PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size |
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Authors: | Kristina Allen-Brady Jathine Wong Nicola J Camp |
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Institution: | (1) Genetic Epidemiology Division, Department of Medical Informatics, University of Utah Salt Lake City, Salt Lake City, Utah, USA |
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Abstract: | Background We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows
for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative
or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related
individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a
time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality
of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide
polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families. |
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