Comment on 'rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing'
Language English Country Great Britain, England Media print
Document type Journal Article
PubMed
37824737
PubMed Central
PMC10569745
DOI
10.1093/bib/bbad354
PII: 7306821
Knihovny.cz E-resources
- Keywords
- RNA sequencing, T-cell receptor, TCR sequencing, benchmarking, cancer immunology, computational methods, immunogenomics,
- MeSH
- B-Lymphocytes MeSH
- Benchmarking * MeSH
- Humans MeSH
- Neoplasms * genetics MeSH
- Receptors, Antigen, T-Cell genetics MeSH
- Sequence Analysis, RNA MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Names of Substances
- Receptors, Antigen, T-Cell MeSH
Transcriptome sequencing has become common in cancer research, resulting in the generation of a substantial volume of RNA sequencing (RNA-Seq) data. The ability to extract immune repertoires from these data is crucial for obtaining information on infiltrating T- and B-lymphocyte clones when dedicated amplicon T-cell/B-cell receptors sequencing (TCR-Seq/BCR-Seq) methods are unavailable. In response to this demand, several dedicated computational methods have been developed, including MiXCR, TRUST and ImRep. In the recent publication in Briefings in Bioinformatics, Peng et al. have conducted an intensive, systematic comparison of the three previously mentioned tools. Although their effort is commendable, we do have a few constructive critiques regarding technical elements of their analysis.
See more in PubMed
Peng K, Nowicki TS, Campbell K, et al. . Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Brief Bioinform 2023;24(4):1–12. PubMed PMC
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Hu X, Zhang J, Wang J, et al. . Landscape of B cell immunity and related immune evasion in human cancers. Nat Genet 2019;51:560–7. PubMed PMC
Mandric I, Rotman J, Yang HT, et al. . Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nat Commun 2020;11:3126. PubMed PMC
Bolotin DA, Poslavsky S, Mitrophanov I, et al. . MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods 2015;12:380–1. PubMed
Bolotin DA, Poslavsky S, Davydov AN, Chudakov DM. Reply to "evaluation of immune repertoire inference methods from RNA-seq data". Nat Biotechnol 2018;36:1035–6. PubMed
Bolotin DA, Poslavsky S, Davydov AN, et al. . Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol 2017;35:908–11. PubMed PMC
