ADMIXMAP a program to model admixture using marker genotype data

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Introduction

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.

Possible uses of the ADMIXMAP program

1. Modelling the distribution of individual admixture values and the history of admixture (inferred by modelling the stochastic variation of ancestry along chromosomes).

2. Case-control, cross-sectional or cohort studies that test for a relationship between disease risk and individual admixture

3. Localizing genes underlying ethnic differences in disease risk by admixture mapping

4. Controlling for population structure (variation in individual admixture) in genetic association studies so as to eliminate associations with unlinked genes

5. Reconstructing the genetic structure of an ancestral population where unadmixed modern descendants are not available for study

ADMIXMAP can model admixture between more than two populations, and can use data from multi-allelic or biallelic marker polymorphisms. The program has been developed for application to admixed human populations, but can also be used to model admixture in livestock or for fine mapping of quantitative trait loci in outbred stocks of mice.

A manual for the program is available which describes the statistical model in more detail. Downloads of the program compiled for various platforms are also available. We recommend that before trying to run the program, you consult us first about your requirements.