Record added by Jurg Ott (the original Rockefeller list)
(haplotype) Family Based Association Test
Haplotype FBAT is a user-friendly, well-documented software that allows the user to test for association/linkage between disease phenotypes and haplotypes by utilizing family-based controls. The method extends the approach for testing described in Rabinowitz and Laird (2000) to handle multiple tightly linked markers. It is robust to population admixture, yet efficient in the sense that it utilizes data from families where phase cannot be completely resolved in all individuals by using weights, which are estimated from the sample. However, the method remains robust to population stratification and population admixture. The method can handle any type of phenotype, including multiple phenotypes and missing parents, marker data, and/or phase, and provides both bi-allelic and multi-allelic tests. PowerFBAT is a tool for power simulation of association analysis using FBAT with binary outcomes. XWXW is an extension to the Haseman-Elston method for non-parametric linkage test with quantitative traits. XDT is a software that performs classical TDT, “SDT” and “Rabinowitz TDT” for nuclear families (not supported anymore).
Nan Laird (Harvard Univ)
UNIX(Solaris, Linux, MS-Windows, Mac(MacOS X/Darwin)
fbat, pbat, powerfbat, xwxw, xdt
Laird NM (2004) Family based tests for associating haplotypes with general phenotype data: application to asthma genetics. Genetic Epidemiology, 26(1):61-69;
Laird, Horvath, Xu (2000), Implementing a unified approach to family based tests of association, Genetic Epi, supp 1, 19:36-42; Rabinowitz, Laird (2000), A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information, Human Heredity, 50:211-223.
Horvath, Xu, Laird (2001), The family based association test method: strategies for studying general genotype-phenotype associations, European J Hum Genet. 9:301-306.