Record added by Jurg Ott (the original Rockefeller list)
GENIE (previously PEDGENIE and HAPMC) performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests.
PedGenie, hapMC, hapConstructor
Allen-Brady, Farnham, Weiler, Camp (2003), “A cautionary note on the appropriateness of using a linkage resource for an association study”, BMC Genetics, 4(suppl 1):S89.
Allen-Brady, Wong, Camp (2006), “PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size”, BMC Bioinformatics, 7:209.
Curtin, Wong, Allen-Brady, Camp (2007), “PedGenie: meta genetic association testing in mixed family and case-control designs”, BMC Bioinformatics, 8:448.
Abo, Knight, Wong, Cox, Camp (2008), “hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework”, Bioinformatics, 24(18):2105-2107.