CCNF.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CCNF
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@abateDistinctViralMutational2015a]|
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
<!-- BL: abateDistinctViralMutational2015a -->
46 51
47 52
## References
48
-1. Abate F, Ambrosio M, Mundo L, Laginestra M, Fuligni F, Rossi M, Zairis S, Gazaneo S, Falco GD, Lazzi S, Bellan C, Rocca BJ, Amato T, Marasco E, Etebari M, Ogwang M, Calbi V, Ndede I, Patel K, Chumba D, Piccaluga P, Pileri S, Leoncini L, Rabadán R. Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma. PLoS Pathogens. 2015;11.
CCT6B.md
... ...
@@ -1,4 +1,10 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CCT6B
7
+
2 8
## Overview
3 9
4 10
Due to [minimal support](CCT6B#representative-mutations) in the original primary data and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL.
... ...
@@ -17,7 +23,7 @@ timeline
17 23
18 24
|Entity|Tier|Description |
19 25
|:------:|:----:|--------------------------------------|
20
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
26
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]|
21 27
22 28
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 29
... ...
@@ -64,4 +70,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
64 70
[670](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/670_reports.html)
65 71
66 72
## 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
CD22.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CD22
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
... ...
@@ -46,7 +51,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
46 51
![](images/gene_expression/CD22_by_pathology.svg)
47 52
48 53
## References
49
-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.*
54
+
50 55
51 56
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
52 57
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
CD36.md
... ...
@@ -1,6 +1,12 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CD36
2 7
3 8
CD36 is a transmembrane glycoprotein involved in fatty acid metabolism, glucose intolerance, and immune responses. It is expressed on various cell types, including platelets, monocytes, and some lymphocytes. One study showed higher rates of CD36 mutations in FL relative to DLBCLs.<sup>1</sup>
9
+
4 10
## History
5 11
```mermaid
6 12
%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
... ...
@@ -13,7 +19,7 @@ timeline
13 19
14 20
|Entity|Tier|Description |
15 21
|:------:|:----:|--------------------------|
16
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@pasqualucciAnalysisCodingGenome2011]|
17 23
18 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 25
... ...
@@ -45,7 +51,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
45 51
46 52
## References
47 53
48
-1. *Carreras J, Ikoma H, Kikuti YY, Miyaoka M, Hiraiwa S, Tomita S, Kondo Y, Ito A, Nagase S, Miura H, Kawada H, Roncador G, Campo E, Hamoudi R, Nakamura N. Mutational, immune microenvironment, and clinicopathological profiles of diffuse large B-cell lymphoma and follicular lymphoma with BCL6 rearrangement. Virchows Arch. 2024 Apr;484(4):657-676. doi: 10.1007/s00428-024-03774-z. Epub 2024 Mar 11. PMID: 38462571.*
54
+
49 55
## CD36 Expression
50 56
![](images/gene_expression/CD36_by_pathology.svg)
51 57
<!-- ORIGIN: pasqualucciAnalysisCodingGenome2011 -->
CD44.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CD44
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-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
21
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
19 24
... ...
@@ -54,4 +59,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
54 59
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
55 60
56 61
## References
57
-1. 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
CD74.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# CD74
2 7
##History
3 8
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous [@arthurGenomewideDiscoverySomatic2018]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -53,4 +58,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
53 58
<!-- DLBCL: arthurGenomewideDiscoverySomatic2018 -->
54 59
55 60
## References
56
-1. 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
CHMP4C.md
... ...
@@ -0,0 +1,37 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CHMP4C
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 |1.149 |
31
+|DLBCL|GAMBL Exome |0.485 |
32
+|DLBCL|GAMBL Genome |0.376 |
33
+
34
+
35
+## References
36
+
37
+
CPS1.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CPS1
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 |5.172 |
31
+|BL|GAMBL Genome |1.931 |
32
+|DLBCL|GAMBL Exome |2.857 |
33
+|DLBCL|GAMBL Genome |3.008 |
34
+|FL|GAMBL Exome |1.146 |
35
+
36
+
37
+## References
38
+
39
+
CRYBG3.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CRYBG3
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 |9.77 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |3.935 |
33
+|DLBCL|GAMBL Genome |3.195 |
34
+|FL|GAMBL Exome |0.287 |
35
+|MCL|GAMBL Genome |2.339 |
36
+
37
+
38
+## References
39
+
40
+
CSF2RB.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# CSF2RB
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2015-02-12 : Reichel : 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[@reichelFlowSortingExome2015a]|
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 |0.772 |
32
+|DLBCL|GAMBL Exome |1.941 |
33
+|DLBCL|GAMBL Genome |0.376 |
34
+
35
+
36
+## References
37
+
38
+
DCP1B.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DCP1B
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 |1.724 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |0.539 |
33
+|DLBCL|GAMBL Genome |0.376 |
34
+|MCL|GAMBL Genome |0.585 |
35
+
36
+
37
+## References
38
+
39
+
DGKB.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DGKB
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 |2.874 |
31
+|BL|GAMBL Genome |2.317 |
32
+|DLBCL|GAMBL Exome |2.588 |
33
+|DLBCL|GAMBL Genome |1.88 |
34
+|FL|GAMBL Exome |1.433 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
DHCR7.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DHCR7
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
+|BL|GAMBL Exome |1.724 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |1.186 |
33
+|DLBCL|GAMBL Genome |0.188 |
34
+
35
+
36
+## References
37
+
38
+
DLGAP2.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DLGAP2
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 |2.299 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |3.073 |
33
+|DLBCL|GAMBL Genome |2.82 |
34
+|FL|GAMBL Exome |0.86 |
35
+|MCL|GAMBL Genome |1.17 |
36
+
37
+
38
+## References
39
+
40
+
DMD.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DMD
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2015-02-12 : Reichel : 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[@reichelFlowSortingExome2015a]|
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 |5.405 |
32
+|DLBCL|GAMBL Exome |7.332 |
33
+|DLBCL|GAMBL Genome |6.015 |
34
+|FL|GAMBL Exome |4.298 |
35
+|MCL|GAMBL Genome |1.754 |
36
+
37
+
38
+## References
39
+
40
+
DNAI1.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DNAI1
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 |1.724 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |1.024 |
33
+|DLBCL|GAMBL Genome |0.376 |
34
+|FL|GAMBL Exome |0.287 |
35
+|MCL|GAMBL Genome |0.585 |
36
+
37
+
38
+## References
39
+
40
+
DNAJC6.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# DNAJC6
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 |2.874 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |1.509 |
33
+|DLBCL|GAMBL Genome |0.564 |
34
+|FL|GAMBL Exome |0.287 |
35
+
36
+
37
+## References
38
+
39
+
HIST1H2AD.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# HIST1H2AD
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 |1.149 |
31
+|BL|GAMBL Genome |0.386 |
32
+|DLBCL|GAMBL Exome |1.779 |
33
+|DLBCL|GAMBL Genome |2.068 |
34
+|FL|GAMBL Exome |0.573 |
35
+
36
+
37
+## References
38
+
39
+
HIST1H2AL.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# HIST1H2AL
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 |0.575 |
31
+|DLBCL|GAMBL Exome |1.509 |
32
+|DLBCL|GAMBL Genome |0.94 |
33
+|FL|GAMBL Exome |0.573 |
34
+
35
+
36
+## References
37
+
38
+
HIST1H2BO.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# HIST1H2BO
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 |1.724 |
31
+|BL|GAMBL Genome |1.931 |
32
+|DLBCL|GAMBL Exome |1.887 |
33
+|DLBCL|GAMBL Genome |2.82 |
34
+|FL|GAMBL Exome |0.573 |
35
+
36
+
37
+## References
38
+
39
+
HIST1H4E.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# HIST1H4E
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_tier2.png)|2|relevance in PMBL/cHL/GZL not firmly established[@mottokIntegrativeGenomicAnalysis2019b]|
24
+
25
+
26
+## Mutation incidence in large patient cohorts (GAMBL reanalysis)
27
+
28
+|Entity|source |frequency (%)|
29
+|:------:|:----:|:----:|
30
+|BL|GAMBL Exome |1.149 |
31
+|BL|GAMBL Genome |1.544 |
32
+|DLBCL|GAMBL Exome |1.24 |
33
+|DLBCL|GAMBL Genome |2.632 |
34
+|FL|GAMBL Exome |0.573 |
35
+
36
+
37
+## References
38
+
39
+
HIST4H4.md
... ...
@@ -0,0 +1,37 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# HIST4H4
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 |1.724 |
31
+|DLBCL|GAMBL Exome |2.426 |
32
+|DLBCL|GAMBL Genome |1.504 |
33
+
34
+
35
+## References
36
+
37
+
KRTAP5-5.md
... ...
@@ -0,0 +1,35 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# KRTAP5-5
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
+|DLBCL|GAMBL Exome |0.216 |
31
+
32
+
33
+## References
34
+
35
+
NRAS.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# NRAS
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 |0.575 |
31
+|BL|GAMBL Genome |0.772 |
32
+|DLBCL|GAMBL Exome |0.485 |
33
+|DLBCL|GAMBL Genome |1.504 |
34
+|MCL|GAMBL Genome |1.754 |
35
+
36
+
37
+## References
38
+
39
+
NUP214.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# NUP214
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 |0.772 |
32
+|DLBCL|GAMBL Exome |3.073 |
33
+|DLBCL|GAMBL Genome |0.752 |
34
+|FL|GAMBL Exome |1.146 |
35
+|MCL|GAMBL Genome |2.339 |
36
+
37
+
38
+## References
39
+
40
+
OR13C2.md
... ...
@@ -0,0 +1,37 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# OR13C2
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
+|DLBCL|GAMBL Exome |0.755 |
32
+|DLBCL|GAMBL Genome |0.376 |
33
+
34
+
35
+## References
36
+
37
+
OR6K3.md
... ...
@@ -0,0 +1,37 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# OR6K3
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 |0.575 |
31
+|DLBCL|GAMBL Exome |0.809 |
32
+|DLBCL|GAMBL Genome |0.188 |
33
+
34
+
35
+## References
36
+
37
+
PDCD11.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# PDCD11
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
20
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@schmitzBurkittLymphomaPathogenesis2012]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
46 51
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
47 52
48 53
## References
49
-1. Schmitz R, Young RM, Ceribelli M, Jhavar S, Xiao W, Zhang M, Wright G, Shaffer AL, Hodson DJ, Buras E, Liu X, Powell J, Yang Y, Xu W, Zhao H, Kohlhammer H, Rosenwald A, Kluin P, Müller-Hermelink HK, Ott G, Gascoyne RD, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Ogwang MD, Reynolds SJ, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pittaluga S, Wilson W, Waldmann TA, Rowe M, Mbulaiteye SM, Rickinson AB, Staudt LM. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature. 2012 Oct 4;490(7418):116–120. PMCID: PMC3609867
PDGFC.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# PDGFC
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 |1.149 |
31
+|BL|GAMBL Genome |1.158 |
32
+|DLBCL|GAMBL Exome |2.049 |
33
+|DLBCL|GAMBL Genome |1.316 |
34
+
35
+
36
+## References
37
+
38
+
PDLIM3.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# PDLIM3
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 |1.149 |
31
+|DLBCL|GAMBL Exome |0.809 |
32
+|DLBCL|GAMBL Genome |0.564 |
33
+|FL|GAMBL Exome |0.287 |
34
+
35
+
36
+## References
37
+
38
+