Admixmap

Record added by Jurg Ott (the original Rockefeller list)

Admixture mapping

3.7 (2007)

ADMIXMAP is a general-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus.

• Clive Hoggart
• Nigel Wetters
• David Clayton
• David O’Donnell (email: david.odonnell@ucd.ie)
• Paul McKeigue (email: paul.mckeigue@ucd.ie)

http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

C++

Linux, MS-Windows

admixmap, admixmap.pl, and some R scripts to process the output

• PM McKeigue (2005), “Prospects for admixture mapping of complex traits”, American Journal of Human Genetics, 76(1):1-7
• CJ Hoggart, MD Shriver, RA Kittles, DG Clayton, PM McKeigue (2004), “Design and analysis of admixture mapping studies”, American Journal of Human Genetics, 74(5):965-978
• CJ Hoggart, EJ Parra, MD Shriver, C Bonilla, RA Kittles, DC Clayton, PM McKeigue (2003), “Control of confounding of genetic associations in stratified populations”, American Journal of Human Genetics, 72(6):1492-1504
• PM McKeigue, J Carpenter, EJ Parra, MD Shriver (2000), “Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations”, Annals of Human Genetics, 64:171-186.