Nov 8, 2018

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

BioRxiv : the Preprint Server for Biology
Fan ZhangHyun Min Kang

Abstract

Detecting and estimating DNA sample contamination are important steps to ensure high quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process samples from multiple studies across diverse populations. On the other hand, incorrectly specified allele frequencies may result in substantial bias in estimated contamination rates. For example, we observed that existing methods often fail to identify 10% contaminated samples at a typical 3% contamination exclusion threshold when genetic ancestry is misspecified. Such an incomplete screening of contaminated samples substantially inflates the estimated rate of genotyping errors even in deeply sequenced genomes and exomes. We propose a robust statistical method that accurately estimates DNA contamination and is agnostic to genetic ancestry of the intended or contaminating sample. Our method integrates the estimation of genetic ancestry and DNA contamination in a unified likeliho...Continue Reading

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Mentioned in this Paper

Study
Genome
Medical Devices
Genetic Activator
Sequence Analysis
Screening Generic
Statistical Technique
Analysis
Alleles
Gene Therapy

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