A Novel Quality-Control Procedure to Improve the Accuracy of Rare Variant Calling in SNP Arrays.

ABSTRACT: Background: Single-nucleotide polymorphism (SNP) arrays are an ideal technology for genotyping genetic variants in mass screening. However, using SNP arrays to detect rare variants [with a minor allele frequency (MAF) of <1%] is still a challenge because of noise signals and batch effects. An approach that improves the genotyping quality is needed for clinical applications. Methods: We developed a quality-control procedure for rare variants which integrates different algorithms, filters, and experiments to increase the accuracy of variant calling. Using data from the TWB 2.0 custom Axiom array, we adopted an advanced normalization adjustment to prevent false calls caused by splitting the cluster and a rare het adjustment which decreases false calls in rare variants. The conco

SUBMITTER: Sun TH 

PROVIDER: S-EPMC8577504 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature