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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.    Results  The results from PedGenie were shown to be valid both for accurate  p -value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the  NBS1  tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10–2.35, p = 0.019).    Conclusion  PedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate  NBS1  may play a role in the genetic etiology of heritable breast cancer.

PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size