EP138: An informatics star allele calling workflow for direct typing of CYP2D6 from fully phased variants using PacBio HiFi reads

Abstract

The CYP2D6 locus is well known for its importance to pharmacogenetics as well as for its high diversity and complex genomic setting, including gene duplications, gene fusions, gene conversion, and large deletions that can be found in all populations. Resolving individual alleles at this locus using short-read sequencing technologies requires inference-based methods due to ambiguous mapping in the presence of highly homologous pseudogenes, and typically imputation because short reads are unable to phase variants over kilobase-long stretches of sequence.