Whole-exome sequencing (WES) has been widely used for analysis of human genetic diseases, but its value for the pharmacogenomic profiling of individuals is not well studied. Initially, we performed an in-depth evaluation of the accuracy of WES variant calling in the pharmacogenes CYP2D6 and CYP2C19 by comparison with MiSeq® amplicon sequencing data (n = 36). This analysis revealed that the concordance rate between WES and MiSeq® was high, achieving 99.60% for variants that were called without exceeding the truth-sensitivity threshold (99%), defined during variant quality score recalibration (VQSR). Beyond this threshold, the proportion of discordant calls increased markedly. Subsequently, we expanded our findings beyond CYP2D6 and CYP2C19 to include more genes genotyped by the iPLEX® ADME PGx Panel in the subset of twelve samples. WES performed well, agreeing with the genotyping panel in approximately 99% of the selected pass-filter variant calls. Overall, our results have demonstrated WES to be a promising approach for pharmacogenomic profiling, with an estimated error rate of lower than 1%. Quality filters, particularly VQSR, are important for reducing the number of false variants. Future studies may benefit from examining the role of WES in the clinical setting for guiding drug therapy.

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.

A functional polymorphism rs1799971 (A118G) in the μ-opioid receptor gene (OPRM1) produces an amino acid substitution Asn40Asp, which is believed to influence naltrexone response in nondepressed alcohol-dependent patients. In this study, patients with alcohol dependence and major depression (n=108) received open-label naltrexone and clinical case management for 12 weeks, and were randomized to citalopram or placebo. General linear mixed models examined the effect of the OPRM1 A118G genotype on alcohol outcomes during treatment. There was no evidence of any difference in the percentage of days abstinent, drinks per drinking day or percentage of heavy drinking days between Asp40 carriers and noncarriers during treatment. This study therefore failed to replicate the previous positive findings for this single nucleotide polymorphism in relation to naltrexone response, possibly indicating that the effect is not present in depressed patients.

The human leukocyte antigen (HLA) system is a gene family that encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region, comprised of 4,765 HLA-B alleles (IPD-IMGT/HLA Database Release 3.28). Many HLA-B alleles have been associated with adverse drug reactions and disease risks, and we are interested in developing efficient methods for analysis of HLA alleles in this context. Here we describe an approach to HLA-B typing using multiplexed next generation sequencing on the MinION™ nanopore sequencer (Oxford Nanopore Technologies), combined with data analysis with the SeqNext-HLA software package (JSI Medical Systems GmbH, Ettenheim, Germany). 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 of known HLA-B type as well as individuals of New Zealand Māori or Pacific Island (Polynesian) 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, on one R9.4 flowcell (Oxford Nanopore Technologies), generated ample read depth for all samples. Sequence analysis using SeqNext-HLA software assigned HLA-B alleles to all samples at high-resolution with very little ambiguity. Our PCRbased next generation sequencing 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 Polynesian people.