Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence and standard benchmark datasets.

ABSTRACT:

Background

Clinical use of genotype data requires high positive predictive value (PPV) and thorough understanding of the genotyping platform characteristics. BeadChip arrays, such as the Global Screening Array (GSA), potentially offer a high-throughput, low-cost clinical screen for known variants. We hypothesize that quality assessment and comparison to whole-genome sequence and benchmark data establish the analytical validity of GSA genotyping.

Methods

To test this hypothesis, we selected 263 samples from Coriell, generated GSA genotypes in triplicate, generated whole genome sequence (rWGS) genotypes, assessed the quality of each set of genotypes, and compared each set of genotypes to each other and to the 1000 Genomes Phase 3 (1KG) genotypes, a performance benchmark. For 5

SUBMITTER: Cherukuri PF 

PROVIDER: S-EPMC8919546 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature