BioProject

Utilization of array- or PCR-based commercial platforms by clinical pharmacogenetic (PGx) testing laboratories may lead to inconsistent star allele calls and reported clinical drug response phenotypes, largely due to differences in platform content and annotation. More...

Utilization of array- or PCR-based commercial platforms by clinical pharmacogenetic (PGx) testing laboratories may lead to inconsistent star allele calls and reported clinical drug response phenotypes, largely due to differences in platform content and annotation. Whole genome sequencing (WGS) allows for higher-resolution genotyping, and may be used to call haplotypes and CNVs that are the basis of PGx star alleles and metabolizer phenotypes. However, multiple challenges exist and calling PGx star alleles using standard NGS variant calling pipelines has not been fully developed and validated. In this study, we generated deep, whole-genome sequence data with 10X linked read sequencing for selected NHGRI and NIGMS samples (with PIGI consent), chosen to represent a diversity of PGx alleles. DNA samples were obtained from the Coriell Institute for Medical Research. The samples in this study have previously been characterized by the Genetic Testing Reference Materials Coordination Program (GeT-RM) and include consensus calls from volunteer testing laboratories for up to 28 PGx genes. The data from this study serve as a resource for the pharmacogenomics community to better characterize PGx variation and improve calling and reporting of PGx alleles from WGS. Less...