPK2.md
... ...
@@ -1,11 +1,12 @@
1
-# [ALPK2]
1
+# ALPK2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |5.10 |
14 15
|BL |Panea cohort |9.90 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ANK2.md
... ...
@@ -1,17 +1,18 @@
1
-# [ANK2]
1
+# ANK2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|1.9 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ANKRD12.md
... ...
@@ -1,11 +1,12 @@
1
-# [ANKRD12]
1
+# ANKRD12
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.10 |
15 16
|DLBCL |Chapuy cohort |5.13 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ANKRD17.md
... ...
@@ -1,11 +1,12 @@
1
-# [ANKRD17]
1
+# ANKRD17
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.80 |
15 16
|DLBCL |Chapuy cohort |2.14 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ARHGEF1.md
... ...
@@ -1,11 +1,12 @@
1
-# [ARHGEF1]
1
+# ARHGEF1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |2.00 |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
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-.page {
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-}
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-</style>
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-
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-<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
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-</head>
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-<body>
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- <script>
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- mermaid.initialize({
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- theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
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- ? 'dark'
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- : 'default'
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- });
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- </script>
368
-<h1 id="arid1a">[ARID1A]</h1>
369
-<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>
371
-<table>
372
-<thead>
373
-<tr>
374
-<th style="text-align:center">Entity</th>
375
-<th style="text-align:center">Tier</th>
376
-<th>Description</th>
377
-</tr>
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-</thead>
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-<tbody>
380
-<tr>
381
-<td style="text-align:center">BL</td>
382
-<td style="text-align:center">1</td>
383
-<td>high-confidence BL gene</td>
384
-</tr>
385
-<tr>
386
-<td style="text-align:center">DLBCL</td>
387
-<td style="text-align:center">1</td>
388
-<td>high-confidence DLBCL gene</td>
389
-</tr>
390
-<tr>
391
-<td style="text-align:center">FL</td>
392
-<td style="text-align:center">1</td>
393
-<td>high-confidence FL gene</td>
394
-</tr>
395
-</tbody>
396
-</table>
397
-<h2 id="mutation-incidence">Mutation incidence</h2>
398
-<table>
399
-<thead>
400
-<tr>
401
-<th style="text-align:center">Entity</th>
402
-<th style="text-align:center">source</th>
403
-<th style="text-align:center">frequency (%)</th>
404
-</tr>
405
-</thead>
406
-<tbody>
407
-<tr>
408
-<td style="text-align:center">BL</td>
409
-<td style="text-align:center">GAMBL genomes+capture</td>
410
-<td style="text-align:center">28.64</td>
411
-</tr>
412
-<tr>
413
-<td style="text-align:center">BL</td>
414
-<td style="text-align:center">Thomas cohort</td>
415
-<td style="text-align:center">36.00</td>
416
-</tr>
417
-<tr>
418
-<td style="text-align:center">BL</td>
419
-<td style="text-align:center">Panea cohort</td>
420
-<td style="text-align:center">19.80</td>
421
-</tr>
422
-<tr>
423
-<td style="text-align:center">DLBCL</td>
424
-<td style="text-align:center">GAMBL genomes</td>
425
-<td style="text-align:center">8.80</td>
426
-</tr>
427
-<tr>
428
-<td style="text-align:center">DLBCL</td>
429
-<td style="text-align:center">Schmitz cohort</td>
430
-<td style="text-align:center">8.94</td>
431
-</tr>
432
-<tr>
433
-<td style="text-align:center">DLBCL</td>
434
-<td style="text-align:center">Reddy cohort</td>
435
-<td style="text-align:center">4.40</td>
436
-</tr>
437
-<tr>
438
-<td style="text-align:center">DLBCL</td>
439
-<td style="text-align:center">Chapuy cohort</td>
440
-<td style="text-align:center">4.27</td>
441
-</tr>
442
-<tr>
443
-<td style="text-align:center">FL</td>
444
-<td style="text-align:center">GAMBL genomes</td>
445
-<td style="text-align:center">12.47</td>
446
-</tr>
447
-</tbody>
448
-</table>
449
-<h2 id="mutation-pattern">Mutation pattern</h2>
450
-<table>
451
-<thead>
452
-<tr>
453
-<th style="text-align:center">Entity</th>
454
-<th style="text-align:center">aSHM</th>
455
-<th style="text-align:center">Significant selection</th>
456
-<th style="text-align:center">dN/dS (missense)</th>
457
-<th style="text-align:center">dN/dS (nonsense)</th>
458
-</tr>
459
-</thead>
460
-<tbody>
461
-<tr>
462
-<td style="text-align:center">BL</td>
463
-<td style="text-align:center">No</td>
464
-<td style="text-align:center">Yes</td>
465
-<td style="text-align:center">3.218</td>
466
-<td style="text-align:center">130.201</td>
467
-</tr>
468
-<tr>
469
-<td style="text-align:center">DLBCL</td>
470
-<td style="text-align:center">No</td>
471
-<td style="text-align:center">Yes</td>
472
-<td style="text-align:center">2.364</td>
473
-<td style="text-align:center">38.689</td>
474
-</tr>
475
-<tr>
476
-<td style="text-align:center">FL</td>
477
-<td style="text-align:center">No</td>
478
-<td style="text-align:center">Yes</td>
479
-<td style="text-align:center">3.794</td>
480
-<td style="text-align:center">248.722</td>
481
-</tr>
482
-</tbody>
483
-</table>
484
-<blockquote>
485
-<p>[!NOTE]
486
-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>
487
-</blockquote>
488
-<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>
489
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARID1A_NM_006015.svg" alt="image"></p>
490
-<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>
491
-<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/ARID1A.svg" alt="image"></p>
492
-
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-</body>
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-</html>
ARID1B.md
... ...
@@ -1,12 +1,13 @@
1
-# [ARID1B]
1
+# ARID1B
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8 8
|MCL |2 |relevance in MCL not firmly established |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.14 |
17 18
|MCL |GAMBL genomes |1.90 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ARID5B.md
... ...
@@ -1,11 +1,12 @@
1
-# [ARID5B]
1
+# ARID5B
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.30 |
15 16
|DLBCL |Chapuy cohort |2.60 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATM.md
... ...
@@ -1,12 +1,13 @@
1
-# [ATM]
1
+# ATM
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|MCL |1 |high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort | 4.70 |
17 18
|MCL |GAMBL genomes |45.02 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATP11C.md
... ...
@@ -1,17 +1,18 @@
1
-# [ATP11C]
1
+# ATP11C
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|---------------------------------------|
7 7
|MCL |2 |relevance in MCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|0 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATP2C2.md
... ...
@@ -1,11 +1,12 @@
1
-# [ATP2C2]
1
+# ATP2C2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATP6AP1.md
... ...
@@ -1,17 +1,18 @@
1
-# [ATP6AP1]
1
+# ATP6AP1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7 7
|FL |1 |high-confidence FL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|4.85 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATP6V1A.md
... ...
@@ -1,17 +1,18 @@
1
-# [ATP6V1A]
1
+# ATP6V1A
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|1.15 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATP6V1B2.md
... ...
@@ -1,17 +1,18 @@
1
-# [ATP6V1B2]
1
+# ATP6V1B2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7 7
|FL |1 |high-confidence FL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|7.39 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
ATR.md
... ...
@@ -1,11 +1,12 @@
1
-# [ATR]
1
+# ATR
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |2.80 |
15 16
|DLBCL |Chapuy cohort |3.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
B2M.md
... ...
@@ -1,7 +1,10 @@
1 1
2
+# B2M
3
+## Overview
4
+
2 5
The B2M (β2-microglobulin) gene plays a crucial role in the function of the major histocompatibility complex (MHC) class I molecules, which are essential for immune system recognition of infected or malignant cells. B2M mutations in B-cell lymphomas, particularly in DLBCL and PMBCL, lead to reduced MHC class I expression, enabling tumor cells to evade immune detection and destruction by cytotoxic T cells.
3 6
4
-## Mutation tier
7
+## Relevance tier by entity
5 8
6 9
|Entity|Tier|Description |
7 10
|:------:|:----:|---------------------------------------|
... ...
@@ -9,7 +12,8 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
9 12
|DLBCL |1 |high-confidence DLBCL gene |
10 13
|FL |1 |high-confidence FL gene |
11 14
|MCL |2 |relevance in MCL not firmly established|
12
-## Mutation incidence
15
+
16
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 17
14 18
|Entity|source |frequency (%)|
15 19
|:------:|:---------------------:|:-------------:|
... ...
@@ -23,7 +27,7 @@ The B2M (β2-microglobulin) gene plays a crucial role in the function of the maj
23 27
|FL |GAMBL genomes | 8.55 |
24 28
|MCL |GAMBL genomes | 1.42 |
25 29
26
-## Mutation pattern
30
+## Mutation pattern and selective pressure estimates
27 31
28 32
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
29 33
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BACH2.md
... ...
@@ -1,11 +1,12 @@
1
-# [BACH2]
1
+# BACH2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |0.40 |
14 15
|BL |Panea cohort |5.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL10.md
... ...
@@ -1,13 +1,16 @@
1
+# BCL10
2
+## Overview
1 3
BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling and immune response regulation. Mutations in BCL10 have been implicated in the pathogenesis of various lymphomas, particularly mucosa-associated lymphoid tissue (MALT) lymphomas. They have also been reproducibly observed in a smaller proportion of DLBCLs with the frequency in non-MALT lymphomas under some debate.<sup>1</sup>
2 4
3
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2 |relevance in BL not firmly established|
8 10
|DLBCL |1 |high-confidence DLBCL gene |
9 11
|FL |2 |relevance in FL not firmly established|
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ BCL10 (B-cell lymphoma/leukemia 10) is a gene involved in apoptosis signaling an
20 23
|DLBCL |Chapuy cohort |6.41 |
21 24
|FL |GAMBL genomes |2.31 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL11A.md
... ...
@@ -1,12 +1,15 @@
1
+# BCL11A
2
+## Overview
1 3
BCL11A (B-cell lymphoma/leukemia 11A) is a transcription factor involved in the regulation of gene expression, particularly in lymphoid cells. Mutations in BCL11A have been linked to various lymphoid malignancies, including B-cell lymphomas. Amplification of the 2p13 region, where BCL11A is located, has been observed in various B-cell non-Hodgkin lymphomas (B-NHL) and Hodgkin disease (HD). Although this suggests that BCL11A amplification contributes to the malignancy through increased expression, the gene is commonly co-amplified with the REL gene.<sup>1</sup> The functional role of somatic mutations of BCL11A in B-cell lymphomas remains unclear. This 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
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 13
11 14
|Entity|source |frequency (%)|
12 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +21,7 @@ BCL11A (B-cell lymphoma/leukemia 11A) is a transcription factor involved in the
18 21
|DLBCL |Reddy cohort |1.60 |
19 22
|DLBCL |Chapuy cohort |3.42 |
20 23
21
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
22 25
23 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL2.md
... ...
@@ -1,13 +1,17 @@
1
+# BCL2
2
+## Overview
3
+
1 4
BCL2 mutations are frequently found in DLBCL, particularly in the germinal center B-cell (GCB) subtype, and are often located in the flexible loop domain and outside the BCL2-homology domains. These mutations are caused by the somatic hypermutation process.<sup>1</sup> The presence of these mutations are strongly correlated with the presence of a translocation between BCL2 and one of the immunoglobulin loci. <sup>2</sup> Although missense mutations may not be under positive selective pressure in the context of lymphomagenesis, some of these mutations may interfere with the function of BCL2 antagonists.<sup>3</sup>
2 5
3
-## Mutation tier
6
+## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
6 9
|:------:|:----:|--------------------------------------|
7 10
|BL |2 |relevance in BL not firmly established|
8 11
|DLBCL |1-a |high-confidence DLBCL gene, hypermutated |
9 12
|FL |1-a |high-confidence FL gene, hypermutated |
10
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 15
12 16
|Entity|source |frequency (%)|
13 17
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +24,7 @@ BCL2 mutations are frequently found in DLBCL, particularly in the germinal cente
20 24
|DLBCL |Chapuy cohort |15.80 |
21 25
|FL |GAMBL genomes |50.35 |
22 26
23
-## Mutation pattern
27
+## Mutation pattern and selective pressure estimates
24 28
25 29
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 30
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL2L11.md
... ...
@@ -1,11 +1,12 @@
1
-# [BCL2L11]
1
+# BCL2L11
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |2.10 |
14 15
|BL |Panea cohort |1.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL6.md
... ...
@@ -1,14 +1,18 @@
1 1
2
+# BCL6
3
+## Overview
4
+
2 5
BCL6 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. Although common, particularly in DLBCL, the function of many of these mutations remains unclear but some have been shown to affect the regulation of BCL6 expression.<sup>1,2</sup> The role of BCL6 missense mutations, seen over 9% of patients,<sup>3</sup> remains unclear.
3 6
4
-## Mutation tier
7
+## Relevance tier by entity
5 8
6 9
|Entity|Tier|Description |
7 10
|:------:|:----:|--------------------------------------|
8 11
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
9 12
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
10 13
|FL |1-a | aSHM target and high-confidence FL gene |
11
-## Mutation incidence
14
+
15
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 16
13 17
|Entity|source |frequency (%)|
14 18
|:------:|:---------------------:|:-------------:|
... ...
@@ -21,7 +25,7 @@ BCL6 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
21 25
|DLBCL |Chapuy cohort | 5.13 |
22 26
|FL |GAMBL genomes | 5.77 |
23 27
24
-## Mutation pattern
28
+## Mutation pattern and selective pressure estimates
25 29
26 30
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
27 31
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCL7A.md
... ...
@@ -1,13 +1,17 @@
1
+# BCL7A
2
+## Overview
3
+
1 4
BCL7A protein interacts with components of the SWI/SNF chromatin remodeling complex, implicating it in chromatin remodeling processes essential for normal cellular function.<sup>1</sup> Mutations in the BCL7A gene have been identified in diffuse large B-cell lymphoma (DLBCL) and other B-cell lymphomas, implicating this gene in the pathogenesis of these cancers. Importantly, BCL7A 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. Due to the presence of some loss-of-function mutations, BCL7A has been described as a tumour-suppressor gene in DLBCL.<sup>3</sup> The rate of DLBCLs with biallelic loss of this locus remains unclear.
2 5
3
-## Mutation tier
6
+## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
6 9
|:------:|:----:|--------------------------------------|
7 10
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 11
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 12
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
13
+
14
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 15
12 16
|Entity|source |frequency (%)|
13 17
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +24,7 @@ BCL7A protein interacts with components of the SWI/SNF chromatin remodeling comp
20 24
|DLBCL |Chapuy cohort | 6.41 |
21 25
|FL |GAMBL genomes |13.86 |
22 26
23
-## Mutation pattern
27
+## Mutation pattern and selective pressure estimates
24 28
25 29
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 30
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
... ...
@@ -49,4 +53,4 @@ View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/
49 53
## References
50 54
1. *Ramos-Medina R, Montes-Moreno S, Maestre L, Cañamero M, Rodríguez-Pinilla M, Martínez-Torrecuadrada J, Piris MÁ, Majid A, Dyer MJ, Pulford K, Roncador G. BCL7A protein expression in normal and malignant lymphoid tissues. Br J Haematol. 2013 Jan;160(1):106-9. doi: 10.1111/bjh.12080. Epub 2012 Oct 9. PMID: 23043359.*
51 55
2. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313-1324. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.*
52
-3. *Baliñas-Gavira C, Rodríguez MI, Andrades A, Cuadros M, Álvarez-Pérez JC, Álvarez-Prado ÁF, de Yébenes VG, Sánchez-Hernández S, Fernández-Vigo E, Muñoz J, Martín F, Ramiro AR, Martínez-Climent JA, Medina PP. Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia. 2020 Oct;34(10):2722-2735. doi: 10.1038/s41375-020-0919-5. Epub 2020 Jun 24. PMID: 32576963.*
... ...
\ No newline at end of file
0
+3. *Baliñas-Gavira C, Rodríguez MI, Andrades A, Cuadros M, Álvarez-Pérez JC, Álvarez-Prado ÁF, de Yébenes VG, Sánchez-Hernández S, Fernández-Vigo E, Muñoz J, Martín F, Ramiro AR, Martínez-Climent JA, Medina PP. Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL. Leukemia. 2020 Oct;34(10):2722-2735. doi: 10.1038/s41375-020-0919-5. Epub 2020 Jun 24. PMID: 32576963.*
BCOR.md
... ...
@@ -1,12 +1,13 @@
1
-# [BCOR]
1
+# BCOR
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|MCL |1 |high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.56 |
17 18
|MCL |GAMBL genomes |3.79 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCR.md
... ...
@@ -1,12 +1,13 @@
1 1
BCR (Breakpoint Cluster Region Protein) 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 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 8
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@ BCR (Breakpoint Cluster Region Protein) is one of [a number of genes](https://gi
18 19
|DLBCL |Reddy cohort | 3.90 |
19 20
|DLBCL |Chapuy cohort | 4.27 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BCR.pdf
... ...
Binary files /dev/null and b/BCR.pdf differ
BIRC3.md
... ...
@@ -1,12 +1,13 @@
1
-# [BIRC3]
1
+# BIRC3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8 8
|MCL |1-a | aSHM target and high-confidence MCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |1.71 |
17 18
|MCL |GAMBL genomes |7.11 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BIRC6.md
... ...
@@ -1,13 +1,14 @@
1
-# [BIRC6]
1
+# BIRC6
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
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
-## Mutation incidence
10
+
11
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 12
12 13
|Entity|source |frequency (%)|
13 14
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +21,7 @@
20 21
|DLBCL |Chapuy cohort | 4.70 |
21 22
|FL |GAMBL genomes | 3.70 |
22 23
23
-## Mutation pattern
24
+## Mutation pattern and selective pressure estimates
24 25
25 26
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 27
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BLK.md
... ...
@@ -1,11 +1,12 @@
1
-# [BLK]
1
+# BLK
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.70 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BMP7.md
... ...
@@ -1,11 +1,12 @@
1
-# [BMP7]
1
+# BMP7
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------|
7 7
|BL |1 |high-confidence BL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |8.90 |
14 15
|BL |Panea cohort |5.00 |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BRAF.md
... ...
@@ -1,12 +1,13 @@
1
-# [BRAF]
1
+# BRAF
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:---------------------:|:-------------:|
... ...
@@ -18,7 +19,7 @@
18 19
|DLBCL |Reddy cohort |2.00 |
19 20
|DLBCL |Chapuy cohort |5.56 |
20 21
21
-## Mutation pattern
22
+## Mutation pattern and selective pressure estimates
22 23
23 24
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
24 25
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BRD4.md
... ...
@@ -1,11 +1,12 @@
1
-# [BRD4]
1
+# BRD4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BRINP3.md
... ...
@@ -1,11 +1,12 @@
1
-# [BRINP3]
1
+# BRINP3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |3.30 |
15 16
|DLBCL |Chapuy cohort |2.99 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BTBD3.md
... ...
@@ -1,11 +1,12 @@
1
-# [BTBD3]
1
+# BTBD3
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.80 |
15 16
|DLBCL |Chapuy cohort |0.85 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BTG1.md
... ...
@@ -1,13 +1,16 @@
1
+# BTG1
2
+## Overview
1 3
BTG1 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
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ BTG1 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort |14.53 |
21 24
|FL |GAMBL genomes | 6.47 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BTG2.md
... ...
@@ -1,13 +1,16 @@
1
+# BTG2
2
+## Overview
1 3
BTG2 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
-## Mutation tier
5
+## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------------------|
7 9
|BL |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
8 10
|DLBCL |1-a | aSHM target and high-confidence DLBCL gene |
9 11
|FL |1-a | aSHM target and high-confidence FL gene |
10
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
12 15
|Entity|source |frequency (%)|
13 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -20,7 +23,7 @@ BTG2 is one of [a number of genes](https://github.com/morinlab/LLMPP/wiki/ashm)
20 23
|DLBCL |Chapuy cohort | 5.98 |
21 24
|FL |GAMBL genomes | 4.39 |
22 25
23
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
24 27
25 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
26 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
BTK.md
... ...
@@ -1,12 +1,13 @@
1
-# [BTK]
1
+# BTK
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8 8
|FL |1 |high-confidence FL gene |
9
-## Mutation incidence
9
+
10
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 11
11 12
|Entity|source |frequency (%)|
12 13
|:------:|:--------------:|:-------------:|
... ...
@@ -16,7 +17,7 @@
16 17
|DLBCL |Chapuy cohort |2.14 |
17 18
|FL |GAMBL genomes |6.93 |
18 19
19
-## Mutation pattern
20
+## Mutation pattern and selective pressure estimates
20 21
21 22
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
22 23
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
C10orf12.md
... ...
@@ -1,11 +1,12 @@
1
-# [C10orf12]
1
+# C10orf12
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |0.00 |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
C6orf27.md
... ...
@@ -1,11 +1,12 @@
1
-# [C6orf27]
1
+# C6orf27
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |NA |
14 15
|BL |Panea cohort |NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|
19 20
CAD.md
... ...
@@ -1,11 +1,12 @@
1
-# [CAD]
1
+# CAD
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CADPS2.md
... ...
@@ -1,11 +1,12 @@
1
-# [CADPS2]
1
+# CADPS2
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |4.30 |
15 16
|DLBCL |Chapuy cohort |1.71 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CARD11.md
... ...
@@ -1,6 +1,6 @@
1
-# [CARD11]
1
+# CARD11
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
... ...
@@ -8,7 +8,8 @@
8 8
|DLBCL |1 |high-confidence DLBCL gene |
9 9
|FL |1 |high-confidence FL gene |
10 10
|MCL |1 |high-confidence MCL gene |
11
-## Mutation incidence
11
+
12
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 13
13 14
|Entity|source |frequency (%)|
14 15
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +23,7 @@
22 23
|FL |GAMBL genomes |14.78 |
23 24
|MCL |GAMBL genomes | 1.42 |
24 25
25
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
26 27
27 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CARD4.md
... ...
@@ -1,11 +1,12 @@
1
-# [CARD4]
1
+# CARD4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort |NA |
14 15
|BL |Panea cohort |NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|
19 20
CASP8.md
... ...
@@ -1,11 +1,12 @@
1
-# [CASP8]
1
+# CASP8
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------|
7 7
|DLBCL |1 |high-confidence DLBCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.20 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CBLB.md
... ...
@@ -1,11 +1,12 @@
1
-# [CBLB]
1
+# CBLB
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |1.60 |
15 16
|DLBCL |Chapuy cohort |1.71 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CCDC42BPB.md
... ...
@@ -1,17 +1,18 @@
1
-# [CCDC42BPB]
1
+# CCDC42BPB
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|FL |2 |relevance in FL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|FL |GAMBL genomes|NA |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|
17 18
CCL4.md
... ...
@@ -1,11 +1,12 @@
1
-# [CCL4]
1
+# CCL4
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|-----------------------------------------|
7 7
|DLBCL |2 |relevance in DLBCL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:--------------:|:-------------:|
... ...
@@ -14,7 +15,7 @@
14 15
|DLBCL |Reddy cohort |0.60 |
15 16
|DLBCL |Chapuy cohort |1.28 |
16 17
17
-## Mutation pattern
18
+## Mutation pattern and selective pressure estimates
18 19
19 20
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
20 21
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CCND1.md
... ...
@@ -1,17 +1,18 @@
1
-# [CCND1]
1
+# CCND1
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|------------------------|
7 7
|MCL |1 |high-confidence MCL gene|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:-------------:|:-------------:|
12 13
|MCL |GAMBL genomes|14.69 |
13 14
14
-## Mutation pattern
15
+## Mutation pattern and selective pressure estimates
15 16
16 17
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
17 18
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CCND3.md
... ...
@@ -1,15 +1,16 @@
1
-# [CCND3]
2
-
1
+# CCND3
2
+## Overview
3 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
-## Mutation tier
5
+## Relevance tier by entity
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------|
9 9
|BL |1 |high-confidence BL gene |
10 10
|DLBCL |1 |high-confidence DLBCL gene|
11 11
|FL |1 |high-confidence FL gene |
12
-## Mutation incidence
12
+
13
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
13 14
14 15
|Entity|source |frequency (%)|
15 16
|:------:|:---------------------:|:-------------:|
... ...
@@ -22,7 +23,7 @@ CCND3 (Cyclin D3) is a gene that encodes a protein involved in the regulation of
22 23
|DLBCL |Chapuy cohort | 4.70 |
23 24
|FL |GAMBL genomes | 3.23 |
24 25
25
-## Mutation pattern
26
+## Mutation pattern and selective pressure estimates
26 27
27 28
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
28 29
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
... ...
@@ -86,4 +87,4 @@ View all variants in GenomePaint [hg19](https://www.bcgsc.ca/downloads/morinlab/
86 87
87 88
## References
88 89
89
-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
0
+1. *Schmitz, R., et al. (2012). "Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics." Nature, 490(7418), 116-120.*
CCNF.md
... ...
@@ -1,11 +1,12 @@
1
-# [CCNF]
1
+# CCNF
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
CCT6B.md
... ...
@@ -1,11 +1,12 @@
1
-# [CCT6B]
1
+# CCT6B
2 2
3
-## Mutation tier
3
+## Relevance tier by entity
4 4
5 5
|Entity|Tier|Description |
6 6
|:------:|:----:|--------------------------------------|
7 7
|BL |2 |relevance in BL not firmly established|
8
-## Mutation incidence
8
+
9
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
9 10
10 11
|Entity|source |frequency (%)|
11 12
|:------:|:---------------------:|:-------------:|
... ...
@@ -13,7 +14,7 @@
13 14
|BL |Thomas cohort | NA |
14 15
|BL |Panea cohort | NA |
15 16
16
-## Mutation pattern
17
+## Mutation pattern and selective pressure estimates
17 18
18 19
|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|
19 20
|:------:|:----:|:---------------------:|:----------------:|:----------------:|
SETD1B.pdf
... ...
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