ETS1 - morinlab/LLMPP GitHub Wiki

ETS1

<<Warn("The variants reported in this gene in BL failed QC")>>

See below or the study page for more information

Overview

ETS1 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. This gene has some recurrent sites of mutations (hot spots). The mutation pattern in DLBCL implies the preferential accumulation of inactivating mutations.

History

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timeline
    title Publication timing
      2011-07-27 : Morin : DLBCL
      2019-09-26 : Panea : BL

Relevance tier by entity

Entity Tier Description
PMBL 1 high-confidence PMBL/cHL/GZL gene
DLBCL 1-a aSHM target and high-confidence DLBCL gene
BL 2-a aSHM target; Although recurrent, the relevance of mutations in BL is tenuous

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity source frequency (%)
DLBCL GAMBL genomes 4.59
DLBCL Schmitz cohort 7.87
DLBCL Reddy cohort 4.40
DLBCL Chapuy cohort 5.56
BL GAMBL genomes+capture 7.62
BL Thomas cohort 7.60
BL Panea cohort 11.90

Mutation pattern and selective pressure estimates

Entity aSHM Significant selection dN/dS (missense) dN/dS (nonsense)
DLBCL Yes No 2.987 0.000
FL Yes No 5.163 25.463
BL Yes No 5.097 18.417

aSHM regions

chr_name hg19_start hg19_end region regulatory_comment
chr11 128339774 128345731 intron enhancer
chr11 128388492 128394163 TSS-2 active_promoter

ETS1 Hotspots

Chromosome Coordinate (hg19) ref>alt HGVSp
chr11 128391889 T>A M1?
chr11 128391888 A>C M1?
chr11 128391871 G>A L7F
chr11 128391867 T>C K8R
chr11 128391865 GC>CT P9A
chr11 128391865 G>C P9A
chr11 128391865 G>A P9S
chr11 128391861 G>A T10I
chr11 128391859 G>C L11V
chr11 128391855 G>C T12S
chr11 128391855 G>A T12I
chr11 128391853 T>C I13V
chr11 128391853 T>A I13F
chr11 128391848 G>C I14M
chr11 128391846 T>C K15R
chr11 128391841 C>G E17Q
chr11 128391841 C>A E17*
chr11 128391824 C>G E22D
chr11 128391823 G>A L23F

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38

ETS1 Expression

Representative Mutations

BL2

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References

  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 SJ, Connors JM, Hirst M, Gascoyne RD, Marra MA. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351. PMID: 21796119; PMCID: PMC3210554.
  2. 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;
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