A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma.

Abstract

It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.

• Authors: Dhruv N Patel, Michelle Yeagley, Juan F Arturo, Shayan Falasiri, Boris I Chobrutskiy, Etienne C Gozlan, George Blanck
• Journal: International journal of immunogenetics (Int J Immunogenet) Vol. 48 Issue 5 Pg. 409-418 (Oct 2021) ISSN: 1744-313X [Electronic] England
• PMID: 34298587 (Publication Type: Journal Article)
• Copyright: © 2021 John Wiley & Sons Ltd.

Chemical References

• Receptors, Antigen, T-Cell

Topics

• Exome (genetics)
• Genomics
• Humans
• Melanoma (genetics)
• Receptors, Antigen, T-Cell (genetics)
• Recombination, Genetic