Table of Contents
Overview
PIM2 is one of a number of genes affected by aberrant somatic hypermutation in B-cell lymphomas, which complicates the interpretation of mutations at this locus.
Relevance tier by entity
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Mutation incidence in large patient cohorts (GAMBL reanalysis)
DLBCL
| Entity | Collection | N | mutated | Incidence | 95% CI |
|---|---|---|---|---|---|
| DLBCL | GAMBL without Reddy | 1,089 | 55 | 0.0505 | [0.0375,0.0635] |
| DLBCL | GAMBL with Reddy | 2,088 | 95 | 0.0455 | [0.0366,0.0544] |
| DLBCL | BC | 231 | 12 | 0.0519 | [0.0233,0.0806] |
| DLBCL | Dana-Farber | 303 | 10 | 0.0330 | [0.0129,0.0531] |
| DLBCL | NCI | 470 | 30 | 0.0638 | [0.0417,0.0859] |
| DLBCL | Reddy | 999 | 40 | 0.0400 | [0.0279,0.0522] |
| DLBCL | DLBCL_ICGC | 85 | 3 | 0.0353 | [0,0.0745] |
Mutation pattern and selective pressure estimates
| Entity | Missense dN/dS | Nonsense dN/dS | Q value |
|---|---|---|---|
| BL | 0.0000 | 0.0000 | 1 |
| FL | 0.4494 | 13.4495 | 1 |
| DLBCL | 0.7409 | 3.9564 | 0 |
aSHM regions
| chr_name | hg19_start | hg19_end | region | regulatory_comment |
|---|---|---|---|---|
| chrX | 48774756 | 48776255 | TSS | active_promoter |
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Expression
History
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timeline
title Publication timing
2015-02-12 : Reichel : PMBL
2017-10-10 : Reddy : DLBCL
2018-04-12 : Schmitz : DLBCL
2018-10-01 : Arthur : DLBCL
References
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
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. PMCID: PMC5659841
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.
4.
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