HLA A - morinlab/LLMPP GitHub Wiki


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HLA-A

Overview

Mutations in the HLA-B gene have been associated with a loss of cell surface expression of HLA class I molecules, which are essential for presenting tumor antigens to cytotoxic T cells. This is a common mechanism of immune escape in DLBCL. Deletions of this gene are more commonly reported than HLA-B mutations. The mutation pattern in DLBCL implies the preferential accumulation of inactivating mutations. Different analytical strategies relating to the mapping of sequencing data and subtracting common germline variants can complicate the detection of mutations in this and other HLA genes. Likely owing to this, the rate of mutations is highly variable across studies and the true mutation rate has not been firmly established.

History

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timeline
    title Publication timing
      2019-08-20 : Desch : PMBL

Relevance tier by entity

Entity Tier Description
PMBL 2 relevance in PMBL/cHL/GZL not firmly established[@deschGenotypingCirculatingTumor2020]
BL 2 relevance in BL not firmly established
DLBCL 1 high-confidence DLBCL gene [@lohrDiscoveryPrioritizationSomatic2012a]

Mutation incidence in large patient cohorts (GAMBL reanalysis)

Entity source frequency (%)
DLBCL GAMBL genomes 7.46
DLBCL Schmitz cohort 11.06
DLBCL Reddy cohort 0.20
DLBCL Chapuy cohort 8.97
BL GAMBL genomes+capture 1.39
BL Thomas cohort 1.30
BL Panea cohort NA

Mutation pattern and selective pressure estimates

Entity aSHM Significant selection dN/dS (missense) dN/dS (nonsense)
BL No No 4.995 22.371
DLBCL No Yes 14.841 190.534
FL No No 0.000 0.000

HLA-A Hotspots

Chromosome Coordinate (hg19) ref>alt HGVSp
chr6 29910596 T>A F46I
chr6 29910609 G>A G50D

View coding variants in ProteinPaint hg19 or hg38

View all variants in GenomePaint hg19 or hg38

References

HLA-A Expression