ROADTRIPS: case-control association testing with partially or completely unknown population and pedigree structure.

American Journal of Human Genetics
Timothy Thornton, Mary Sara McPeek

Abstract

Genome-wide association studies are routinely conducted to identify genetic variants that influence complex disorders. It is well known that failure to properly account for population or pedigree structure can lead to spurious association as well as reduced power. We propose a method, ROADTRIPS, for case-control association testing in samples with partially or completely unknown population and pedigree structure. ROADTRIPS uses a covariance matrix estimated from genome-screen data to correct for unknown population and pedigree structure while maintaining high power by taking advantage of known pedigree information when it is available. ROADTRIPS can incorporate data on arbitrary combinations of related and unrelated individuals and is computationally feasible for the analysis of genetic studies with millions of markers. In simulations with related individuals and population structure, including admixture, we demonstrate that ROADTRIPS provides a substantial improvement over existing methods in terms of power and type 1 error. The ROADTRIPS method can be used across a variety of study designs, ranging from studies that have a combination of unrelated individuals and small pedigrees to studies of isolated founder populations with...Continue Reading

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Citations

Aug 2, 2011·Human Genetics·Ani ManichaikulJosyf C Mychaleckyj
Jun 16, 2010·Nature Reviews. Genetics·Alkes L PriceNick Patterson
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