Correcting for Sample Contamination in Genotype Calling of DNA Sequence Data

DNA sample contamination is a frequent problem in DNA sequencing studies and can result in genotyping errors and reduced power for association testing. We recently described methods to identify within-species DNA sample contamination based on sequencing read data, showed that our methods can reliably detect and estimate contamination levels as low as 1%, and suggested strategies to identify and remove contaminated samples from sequencing studies. Here we propose methods to model contamination during genotype calling as an alternative to removal of contaminated samples from further analyses.

Source: The American Journal of Human Genetics - July 30, 2015 Category: Genetics & Stem Cells Authors: Matthew Flickinger, Goo Jun, Gonçalo R. Abecasis, Michael Boehnke, Hyun Min Kang Tags: Article Source Type: research