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

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 re

SUBMITTER: Allen-Brady K 

PROVIDER: S-EPMC1459209 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature