Nanopore sequencing enables improvements in Pharmacogenomic CYP2D6 Haplotyping

Long-read single-molecule sequencers, such as those provided by Oxford Nanopore, offer the capability to direct detection and phasing of variants across the CYP2D6 gene. We performed replicate sequencing on the MinION and compared results to the same diagnostic controls on our current MALDI-TOF diagnostic platform (based on 18 SNPs and Indels). Results are highly comparable to current diagnostic genotyping methods (>98.8% concordance), even when downsampled to only 100 reads. While SNP calls were relatively concordant across runs (94%), indels were far less indicating needed future improvements in sequencing, base calling, and/or variant calling. We fully phased all samples into two alleles.