Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.
Am J Hum Genet
; 91(5): 839-48, 2012 Nov 02.
Article
en En
| MEDLINE
| ID: mdl-23103226
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 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.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Análisis de Secuencia de ADN
/
Contaminación de ADN
/
Genotipo
Tipo de estudio:
Diagnostic_studies
/
Prognostic_studies
Límite:
Humans
Idioma:
En
Año:
2012
Tipo del documento:
Article