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

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...

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Vydáno v:American journal of human genetics Ročník 91; číslo 5; s. 839
Hlavní autoři: Jun, Goo, Flickinger, Matthew, Hetrick, Kurt N, Romm, Jane M, Doheny, Kimberly F, Abecasis, Gonçalo R, Boehnke, Michael, Kang, Hyun Min
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 02.11.2012
Témata:
Diabetes Mellitus, Type 2 - diagnosis
Diabetes Mellitus, Type 2 - genetics
DNA Contamination
Genotype
Humans
Sequence Analysis, DNA
ISSN:1537-6605, 1537-6605
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Shrnutí: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 combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies.
Bibliografie:ObjectType-Article-1
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ISSN:1537-6605
1537-6605
DOI:10.1016/j.ajhg.2012.09.004