Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.

ABSTRACT: DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combinatio

SUBMITTER: Jun G 

PROVIDER: S-EPMC3487130 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature