Identification and characterization of novel HLA alleles: Utility of next-generation sequencing methods

Human Immunology
Nicholas K BrownSusana R Marino

Abstract

The HLA genes are the most polymorphic of the human genome, and novel HLA alleles are continuously identified, often by clinical Sanger sequencing-based typing (SBT) assays. Introduction of next-generation sequencing (NGS) technologies for clinical HLA typing may significantly improve this process. Here we compare four cases of novel HLA alleles identified and characterized by both SBT and NGS. The tested NGS system sequenced broader regions of the HLA loci, and identified novel polymorphisms undetected by SBT. Subsequent characterization of the novel alleles in isolation of coencoded alleles by SBT required custom-designed primers, while the NGS system was able to sequence both alleles in phase. However, the tested assay was unable to amplify buccal cell DNA for subsequent NGS sequencing, presumably due to the lower quality of these samples. While NGS assays will undoubtedly increase novel allele identification, more stringent DNA sample requirements may be necessary for this new technology.

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Citations

Aug 12, 2016·International Journal of Immunogenetics·Steven G E Marsh
Sep 2, 2016·HLA : Immune Response Genetics·S G E Marsh, UNKNOWN WHO Nomenclature Committee for Factors of the HLA System
Oct 6, 2016·Human Immunology·Steven G E Marsh, UNKNOWN WHO Nomenclature Committee for Factors of the HLA System
Jan 12, 2020·Science & Justice : Journal of the Forensic Science Society·Agnieszka KuffelNiamh Nic Daeid
Mar 17, 2021·HLA : Immune Response Genetics·Nanying ChenFaming Zhu
Jul 31, 2021·Immunology Letters·Constantina A SarriZissis Mamuris
Aug 15, 2021·HLA : Immune Response Genetics·Yanmin HeFaming Zhu

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