MEF2B.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# MEF2B
2 7
3 8
## Overview
... ...
@@ -16,10 +21,10 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------------------|
19
-|![MCL](images/icons/MCL_tier2.png)|2|relevance in MCL not firmly established|
24
+|![MCL](images/icons/MCL_tier2.png)|2|relevance in MCL not firmly established[@beaLandscapeSomaticMutations2013]|
20 25
|![BL](images/icons/BL_tier2.png) |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous |
21
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene |
22
-|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene |
26
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]|
27
+|![FL](images/icons/FL_tier1.png) |1-a | aSHM target and high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
23 28
24 29
25 30
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -99,5 +104,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
99 104
<!-- BL: 2 -->
100 105
101 106
## 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. 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
MGEA5.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# MGEA5
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3 8
## History
... ...
@@ -14,7 +19,7 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|--------------------------------------|
17
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
22
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -49,7 +54,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/M
49 54
[SP116649](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP116649.html)
50 55
51 56
## References
52
-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
57
+
53 58
54 59
<!-- ORIGIN: hubschmannMutationalMechanismsShaping2021b -->
55 60
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
MKI67.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# MKI67
2 7
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## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------------------|
16
-|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established|
17
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
21
+|![BL](images/icons/BL_tier2.png) |2 |relevance in BL not firmly established[@schmitzBurkittLymphomaPathogenesis2012]|
22
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]|
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/M
51 56
<!-- FL: russler-germainMutationsAssociatedProgression2023b -->
52 57
53 58
## References
54
-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
55
-2. Russler-Germain DA, Krysiak K, Ramirez CA, Mosior M, Watkins MP, Gomez F, Skidmore ZL, Trani L, Gao F, Geyer S, Cashen A, Mehta-Shah N, Kahl B, Bartlett N, Alderuccio J, Lossos I, Ondrejka S, Hsi E, Martin P, Leonard J, Griffith M, Griffith O, Fehniger T. Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303. Blood Advances. 2023;7:5524–5539.
TERT.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# TERT
2 7
3 8
## History
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@@ -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[@nadeuGenomicEpigenomicInsights2020b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -45,4 +50,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
45 50
<!-- MCL: nadeuGenomicEpigenomicInsights2020b -->
46 51
47 52
## References
48
-1. Nadeu F, Martín-García D, Clot G, Díaz-Navarro A, Duran-Ferrer M, Navarro A, Vilarrasa-Blasi R, Kulis M, Royo R, Gutiérrez-Abril J, Valdés-Mas R, López C, Chapaprieta V, Puiggrós M, Castellano G, Costa D, Aymerich M, Jares P, Espinet B, Muntañola A, Ribera‐Cortada I, Siebert R, Colomer D, Torrents D, Giné E, López-Guillermo A, Küppers R, Martín-Subero J, Puente X, Beà S, Campo E. Genomic and epigenomic insights into the origin, pathogenesis and clinical behavior of mantle cell lymphoma subtypes. Blood. 2020;
53
+
TOX.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# TOX
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
20
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@reddyGeneticFunctionalDrivers2017]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -56,4 +61,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
56 61
<!-- DLBCL: reddyGeneticFunctionalDrivers2017 -->
57 62
58 63
## References
59
-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.
TP53.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# TP53
2 7
3 8
## History
... ...
@@ -17,12 +22,12 @@ timeline
17 22
18 23
|Entity|Tier|Description |
19 24
|:------:|:----:|--------------------------|
20
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
21
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
22
-|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene |
23
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
24
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene |
25
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
25
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiCodingGenomeSplenic2012c]|
26
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@tiacciPervasiveMutationsJAKSTAT2018b]|
27
+|![BL](images/icons/BL_tier1.png) |1 |high-confidence BL gene [@wildaInactivationARFMDM2p53Pathway2004]|
28
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
29
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene [@morinFrequentMutationHistonemodifying2011]|
30
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@beaLandscapeSomaticMutations2013]|
26 31
27 32
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
28 33
... ...
@@ -69,8 +74,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
69 74
<!-- PMBL: tiacciPervasiveMutationsJAKSTAT2018b -->
70 75
71 76
## References
72
-1. Wilda M, Bruch J, Harder L, Rawer D, Reiter A, Borkhardt A, Woessmann W. Inactivation of the ARF-MDM-2-p53 pathway in sporadic Burkitt’s lymphoma in children. Leukemia. 2004 Mar;18(3):584–588. PMID: 14712292
73
-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
74
-3. 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
75
-4. 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
76
-5. Tiacci E, Ladewig E, Schiavoni G, Penson A, Fortini E, Pettirossi V, Wang Y, Rosseto A, Venanzi A, Vlasevska S, Pacini R, Piattoni S, Tabarrini A, Pucciarini A, Bigerna B, Santi A, Gianni AM, Viviani S, Cabras A, Ascani S, Crescenzi B, Mecucci C, Pasqualucci L, Rabadan R, Falini B. Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma. Blood. 2018 May 31;131(22):2454–2465. PMCID: PMC6634958
TPP1.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
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# TPP1
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|--------------------------------------|
15
-|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established|
20
+|![FL](images/icons/FL_tier2.png) |2 |relevance in FL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -53,4 +58,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
53 58
[SP59416](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59416.html)
54 59
55 60
## References
56
-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
+
TPST2.md
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@@ -1,3 +1,8 @@
1
+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# TPST2
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[@loveGeneticLandscapeMutations2012]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -55,4 +60,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
55 60
56 61
57 62
## References
58
-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
63
+
TRAF3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# TRAF3
2 7
3 8
## History
... ...
@@ -14,9 +19,9 @@ timeline
14 19
15 20
|Entity|Tier|Description |
16 21
|:------:|:----:|-----------------------------------------|
17
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
18
-|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene|
19
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
22
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@ottoGeneticLesionsTRAF32012a]|
23
+|![MZL](images/icons/MZL_tier1.png)|1|high-confidence MZL gene[@rossiAlterationBIRC3Multiple2011a]|
24
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@pasqualucciAnalysisCodingGenome2011]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -53,6 +58,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
53 58
<!-- PMBL: ottoGeneticLesionsTRAF32012a -->
54 59
55 60
## References
56
-1. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat Genet. 2011 Jul 31;43(9):830–837. PMCID: PMC3297422
57
-2. 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
58
-3. Otto C, Giefing M, Massow A, Vater I, Gesk S, Schlesner M, Richter J, Klapper W, Hansmann ML, Siebert R, Küppers R. Genetic lesions of the TRAF3 and MAP3K14 genes in classical Hodgkin lymphoma. Br J Haematol. 2012 Jun;157(6):702–708. PMID: 22469134
TRAF6.md
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+---
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+bibliography: 'morinlab.bib'
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+csl: 'NLM.csl'
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+link-citations: true
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+---
1 6
# TRAF6
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -62,4 +67,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
62 67
[SP59456](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59456.html)
63 68
64 69
## References
65
-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
TRIP12.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# TRIP12
2 7
3 8
## Relevance tier by entity
TRRAP.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# TRRAP
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_tier1.png) |1 |high-confidence DLBCL gene|
21
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@parryWholeExomeSequencing2013]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -57,5 +62,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
57 62
<!-- MZL: rossiCodingGenomeSplenic2012c -->
58 63
59 64
## References
60
-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
61
-2. Parry M, Rose-Zerilli MJJ, Gibson J, Ennis S, Walewska R, Forster J, Parker H, Davis Z, Gardiner A, Collins A, Oscier DG, Strefford JC. Whole exome sequencing identifies novel recurrently mutated genes in patients with splenic marginal zone lymphoma. PLoS One. 2013;8(12):e83244. PMCID: PMC3862727
TTN.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# TTN
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[@burkhardtClinicalRelevanceMolecular2022b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -51,4 +56,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/T
51 56
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
52 57
53 58
## References
54
-1. 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
UBE2A.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UBE2A
2 7
3 8
## History
... ...
@@ -13,8 +18,8 @@ timeline
13 18
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|--------------------------------------|
16
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
17
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene |
21
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
22
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]|
18 23
19 24
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
20 25
... ...
@@ -50,5 +55,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
50 55
<!-- PMBL: reichelFlowSortingExome2015a -->
51 56
52 57
## References
53
-1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972
54
-2. 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.
58
+
UBE2J1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UBE2J1
2 7
3 8
## Relevance tier by entity
UBR5.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UBR5
2 7
3 8
## History
... ...
@@ -14,8 +19,8 @@ timeline
14 19
|Entity|Tier|Description |
15 20
|:------:|:----:|-----------------------------------------|
16 21
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
17
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
18
-|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene |
22
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@zhangGeneticHeterogeneityDiffuse2013]|
23
+|![MCL](images/icons/MCL_tier1.png) |1 |high-confidence MCL gene [@pararajalingamCodingNoncodingDrivers2020]|
19 24
20 25
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
21 26
... ...
@@ -53,5 +58,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
53 58
<!-- MCL: pararajalingamCodingNoncodingDrivers2020 -->
54 59
55 60
## References
56
-1. Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers C, Naresh K, Evens A, Gordon LI, Czader M, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima D, Smith LL, Johnson AJ, Byrd JC, Luftig MA, Ni T, Zhu J, Chadburn A, Levy S, Dunson D, Dave SS. Genetic heterogeneity of diffuse large B-cell lymphoma. 2013 Jan;
57
-2. Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood. 2020 Jul 30;136(5):572–584. PMCID: PMC7440974
61
+
UNC5B.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UNC5B
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -53,4 +58,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
53 58
[SP59448](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59448.html)
54 59
55 60
## References
56
-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
+
UNC5C.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UNC5C
2 7
3 8
## Relevance tier by entity
... ...
@@ -5,7 +10,7 @@
5 10
|Entity|Tier|Description |
6 11
|:------:|:----:|--------------------------|
7 12
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
8
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
9 14
10 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 16
UNC5D.md
... ...
@@ -1,10 +1,15 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# UNC5D
2 7
3 8
## Relevance tier by entity
4 9
5 10
|Entity|Tier|Description |
6 11
|:------:|:----:|--------------------------|
7
-|![DLBCL](images/icons/DLBCL_tier2.png) | 2 |low-confidence DLBCL gene|
12
+|![DLBCL](images/icons/DLBCL_tier2.png) | 2 |low-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
8 13
9 14
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
10 15
USH2A.md
... ...
@@ -0,0 +1,40 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# USH2A
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 |14.943 |
31
+|BL|GAMBL Genome |6.95 |
32
+|DLBCL|GAMBL Exome |15.094 |
33
+|DLBCL|GAMBL Genome |12.218 |
34
+|FL|GAMBL Exome |3.725 |
35
+|MCL|GAMBL Genome |6.433 |
36
+
37
+
38
+## References
39
+
40
+
USP7.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# USP7
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 [@grandeGenomewideDiscoverySomatic2019]|
16 21
|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
17 22
18 23
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
... ...
@@ -49,6 +54,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/U
49 54
![](images/gene_expression/USP7_by_pathology.svg)
50 55
51 56
## References
52
-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. doi: 10.1182/blood-2018-09-871418. Epub 2019 Jan 7. PMID: 30617194; PMCID: PMC6428665.*
57
+
53 58
<!-- ORIGIN: grandeGenomewideDiscoverySomatic2019 -->
54 59
<!-- BL: grandeGenomewideDiscoverySomatic2019 -->
VMA21.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# VMA21
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------|
15
-|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene|
20
+|![FL](images/icons/FL_tier1.png) |1 |high-confidence FL gene[@hubschmannMutationalMechanismsShaping2021b]|
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/V
45 50
<!-- FL: hubschmannMutationalMechanismsShaping2021b -->
46 51
47 52
## References
48
-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
VMP1.md
... ...
@@ -0,0 +1,38 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# VMP1
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 |0.575 |
31
+|DLBCL|GAMBL Exome |4.69 |
32
+|DLBCL|GAMBL Genome |2.632 |
33
+|FL|GAMBL Exome |0.573 |
34
+
35
+
36
+## References
37
+
38
+
VPS13B.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# VPS13B
2 7
3 8
## Relevance tier by entity
... ...
@@ -5,7 +10,7 @@
5 10
|Entity|Tier|Description |
6 11
|:------:|:----:|--------------------------|
7 12
|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
8
-|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene|
13
+|![DLBCL](images/icons/DLBCL_tier1.png) |1 |high-confidence DLBCL gene[@lohrDiscoveryPrioritizationSomatic2012a]|
9 14
10 15
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
11 16
VWA7.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# VWA7
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[@burkhardtClinicalRelevanceMolecular2022b]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -47,4 +52,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/V
47 52
<!-- BL: burkhardtClinicalRelevanceMolecular2022b -->
48 53
49 54
## References
50
-1. 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
WAC.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WAC
2 7
3 8
<<Warn("The variants reported in this gene in DLBCL failed QC")>>
... ...
@@ -15,8 +20,8 @@ timeline
15 20
16 21
|Entity|Tier|Description |
17 22
|:------:|:----:|-----------------------------------------|
18
-|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established|
19
-|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC|
23
+|![MZL](images/icons/MZL_tier2.png)|2|relevance in MZL not firmly established[@rossiCodingGenomeSplenic2012c]|
24
+|![DLBCL](images/icons/DLBCL_tier2.png) |2-F |failed QC[@reddyGeneticFunctionalDrivers2017]|
20 25
21 26
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
22 27
... ...
@@ -78,5 +83,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
78 83
[Reddy_3977T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_3977T.html)
79 84
80 85
## References
81
-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
82
-2. 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.
WDFY3.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WDFY3
2 7
3 8
## History
... ...
@@ -12,7 +17,7 @@ timeline
12 17
13 18
|Entity|Tier|Description |
14 19
|:------:|:----:|-----------------------------------------|
15
-|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established|
20
+|![DLBCL](images/icons/DLBCL_tier2.png) |2 |relevance in DLBCL not firmly established[@morinMutationalStructuralAnalysis2013]|
16 21
17 22
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18 23
... ...
@@ -48,4 +53,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
48 53
<!-- DLBCL: morinMutationalStructuralAnalysis2013 -->
49 54
50 55
## References
51
-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
WDR7.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WDR7
2 7
3 8
<<Warn("The variants reported in this gene failed QC")>>
... ...
@@ -63,4 +68,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
63 68
64 69
65 70
## References
66
-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;
WDR87.md
... ...
@@ -0,0 +1,39 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
6
+
7
+# WDR87
8
+
9
+## History
10
+
11
+```mermaid
12
+%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
13
+timeline
14
+ title Publication timing
15
+ 2021-07-15 : Duns : 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[@dunsCharacterizationDLBCLPMBL2021b]|
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 |2.317 |
32
+|DLBCL|GAMBL Exome |3.935 |
33
+|DLBCL|GAMBL Genome |3.195 |
34
+|FL|GAMBL Exome |0.287 |
35
+
36
+
37
+## References
38
+
39
+
WDR90.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WDR90
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
... ...
@@ -47,4 +52,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
47 52
<!-- BL: schmitzBurkittLymphomaPathogenesis2012 -->
48 53
49 54
## References
50
-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
WEE1.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WEE1
2 7
3 8
## Overview
... ...
@@ -16,8 +21,8 @@ timeline
16 21
17 22
|Entity|Tier|Description |
18 23
|:------:|:----:|--------------------------|
19
-|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene|
20
-|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene|
24
+|![PMBL](images/icons/PMBL_tier1.png)|1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]|
25
+|![DLBCL](images/icons/DLBCL_tier1.png) |1-a | aSHM target and high-confidence DLBCL gene[@schmitzGeneticsPathogenesisDiffuse2018a]|
21 26
22 27
## Mutation incidence in large patient cohorts (GAMBL reanalysis)
23 28
... ...
@@ -68,5 +73,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W
68 73
<!-- DLBCL: schmitzGeneticsPathogenesisDiffuse2018a -->
69 74
70 75
## References
71
-1. Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G, Carlo-Stella C, Santoro A, Rahal D, Totonchy J, Elemento O, Cesarman E, Roshal M. Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells. Blood. 2015 Feb 12;125(7):1061–1072. PMID: 25488972
72
-2. Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM. Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma. N Engl J Med. 2018 Apr 12;378(15):1396–1407. PMCID: PMC6010183
WHAMM.md
... ...
@@ -1,3 +1,8 @@
1
+---
2
+bibliography: 'morinlab.bib'
3
+csl: 'NLM.csl'
4
+link-citations: true
5
+---
1 6
# WHAMM
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/W
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