Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa

Human Immunology
Yvonne R ThorstensonMark M Davis

Abstract

The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4...Continue Reading

Citations

May 11, 2019·HLA : Immune Response Genetics·Steven G E Marsh, UNKNOWN WHO Nomenclature Committee for Factors of the HLA System
May 12, 2019·International Journal of Immunogenetics·Steven G E Marsh
Sep 4, 2019·HLA : Immune Response Genetics·Shayne LoubserCaroline T Tiemessen
Aug 30, 2019·HLA : Immune Response Genetics·Shayne LoubserCaroline T Tiemessen
Jul 31, 2019·Nature Medicine·Kathryn E YostHoward Y Chang
Jul 2, 2019·Human Immunology·Kazutoyo OsoegawaMarcelo A Fernández-Viña
Jan 12, 2020·Science & Justice : Journal of the Forensic Science Society·Agnieszka KuffelNiamh Nic Daeid
Apr 25, 2021·Human Immunology·Yuxin YinQiuheng Zhang
Jul 31, 2021·Immunology Letters·Constantina A SarriZissis Mamuris

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