Author
Listed:
- Naveen K Kadri
- Bernt Guldbrandtsen
- Peter Sørensen
- Goutam Sahana
Abstract
Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic markers. Linear models that ignored K were also tested. Correction for P was performed using principal component or structured association analysis. In analyses of simulated and real data, linear mixed models that corrected for K were able to control for type-I error, regardless of whether they also corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree and genomic relationships. In summary, in association studies using samples with both P and K, ancestries estimated using principal components or structured assignment were not sufficient to correct type-I errors. In such cases type-I errors may be controlled by use of linear mixed models with relationships derived from either pedigree or from genetic markers.
Suggested Citation
Naveen K Kadri & Bernt Guldbrandtsen & Peter Sørensen & Goutam Sahana, 2014.
"Comparison of Genome-Wide Association Methods in Analyses of Admixed Populations with Complex Familial Relationships,"
PLOS ONE, Public Library of Science, vol. 9(3), pages 1-8, March.
Handle:
RePEc:plo:pone00:0088926
DOI: 10.1371/journal.pone.0088926
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