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Population matched (pm) germline allelic variants of T-cell receptor (TR) loci

Journal Article (2022)
Author(s)

Julian Dekker (University of Applied Sciences Leiden, Leiden University Medical Center, TU Delft - Pattern Recognition and Bioinformatics)

Jacques J.M. van Dongen (Leiden University Medical Center)

MJT Reinders (Leiden University Medical Center, TU Delft - Pattern Recognition and Bioinformatics, Delft Bioinformatics Lab)

Indu Khatri (Leiden University Medical Center)

Research Group
Pattern Recognition and Bioinformatics
Copyright
© 2022 J.J. Dekker, Jacques J.M. van Dongen, M.J.T. Reinders, Indu Khatri
DOI related publication
https://doi.org/10.1038/s41435-022-00171-x
More Info
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Publication Year
2022
Language
English
Copyright
© 2022 J.J. Dekker, Jacques J.M. van Dongen, M.J.T. Reinders, Indu Khatri
Research Group
Pattern Recognition and Bioinformatics
Issue number
2
Volume number
23
Pages (from-to)
99-110
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Abstract

The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information when studying the genetic basis of population-specific immune responses in disease and in vaccination. Therefore, we meticulously identified true germline alleles enriched with complete TR allele sequences and their frequencies across 26 different human populations, profiled by “1000 Genomes data”. We identified 205 TRAV, 249 TRBV, 16 TRGV and 5 TRDV germline alleles supported by at least four haplotypes. The diversity of germline allelic variants in the TR loci is the highest in Africans, while the majority of the Non-African alleles are specific to the Asian populations, suggesting a diverse profile of TR germline alleles in different human populations. Interestingly, the alleles in the IMGT database are frequent and common across all five super-populations. We believe that this new set of germline TR sequences represents a valuable new resource which we have made available through the new population-matched TR (pmTR) database, accessible via https://pmtrig.lumc.nl/.