MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

Harm-Jan Westra, Ritsert C Jansen, Rudolf S N Fehrmann, Gerard J te Meerman, David van Heel, Cisca Wijmenga, Lude Franke*, Gerhardus te Meerman

*Bijbehorende auteur voor dit werk

OnderzoeksoutputAcademicpeer review

45 Citaten (Scopus)
472 Downloads (Pure)

Samenvatting

MOTIVATION: Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels.

RESULTS: We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets.

AVAILABILITY AND IMPLEMENTATION: MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/

Originele taal-2English
Pagina's (van-tot)2104-2111
Aantal pagina's8
TijdschriftBioinformatics
Volume27
Nummer van het tijdschrift15
DOI's
StatusPublished - 1-aug-2011

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