ARID5B.md
... ...
@@ -1,10 +1,15 @@
1 1
# ARID5B
2
+## History
3
+Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
4
+
5
+> [!WARNING]
6
+> Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1)
2 7
3 8
## Relevance tier by entity
4 9
5 10
|Entity|Tier|Description |
6 11
|:------:|:----:|-----------------------------------------|
7
-|DLBCL |2 |relevance in DLBCL not firmly established|
12
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
8 13
9 14
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 15
... ...
@@ -23,13 +28,6 @@
23 28
|DLBCL |No |No |2.263 |0 |
24 29
|FL |No |No |0.000 |0 |
25 30
26
-
27
-> [!NOTE]
28
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567)
29
-
30
-> [!WARNING]
31
-> Mutations in this gene were reported to be inflated in the original results according to [Dreval K](https://www.biorxiv.org/content/10.1101/2023.11.21.567983v1)
32
-
33 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ARID5B_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ARID5B_protein_hg38.html)
34 32
35 33
![image](images/proteinpaint/ARID5B_NM_032199.svg)
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@@ -39,4 +37,11 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39 37
![image](images/proteinpaint/ARID5B.svg)
40 38
## ARID5B Expression
41 39
![image](images/gene_expression/ARID5B_by_pathology.svg)
40
+
41
+## References
42
+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.*
43
+
44
+
42 45
<!-- ORIGIN: reddyGeneticFunctionalDrivers2017 -->
46
+<!-- PMBL: gomezUltraDeepSequencingReveals2023 -->
47
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
ATM.md
... ...
@@ -1,11 +1,13 @@
1 1
# ATM
2
+## History
3
+Mutations in this gene were first described in MZL by Braggio et al,<sup>1</sup> then in MCL by Bea et al.<sup>2</sup> ATM mutations were later described in DLBCL by Reddy et al.<sup>3</sup>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7
-|DLBCL |1 |high-confidence DLBCL gene|
8
-|MCL |1 |high-confidence MCL gene |
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
10
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
9 11
10 12
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 13
... ...
@@ -26,10 +28,6 @@
26 28
|FL |No |No |1.679 |6.201 |
27 29
28 30
29
-> [!NOTE]
30
-> First described in DLBCL in 2017 by [Reddy A](https://pubmed.ncbi.nlm.nih.gov/28985567). First described in MCL in 2013 by [Beà S](https://pubmed.ncbi.nlm.nih.gov/24145436)
31
-
32
-
33 31
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATM_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATM_protein_hg38.html)
34 32
35 33
![image](images/proteinpaint/ATM_NM_000051.svg)
... ...
@@ -39,4 +37,14 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
39 37
![image](images/proteinpaint/ATM.svg)
40 38
## ATM Expression
41 39
![image](images/gene_expression/ATM_by_pathology.svg)
42
-<!-- ORIGIN: beaLandscapeSomaticMutations2013 -->
40
+
41
+## References
42
+1. *Braggio E, Dogan A, Keats JJ, Chng WJ, Huang G, Matthews JM, Maurer MJ, Law ME, Bosler DS, Barrett M, Lossos IS, Witzig TE, Fonseca R. Genomic analysis of marginal zone and lymphoplasmacytic lymphomas identified common and disease-specific abnormalities. Mod Pathol. 2012 May;25(5):651–660. PMCID: PMC3341516*
43
+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*
44
+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.*
45
+
46
+
47
+<!-- ORIGIN: braggioGenomicAnalysisMarginal2012 -->
48
+<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
49
+<!-- MZL: braggioGenomicAnalysisMarginal2012 -->
50
+<!-- MCL: beaLandscapeSomaticMutations2013 -->
ATP2C2.md
... ...
@@ -37,3 +37,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
37 37
## ATP2C2 Expression
38 38
![image](images/gene_expression/ATP2C2_by_pathology.svg)
39 39
<!-- ORIGIN: loveGeneticLandscapeMutations2012 -->
40
+<!-- BL: loveGeneticLandscapeMutations2012 -->
ATP6AP1.md
... ...
@@ -32,3 +32,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/A
32 32
## ATP6AP1 Expression
33 33
![image](images/gene_expression/ATP6AP1_by_pathology.svg)
34 34
<!-- ORIGIN: okosunRecurrentMTORC1activatingRRAGC2016a -->
35
+<!-- FL: okosunRecurrentMTORC1activatingRRAGC2016a -->
ATP6V1A.md
... ...
@@ -1,5 +1,8 @@
1 1
# ATP6V1A
2 2
3
+## History
4
+Mutations in this gene were first described in DLBCL in 2021 by Hübschmann et al.<sup>1</sup>
5
+
3 6
## Relevance tier by entity
4 7
5 8
|Entity|Tier|Description |
... ...
@@ -20,8 +23,6 @@
20 23
|DLBCL |No |No |7.648 |0 |
21 24
|FL |No |No |8.783 |0 |
22 25
23
-
24
-> [!NOTE]
25 26
## ATP6V1A Hotspots
26 27
27 28
| Chromosome |Coordinate (hg19) | ref>alt | HGVSp |
... ...
@@ -35,6 +36,12 @@ View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAM
35 36
View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ATP6V1A_hg38.html)
36 37
37 38
![image](images/proteinpaint/ATP6V1A.svg)
39
+
38 40
## ATP6V1A Expression
39 41
![image](images/gene_expression/ATP6V1A_by_pathology.svg)
42
+
43
+## References
44
+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
45
+
40 46
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
47
+<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
BMP7.md
... ...
@@ -58,3 +58,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/B
58 58
## BMP7 Expression
59 59
![image](images/gene_expression/BMP7_by_pathology.svg)
60 60
<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
61
+<!-- BL: paneaWholeGenomeLandscape2019 -->
CIITA.md
... ...
@@ -52,3 +52,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C
52 52
3. *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 SJ, 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. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.*
53 53
54 54
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
55
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
56
+<!-- PMBL: mottokGenomicAlterationsCIITA2015b -->
EBF1.md
... ...
@@ -69,4 +69,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
69 69
1. *Györy I, Boller S, Nechanitzky R, Mandel E, Pott S, Liu E, Grosschedl R. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev. 2012 Apr 1;26(7):668-82. doi: 10.1101/gad.187328.112. Epub 2012 Mar 19. PMID: 22431510; PMCID: PMC3323878.*
70 70
## EBF1 Expression
71 71
![image](images/gene_expression/EBF1_by_pathology.svg)
72
-<!-- ORIGIN: bohleRoleEarlyBcell2013 -->
72
+<!-- ORIGIN: 23174882 -->
73
+<!-- BL: 2 -->
74
+<!-- PMBL: reichelFlowSortingExome2015a -->
75
+<!-- DLBCL: bohleRoleEarlyBcell2013 -->
EZH2.md
... ...
@@ -6,9 +6,13 @@ EZH2 encodes a histone methyltransferase that is a component of the polycomb rep
6 6
7 7
|Entity|Tier|Description |
8 8
|:------:|:----:|--------------------------------------|
9
-|DLBCL |1 |high-confidence DLBCL gene |
10
-|FL |1 |high-confidence FL gene |
11
-|BL |2 |relevance in BL not firmly established|
9
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
10
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
11
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
12
+
13
+
14
+
15
+
12 16
13 17
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
14 18
... ...
@@ -71,3 +75,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
71 75
4. *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. doi: 10.1182/blood.2022016534. PMID: 36201743; PMCID: PMC10023728.*
72 76
73 77
<!-- ORIGIN: morinSomaticMutationsAltering2010 -->
78
+<!-- BL: loveGeneticLandscapeMutations2012 -->
79
+<!-- FL: morinSomaticMutationsAltering2010 -->
80
+<!-- BL: loveGeneticLandscapeMutations2012 -->
81
+<!-- DLBCL: morinSomaticMutationsAltering2010 -->
EZR.md
... ...
@@ -39,4 +39,5 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/E
39 39
![image](images/proteinpaint/EZR.svg)
40 40
## EZR Expression
41 41
![image](images/gene_expression/EZR_by_pathology.svg)
42
-<!-- ORIGIN: Unknown -->
42
+<!-- ORIGIN: deschGenotypingCirculatingTumor2020 -->
43
+<!-- PMBL: deschGenotypingCirculatingTumor2020 -->
FBXO11.md
... ...
@@ -2,6 +2,9 @@
2 2
## Overview
3 3
Somatic mutations in FBXO11 are common in BL<sup>1,2</sup> and appear in a small number of DLBCLs.<sup>3</sup> This gene has some recurrent sites of mutations (hot spots). Mutations lead to stabilization of BCL6, an important transcriptional repressor involved in lymphomagenesis.<sup>4</sup> These mutations present a potential novel target for therapeutic intervention, particularly through strategies aimed at degrading BCL6 or inhibiting its function.<sup>4</sup>
4 4
5
+## History
6
+Mutations in this gene were first described in BL in 2015 by Pighi et al<sup>4</sup> and in DLBCL by Hübschmann et al.<sup>5</sup>
7
+
5 8
## Relevance tier by entity
6 9
7 10
|Entity|Tier|Description |
... ...
@@ -69,4 +72,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
69 72
5. *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. doi: 10.1038/s41375-021-01251-z. Epub 2021 May 5. PMID: 33953289; PMCID: PMC8257491.*
70 73
## FBXO11 Expression
71 74
![image](images/gene_expression/FBXO11_by_pathology.svg)
72
-<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
75
+<!-- ORIGIN: parryWholeExomeSequencing2013 -->
76
+<!-- BL: richterRecurrentMutationID32012a -->
77
+<!-- MZL: parryWholeExomeSequencing2013 -->
78
+<!-- DLBCL: hubschmannMutationalMechanismsShaping2021b -->
FBXW7.md
... ...
@@ -41,3 +41,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
41 41
## FBXW7 Expression
42 42
![image](images/gene_expression/FBXW7_by_pathology.svg)
43 43
<!-- ORIGIN: zhangGeneticHeterogeneityDiffuse2013 -->
44
+<!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 -->
FOXC1.md
... ...
@@ -44,3 +44,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
44 44
45 45
<!-- FLAGGED FOR TIER 2 -->
46 46
<!-- ORIGIN: schmitzGeneticsPathogenesisDiffuse2018a -->
47
+<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
FOXO1.md
... ...
@@ -79,3 +79,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/F
79 79
## FOXO1 Expression
80 80
![image](images/gene_expression/FOXO1_by_pathology.svg)
81 81
<!-- ORIGIN: morinFrequentMutationHistonemodifying2011 -->
82
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
83
+<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
84
+<!-- FL: morinFrequentMutationHistonemodifying2011 -->
85
+<!-- DLBCL: morinFrequentMutationHistonemodifying2011 -->
ID3.md
... ...
@@ -1,12 +1,14 @@
1 1
# ID3
2
-
2
+## History
3
+ID3 was first reported as mutated in BL in 2012 by Richter et al.<sup>1</sup> The existence of mutations in DLBCL were described in 2012 by Schmitz et al<sup>2</sup> and later in MZL by Spina et al.<sup>3</sup>
4
+
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|-----------------------------------------|
7
-|BL |1-a | aSHM target and high-confidence BL gene |
8
-|DLBCL |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous |
9
-|FL |2-a | aSHM target; Although recurrent, the relevance of mutations in FL is tenuous |
9
+|![BL](images/icons/BL_tier1.png) |1 | high-confidence BL gene |
10
+|![MZL](images/icons/MZL_tier1.png) |1 | high-confidence MZL gene |
11
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 | Although recurrent, the relevance of mutations in DLBCL is tenuous |
10 12
11 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
12 14
... ...
@@ -35,10 +37,6 @@
35 37
|:--------:|:----------:|:--------:|:-----------------------------------------------------------------------------------------:|:------------------:|
36 38
|chr1 |23885584 |23885835|[TSS](https://genome.ucsc.edu/s/rdmorin/GAMBL%20hg19?position=chr1%3A23885584%2D23885835)|NA |
37 39
38
-> [!NOTE]
39
-> First described in BL in 2012 by [Richter J](https://pubmed.ncbi.nlm.nih.gov/23143595). First described in FL in 2023 by [Russler-Germain DA](https://pubmed.ncbi.nlm.nih.gov/37493986)
40
-
41
-
42 40
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/ID3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/ID3_protein_hg38.html)
43 41
44 42
![image](images/proteinpaint/ID3_NM_002167.svg)
... ...
@@ -48,4 +46,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/I
48 46
![image](images/proteinpaint/ID3.svg)
49 47
## ID3 Expression
50 48
![image](images/gene_expression/ID3_by_pathology.svg)
51
-<!-- ORIGIN: schmitzBurkittLymphomaPathogenesis2012 -->
49
+
50
+## References
51
+1. *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*
52
+2. *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*
53
+3. *Spina V, Khiabanian H, Messina M, Monti S, Cascione L, Bruscaggin A, Spaccarotella E, Holmes AB, Arcaini L, Lucioni M, Tabbò F, Zairis S, Diop F, Cerri M, Chiaretti S, Marasca R, Ponzoni M, Deaglio S, Ramponi A, Tiacci E, Pasqualucci L, Paulli M, Falini B, Inghirami G, Bertoni F, Foà R, Rabadan R, Gaidano G, Rossi D. The genetics of nodal marginal zone lymphoma. Blood. 2016 Sep 8;128(10):1362–1373.*
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+
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+<!-- ORIGIN: 22885699 -->
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+<!-- BL: richterRecurrentMutationID32012a -->
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+<!-- DLBCL: schmitzBurkittLymphomaPathogenesis2012 -->
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+<!-- MZL: spinaGeneticsNodalMarginal2016b -->
SIN3A.md
... ...
@@ -1,11 +1,14 @@
1 1
# SIN3A
2
+## History
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>
2 4
3 5
## Relevance tier by entity
4 6
5 7
|Entity|Tier|Description |
6 8
|:------:|:----:|--------------------------|
7
-|BL |1 |high-confidence BL gene |
8
-|DLBCL |1 |high-confidence DLBCL gene|
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+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
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+|![MZL](images/icons/MZL_tier1.png) |1 |high-confidence MZL gene |
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+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
9 12
10 13
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 14
... ...
@@ -28,10 +31,6 @@
28 31
|FL |No |No |0.000 |20.676 |
29 32
30 33
31
-> [!NOTE]
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-> First described in BL in 2019 by [Grande BM](https://pubmed.ncbi.nlm.nih.gov/30617194)
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-
34
-
35 34
View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SIN3A_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SIN3A_protein_hg38.html)
36 35
37 36
![image](images/proteinpaint/SIN3A_NM_001145358.svg)
... ...
@@ -41,4 +40,13 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/S
41 40
![image](images/proteinpaint/SIN3A.svg)
42 41
## SIN3A Expression
43 42
![image](images/gene_expression/SIN3A_by_pathology.svg)
44
-<!-- ORIGIN: NA -->
43
+
44
+## References
45
+
46
+1. *Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941*
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+
48
+2. *Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood. 2019 Mar 21;133(12):1313–1324.*
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+
50
+<!-- ORIGIN: rossiCodingGenomeSplenic2012c -->
51
+<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
52
+<!-- MZL: rossiCodingGenomeSplenic2012c -->