Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples

Frontiers in Genetics
Kim N T TonMartin A Kennedy

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 alle...Continue Reading

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Datasets Mentioned

BETA
SRP138979

Methods Mentioned

BETA
genotyping
exome sequencing
Genome Sequencing
PCR
electrophoresis

Software Mentioned

Geneious
SeqPilot
MinION
SBTengine
Nanopolish
BWA
Metrichor
PromethION
MEM
GridION

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