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Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples.
Front Genet. 2018; 9:152.FG

Abstract

The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles. Here, we describe an approach to HLA-B typing using next generation sequencing (NGS) on the MinION™ nanopore sequencer, combined with data analysis with the SeqNext-HLA software package. The nanopore sequencer offers the advantages of long-read capability and single molecule reads, which can facilitate effective haplotyping. We developed this method using reference samples as well as individuals of New Zealand Māori or Pacific Island descent, because HLA-B diversity in these populations is not well understood. We demonstrate here that nanopore sequencing of barcoded, pooled, 943 bp polymerase chain reaction (PCR) amplicons of 49 DNA samples generated ample read depth for all samples. HLA-B alleles were assigned to all samples at high-resolution with very little ambiguity. Our method is a scaleable and efficient approach for genotyping HLA-B and potentially any other HLA locus. Finally, we report our findings on HLA-B genotypes of this cohort, which adds to our understanding of HLA-B allele frequencies among Māori and Pacific Island people.

Authors+Show Affiliations

Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.JSI Medical Systems GmbH, Ettenheim, Germany.Biochemistry Department, University of Otago, Dunedin, New Zealand.Department of Medicine, University of Otago, Christchurch, New Zealand.Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29760718

Citation

Ton, Kim N T., et al. "Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples." Frontiers in Genetics, vol. 9, 2018, p. 152.
Ton KNT, Cree SL, Gronert-Sum SJ, et al. Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Front Genet. 2018;9:152.
Ton, K. N. T., Cree, S. L., Gronert-Sum, S. J., Merriman, T. R., Stamp, L. K., & Kennedy, M. A. (2018). Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Frontiers in Genetics, 9, 152. https://doi.org/10.3389/fgene.2018.00152
Ton KNT, et al. Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Front Genet. 2018;9:152. PubMed PMID: 29760718.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. AU - Ton,Kim N T, AU - Cree,Simone L, AU - Gronert-Sum,Sabine J, AU - Merriman,Tony R, AU - Stamp,Lisa K, AU - Kennedy,Martin A, Y1 - 2018/04/30/ PY - 2017/12/21/received PY - 2018/04/12/accepted PY - 2018/5/16/entrez PY - 2018/5/16/pubmed PY - 2018/5/16/medline KW - HLA-B KW - Māori KW - Pacific Island KW - Polynesian KW - nanopore sequencing KW - pharmacogenetics SP - 152 EP - 152 JF - Frontiers in genetics JO - Front Genet VL - 9 N2 - The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles. Here, we describe an approach to HLA-B typing using next generation sequencing (NGS) on the MinION™ nanopore sequencer, combined with data analysis with the SeqNext-HLA software package. The nanopore sequencer offers the advantages of long-read capability and single molecule reads, which can facilitate effective haplotyping. We developed this method using reference samples as well as individuals of New Zealand Māori or Pacific Island descent, because HLA-B diversity in these populations is not well understood. We demonstrate here that nanopore sequencing of barcoded, pooled, 943 bp polymerase chain reaction (PCR) amplicons of 49 DNA samples generated ample read depth for all samples. HLA-B alleles were assigned to all samples at high-resolution with very little ambiguity. Our method is a scaleable and efficient approach for genotyping HLA-B and potentially any other HLA locus. Finally, we report our findings on HLA-B genotypes of this cohort, which adds to our understanding of HLA-B allele frequencies among Māori and Pacific Island people. SN - 1664-8021 UR - https://www.unboundmedicine.com/medline/citation/29760718/Multiplexed_Nanopore_Sequencing_of_HLA_B_Locus_in_Māori_and_Pacific_Island_Samples_ L2 - https://doi.org/10.3389/fgene.2018.00152 DB - PRIME DP - Unbound Medicine ER -
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