Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening.

ABSTRACT:

Purpose

The aim of the study was to assess exome data for preemptive pharmacogenetic screening for 203 clinically relevant pharmacogenetic variant positions from the Pharmacogenomics Knowledgebase and Clinical Pharmacogenetics Implementation Consortium and identify copy-number variants (CNVs) in CYP2D6.

Methods

We examined the coverage and genotype quality of 203 pharmacogenetic variant positions in 973 exomes compared with five genomes and with five genotyping chip data sets. Then, we determined the agreement of exome and chip genotypes by evaluating concordance in a three-way comparison of exome, genome, and chip-based genotyping at 1,929 variant positions in five individuals. Finally, we evaluated the utility of exomes for detecting CYP2D6 CNVs.

Results

For 5 indiv

SUBMITTER: Ng D 

PROVIDER: S-EPMC5316383 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature