PHF6.md
... ...
@@ -1,5 +1,12 @@
1 1
# PHF6
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+ 2023-02-03 : Thomas : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -44,3 +51,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
44 51
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
45 52
<!-- BL: thomasGeneticSubgroupsInform2023 -->
46 53
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
54
+## References
55
+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.
56
+2. Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood. 2023 Feb 23;141(8):904–916.
PTEN.md
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@@ -1,5 +1,11 @@
1 1
# PTEN
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2012-12-01 : Love : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -40,3 +46,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/P
40 46
![image](images/gene_expression/PTEN_by_pathology.svg)
41 47
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
42 48
<!-- BL: loveGeneticLandscapeMutations2012 -->
49
+## References
50
+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
RFX7.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
First described as mutated in BL in 2009 by Grande et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2019-03-21 : Grande : BL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
RHOA.md
... ...
@@ -1,5 +1,12 @@
1 1
# RHOA
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2001-07-19 : Pasqualucci : DLBCL
8
+ 2012-11-11 : Richter : BL
9
+```
3 10
## Relevance tier by entity
4 11
5 12
|Entity|Tier|Description |
... ...
@@ -56,3 +63,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/R
56 63
<!-- ORIGIN: pasqualucciHypermutationMultipleProtooncogenes2001a -->
57 64
<!-- DLBCL: pasqualucciHypermutationMultipleProtooncogenes2001a -->
58 65
<!-- BL: richterRecurrentMutationID32012a -->
66
+## References
67
+1. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Küppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001 Jul 19;412(6844):341–346. PMID: 11460166
68
+2. Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012 Dec;44(12):1316–1320. PMID: 23143595
SIN3A.md
... ...
@@ -2,6 +2,13 @@
2 2
## History
3 3
Mutations in this gene were first described in MZL in 2012 by Rossi et al<sup>1</sup> and in BL in 2019 by Grande et al.<sup>2</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2012-08-27 : Rossi : MZL
10
+ 2019-03-21 : Grande : BL
11
+```
5 12
## Relevance tier by entity
6 13
7 14
|Entity|Tier|Description |
STAT3.md
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@@ -1,5 +1,11 @@
1 1
# STAT3
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2014-07-01 : Ohgami : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -48,3 +54,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
48 54
![image](images/gene_expression/STAT3_by_pathology.svg)
49 55
<!-- ORIGIN: ohgamiSTAT3MutationsAre2014 -->
50 56
<!-- DLBCL: ohgamiSTAT3MutationsAre2014 -->
57
+## References
58
+1. Ohgami RS, Ma L, Monabati A, Zehnder JL, Arber DA. STAT3 mutations are present in aggressive B-cell lymphomas including a subset of diffuse large B-cell lymphomas with CD30 expression. Haematologica. 2014 Jul;99(7):e105-107. PMCID: PMC4077094
SYK.md
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@@ -1,5 +1,11 @@
1 1
# SYK
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-10-10 : Reddy : DLBCL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
... ...
@@ -24,9 +30,6 @@
24 30
|FL |No |No |0.000 | 0.00 |
25 31
26 32
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30 33
31 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SYK_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SYK_protein_hg38.html)
32 35
... ...
@@ -39,3 +42,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
39 42
![image](images/gene_expression/SYK_by_pathology.svg)
40 43
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
41 44
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
45
+## References
46
+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.
TCL1A.md
... ...
@@ -1,5 +1,11 @@
1 1
# TCL1A
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-03-21 : Grande : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
TFAP4.md
... ...
@@ -2,6 +2,12 @@
2 2
## History
3 3
Mutations in BL were first described by Grande et al.<sup>1</sup>
4 4
5
+```mermaid
6
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
7
+timeline
8
+ title Publication timing
9
+ 2019-03-21 : Grande : BL
10
+```
5 11
## Relevance tier by entity
6 12
7 13
|Entity|Tier|Description |
USP7.md
... ...
@@ -1,5 +1,11 @@
1 1
# USP7
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2019-03-21 : Grande : BL
8
+```
3 9
## Relevance tier by entity
4 10
5 11
|Entity|Tier|Description |
WNK1.md
... ...
@@ -1,9 +1,18 @@
1 1
# WNK1
2
-
2
+## History
3
+```mermaid
4
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
5
+timeline
6
+ title Publication timing
7
+ 2017-07-27 : Jallades : MZL
8
+ 2021-05-05 : H : DLBCL
9
+ 2023-02-03 : Thomas : BL
10
+```
3 11
## Relevance tier by entity
4 12
5 13
|Entity|Tier|Description |
6 14
|:------:|:----:|-----------------------------------------|
15
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
7 16
|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
8 17
|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
9 18