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

Area of Science:

• Immunogenetics
• Genomic Sequencing
• Population Genetics

Background:

• The human leukocyte antigen (HLA) system, particularly HLA-B, is highly polymorphic and linked to adverse drug reactions and disease susceptibility.
• Understanding HLA-B allele frequencies across diverse ethnic groups, such as New Zealand Māori and Pacific Islanders, is crucial but often limited by current genotyping methods.
• Improved HLA-B genotyping techniques are needed to facilitate research into HLA associations with diseases and drug responses.

Purpose of the Study:

• To develop and validate a novel, efficient, and scalable method for high-resolution HLA-B genotyping.
• To apply this method to a cohort of New Zealand Māori and Pacific Island descent to investigate HLA-B allele diversity.
• To enhance the understanding of HLA-B allele frequencies in underrepresented populations.

Main Methods:

• Utilized next-generation sequencing (NGS) on a MinION™ nanopore sequencer.
• Employed the SeqNext-HLA software package for data analysis.
• Sequenced barcoded, pooled polymerase chain reaction (PCR) amplicons (943 bp) from 49 DNA samples, including reference and Māori/Pacific Islander individuals.

Main Results:

• Nanopore sequencing generated sufficient read depth for all 49 samples.
• High-resolution HLA-B typing was achieved with minimal ambiguity across all samples.
• The method proved scalable and efficient for genotyping HLA-B and potentially other HLA loci.

Conclusions:

• The developed nanopore sequencing approach combined with SeqNext-HLA software provides an effective and accurate method for HLA-B genotyping.
• This technique facilitates haplotyping due to its long-read capability.
• The study reports novel HLA-B genotype data for Māori and Pacific Island populations, contributing valuable insights into their genetic diversity.