ABCA13.md
... ...
@@ -0,0 +1,42 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ABCA13
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+ 2021-04-01 : Sarkozy : PMBL
17
+```
18
+
19
+
20
+## Relevance tier by entity
21
+
22
+|Entity|Tier|Description|
23
+|:------:|:----:|--------------------------------------|
24
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
25
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021a]|
26
+
27
+
28
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
29
+
30
+|Entity|source |frequency (%)|
31
+|:------:|:----:|:----:|
32
+|BL|GAMBL Exome |16.092 |
33
+|BL|GAMBL Genome |6.178 |
34
+|DLBCL|GAMBL Exome |10.189 |
35
+|DLBCL|GAMBL Genome |7.895 |
36
+|FL|GAMBL Exome |2.006 |
37
+|MCL|GAMBL Genome |3.509 |
38
+
39
+
40
+## References
41
+
42
+
ABCA3.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ABCA3
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2013-11-05 : Be : MCL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MCL](images/icons/MCL_tier2.png)|2|relevance in MCL not firmly established[@beaLandscapeSomaticMutations2013]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |7.471 |
31
+|BL|GAMBL Genome |2.703 |
32
+|DLBCL|GAMBL Exome |2.911 |
33
+|DLBCL|GAMBL Genome |0.94 |
34
+|FL|GAMBL Exome |0.287 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
ABCC9.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ABCC9
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2013-11-05 : Be : MCL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MCL](images/icons/MCL_tier2.png)|2|relevance in MCL not firmly established[@beaLandscapeSomaticMutations2013]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |4.598 |
31
+|BL|GAMBL Genome |2.703 |
32
+|DLBCL|GAMBL Exome |3.504 |
33
+|DLBCL|GAMBL Genome |2.632 |
34
+|FL|GAMBL Exome |0.573 |
35
+
36
+
37
+## References
38
+
39
+
ADD2.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ADD2
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |4.023 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |1.078 |
33
+|DLBCL|GAMBL Genome |0.94 |
34
+
35
+
36
+## References
37
+
38
+
AKAP6.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# AKAP6
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2018-05-31 : Tiacci : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@tiacciPervasiveMutationsJAKSTAT2018b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |6.897 |
31
+|BL|GAMBL Genome |1.544 |
32
+|DLBCL|GAMBL Exome |4.151 |
33
+|DLBCL|GAMBL Genome |3.195 |
34
+|FL|GAMBL Exome |2.292 |
35
+
36
+
37
+## References
38
+
39
+
AMN.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# AMN
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.724 |
31
+|DLBCL|GAMBL Exome |0.863 |
32
+|DLBCL|GAMBL Genome |0.564 |
33
+|MCL|GAMBL Genome |0.585 |
34
+
35
+
36
+## References
37
+
38
+
AOC2.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# AOC2
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |3.448 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |1.563 |
33
+|FL|GAMBL Exome |0.287 |
34
+
35
+
36
+## References
37
+
38
+
ARHGAP20.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ARHGAP20
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2017-07-27 : Jallades : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |4.023 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |1.941 |
33
+|DLBCL|GAMBL Genome |1.128 |
34
+|FL|GAMBL Exome |0.287 |
35
+
36
+
37
+## References
38
+
39
+
ARHGEF17.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# ARHGEF17
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2017-07-27 : Jallades : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |4.023 |
31
+|BL|GAMBL Genome |1.931 |
32
+|DLBCL|GAMBL Exome |3.558 |
33
+|DLBCL|GAMBL Genome |1.88 |
34
+|MCL|GAMBL Genome |1.17 |
35
+
36
+
37
+## References
38
+
39
+
ATR.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# ATR
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -106,7 +111,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
106 111
107 112
108 113
## References
109
-1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
114
+
110 115
111 116
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
112 117
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
AXDND1.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# AXDND1
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2023-11-15 : Gomez : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@gomezUltraDeepSequencingReveals2023]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.724 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |0.863 |
33
+|DLBCL|GAMBL Genome |1.128 |
34
+|MCL|GAMBL Genome |1.17 |
35
+
36
+
37
+## References
38
+
39
+
BACH2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BACH2
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|--------------------------------------|
17
-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
22
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@grandeGenomewideDiscoverySomatic2019]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -51,7 +56,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
51 56
![](images/gene_expression/BACH2_by_pathology.svg)
52 57
53 58
## References
54
-1. 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.
55 59
56 60
57 61
<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
BACH2_tmp.html
... ...
@@ -0,0 +1,487 @@
1
+<!DOCTYPE html>
2
+<html>
3
+<head>
4
+<title>BACH2.md</title>
5
+<meta http-equiv="Content-type" content="text/html;charset=UTF-8">
6
+
7
+<style>
8
+/* https://github.com/microsoft/vscode/blob/master/extensions/markdown-language-features/media/markdown.css */
9
+/*---------------------------------------------------------------------------------------------
10
+ * Copyright (c) Microsoft Corporation. All rights reserved.
11
+ * Licensed under the MIT License. See License.txt in the project root for license information.
12
+ *--------------------------------------------------------------------------------------------*/
13
+
14
+body {
15
+ font-family: var(--vscode-markdown-font-family, -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif);
16
+ font-size: var(--vscode-markdown-font-size, 14px);
17
+ padding: 0 26px;
18
+ line-height: var(--vscode-markdown-line-height, 22px);
19
+ word-wrap: break-word;
20
+}
21
+
22
+#code-csp-warning {
23
+ position: fixed;
24
+ top: 0;
25
+ right: 0;
26
+ color: white;
27
+ margin: 16px;
28
+ text-align: center;
29
+ font-size: 12px;
30
+ font-family: sans-serif;
31
+ background-color:#444444;
32
+ cursor: pointer;
33
+ padding: 6px;
34
+ box-shadow: 1px 1px 1px rgba(0,0,0,.25);
35
+}
36
+
37
+#code-csp-warning:hover {
38
+ text-decoration: none;
39
+ background-color:#007acc;
40
+ box-shadow: 2px 2px 2px rgba(0,0,0,.25);
41
+}
42
+
43
+body.scrollBeyondLastLine {
44
+ margin-bottom: calc(100vh - 22px);
45
+}
46
+
47
+body.showEditorSelection .code-line {
48
+ position: relative;
49
+}
50
+
51
+body.showEditorSelection .code-active-line:before,
52
+body.showEditorSelection .code-line:hover:before {
53
+ content: "";
54
+ display: block;
55
+ position: absolute;
56
+ top: 0;
57
+ left: -12px;
58
+ height: 100%;
59
+}
60
+
61
+body.showEditorSelection li.code-active-line:before,
62
+body.showEditorSelection li.code-line:hover:before {
63
+ left: -30px;
64
+}
65
+
66
+.vscode-light.showEditorSelection .code-active-line:before {
67
+ border-left: 3px solid rgba(0, 0, 0, 0.15);
68
+}
69
+
70
+.vscode-light.showEditorSelection .code-line:hover:before {
71
+ border-left: 3px solid rgba(0, 0, 0, 0.40);
72
+}
73
+
74
+.vscode-light.showEditorSelection .code-line .code-line:hover:before {
75
+ border-left: none;
76
+}
77
+
78
+.vscode-dark.showEditorSelection .code-active-line:before {
79
+ border-left: 3px solid rgba(255, 255, 255, 0.4);
80
+}
81
+
82
+.vscode-dark.showEditorSelection .code-line:hover:before {
83
+ border-left: 3px solid rgba(255, 255, 255, 0.60);
84
+}
85
+
86
+.vscode-dark.showEditorSelection .code-line .code-line:hover:before {
87
+ border-left: none;
88
+}
89
+
90
+.vscode-high-contrast.showEditorSelection .code-active-line:before {
91
+ border-left: 3px solid rgba(255, 160, 0, 0.7);
92
+}
93
+
94
+.vscode-high-contrast.showEditorSelection .code-line:hover:before {
95
+ border-left: 3px solid rgba(255, 160, 0, 1);
96
+}
97
+
98
+.vscode-high-contrast.showEditorSelection .code-line .code-line:hover:before {
99
+ border-left: none;
100
+}
101
+
102
+img {
103
+ max-width: 100%;
104
+ max-height: 100%;
105
+}
106
+
107
+a {
108
+ text-decoration: none;
109
+}
110
+
111
+a:hover {
112
+ text-decoration: underline;
113
+}
114
+
115
+a:focus,
116
+input:focus,
117
+select:focus,
118
+textarea:focus {
119
+ outline: 1px solid -webkit-focus-ring-color;
120
+ outline-offset: -1px;
121
+}
122
+
123
+hr {
124
+ border: 0;
125
+ height: 2px;
126
+ border-bottom: 2px solid;
127
+}
128
+
129
+h1 {
130
+ padding-bottom: 0.3em;
131
+ line-height: 1.2;
132
+ border-bottom-width: 1px;
133
+ border-bottom-style: solid;
134
+}
135
+
136
+h1, h2, h3 {
137
+ font-weight: normal;
138
+}
139
+
140
+table {
141
+ border-collapse: collapse;
142
+}
143
+
144
+table > thead > tr > th {
145
+ text-align: left;
146
+ border-bottom: 1px solid;
147
+}
148
+
149
+table > thead > tr > th,
150
+table > thead > tr > td,
151
+table > tbody > tr > th,
152
+table > tbody > tr > td {
153
+ padding: 5px 10px;
154
+}
155
+
156
+table > tbody > tr + tr > td {
157
+ border-top: 1px solid;
158
+}
159
+
160
+blockquote {
161
+ margin: 0 7px 0 5px;
162
+ padding: 0 16px 0 10px;
163
+ border-left-width: 5px;
164
+ border-left-style: solid;
165
+}
166
+
167
+code {
168
+ font-family: Menlo, Monaco, Consolas, "Droid Sans Mono", "Courier New", monospace, "Droid Sans Fallback";
169
+ font-size: 1em;
170
+ line-height: 1.357em;
171
+}
172
+
173
+body.wordWrap pre {
174
+ white-space: pre-wrap;
175
+}
176
+
177
+pre:not(.hljs),
178
+pre.hljs code > div {
179
+ padding: 16px;
180
+ border-radius: 3px;
181
+ overflow: auto;
182
+}
183
+
184
+pre code {
185
+ color: var(--vscode-editor-foreground);
186
+ tab-size: 4;
187
+}
188
+
189
+/** Theming */
190
+
191
+.vscode-light pre {
192
+ background-color: rgba(220, 220, 220, 0.4);
193
+}
194
+
195
+.vscode-dark pre {
196
+ background-color: rgba(10, 10, 10, 0.4);
197
+}
198
+
199
+.vscode-high-contrast pre {
200
+ background-color: rgb(0, 0, 0);
201
+}
202
+
203
+.vscode-high-contrast h1 {
204
+ border-color: rgb(0, 0, 0);
205
+}
206
+
207
+.vscode-light table > thead > tr > th {
208
+ border-color: rgba(0, 0, 0, 0.69);
209
+}
210
+
211
+.vscode-dark table > thead > tr > th {
212
+ border-color: rgba(255, 255, 255, 0.69);
213
+}
214
+
215
+.vscode-light h1,
216
+.vscode-light hr,
217
+.vscode-light table > tbody > tr + tr > td {
218
+ border-color: rgba(0, 0, 0, 0.18);
219
+}
220
+
221
+.vscode-dark h1,
222
+.vscode-dark hr,
223
+.vscode-dark table > tbody > tr + tr > td {
224
+ border-color: rgba(255, 255, 255, 0.18);
225
+}
226
+
227
+</style>
228
+
229
+<style>
230
+/* Tomorrow Theme */
231
+/* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
232
+/* Original theme - https://github.com/chriskempson/tomorrow-theme */
233
+
234
+/* Tomorrow Comment */
235
+.hljs-comment,
236
+.hljs-quote {
237
+ color: #8e908c;
238
+}
239
+
240
+/* Tomorrow Red */
241
+.hljs-variable,
242
+.hljs-template-variable,
243
+.hljs-tag,
244
+.hljs-name,
245
+.hljs-selector-id,
246
+.hljs-selector-class,
247
+.hljs-regexp,
248
+.hljs-deletion {
249
+ color: #c82829;
250
+}
251
+
252
+/* Tomorrow Orange */
253
+.hljs-number,
254
+.hljs-built_in,
255
+.hljs-builtin-name,
256
+.hljs-literal,
257
+.hljs-type,
258
+.hljs-params,
259
+.hljs-meta,
260
+.hljs-link {
261
+ color: #f5871f;
262
+}
263
+
264
+/* Tomorrow Yellow */
265
+.hljs-attribute {
266
+ color: #eab700;
267
+}
268
+
269
+/* Tomorrow Green */
270
+.hljs-string,
271
+.hljs-symbol,
272
+.hljs-bullet,
273
+.hljs-addition {
274
+ color: #718c00;
275
+}
276
+
277
+/* Tomorrow Blue */
278
+.hljs-title,
279
+.hljs-section {
280
+ color: #4271ae;
281
+}
282
+
283
+/* Tomorrow Purple */
284
+.hljs-keyword,
285
+.hljs-selector-tag {
286
+ color: #8959a8;
287
+}
288
+
289
+.hljs {
290
+ display: block;
291
+ overflow-x: auto;
292
+ color: #4d4d4c;
293
+ padding: 0.5em;
294
+}
295
+
296
+.hljs-emphasis {
297
+ font-style: italic;
298
+}
299
+
300
+.hljs-strong {
301
+ font-weight: bold;
302
+}
303
+</style>
304
+
305
+<style>
306
+/*
307
+ * Markdown PDF CSS
308
+ */
309
+
310
+ body {
311
+ font-family: -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif, "Meiryo";
312
+ padding: 0 12px;
313
+}
314
+
315
+pre {
316
+ background-color: #f8f8f8;
317
+ border: 1px solid #cccccc;
318
+ border-radius: 3px;
319
+ overflow-x: auto;
320
+ white-space: pre-wrap;
321
+ overflow-wrap: break-word;
322
+}
323
+
324
+pre:not(.hljs) {
325
+ padding: 23px;
326
+ line-height: 19px;
327
+}
328
+
329
+blockquote {
330
+ background: rgba(127, 127, 127, 0.1);
331
+ border-color: rgba(0, 122, 204, 0.5);
332
+}
333
+
334
+.emoji {
335
+ height: 1.4em;
336
+}
337
+
338
+code {
339
+ font-size: 14px;
340
+ line-height: 19px;
341
+}
342
+
343
+/* for inline code */
344
+:not(pre):not(.hljs) > code {
345
+ color: #C9AE75; /* Change the old color so it seems less like an error */
346
+ font-size: inherit;
347
+}
348
+
349
+/* Page Break : use <div class="page"/> to insert page break
350
+-------------------------------------------------------- */
351
+.page {
352
+ page-break-after: always;
353
+}
354
+
355
+</style>
356
+
357
+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
358
+</head>
359
+<body>
360
+ <script>
361
+ mermaid.initialize({
362
+ startOnLoad: true,
363
+ theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
364
+ ? 'dark'
365
+ : 'default'
366
+ });
367
+ </script>
368
+<h1 id="bach2">BACH2</h1>
369
+<h2 id="history">History</h2>
370
+<p>Mutations in this gene were first described in BL in 2019 by Grande et al.<sup>1</sup></p>
371
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
372
+timeline
373
+ title Publication timing
374
+ 2019-03-21 : Grande : BL
375
+</div></code></pre>
376
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
377
+<table>
378
+<thead>
379
+<tr>
380
+<th style="text-align:center">Entity</th>
381
+<th style="text-align:center">Tier</th>
382
+<th>Description</th>
383
+</tr>
384
+</thead>
385
+<tbody>
386
+<tr>
387
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
388
+<td style="text-align:center">2-a</td>
389
+<td>aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@grandeGenomewideDiscoverySomatic2019]</td>
390
+</tr>
391
+</tbody>
392
+</table>
393
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
394
+<table>
395
+<thead>
396
+<tr>
397
+<th style="text-align:center">Entity</th>
398
+<th style="text-align:center">source</th>
399
+<th style="text-align:center">frequency (%)</th>
400
+</tr>
401
+</thead>
402
+<tbody>
403
+<tr>
404
+<td style="text-align:center">BL</td>
405
+<td style="text-align:center">GAMBL genomes+capture</td>
406
+<td style="text-align:center">1.85</td>
407
+</tr>
408
+<tr>
409
+<td style="text-align:center">BL</td>
410
+<td style="text-align:center">Thomas cohort</td>
411
+<td style="text-align:center">0.40</td>
412
+</tr>
413
+<tr>
414
+<td style="text-align:center">BL</td>
415
+<td style="text-align:center">Panea cohort</td>
416
+<td style="text-align:center">5.00</td>
417
+</tr>
418
+</tbody>
419
+</table>
420
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
421
+<table>
422
+<thead>
423
+<tr>
424
+<th style="text-align:center">Entity</th>
425
+<th style="text-align:center">aSHM</th>
426
+<th style="text-align:center">Significant selection</th>
427
+<th style="text-align:center">dN/dS (missense)</th>
428
+<th style="text-align:center">dN/dS (nonsense)</th>
429
+</tr>
430
+</thead>
431
+<tbody>
432
+<tr>
433
+<td style="text-align:center">BL</td>
434
+<td style="text-align:center">Yes</td>
435
+<td style="text-align:center">No</td>
436
+<td style="text-align:center">0.652</td>
437
+<td style="text-align:center">0.000</td>
438
+</tr>
439
+<tr>
440
+<td style="text-align:center">DLBCL</td>
441
+<td style="text-align:center">Yes</td>
442
+<td style="text-align:center">No</td>
443
+<td style="text-align:center">0.949</td>
444
+<td style="text-align:center">0.000</td>
445
+</tr>
446
+<tr>
447
+<td style="text-align:center">FL</td>
448
+<td style="text-align:center">Yes</td>
449
+<td style="text-align:center">No</td>
450
+<td style="text-align:center">0.000</td>
451
+<td style="text-align:center">28.997</td>
452
+</tr>
453
+</tbody>
454
+</table>
455
+<h2 id="ashm-regions">aSHM regions</h2>
456
+<table>
457
+<thead>
458
+<tr>
459
+<th style="text-align:center">chr_name</th>
460
+<th style="text-align:center">hg19_start</th>
461
+<th style="text-align:center">hg19_end</th>
462
+<th style="text-align:center">region</th>
463
+<th style="text-align:center">regulatory_comment</th>
464
+</tr>
465
+</thead>
466
+<tbody>
467
+<tr>
468
+<td style="text-align:center">chr6</td>
469
+<td style="text-align:center">90981034</td>
470
+<td style="text-align:center">91016134</td>
471
+<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr6%3A90981034%2D91016134">TSS</a></td>
472
+<td style="text-align:center">NA</td>
473
+</tr>
474
+</tbody>
475
+</table>
476
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_protein_hg38.html">hg38</a></p>
477
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BACH2_NM_021813.svg" alt=""></p>
478
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BACH2_hg38.html">hg38</a></p>
479
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BACH2.svg" alt=""></p>
480
+<h2 id="bach2-expression">BACH2 Expression</h2>
481
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BACH2_by_pathology.svg" alt=""></p>
482
+<h2 id="references">References</h2>
483
+<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
484
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
485
+
486
+</body>
487
+</html>
BCL11A.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BCL11A
2 7
3 8
## Overview
... ...
@@ -57,9 +62,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
57 62
58 63
![](images/proteinpaint/BCL11A.svg)
59 64
60
-## References
61
-
62
-1. *Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood. 2001 Dec 1;98(12):3413-20. doi: 10.1182/blood.v98.12.3413. PMID: 11719382.*
63 65
## BCL11A Expression
64 66
![](images/gene_expression/BCL11A_by_pathology.svg)
65 67
<!-- ORIGIN: Unknown -->
68
+
69
+
70
+## References
71
+
72
+1. *Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood. 2001 Dec 1;98(12):3413-20. doi: 10.1182/blood.v98.12.3413. PMID: 11719382.*
BCL2.md
... ...
@@ -1,8 +1,15 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BCL2
2 7
3 8
## Overview
4 9
5
-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>
10
+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.
11
+These mutations are caused by the somatic hypermutation process. The presence of these mutations are strongly correlated with the presence of a translocation between BCL2 and one of the immunoglobulin loci.
12
+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.
6 13
7 14
```mermaid
8 15
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -18,10 +25,10 @@ timeline
18 25
19 26
|Entity|Tier|Description |
20 27
|:------:|:----:|--------------------------------------|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated |
28
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a |high-confidence DLBCL gene, hypermutated [@tanakaFrequentIncidenceSomatic1992]|
22 29
|![FL](images/icons/FL_tier1.png) |1-a |high-confidence FL gene, hypermutated
23
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
24
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
30
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@sarkozyMutationalLandscapeGray2021a]|
31
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]|
25 32
|
26 33
27 34
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -88,8 +95,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
88 95
<!-- DLBCL: tanakaFrequentIncidenceSomatic1992 -->
89 96
90 97
## References
91
-1. Tanaka S, Louie DC, Kant JA, Reed JC. Frequent incidence of somatic mutations in translocated BCL2 oncogenes of non-Hodgkin’s lymphomas. Blood. 1992 Jan 1;79(1):229–237. PMID: 1339299
92
-2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554
93
-3. Sarkozy C, Hung SS, Chavez EA, Duns G, Takata K, Chong LC, Aoki T, Jiang A, Miyata-Takata T, Telenius A, Slack GW, Molina TJ, Ben-Neriah S, Farinha P, Dartigues P, Damotte D, Mottok A, Salles GA, Casasnovas RO, Savage KJ, Laurent C, Scott DW, Traverse-Glehen A, Steidl C. Mutational landscape of gray zone lymphoma. Blood. 2021 Apr 1;137(13):1765–1776. PMID: 32961552
94
-4. Burkhardt B, Michgehl U, Rohde J, Erdmann T, Berning P, Reutter K, Rohde M, Borkhardt A, Burmeister T, Dave S, Tzankov A, Dugas M, Sandmann S, Fend F, Finger J, Mueller S, Gökbuget N, Haferlach T, Kern W, Hartmann W, Klapper W, Oschlies I, Richter J, Kontny U, Lutz M, Maecker-Kolhoff B, Ott G, Rosenwald A, Siebert R, von Stackelberg A, Strahm B, Woessmann W, Zimmermann M, Zapukhlyak M, Grau M, Lenz G. Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age. Nat Commun. 2022 Jul 6;13(1):3881. PMCID: PMC9259584
98
+
99
+2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, L
95 100
<!-- PMBL: sarkozyMutationalLandscapeGray2021a -->
BCL6.md
... ...
@@ -1,8 +1,14 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BCL6
2 7
3 8
## Overview
4 9
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.
10
+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.
11
+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. The role of BCL6 missense mutations, seen over 9% of patients remains unclear.
6 12
7 13
```mermaid
8 14
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -16,8 +22,8 @@ timeline
16 22
17 23
|Entity|Tier|Description |
18 24
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
20
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
25
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@loveGeneticLandscapeMutations2012]|
26
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
21 27
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
22 28
23 29
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -99,5 +105,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
99 105
100 106
101 107
## References
102
-1. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554
103
-2. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
BCR.md
... ...
@@ -1,10 +1,28 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+## Overview
8
+
1 9
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. This gene has some recurrent sites of mutations (hot spots).
2 10
11
+## History
12
+
13
+```mermaid
14
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
15
+timeline
16
+ title Publication timing
17
+ 2012-03-06 : Lohr : DLBCL
18
+```
19
+
20
+
3 21
## Relevance tier by entity
4 22
5 23
|Entity|Tier|Description |
6 24
|:------:|:----:|--------------------------------------|
7
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]|
8 26
9 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 28
BIRC3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BIRC3
2 7
3 8
## History
... ...
@@ -15,10 +20,10 @@ timeline
15 20
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|-----------------------------------------|
18
-|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established|
19
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
21
-|![MCL](images/icons/MCL_tier1.png) |1-a | aSHM target and high-confidence MCL gene |
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]|
24
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]|
25
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]|
26
+|![MCL](images/icons/MCL_tier1.png) |1-a | aSHM target and high-confidence MCL gene [@beaLandscapeSomaticMutations2013]|
22 27
23 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
24 29
... ...
@@ -63,7 +68,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
63 68
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
64 69
65 70
## References
66
-1. Rossi D, Deaglio S, Dominguez-Sola D, Rasi S, Vaisitti T, Agostinelli C, Spina V, Bruscaggin A, Monti S, Cerri M, Cresta S, Fangazio M, Arcaini L, Lucioni M, Marasca R, Thieblemont C, Capello D, Facchetti F, Kwee I, Pileri SA, Foà R, Bertoni F, Dalla-Favera R, Pasqualucci L, Gaidano G. Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. Blood. 2011 Nov 3;118(18):4930–4934. PMID: 21881048
67
-2. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436
68
-3. Arthur SE, Jiang A, Grande BM, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma. Nat Commun. 2018 Oct 1;9(1):4001. PMCID: PMC6167379
69
-4. Duns G, Viganò E, Ennishi D, Sarkozy C, Hung SS, Chavez E, Takata K, Rushton C, Jiang A, Ben-Neriah S, Woolcock BW, Slack GW, Hsi ED, Craig JW, Hilton LK, Shah SP, Farinha P, Mottok A, Gascoyne RD, Morin RD, Savage KJ, Scott DW, Steidl C. Characterization of DLBCL with a PMBL gene expression signature. Blood. 2021 Jul 15;138(2):136–148. PMID: 33684939
BIRC3_tmp.html
... ...
@@ -0,0 +1,517 @@
1
+<!DOCTYPE html>
2
+<html>
3
+<head>
4
+<title>BIRC3.md</title>
5
+<meta http-equiv="Content-type" content="text/html;charset=UTF-8">
6
+
7
+<style>
8
+/* https://github.com/microsoft/vscode/blob/master/extensions/markdown-language-features/media/markdown.css */
9
+/*---------------------------------------------------------------------------------------------
10
+ * Copyright (c) Microsoft Corporation. All rights reserved.
11
+ * Licensed under the MIT License. See License.txt in the project root for license information.
12
+ *--------------------------------------------------------------------------------------------*/
13
+
14
+body {
15
+ font-family: var(--vscode-markdown-font-family, -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif);
16
+ font-size: var(--vscode-markdown-font-size, 14px);
17
+ padding: 0 26px;
18
+ line-height: var(--vscode-markdown-line-height, 22px);
19
+ word-wrap: break-word;
20
+}
21
+
22
+#code-csp-warning {
23
+ position: fixed;
24
+ top: 0;
25
+ right: 0;
26
+ color: white;
27
+ margin: 16px;
28
+ text-align: center;
29
+ font-size: 12px;
30
+ font-family: sans-serif;
31
+ background-color:#444444;
32
+ cursor: pointer;
33
+ padding: 6px;
34
+ box-shadow: 1px 1px 1px rgba(0,0,0,.25);
35
+}
36
+
37
+#code-csp-warning:hover {
38
+ text-decoration: none;
39
+ background-color:#007acc;
40
+ box-shadow: 2px 2px 2px rgba(0,0,0,.25);
41
+}
42
+
43
+body.scrollBeyondLastLine {
44
+ margin-bottom: calc(100vh - 22px);
45
+}
46
+
47
+body.showEditorSelection .code-line {
48
+ position: relative;
49
+}
50
+
51
+body.showEditorSelection .code-active-line:before,
52
+body.showEditorSelection .code-line:hover:before {
53
+ content: "";
54
+ display: block;
55
+ position: absolute;
56
+ top: 0;
57
+ left: -12px;
58
+ height: 100%;
59
+}
60
+
61
+body.showEditorSelection li.code-active-line:before,
62
+body.showEditorSelection li.code-line:hover:before {
63
+ left: -30px;
64
+}
65
+
66
+.vscode-light.showEditorSelection .code-active-line:before {
67
+ border-left: 3px solid rgba(0, 0, 0, 0.15);
68
+}
69
+
70
+.vscode-light.showEditorSelection .code-line:hover:before {
71
+ border-left: 3px solid rgba(0, 0, 0, 0.40);
72
+}
73
+
74
+.vscode-light.showEditorSelection .code-line .code-line:hover:before {
75
+ border-left: none;
76
+}
77
+
78
+.vscode-dark.showEditorSelection .code-active-line:before {
79
+ border-left: 3px solid rgba(255, 255, 255, 0.4);
80
+}
81
+
82
+.vscode-dark.showEditorSelection .code-line:hover:before {
83
+ border-left: 3px solid rgba(255, 255, 255, 0.60);
84
+}
85
+
86
+.vscode-dark.showEditorSelection .code-line .code-line:hover:before {
87
+ border-left: none;
88
+}
89
+
90
+.vscode-high-contrast.showEditorSelection .code-active-line:before {
91
+ border-left: 3px solid rgba(255, 160, 0, 0.7);
92
+}
93
+
94
+.vscode-high-contrast.showEditorSelection .code-line:hover:before {
95
+ border-left: 3px solid rgba(255, 160, 0, 1);
96
+}
97
+
98
+.vscode-high-contrast.showEditorSelection .code-line .code-line:hover:before {
99
+ border-left: none;
100
+}
101
+
102
+img {
103
+ max-width: 100%;
104
+ max-height: 100%;
105
+}
106
+
107
+a {
108
+ text-decoration: none;
109
+}
110
+
111
+a:hover {
112
+ text-decoration: underline;
113
+}
114
+
115
+a:focus,
116
+input:focus,
117
+select:focus,
118
+textarea:focus {
119
+ outline: 1px solid -webkit-focus-ring-color;
120
+ outline-offset: -1px;
121
+}
122
+
123
+hr {
124
+ border: 0;
125
+ height: 2px;
126
+ border-bottom: 2px solid;
127
+}
128
+
129
+h1 {
130
+ padding-bottom: 0.3em;
131
+ line-height: 1.2;
132
+ border-bottom-width: 1px;
133
+ border-bottom-style: solid;
134
+}
135
+
136
+h1, h2, h3 {
137
+ font-weight: normal;
138
+}
139
+
140
+table {
141
+ border-collapse: collapse;
142
+}
143
+
144
+table > thead > tr > th {
145
+ text-align: left;
146
+ border-bottom: 1px solid;
147
+}
148
+
149
+table > thead > tr > th,
150
+table > thead > tr > td,
151
+table > tbody > tr > th,
152
+table > tbody > tr > td {
153
+ padding: 5px 10px;
154
+}
155
+
156
+table > tbody > tr + tr > td {
157
+ border-top: 1px solid;
158
+}
159
+
160
+blockquote {
161
+ margin: 0 7px 0 5px;
162
+ padding: 0 16px 0 10px;
163
+ border-left-width: 5px;
164
+ border-left-style: solid;
165
+}
166
+
167
+code {
168
+ font-family: Menlo, Monaco, Consolas, "Droid Sans Mono", "Courier New", monospace, "Droid Sans Fallback";
169
+ font-size: 1em;
170
+ line-height: 1.357em;
171
+}
172
+
173
+body.wordWrap pre {
174
+ white-space: pre-wrap;
175
+}
176
+
177
+pre:not(.hljs),
178
+pre.hljs code > div {
179
+ padding: 16px;
180
+ border-radius: 3px;
181
+ overflow: auto;
182
+}
183
+
184
+pre code {
185
+ color: var(--vscode-editor-foreground);
186
+ tab-size: 4;
187
+}
188
+
189
+/** Theming */
190
+
191
+.vscode-light pre {
192
+ background-color: rgba(220, 220, 220, 0.4);
193
+}
194
+
195
+.vscode-dark pre {
196
+ background-color: rgba(10, 10, 10, 0.4);
197
+}
198
+
199
+.vscode-high-contrast pre {
200
+ background-color: rgb(0, 0, 0);
201
+}
202
+
203
+.vscode-high-contrast h1 {
204
+ border-color: rgb(0, 0, 0);
205
+}
206
+
207
+.vscode-light table > thead > tr > th {
208
+ border-color: rgba(0, 0, 0, 0.69);
209
+}
210
+
211
+.vscode-dark table > thead > tr > th {
212
+ border-color: rgba(255, 255, 255, 0.69);
213
+}
214
+
215
+.vscode-light h1,
216
+.vscode-light hr,
217
+.vscode-light table > tbody > tr + tr > td {
218
+ border-color: rgba(0, 0, 0, 0.18);
219
+}
220
+
221
+.vscode-dark h1,
222
+.vscode-dark hr,
223
+.vscode-dark table > tbody > tr + tr > td {
224
+ border-color: rgba(255, 255, 255, 0.18);
225
+}
226
+
227
+</style>
228
+
229
+<style>
230
+/* Tomorrow Theme */
231
+/* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
232
+/* Original theme - https://github.com/chriskempson/tomorrow-theme */
233
+
234
+/* Tomorrow Comment */
235
+.hljs-comment,
236
+.hljs-quote {
237
+ color: #8e908c;
238
+}
239
+
240
+/* Tomorrow Red */
241
+.hljs-variable,
242
+.hljs-template-variable,
243
+.hljs-tag,
244
+.hljs-name,
245
+.hljs-selector-id,
246
+.hljs-selector-class,
247
+.hljs-regexp,
248
+.hljs-deletion {
249
+ color: #c82829;
250
+}
251
+
252
+/* Tomorrow Orange */
253
+.hljs-number,
254
+.hljs-built_in,
255
+.hljs-builtin-name,
256
+.hljs-literal,
257
+.hljs-type,
258
+.hljs-params,
259
+.hljs-meta,
260
+.hljs-link {
261
+ color: #f5871f;
262
+}
263
+
264
+/* Tomorrow Yellow */
265
+.hljs-attribute {
266
+ color: #eab700;
267
+}
268
+
269
+/* Tomorrow Green */
270
+.hljs-string,
271
+.hljs-symbol,
272
+.hljs-bullet,
273
+.hljs-addition {
274
+ color: #718c00;
275
+}
276
+
277
+/* Tomorrow Blue */
278
+.hljs-title,
279
+.hljs-section {
280
+ color: #4271ae;
281
+}
282
+
283
+/* Tomorrow Purple */
284
+.hljs-keyword,
285
+.hljs-selector-tag {
286
+ color: #8959a8;
287
+}
288
+
289
+.hljs {
290
+ display: block;
291
+ overflow-x: auto;
292
+ color: #4d4d4c;
293
+ padding: 0.5em;
294
+}
295
+
296
+.hljs-emphasis {
297
+ font-style: italic;
298
+}
299
+
300
+.hljs-strong {
301
+ font-weight: bold;
302
+}
303
+</style>
304
+
305
+<style>
306
+/*
307
+ * Markdown PDF CSS
308
+ */
309
+
310
+ body {
311
+ font-family: -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif, "Meiryo";
312
+ padding: 0 12px;
313
+}
314
+
315
+pre {
316
+ background-color: #f8f8f8;
317
+ border: 1px solid #cccccc;
318
+ border-radius: 3px;
319
+ overflow-x: auto;
320
+ white-space: pre-wrap;
321
+ overflow-wrap: break-word;
322
+}
323
+
324
+pre:not(.hljs) {
325
+ padding: 23px;
326
+ line-height: 19px;
327
+}
328
+
329
+blockquote {
330
+ background: rgba(127, 127, 127, 0.1);
331
+ border-color: rgba(0, 122, 204, 0.5);
332
+}
333
+
334
+.emoji {
335
+ height: 1.4em;
336
+}
337
+
338
+code {
339
+ font-size: 14px;
340
+ line-height: 19px;
341
+}
342
+
343
+/* for inline code */
344
+:not(pre):not(.hljs) > code {
345
+ color: #C9AE75; /* Change the old color so it seems less like an error */
346
+ font-size: inherit;
347
+}
348
+
349
+/* Page Break : use <div class="page"/> to insert page break
350
+-------------------------------------------------------- */
351
+.page {
352
+ page-break-after: always;
353
+}
354
+
355
+</style>
356
+
357
+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
358
+</head>
359
+<body>
360
+ <script>
361
+ mermaid.initialize({
362
+ startOnLoad: true,
363
+ theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
364
+ ? 'dark'
365
+ : 'default'
366
+ });
367
+ </script>
368
+<h1 id="birc3">BIRC3</h1>
369
+<h2 id="history">History</h2>
370
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
371
+timeline
372
+ title Publication timing
373
+ 2011-11-03 : Rossi : MZL
374
+ 2013-11-05 : Be : MCL
375
+ 2018-10-01 : Arthur : DLBCL
376
+ 2021-07-15 : Duns : PMBL
377
+</div></code></pre>
378
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
379
+<table>
380
+<thead>
381
+<tr>
382
+<th style="text-align:center">Entity</th>
383
+<th style="text-align:center">Tier</th>
384
+<th>Description</th>
385
+</tr>
386
+</thead>
387
+<tbody>
388
+<tr>
389
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/PMBL_tier2.png" alt="PMBL"></td>
390
+<td style="text-align:center">2</td>
391
+<td>relevance in PMBL/cHL/GZL not firmly established[@dunsCharacterizationDLBCLPMBL2021b]</td>
392
+</tr>
393
+<tr>
394
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/MZL_tier1.png" alt="MZL"></td>
395
+<td style="text-align:center">1</td>
396
+<td>high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]</td>
397
+</tr>
398
+<tr>
399
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/DLBCL_tier2.png" alt="DLBCL"></td>
400
+<td style="text-align:center">2-a</td>
401
+<td>aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]</td>
402
+</tr>
403
+<tr>
404
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/MCL_tier1.png" alt="MCL"></td>
405
+<td style="text-align:center">1-a</td>
406
+<td>aSHM target and high-confidence MCL gene [@beaLandscapeSomaticMutations2013]</td>
407
+</tr>
408
+</tbody>
409
+</table>
410
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
411
+<table>
412
+<thead>
413
+<tr>
414
+<th style="text-align:center">Entity</th>
415
+<th style="text-align:center">source</th>
416
+<th style="text-align:center">frequency (%)</th>
417
+</tr>
418
+</thead>
419
+<tbody>
420
+<tr>
421
+<td style="text-align:center">DLBCL</td>
422
+<td style="text-align:center">GAMBL genomes</td>
423
+<td style="text-align:center">1.53</td>
424
+</tr>
425
+<tr>
426
+<td style="text-align:center">DLBCL</td>
427
+<td style="text-align:center">Schmitz cohort</td>
428
+<td style="text-align:center">1.91</td>
429
+</tr>
430
+<tr>
431
+<td style="text-align:center">DLBCL</td>
432
+<td style="text-align:center">Reddy cohort</td>
433
+<td style="text-align:center">1.30</td>
434
+</tr>
435
+<tr>
436
+<td style="text-align:center">DLBCL</td>
437
+<td style="text-align:center">Chapuy cohort</td>
438
+<td style="text-align:center">1.71</td>
439
+</tr>
440
+<tr>
441
+<td style="text-align:center">MCL</td>
442
+<td style="text-align:center">GAMBL genomes</td>
443
+<td style="text-align:center">7.11</td>
444
+</tr>
445
+</tbody>
446
+</table>
447
+<h2 id="mutation-pattern-and-selective-pressure-estimates">Mutation pattern and selective pressure estimates</h2>
448
+<table>
449
+<thead>
450
+<tr>
451
+<th style="text-align:center">Entity</th>
452
+<th style="text-align:center">aSHM</th>
453
+<th style="text-align:center">Significant selection</th>
454
+<th style="text-align:center">dN/dS (missense)</th>
455
+<th style="text-align:center">dN/dS (nonsense)</th>
456
+</tr>
457
+</thead>
458
+<tbody>
459
+<tr>
460
+<td style="text-align:center">BL</td>
461
+<td style="text-align:center">Yes</td>
462
+<td style="text-align:center">No</td>
463
+<td style="text-align:center">0.000</td>
464
+<td style="text-align:center">0</td>
465
+</tr>
466
+<tr>
467
+<td style="text-align:center">DLBCL</td>
468
+<td style="text-align:center">Yes</td>
469
+<td style="text-align:center">No</td>
470
+<td style="text-align:center">1.404</td>
471
+<td style="text-align:center">0</td>
472
+</tr>
473
+<tr>
474
+<td style="text-align:center">FL</td>
475
+<td style="text-align:center">Yes</td>
476
+<td style="text-align:center">No</td>
477
+<td style="text-align:center">2.427</td>
478
+<td style="text-align:center">0</td>
479
+</tr>
480
+</tbody>
481
+</table>
482
+<h2 id="ashm-regions">aSHM regions</h2>
483
+<table>
484
+<thead>
485
+<tr>
486
+<th style="text-align:center">chr_name</th>
487
+<th style="text-align:center">hg19_start</th>
488
+<th style="text-align:center">hg19_end</th>
489
+<th style="text-align:center">region</th>
490
+<th style="text-align:center">regulatory_comment</th>
491
+</tr>
492
+</thead>
493
+<tbody>
494
+<tr>
495
+<td style="text-align:center">chr11</td>
496
+<td style="text-align:center">102188170</td>
497
+<td style="text-align:center">102190077</td>
498
+<td style="text-align:center"><a href="https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr11%3A102188170%2D102190077">TSS</a></td>
499
+<td style="text-align:center">active_promoter</td>
500
+</tr>
501
+</tbody>
502
+</table>
503
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_protein_hg38.html">hg38</a></p>
504
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BIRC3_NM_001165.svg" alt=""></p>
505
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/BIRC3_hg38.html">hg38</a></p>
506
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/BIRC3.svg" alt=""></p>
507
+<h2 id="birc3-expression">BIRC3 Expression</h2>
508
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/gene_expression/BIRC3_by_pathology.svg" alt=""></p>
509
+<!-- ORIGIN: rossiAlterationBIRC3Multiple2011a -->
510
+<!-- PMBL: dunsCharacterizationDLBCLPMBL2021b -->
511
+<!-- MZL: rossiAlterationBIRC3Multiple2011a -->
512
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
513
+<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
514
+<h2 id="references">References</h2>
515
+
516
+</body>
517
+</html>
BLK.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BLK
2 7
3 8
## Relevance tier by entity
BMP7.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BMP7
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene|
20
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene[@paneaWholeGenomeLandscape2019]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -68,4 +73,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
68 73
<!-- BL: paneaWholeGenomeLandscape2019 -->
69 74
70 75
## References
71
-1. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019;
BRD4.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BRD4
2 7
3 8
## Overview
... ...
@@ -16,7 +21,7 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
24
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -64,4 +69,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
64 69
[747](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html)
65 70
66 71
## References
67
-1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
BRINP3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BRINP3
2 7
3 8
<<Warn("In a subsequent reanalysis, the mutation rate in this gene was found to be inflated in the original results")>>
... ...
@@ -17,7 +22,7 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|-----------------------------------------|
20
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
25
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -115,7 +120,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
115 120
[Reddy_695T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_695T.html)
116 121
117 122
## References
118
-1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
123
+
119 124
120 125
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
121 126
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
BTBD3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BTBD3
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -73,7 +78,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
73 78
[Reddy_759T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_759T.html)
74 79
75 80
## References
76
-1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
77 81
78 82
79 83
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
BTG1.md
... ...
@@ -1,7 +1,14 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# BTG1
2 7
3 8
## Overview
4
-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. These mutations are a feature of the MCD genetic subgroup of DLBCL.<sup>1</sup> Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.<sup>2</sup> Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.<sup>3</sup>
9
+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. These mutations are a feature of the MCD genetic subgroup of DLBCL.
10
+Mutations in the BTG1 gene have been implicated in the pathogenesis and progression of diffuse large B-cell lymphoma (DLBCL) through functional exploration in vivo. Knock-out of BTG1 did not lead to spontaneous lymphomagenesis but enhanced the lymphoproliferation induced by VavP-BCL2 and promoted lymphoma dissemination in xenotransplantation experiments.
11
+Another study demonstrated that specific BTG1 mutations afford germinal center (GC) B cells with a fitness advantage relative to un-mutated counterparts.
5 12
6 13
```mermaid
7 14
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -17,10 +24,10 @@ timeline
17 24
|Entity|Tier|Description |
18 25
|:------:|:----:|--------------------------------------|
19 26
|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
20
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
27
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@sarkozyMutationalLandscapeGray2021a]|
28
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
22 29
|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
23
-|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
30
+|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@burkhardtClinicalRelevanceMolecular2022b]|
24 31
25 32
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
26 33
C16orf48.md
... ...
@@ -0,0 +1,34 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# C16orf48
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2012-10-04 : Schmitz : BL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![BL](images/icons/BL_tier2.png)|2|relevance in BL not firmly established[@schmitzBurkittLymphomaPathogenesis2012]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+
31
+
32
+## References
33
+
34
+
C6orf103.md
... ...
@@ -0,0 +1,34 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# C6orf103
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+
31
+
32
+## References
33
+
34
+
C6orf27.md
... ...
@@ -1,4 +1,10 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# C6orf27
7
+
2 8
## Overview
3 9
4 10
Due to [minimal support](C6orf27#representative-mutation) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
... ...
@@ -16,7 +22,7 @@ timeline
16 22
17 23
|Entity|Tier|Description |
18 24
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
25
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
20 26
21 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 28
... ...
@@ -60,4 +66,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
60 66
61 67
62 68
## References
63
-1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
CAD.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CAD
2 7
3 8
## Overview
... ...
@@ -17,7 +22,7 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
25
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -70,4 +75,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
70 75
[479](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/479_reports.html)
71 76
72 77
## References
73
-1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
CADPS2.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CADPS2
2 7
3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -57,7 +62,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
57 62
[SP192970](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP192970.html)
58 63
59 64
## References
60
-1. Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021 Jul;35(7):2002–2016. PMCID: PMC8257491
61 65
62 66
63 67
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
CARD11.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CARD11
2 7
3 8
## History
... ...
@@ -16,11 +21,12 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------------------|
19
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
20
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
21
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
22
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
24
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@yanBCRTLRSignaling2012a]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@lenzOncogenicCARD11Mutations2008]|
26
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
27
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@wuGeneticHeterogeneityPrimary2016]|
23 28
29
+|![BL](images/icons/BL_tier2.png)|2|relevance in BL not firmly established|
24 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
25 31
26 32
|Entity|source |frequency (%)|
... ...
@@ -84,9 +90,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
84 90
<!-- DLBCL: lenzOncogenicCARD11Mutations2008 -->
85 91
86 92
## References
87
-1. Lenz G, Davis RE, Ngo VN, Lam L, George TC, Wright GW, Dave SS, Zhao H, Xu W, Rosenwald A, Ott G, Müller-Hermelink HK, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Fisher RI, Chan WC, Staudt LM. Oncogenic CARD11 mutations in human diffuse large B cell lymphoma. Science. 2008 Mar;319(5870):1676–1679.
88
-2. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, Tamura-Wells J, Li S, Firme MR, Rogic S, Griffith M, Chan S, Yakovenko O, Meyer IM, Zhao EY, Smailus D, Moksa M, Chittaranjan S, Rimsza L, Brooks-Wilson A, Spinelli JJ, Ben-Neriah S, Meissner B, Woolcock B, Boyle M, McDonald H, Tam A, Zhao Y, Delaney A, Zeng T, Tse K, Butterfield Y, Birol I, Holt R, Schein J, Horsman DE, Moore R, Jones SJM, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298–303. PMCID: PMC3210554
89
-3. Yan Q, Huang Y, Watkins AJ, Kocialkowski S, Zeng N, Hamoudi RA, Isaacson PG, de Leval L, Wotherspoon A, Du MQ. BCR and TLR signaling pathways are recurrently targeted by genetic changes in splenic marginal zone lymphomas. Haematologica. 2012 Apr;97(4):595–598. PMCID: PMC3347666
90
-4. Wu C, de Miranda NF, Chen L, Wasik AM, Mansouri L, Jurczak W, Galazka K, Dlugosz-Danecka M, Machaczka M, Zhang H, Peng R, Morin RD, Rosenquist R, Sander B, Pan-Hammarström Q. Genetic heterogeneity in primary and relapsed mantle cell lymphomas: Impact of recurrent CARD11 mutations. Oncotarget. 2016 Jun 21;7(25):38180–38190. PMCID: PMC5122381
91
-
92
-
CARD4.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CARD4
2 7
3 8
## Overview
... ...
@@ -16,7 +21,7 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------------------|
19
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
24
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -50,4 +55,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
50 55
[747](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html)
51 56
52 57
## References
53
-1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561
CARD4_tmp.html
... ...
@@ -0,0 +1,437 @@
1
+<!DOCTYPE html>
2
+<html>
3
+<head>
4
+<title>CARD4.md</title>
5
+<meta http-equiv="Content-type" content="text/html;charset=UTF-8">
6
+
7
+<style>
8
+/* https://github.com/microsoft/vscode/blob/master/extensions/markdown-language-features/media/markdown.css */
9
+/*---------------------------------------------------------------------------------------------
10
+ * Copyright (c) Microsoft Corporation. All rights reserved.
11
+ * Licensed under the MIT License. See License.txt in the project root for license information.
12
+ *--------------------------------------------------------------------------------------------*/
13
+
14
+body {
15
+ font-family: var(--vscode-markdown-font-family, -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif);
16
+ font-size: var(--vscode-markdown-font-size, 14px);
17
+ padding: 0 26px;
18
+ line-height: var(--vscode-markdown-line-height, 22px);
19
+ word-wrap: break-word;
20
+}
21
+
22
+#code-csp-warning {
23
+ position: fixed;
24
+ top: 0;
25
+ right: 0;
26
+ color: white;
27
+ margin: 16px;
28
+ text-align: center;
29
+ font-size: 12px;
30
+ font-family: sans-serif;
31
+ background-color:#444444;
32
+ cursor: pointer;
33
+ padding: 6px;
34
+ box-shadow: 1px 1px 1px rgba(0,0,0,.25);
35
+}
36
+
37
+#code-csp-warning:hover {
38
+ text-decoration: none;
39
+ background-color:#007acc;
40
+ box-shadow: 2px 2px 2px rgba(0,0,0,.25);
41
+}
42
+
43
+body.scrollBeyondLastLine {
44
+ margin-bottom: calc(100vh - 22px);
45
+}
46
+
47
+body.showEditorSelection .code-line {
48
+ position: relative;
49
+}
50
+
51
+body.showEditorSelection .code-active-line:before,
52
+body.showEditorSelection .code-line:hover:before {
53
+ content: "";
54
+ display: block;
55
+ position: absolute;
56
+ top: 0;
57
+ left: -12px;
58
+ height: 100%;
59
+}
60
+
61
+body.showEditorSelection li.code-active-line:before,
62
+body.showEditorSelection li.code-line:hover:before {
63
+ left: -30px;
64
+}
65
+
66
+.vscode-light.showEditorSelection .code-active-line:before {
67
+ border-left: 3px solid rgba(0, 0, 0, 0.15);
68
+}
69
+
70
+.vscode-light.showEditorSelection .code-line:hover:before {
71
+ border-left: 3px solid rgba(0, 0, 0, 0.40);
72
+}
73
+
74
+.vscode-light.showEditorSelection .code-line .code-line:hover:before {
75
+ border-left: none;
76
+}
77
+
78
+.vscode-dark.showEditorSelection .code-active-line:before {
79
+ border-left: 3px solid rgba(255, 255, 255, 0.4);
80
+}
81
+
82
+.vscode-dark.showEditorSelection .code-line:hover:before {
83
+ border-left: 3px solid rgba(255, 255, 255, 0.60);
84
+}
85
+
86
+.vscode-dark.showEditorSelection .code-line .code-line:hover:before {
87
+ border-left: none;
88
+}
89
+
90
+.vscode-high-contrast.showEditorSelection .code-active-line:before {
91
+ border-left: 3px solid rgba(255, 160, 0, 0.7);
92
+}
93
+
94
+.vscode-high-contrast.showEditorSelection .code-line:hover:before {
95
+ border-left: 3px solid rgba(255, 160, 0, 1);
96
+}
97
+
98
+.vscode-high-contrast.showEditorSelection .code-line .code-line:hover:before {
99
+ border-left: none;
100
+}
101
+
102
+img {
103
+ max-width: 100%;
104
+ max-height: 100%;
105
+}
106
+
107
+a {
108
+ text-decoration: none;
109
+}
110
+
111
+a:hover {
112
+ text-decoration: underline;
113
+}
114
+
115
+a:focus,
116
+input:focus,
117
+select:focus,
118
+textarea:focus {
119
+ outline: 1px solid -webkit-focus-ring-color;
120
+ outline-offset: -1px;
121
+}
122
+
123
+hr {
124
+ border: 0;
125
+ height: 2px;
126
+ border-bottom: 2px solid;
127
+}
128
+
129
+h1 {
130
+ padding-bottom: 0.3em;
131
+ line-height: 1.2;
132
+ border-bottom-width: 1px;
133
+ border-bottom-style: solid;
134
+}
135
+
136
+h1, h2, h3 {
137
+ font-weight: normal;
138
+}
139
+
140
+table {
141
+ border-collapse: collapse;
142
+}
143
+
144
+table > thead > tr > th {
145
+ text-align: left;
146
+ border-bottom: 1px solid;
147
+}
148
+
149
+table > thead > tr > th,
150
+table > thead > tr > td,
151
+table > tbody > tr > th,
152
+table > tbody > tr > td {
153
+ padding: 5px 10px;
154
+}
155
+
156
+table > tbody > tr + tr > td {
157
+ border-top: 1px solid;
158
+}
159
+
160
+blockquote {
161
+ margin: 0 7px 0 5px;
162
+ padding: 0 16px 0 10px;
163
+ border-left-width: 5px;
164
+ border-left-style: solid;
165
+}
166
+
167
+code {
168
+ font-family: Menlo, Monaco, Consolas, "Droid Sans Mono", "Courier New", monospace, "Droid Sans Fallback";
169
+ font-size: 1em;
170
+ line-height: 1.357em;
171
+}
172
+
173
+body.wordWrap pre {
174
+ white-space: pre-wrap;
175
+}
176
+
177
+pre:not(.hljs),
178
+pre.hljs code > div {
179
+ padding: 16px;
180
+ border-radius: 3px;
181
+ overflow: auto;
182
+}
183
+
184
+pre code {
185
+ color: var(--vscode-editor-foreground);
186
+ tab-size: 4;
187
+}
188
+
189
+/** Theming */
190
+
191
+.vscode-light pre {
192
+ background-color: rgba(220, 220, 220, 0.4);
193
+}
194
+
195
+.vscode-dark pre {
196
+ background-color: rgba(10, 10, 10, 0.4);
197
+}
198
+
199
+.vscode-high-contrast pre {
200
+ background-color: rgb(0, 0, 0);
201
+}
202
+
203
+.vscode-high-contrast h1 {
204
+ border-color: rgb(0, 0, 0);
205
+}
206
+
207
+.vscode-light table > thead > tr > th {
208
+ border-color: rgba(0, 0, 0, 0.69);
209
+}
210
+
211
+.vscode-dark table > thead > tr > th {
212
+ border-color: rgba(255, 255, 255, 0.69);
213
+}
214
+
215
+.vscode-light h1,
216
+.vscode-light hr,
217
+.vscode-light table > tbody > tr + tr > td {
218
+ border-color: rgba(0, 0, 0, 0.18);
219
+}
220
+
221
+.vscode-dark h1,
222
+.vscode-dark hr,
223
+.vscode-dark table > tbody > tr + tr > td {
224
+ border-color: rgba(255, 255, 255, 0.18);
225
+}
226
+
227
+</style>
228
+
229
+<style>
230
+/* Tomorrow Theme */
231
+/* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
232
+/* Original theme - https://github.com/chriskempson/tomorrow-theme */
233
+
234
+/* Tomorrow Comment */
235
+.hljs-comment,
236
+.hljs-quote {
237
+ color: #8e908c;
238
+}
239
+
240
+/* Tomorrow Red */
241
+.hljs-variable,
242
+.hljs-template-variable,
243
+.hljs-tag,
244
+.hljs-name,
245
+.hljs-selector-id,
246
+.hljs-selector-class,
247
+.hljs-regexp,
248
+.hljs-deletion {
249
+ color: #c82829;
250
+}
251
+
252
+/* Tomorrow Orange */
253
+.hljs-number,
254
+.hljs-built_in,
255
+.hljs-builtin-name,
256
+.hljs-literal,
257
+.hljs-type,
258
+.hljs-params,
259
+.hljs-meta,
260
+.hljs-link {
261
+ color: #f5871f;
262
+}
263
+
264
+/* Tomorrow Yellow */
265
+.hljs-attribute {
266
+ color: #eab700;
267
+}
268
+
269
+/* Tomorrow Green */
270
+.hljs-string,
271
+.hljs-symbol,
272
+.hljs-bullet,
273
+.hljs-addition {
274
+ color: #718c00;
275
+}
276
+
277
+/* Tomorrow Blue */
278
+.hljs-title,
279
+.hljs-section {
280
+ color: #4271ae;
281
+}
282
+
283
+/* Tomorrow Purple */
284
+.hljs-keyword,
285
+.hljs-selector-tag {
286
+ color: #8959a8;
287
+}
288
+
289
+.hljs {
290
+ display: block;
291
+ overflow-x: auto;
292
+ color: #4d4d4c;
293
+ padding: 0.5em;
294
+}
295
+
296
+.hljs-emphasis {
297
+ font-style: italic;
298
+}
299
+
300
+.hljs-strong {
301
+ font-weight: bold;
302
+}
303
+</style>
304
+
305
+<style>
306
+/*
307
+ * Markdown PDF CSS
308
+ */
309
+
310
+ body {
311
+ font-family: -apple-system, BlinkMacSystemFont, "Segoe WPC", "Segoe UI", "Ubuntu", "Droid Sans", sans-serif, "Meiryo";
312
+ padding: 0 12px;
313
+}
314
+
315
+pre {
316
+ background-color: #f8f8f8;
317
+ border: 1px solid #cccccc;
318
+ border-radius: 3px;
319
+ overflow-x: auto;
320
+ white-space: pre-wrap;
321
+ overflow-wrap: break-word;
322
+}
323
+
324
+pre:not(.hljs) {
325
+ padding: 23px;
326
+ line-height: 19px;
327
+}
328
+
329
+blockquote {
330
+ background: rgba(127, 127, 127, 0.1);
331
+ border-color: rgba(0, 122, 204, 0.5);
332
+}
333
+
334
+.emoji {
335
+ height: 1.4em;
336
+}
337
+
338
+code {
339
+ font-size: 14px;
340
+ line-height: 19px;
341
+}
342
+
343
+/* for inline code */
344
+:not(pre):not(.hljs) > code {
345
+ color: #C9AE75; /* Change the old color so it seems less like an error */
346
+ font-size: inherit;
347
+}
348
+
349
+/* Page Break : use <div class="page"/> to insert page break
350
+-------------------------------------------------------- */
351
+.page {
352
+ page-break-after: always;
353
+}
354
+
355
+</style>
356
+
357
+<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
358
+</head>
359
+<body>
360
+ <script>
361
+ mermaid.initialize({
362
+ startOnLoad: true,
363
+ theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
364
+ ? 'dark'
365
+ : 'default'
366
+ });
367
+ </script>
368
+<h1 id="card4">CARD4</h1>
369
+<h2 id="overview">Overview</h2>
370
+<p><em>CARD4 is now known as NOD1.</em></p>
371
+<h2 id="history">History</h2>
372
+<pre><code class="language-mermaid"><div class="mermaid">%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
373
+timeline
374
+ title Publication timing
375
+ 2012-12-01 : Love : BL
376
+</div></code></pre>
377
+<h2 id="relevance-tier-by-entity">Relevance tier by entity</h2>
378
+<table>
379
+<thead>
380
+<tr>
381
+<th style="text-align:center">Entity</th>
382
+<th style="text-align:center">Tier</th>
383
+<th>Description</th>
384
+</tr>
385
+</thead>
386
+<tbody>
387
+<tr>
388
+<td style="text-align:center"><img src="file:///Users/rmorin/git/LLMPP.wiki/images/icons/BL_tier2.png" alt="BL"></td>
389
+<td style="text-align:center">2</td>
390
+<td>relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]</td>
391
+</tr>
392
+</tbody>
393
+</table>
394
+<h2 id="mutation-incidence-in-large-patient-cohorts-gambl-reanalysis">Mutation incidence in large patient cohorts (GAMBL reanalysis)</h2>
395
+<table>
396
+<thead>
397
+<tr>
398
+<th style="text-align:center">Entity</th>
399
+<th style="text-align:center">source</th>
400
+<th style="text-align:center">frequency (%)</th>
401
+</tr>
402
+</thead>
403
+<tbody>
404
+<tr>
405
+<td style="text-align:center">BL</td>
406
+<td style="text-align:center">GAMBL genomes+capture</td>
407
+<td style="text-align:center">NA</td>
408
+</tr>
409
+<tr>
410
+<td style="text-align:center">BL</td>
411
+<td style="text-align:center">Thomas cohort</td>
412
+<td style="text-align:center">NA</td>
413
+</tr>
414
+<tr>
415
+<td style="text-align:center">BL</td>
416
+<td style="text-align:center">Panea cohort</td>
417
+<td style="text-align:center">NA</td>
418
+</tr>
419
+</tbody>
420
+</table>
421
+<p>View coding variants in ProteinPaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_protein_hg38.html">hg38</a></p>
422
+<p>View all variants in GenomePaint <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4.html">hg19</a> or <a href="https://morinlab.github.io/LLMPP/GAMBL/CARD4_hg38.html">hg38</a></p>
423
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/images/proteinpaint/CARD4.svg" alt=""></p>
424
+<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
425
+<!-- BL: loveGeneticLandscapeMutations2012 -->
426
+<h2 id="representative-mutations">Representative Mutations</h2>
427
+<p><img src="file:///Users/rmorin/git/LLMPP.wiki/primary/Love_CARD4.svg" alt="">
428
+<strong>Rating</strong>
429
+★ ★ ★ ★ ☆</p>
430
+<h2 id="all-mutations">All Mutations</h2>
431
+<p><a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/1092_reports.html">1092</a>
432
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/674_reports.html">674</a>
433
+<a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/747_reports.html">747</a></p>
434
+<h2 id="references">References</h2>
435
+
436
+</body>
437
+</html>
CASP8.md
... ...
@@ -1,9 +1,13 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CASP8
2 7
3 8
## Overview
4 9
5
-Caspase-8 mutations are relatively rare but have been documented in various non-Hodgkin lymphomas (NHLs). One study found no CASP8 mutations in gastrointestinal lymphomas, suggesting that these mutations may not be prevalent in all lymphoma types.<sup>1</sup> Due to the rarity of these mutations, their role remains poorly understood. Loss of caspase-8 may promote lymphomagenesis by impairing cytokinesis and increasing chromosomal aberrations.<sup>2</sup>
6
-
10
+Caspase-8 mutations are relatively rare but have been documented in various non-Hodgkin lymphomas (NHLs). One study found no CASP8 mutations in gastrointestinal lymphomas, suggesting that these mutations may not be prevalent in all lymphoma types. Due to the rarity of these mutations, their role remains poorly understood. Loss of caspase-8 may promote lymphomagenesis by impairing cytokinesis and increasing chromosomal aberrations.
7 11
## History
8 12
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup>
9 13
... ...
@@ -18,7 +22,7 @@ timeline
18 22
19 23
|Entity|Tier|Description |
20 24
|:------:|:----:|--------------------------|
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@reddyGeneticFunctionalDrivers2017]|
22 26
23 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
24 28
... ...
@@ -53,11 +57,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53 57
54 58
## References
55 59
56
-1. *Yoo NJ, Soung YH, Lee SH, Kim KM, Lee SH. Absence of CASP7 and CASP8 mutation in gastrointestinal lymphomas. Eur J Haematol. 2007 Jul;79(1):86-7. doi: 10.1111/j.1600-0609.2007.00865.x. Epub 2007 May 28. PMID: 17532763.*
57
-2. *Hakem A, El Ghamrasni S, Maire G, Lemmers B, Karaskova J, Jurisicova A, Sanchez O, Squire J, Hakem R. Caspase-8 is essential for maintaining chromosomal stability and suppressing B-cell lymphomagenesis. Blood. 2012 Apr 12;119(15):3495-502. doi: 10.1182/blood-2011-07-367532. Epub 2012 Feb 16. PMID: 22343728.*
58
-3. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
59
-
60
-
61 60
62 61
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
63 62
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CBFA2T3.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CBFA2T3
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2013-12-13 : Parry : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@parryWholeExomeSequencing2013]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |2.299 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |1.294 |
33
+|DLBCL|GAMBL Genome |0.564 |
34
+|MCL|GAMBL Genome |0.585 |
35
+
36
+
37
+## References
38
+
39
+
CBLB.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CBLB
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -85,7 +90,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
85 90
[Reddy_4000T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_4000T.html)
86 91
87 92
## References
88
-1. *Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct;171(2):481-494.e15.*
89 93
90 94
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
91 95
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CCL4.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CCL4
2 7
3 8
## History
... ...
@@ -13,7 +18,7 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -49,4 +54,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
49 54
<!-- DLBCL: chapuyMolecularSubtypesDiffuse2018b -->
50 55
51 56
## References
52
-1. Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679–690. PMCID: PMC6613387
CCND1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CCND1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|------------------------|
15
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene|
20
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene[@beaLandscapeSomaticMutations2013]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -45,4 +50,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
45 50
<!-- MCL: beaLandscapeSomaticMutations2013 -->
46 51
47 52
## References
48
-1. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436
CCND1.pdf
... ...
Binary files /dev/null and b/CCND1.pdf differ
CD9B.md
... ...
@@ -0,0 +1,34 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CD9B
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-06-14 : van : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@vandenbrandRecurrentMutationsGenes2017]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+
31
+
32
+## References
33
+
34
+
CDH2.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CDH2
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2019-08-20 : Desch : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |4.023 |
31
+|BL|GAMBL Genome |1.931 |
32
+|DLBCL|GAMBL Exome |2.695 |
33
+|DLBCL|GAMBL Genome |2.068 |
34
+|FL|GAMBL Exome |0.86 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
CDH5.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CDH5
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2023-11-15 : Gomez : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@gomezUltraDeepSequencingReveals2023]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |2.874 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |2.21 |
33
+|DLBCL|GAMBL Genome |1.128 |
34
+|FL|GAMBL Exome |0.573 |
35
+
36
+
37
+## References
38
+
39
+
CISH.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CISH
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2019-09-05 : Mottok : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@mottokIntegrativeGenomicAnalysis2019b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |0.575 |
31
+|DLBCL|GAMBL Exome |0.377 |
32
+|DLBCL|GAMBL Genome |0.188 |
33
+|FL|GAMBL Exome |0.573 |
34
+
35
+
36
+## References
37
+
38
+
CLGN.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CLGN
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.724 |
31
+|DLBCL|GAMBL Exome |0.701 |
32
+|DLBCL|GAMBL Genome |0.752 |
33
+|FL|GAMBL Exome |0.573 |
34
+|MCL|GAMBL Genome |0.585 |
35
+
36
+
37
+## References
38
+
39
+
CNBP.md
... ...
@@ -0,0 +1,34 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CNBP
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+
31
+
32
+## References
33
+
34
+
CNKSR2.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CNKSR2
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2016-09-08 : Spina : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@spinaGeneticsNodalMarginal2016b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |2.874 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |1.078 |
33
+|DLBCL|GAMBL Genome |1.692 |
34
+|FL|GAMBL Exome |0.573 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
DNAH12.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DNAH12
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2019-12-10 : Wienand : PMBL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![PMBL](images/icons/PMBL_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@wienandGenomicAnalysesFlowsorted2019b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |6.897 |
31
+|BL|GAMBL Genome |4.247 |
32
+|DLBCL|GAMBL Exome |3.881 |
33
+|DLBCL|GAMBL Genome |2.82 |
34
+|MCL|GAMBL Genome |1.17 |
35
+
36
+
37
+## References
38
+
39
+
DNAH5.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# DNAH5
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
21
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@morinMutationalStructuralAnalysis2013]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -51,5 +56,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D
51 56
<!-- MZL: jalladesExomeSequencingIdentifies2017 -->
52 57
53 58
## References
54
-1. Morin RD, Mungall K, Pleasance E, Mungall AJ, Goya R, Huff RD, Scott DW, Ding J, Roth A, Chiu R, Corbett RD, Chan FC, Mendez-Lago M, Trinh DL, Bolger-Munro M, Taylor G, Hadj Khodabakhshi A, Ben-Neriah S, Pon J, Meissner B, Woolcock B, Farnoud N, Rogic S, Lim EL, Johnson NA, Shah S, Jones S, Steidl C, Holt R, Birol I, Moore R, Connors JM, Gascoyne RD, Marra MA. Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood. 2013 Aug 15;122(7):1256–1265. PMCID: PMC3744992
55
-2. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860
DNAH7.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DNAH7
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2017-07-27 : Jallades : MZL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |6.897 |
31
+|BL|GAMBL Genome |5.019 |
32
+|DLBCL|GAMBL Exome |7.493 |
33
+|DLBCL|GAMBL Genome |3.947 |
34
+|FL|GAMBL Exome |3.152 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
TNF.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# TNF
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2012-03-06 : Lohr : DLBCL
16
+```
17
+
18
+
19
+## Relevance tier by entity
20
+
21
+|Entity|Tier|Description|
22
+|:------:|:----:|--------------------------------------|
23
+|![DLBCL](images/icons/DLBCL_tier2.png)|2|relevance in DLBCL not firmly established[@lohrDiscoveryPrioritizationSomatic2012a]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |2.299 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |0.809 |
33
+|DLBCL|GAMBL Genome |0.94 |
34
+
35
+
36
+## References
37
+
38
+