TY - JOUR
T1 - Haplotype analysis of the t-cell receptor beta (Tcrb) locus by long-amplicon tcrb repertoire sequencing
AU - Looney, Timothy J.
AU - Duose, Dzifa Y.
AU - Lowman, Geoffrey
AU - Linch, Elizabeth
AU - Hajjar, Joud
AU - Topacio-Hall, Denise
AU - Xu, Mingxuan
AU - Zheng, Jianping
AU - Alshawa, Anas
AU - Tapia, Coya
AU - Stephen, Bettzy
AU - Wang, Linghua
AU - Meric-Bernstam, Funda
AU - Miller, Lauren
AU - Glavin, Alexander
AU - Lin, Lifeng
AU - Gong, Jing
AU - Conroy, Jeffrey
AU - Morrison, Carl
AU - Hyland, Fiona
AU - Naing, Aung
N1 - Funding Information:
The authors declare that this study received funding from Thermo Fisher Scientific. The funder is or was the employer of TL, GL, EL, DT, JZ, LM, AG, LL, FH, and supported the procurement and sequencing of samples used in this study. The funder was not involved in the study design, collection, analysis, interpretation of data, nor the writing of this article. The decision to submit this work for publication was agreed upon by all authors.
Publisher Copyright:
© 2019 Journal of Immunotherapy and Precision Oncology | Published by Wolters Kluwer-Medknow.
PY - 2019
Y1 - 2019
N2 - Background: Polymorphism within the human T-cell receptor beta variable (TRBV) gene has been proposed as a risk factor for autoimmune disease and immune-related adverse events (IRAEs) during immunotherapy. Previous efforts to evaluate TRBV polymorphism by whole genome sequencing have been hampered by the repetitive nature of the T-cell receptor beta (TCRB) locus. We present a novel long-amplicon TCRB repertoire sequencing approach to enable TRBV haplotype analysis from peripheral blood. Methods: Peripheral blood leukocyte total RNA from 81 Caucasians was used for sequencing of TCRB chains via the Oncomine TCRB-LR assay (amplicon spanning CDR1, 2 and 3) and the Ion Gene Studio S5. VDJ rearrangements were annotated by comparison to the IMGT database, then mined to construct TRBV allele profiles for each individual including, where detected, novel alleles not present in the ImMunoGeneTics (IMGT) database. Finally, TRBV allele profiles were subjected to principal component analysis and k-means clustering to identify TRBV allele haplotypes. Results: Clustering analysis revealed the presence of six major sets of coincident TRBV alleles, which we term haplotype groups. Allelic diversity varied markedly across haplotype groups, with approximately one third of the cohort showing limited TRBV allelic diversity and few uncommon alleles compared to members of other groups. Analysis revealed 37 putatively novel TRBV alleles that are absent from the IMGT database. Conclusion: We demonstrate a straightforward and cost-efficient method for TRBV haplotype analysis from long-amplicon TCRB sequencing data.
AB - Background: Polymorphism within the human T-cell receptor beta variable (TRBV) gene has been proposed as a risk factor for autoimmune disease and immune-related adverse events (IRAEs) during immunotherapy. Previous efforts to evaluate TRBV polymorphism by whole genome sequencing have been hampered by the repetitive nature of the T-cell receptor beta (TCRB) locus. We present a novel long-amplicon TCRB repertoire sequencing approach to enable TRBV haplotype analysis from peripheral blood. Methods: Peripheral blood leukocyte total RNA from 81 Caucasians was used for sequencing of TCRB chains via the Oncomine TCRB-LR assay (amplicon spanning CDR1, 2 and 3) and the Ion Gene Studio S5. VDJ rearrangements were annotated by comparison to the IMGT database, then mined to construct TRBV allele profiles for each individual including, where detected, novel alleles not present in the ImMunoGeneTics (IMGT) database. Finally, TRBV allele profiles were subjected to principal component analysis and k-means clustering to identify TRBV allele haplotypes. Results: Clustering analysis revealed the presence of six major sets of coincident TRBV alleles, which we term haplotype groups. Allelic diversity varied markedly across haplotype groups, with approximately one third of the cohort showing limited TRBV allelic diversity and few uncommon alleles compared to members of other groups. Analysis revealed 37 putatively novel TRBV alleles that are absent from the IMGT database. Conclusion: We demonstrate a straightforward and cost-efficient method for TRBV haplotype analysis from long-amplicon TCRB sequencing data.
KW - Immune-related adverse events
KW - Immunotherapy
KW - Polymorphism
KW - T-cell receptor
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U2 - 10.4103/JIPO.JIPO_16_19
DO - 10.4103/JIPO.JIPO_16_19
M3 - Article
AN - SCOPUS:85096201681
SN - 2666-2345
VL - 2
SP - 137
EP - 143
JO - Journal of Immunotherapy and Precision Oncology
JF - Journal of Immunotherapy and Precision Oncology
IS - 4
ER -