ce160559e01272f2152b7ac6ebc7b26e86861ef3
CYB5D1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # CYB5D1 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,7 +18,7 @@ timeline |
| 13 | 18 | |
| 14 | 19 | |Entity|Tier|Description | |
| 15 | 20 | |:------:|:----:|--------------------------------------| |
| 16 | -| |2 |relevance in BL not firmly established| |
|
| 21 | +| |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]| |
|
| 17 | 22 | |
| 18 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 24 | |
| ... | ... | @@ -60,4 +65,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C |
| 60 | 65 | [670](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Love/670_reports.html) |
| 61 | 66 | |
| 62 | 67 | ## References |
| 63 | -1. Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012 Dec;44(12):1321–1325. PMCID: PMC3674561 |
CYP2A6.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # CYP2A6 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,7 +18,7 @@ timeline |
| 13 | 18 | |
| 14 | 19 | |Entity|Tier|Description | |
| 15 | 20 | |:------:|:----:|--------------------------------------| |
| 16 | -| |2 |relevance in FL not firmly established| |
|
| 21 | +| |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]| |
|
| 17 | 22 | |
| 18 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 24 | |
| ... | ... | @@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C |
| 46 | 51 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 47 | 52 | |
| 48 | 53 | ## References |
| 49 | -1. 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. |
CYP4F22.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # CYP4F22 |
| 2 | 7 | |
| 3 | 8 | ## Overview |
| ... | ... | @@ -17,7 +22,7 @@ timeline |
| 17 | 22 | |
| 18 | 23 | |Entity|Tier|Description | |
| 19 | 24 | |:------:|:----:|--------------------------------------| |
| 20 | -| |2 |relevance in BL not firmly established| |
|
| 25 | +| |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]| |
|
| 21 | 26 | |
| 22 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 23 | 28 | |
| ... | ... | @@ -66,4 +71,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/C |
| 66 | 71 | |
| 67 | 72 | ## References |
| 68 | 73 | |
| 69 | -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 |
DAZAP1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # DAZAP1 |
| 2 | 7 | |
| 3 | 8 | ## Overview |
| ... | ... | @@ -15,8 +20,8 @@ timeline |
| 15 | 20 | |
| 16 | 21 | |Entity|Tier|Description | |
| 17 | 22 | |:------:|:----:|--------------------------| |
| 18 | -| |1 |high-confidence DLBCL gene| |
|
| 19 | -| |1 |high-confidence MCL gene | |
|
| 23 | +| |1 |high-confidence DLBCL gene[@pararajalingamCodingNoncodingDrivers2020]| |
|
| 24 | +| |1 |high-confidence MCL gene [@pararajalingamCodingNoncodingDrivers2020]| |
|
| 20 | 25 | |
| 21 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 27 | |
| ... | ... | @@ -59,7 +64,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D |
| 59 | 64 |  |
| 60 | 65 | |
| 61 | 66 | ## References |
| 62 | -1. *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. doi: 10.1182/blood.2019002385. PMID: 32160292; PMCID: PMC7440974.* |
|
| 67 | + |
|
| 63 | 68 | <!-- ORIGIN: pararajalingamCodingNoncodingDrivers2020 --> |
| 64 | 69 | <!-- DLBCL: pararajalingamCodingNoncodingDrivers2020 --> |
| 65 | 70 | <!-- MCL: pararajalingamCodingNoncodingDrivers2020 --> |
DCAF6.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # DCAF6 |
| 2 | 7 | |
| 3 | 8 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| ... | ... | @@ -92,7 +97,6 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D |
| 92 | 97 | [Reddy_705T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_705T.html) |
| 93 | 98 | |
| 94 | 99 | ## References |
| 95 | -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.* |
|
| 96 | 100 | |
| 97 | 101 | |
| 98 | 102 | <!-- ORIGIN: reddyGeneticFunctionalDrivers2017 --> |
DDX10.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # DDX10 |
| 2 | 7 | |
| 3 | 8 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| ... | ... | @@ -82,4 +87,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D |
| 82 | 87 | |
| 83 | 88 | |
| 84 | 89 | ## References |
| 85 | -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. |
DHDH.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # DHDH |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,7 +18,7 @@ timeline |
| 13 | 18 | |
| 14 | 19 | |Entity|Tier|Description | |
| 15 | 20 | |:------:|:----:|---------------------------------------| |
| 16 | -| |2 |relevance in MCL not firmly established| |
|
| 21 | +| |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]| |
|
| 17 | 22 | |
| 18 | 23 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 19 | 24 | |
| ... | ... | @@ -46,4 +51,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/D |
| 46 | 51 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 47 | 52 | |
| 48 | 53 | ## References |
| 49 | -1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
WNK1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # WNK1 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -14,9 +19,9 @@ timeline |
| 14 | 19 | |
| 15 | 20 | |Entity|Tier|Description | |
| 16 | 21 | |:------:|:----:|-----------------------------------------| |
| 17 | -||2|relevance in MZL not firmly established| |
|
| 18 | -| |1 |high-confidence BL gene | |
|
| 19 | -| |2 |relevance in DLBCL not firmly established| |
|
| 22 | +||2|relevance in MZL not firmly established[@jalladesExomeSequencingIdentifies2017]| |
|
| 23 | +| |1 |high-confidence BL gene [@thomasGeneticSubgroupsInform2023]| |
|
| 24 | +| |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 20 | 25 | |
| 21 | 26 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 22 | 27 | |
| ... | ... | @@ -74,6 +79,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/W |
| 74 | 79 | [SP59452](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59452.html) |
| 75 | 80 | |
| 76 | 81 | ## References |
| 77 | -1. Jallades L, Baseggio L, Sujobert P, Huet S, Chabane K, Callet-Bauchu E, Verney A, Hayette S, Desvignes JP, Salgado D, Levy N, Béroud C, Felman P, Berger F, Magaud JP, Genestier L, Salles G, Traverse-Glehen A. Exome sequencing identifies recurrent BCOR alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma. Haematologica. 2017 Oct;102(10):1758–1766. PMCID: PMC5622860 |
|
| 78 | -2. 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 |
|
| 79 | -3. 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. |
WNK2.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # WNK2 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | -| |2 |relevance in BL not firmly established| |
|
| 20 | +| |2 |relevance in BL not firmly established[@paneaWholeGenomeLandscape2019]| |
|
| 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/W |
| 53 | 58 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
| 54 | 59 | |
| 55 | 60 | ## References |
| 56 | -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; |
XBP1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # XBP1 |
| 2 | 7 | |
| 3 | 8 | ## Relevance tier by entity |
XIRP2.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # XIRP2 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | -| |2 |relevance in FL not firmly established| |
|
| 20 | +| |2 |relevance in FL not firmly established[@russler-germainMutationsAssociatedProgression2023b]| |
|
| 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/X |
| 51 | 56 | <!-- FL: russler-germainMutationsAssociatedProgression2023b --> |
| 52 | 57 | |
| 53 | 58 | ## References |
| 54 | -1. 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. |
YY1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # YY1 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|-----------------------------------------| |
| 15 | -| |2 |relevance in DLBCL not firmly established| |
|
| 20 | +| |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
|
| 16 | 21 | |
| 17 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 23 | |
| ... | ... | @@ -50,4 +55,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Y |
| 50 | 55 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 51 | 56 | |
| 52 | 57 | ## References |
| 53 | -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. |
YY1AP1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # YY1AP1 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | -| |2 |relevance in BL not firmly established| |
|
| 20 | +| |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/Y |
| 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 |
ZAN.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZAN |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | -| |2 |relevance in BL not firmly established| |
|
| 20 | +| |2 |relevance in BL not firmly established[@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 16 | 21 | |
| 17 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 23 | |
| ... | ... | @@ -43,4 +48,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 43 | 48 | <!-- BL: burkhardtClinicalRelevanceMolecular2022b --> |
| 44 | 49 | |
| 45 | 50 | ## References |
| 46 | -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 |
ZBTB7A.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZBTB7A |
| 2 | 7 | |
| 3 | 8 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| ... | ... | @@ -16,7 +21,7 @@ timeline |
| 16 | 21 | |
| 17 | 22 | |Entity|Tier|Description | |
| 18 | 23 | |:------:|:----:|-----------------------------------------| |
| 19 | -| |2 |relevance in BL not firmly established | |
|
| 24 | +| |2 |relevance in BL not firmly established [@burkhardtClinicalRelevanceMolecular2022b]| |
|
| 20 | 25 | | |2-F |failed QC| |
| 21 | 26 | |
| 22 | 27 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| ... | ... | @@ -105,5 +110,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 105 | 110 | [Reddy_648T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_648T.html) |
| 106 | 111 | |
| 107 | 112 | ## References |
| 108 | -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. |
|
| 109 | -2. 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 |
ZC3H12A.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZC3H12A |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,7 +18,7 @@ timeline |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | 20 | ||2|relevance in MCL not firmly established| |
| 16 | -| |1 |high-confidence DLBCL gene | |
|
| 21 | +| |1 |high-confidence DLBCL gene [@arthurGenomewideDiscoverySomatic2018]| |
|
| 17 | 22 | | |2 |relevance in FL not firmly established| |
| 18 | 23 | |
| 19 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| ... | ... | @@ -50,5 +55,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 50 | 55 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 51 | 56 | |
| 52 | 57 | ## References |
| 53 | -1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
|
| 54 | -2. 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 |
ZCCHC11.md
| ... | ... | @@ -0,0 +1,40 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 6 | + |
|
| 7 | +# ZCCHC11 |
|
| 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 | +||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 |1.544 | |
|
| 32 | +|DLBCL|GAMBL Exome |2.21 | |
|
| 33 | +|DLBCL|GAMBL Genome |0.376 | |
|
| 34 | +|FL|GAMBL Exome |0.287 | |
|
| 35 | +|MCL|GAMBL Genome |1.17 | |
|
| 36 | + |
|
| 37 | + |
|
| 38 | +## References |
|
| 39 | + |
|
| 40 | + |
ZCCHC7.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZCCHC7 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|-----------------------------------------| |
| 15 | -| |2-a | aSHM target; Although recurrent, the relevance of mutations in DLBCL is tenuous | |
|
| 20 | +| |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 | |
| ... | ... | @@ -56,4 +61,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 56 | 61 | <!-- DLBCL: arthurGenomewideDiscoverySomatic2018 --> |
| 57 | 62 | |
| 58 | 63 | ## References |
| 59 | -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 |
ZEB2.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZEB2 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|-----------------------------------------| |
| 15 | -| |2 |relevance in DLBCL not firmly established| |
|
| 20 | +| |2 |relevance in DLBCL not firmly established[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 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/Z |
| 48 | 53 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | 54 | |
| 50 | 55 | ## References |
| 51 | -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; |
ZFAT.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZFAT |
| 2 | 7 | |
| 3 | 8 | <<Warn("The variants reported in this gene in DLBCL failed QC")>> |
| ... | ... | @@ -75,4 +80,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 75 | 80 | [Reddy_4000T](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/Reddy_4000T.html) |
| 76 | 81 | |
| 77 | 82 | ## References |
| 78 | -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. |
|
| 83 | + |
ZFP36L1.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZFP36L1 |
| 2 | 7 | |
| 3 | 8 | ## Overview |
| ... | ... | @@ -18,9 +23,9 @@ timeline |
| 18 | 23 | |Entity|Tier|Description | |
| 19 | 24 | |:------:|:----:|--------------------------------------| |
| 20 | 25 | ||2|relevance in MCL not firmly established| |
| 21 | -||1|high-confidence PMBL/cHL/GZL gene| |
|
| 22 | -| |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous | |
|
| 23 | -| |1-a | aSHM target and high-confidence DLBCL gene | |
|
| 26 | +||1|high-confidence PMBL/cHL/GZL gene[@reichelFlowSortingExome2015a]| |
|
| 27 | +| |2-a | aSHM target; Although recurrent, the relevance of mutations in BL is tenuous [@paneaWholeGenomeLandscape2019]| |
|
| 28 | +| |1-a | aSHM target and high-confidence DLBCL gene [@morinFrequentMutationHistonemodifying2011]| |
|
| 24 | 29 | |
| 25 | 30 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 26 | 31 | |
| ... | ... | @@ -61,10 +66,7 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 61 | 66 |  |
| 62 | 67 | |
| 63 | 68 | ## References |
| 64 | -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 |
|
| 65 | -2. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
|
| 66 | -3. 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 |
|
| 67 | -4. 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; |
|
| 69 | + |
|
| 68 | 70 | <!-- DLBCL: morinFrequentMutationHistonemodifying2011 --> |
| 69 | 71 | <!-- PMBL: reichelFlowSortingExome2015a --> |
| 70 | 72 | <!-- BL: paneaWholeGenomeLandscape2019 --> |
ZFX.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZFX |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|-----------------------------------------| |
| 15 | -| |2 |relevance in DLBCL not firmly established| |
|
| 20 | +| |2 |relevance in DLBCL not firmly established[@reddyGeneticFunctionalDrivers2017]| |
|
| 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/Z |
| 51 | 56 | <!-- DLBCL: reddyGeneticFunctionalDrivers2017 --> |
| 52 | 57 | |
| 53 | 58 | ## References |
| 54 | -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. |
ZNF117.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF117 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|---------------------------------------| |
| 15 | -| |2 |relevance in MCL not firmly established| |
|
| 20 | +| |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]| |
|
| 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/Z |
| 45 | 50 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 46 | 51 | |
| 47 | 52 | ## References |
| 48 | -1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
ZNF217.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF217 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,8 +18,8 @@ timeline |
| 13 | 18 | |
| 14 | 19 | |Entity|Tier|Description | |
| 15 | 20 | |:------:|:----:|-----------------------------------------| |
| 16 | -||2|relevance in PMBL/cHL/GZL not firmly established| |
|
| 17 | -| |2 |relevance in DLBCL not firmly established| |
|
| 21 | +||2|relevance in PMBL/cHL/GZL not firmly established[@reichelFlowSortingExome2015a]| |
|
| 22 | +| |2 |relevance in DLBCL not firmly established[@hubschmannMutationalMechanismsShaping2021b]| |
|
| 18 | 23 | |
| 19 | 24 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 20 | 25 | |
| ... | ... | @@ -59,5 +64,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 59 | 64 | [SP59448](https://www.bcgsc.ca/downloads/morinlab/GAMBL/MALY/SP59448.html) |
| 60 | 65 | |
| 61 | 66 | ## References |
| 62 | -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 |
|
| 63 | -2. 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 |
ZNF229.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF229 |
| 2 | 7 | |
| 3 | 8 | Due to [minimal support](ZNF229#representative-mutation) in the original primary data, [low expression in BL](ZNF229#znf229-expression) and very few mutations reported in subsequent studies, this gene is very unlikely to be relevant in BL. |
| ... | ... | @@ -15,7 +20,7 @@ timeline |
| 15 | 20 | |
| 16 | 21 | |Entity|Tier|Description | |
| 17 | 22 | |:------:|:----:|--------------------------------------| |
| 18 | -| |2 |relevance in BL not firmly established| |
|
| 23 | +| |2 |relevance in BL not firmly established[@loveGeneticLandscapeMutations2012]| |
|
| 19 | 24 | |
| 20 | 25 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 21 | 26 | |
| ... | ... | @@ -59,4 +64,3 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/Z |
| 59 | 64 | |
| 60 | 65 | |
| 61 | 66 | ## References |
| 62 | -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 |
ZNF292.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF292 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------| |
| 15 | -| |1 |high-confidence DLBCL gene| |
|
| 20 | +| |1 |high-confidence DLBCL gene[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 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/Z |
| 48 | 53 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 49 | 54 | |
| 50 | 55 | ## References |
| 51 | -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; |
ZNF296.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF296 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|---------------------------------------| |
| 15 | -| |2 |relevance in MCL not firmly established| |
|
| 20 | +| |2 |relevance in MCL not firmly established[@zhangGenomicLandscapeMantle2014]| |
|
| 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/Z |
| 45 | 50 | <!-- MCL: zhangGenomicLandscapeMantle2014 --> |
| 46 | 51 | |
| 47 | 52 | ## References |
| 48 | -1. Zhang J, Jima D, Moffitt AB, Liu Q, Czader M, Hsi ED, Fedoriw Y, Dunphy CH, Richards KL, Gill JI, Sun Z, Love C, Scotland P, Lock E, Levy S, Hsu DS, Dunson D, Dave SS. The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells. Blood. 2014 May 8;123(19):2988–2996. |
ZNF423.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF423 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|-----------------------------------------| |
| 15 | -| |2 |relevance in DLBCL not firmly established| |
|
| 20 | +| |2 |relevance in DLBCL not firmly established[@chapuyMolecularSubtypesDiffuse2018b]| |
|
| 16 | 21 | |
| 17 | 22 | ## Mutation incidence in large patient cohorts (GAMBL reanalysis) |
| 18 | 23 |
ZNF608.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF608 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -13,8 +18,8 @@ timeline |
| 13 | 18 | |
| 14 | 19 | |Entity|Tier|Description | |
| 15 | 20 | |:------:|:----:|--------------------------| |
| 16 | -||2|relevance in FL not firmly established| |
|
| 17 | -| |1 |high-confidence DLBCL gene| |
|
| 21 | +||2|relevance in FL not firmly established[@krysiakRecurrentSomaticMutations2017b]| |
|
| 22 | +| |1 |high-confidence DLBCL gene[@zhangGeneticHeterogeneityDiffuse2013]| |
|
| 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/Z |
| 51 | 56 | <!-- DLBCL: zhangGeneticHeterogeneityDiffuse2013 --> |
| 52 | 57 | |
| 53 | 58 | ## References |
| 54 | -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; |
|
| 55 | -2. Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma. Blood. 2017 Jan 26;129(4):473–483. PMCID: PMC5270390 |
ZNF85.md
| ... | ... | @@ -1,3 +1,8 @@ |
| 1 | +--- |
|
| 2 | +bibliography: 'morinlab.bib' |
|
| 3 | +csl: 'NLM.csl' |
|
| 4 | +link-citations: true |
|
| 5 | +--- |
|
| 1 | 6 | # ZNF85 |
| 2 | 7 | |
| 3 | 8 | ## History |
| ... | ... | @@ -12,7 +17,7 @@ timeline |
| 12 | 17 | |
| 13 | 18 | |Entity|Tier|Description | |
| 14 | 19 | |:------:|:----:|--------------------------------------| |
| 15 | -| |2 |relevance in BL not firmly established| |
|
| 20 | +| |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/Z |
| 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 |