Establishing analytical validity of BeadChip array genotype data using WGS data and standard benchmark datasets

Clinical genotyping using DNA hybridization, e.g., the Global Screening Array (GSA), requires a comprehensive analytical framework to detect and limit error. Based on current research methodologies, we propose analytical validation of GSA genotyping by assessment of quality metrics and by comparison to truth sets: those of the 1000 Genomes Phase 3 (1KG), the National Institute of Standards and Technology (NIST), and the Genome in a Bottle Consortium (GiAB). To test this, we selected 263 Coriell DNA samples and, for each sample, generated whole genome sequence (rWGS) at an average 37x read depth and GSA genotypes in triplicate. These data were compared to each other and to the corresponding publicly available truth sets.