STRATIFICATION PROGRAMS

 

ADMIXMAP (ADMIXture MAPping)  video
*Description This is a general-purpose program for modelling admixture using marker genotypes and trait data of individuals from an admixed population (such as African-Americans). 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. The ADMIXMAP program can be used to estimate individual and population level admixture, test for a relationship between disease risk and individual admixture in case-control, cross-sectional or cohort studies, localize genes underlying ethnic differences in disease risk by admixture mapping and control for population structure (variation in individual admixture) in genetic association studies so as to eliminate associations with unlinked genes.
Authors Clive Hoggart, Nigel Wetters, David Clayton and Paul McKeigue
References Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DC, McKeigue PM. (2003). Control of confounding of genetic associations in stratified populations. American Journal of Human Genetics, 72, 1492-1504.
Website http://admixmap.sourceforge.net/

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ANCESTRYMAP   video
Description This program uses admixture mapping to isolate disease causing genes that differ in frequency across populations. Admixture mapping is a method for localizing disease causing genetic variants that differ in frequency across populations.
Authors Nick Patterson, David Reich
References Patterson et al (2004) Methods for High-Density Admixture Mapping of Disease Genes Am. J. Hum Genet. 74: 979-1000
Website http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

 

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STRAT   video
Description STRAT is a companion program to structure. This is a structured association method, for use in association mapping, enabling valid case-control studies even in the presence of population structure. This method was described in an article in Am. J. Hum Genet 2000 (67:170-181). Collaborators: Matthew Stephens, Noah Rosenberg, Peter Donnelly. (Description retrieved from http://pritchardlab.stanford.edu/software.html)
Authors Jonathan Pritchard
References Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. (2000). Association mapping in structured populations. American Journal of Human Genetics, 67, 170-181.
Website http://pritchardlab.stanford.edu/software.html

 

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STRUCTURE   video
Description The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs. (Description retrieved from http://pritchardlab.stanford.edu/structure.html)
Authors Jonathan Pritchard
References Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. (2000). Association mapping in structured populations. American Journal of Human Genetics, 67, 170-181.
Website http://pritchardlab.stanford.edu/structure.html

 

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Genomic Control  video
Description The program implements the genomic control (GC) models. The program runs in two steps. First, it estimates the inflation factor(s) from a set of "null" loci specified by the user. The program then uses these estimates to test for effects at either a single loci (marginal) or two loci (interaction) with relation to a user specified response variable.
Authors Devlin B, Roeder K.
References
  • Bacanu, S., Devlin, B., Roeder, K. (2002). Association Studies for Quantitative Traits in Structured Populations. Genetic Epidemiology, 22, 78-93.
  • Devlin B, Roeder K. (1999). Genomic control for association studies. Biometrics, 55(4), 997-1004.
Website http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm
http://wpicr.wpic.pitt.edu/WPICCompGen/software.html

 

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L-POP   video
*Description L-POP detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. Using a latent class analysis model, population strata are defined such that unlinked markers are in Hardy-Weinberg equilibrium and linkage equilibrium within classes. L-POP calculates the posterior probabilities for each individual belonging to each of K classes, which can be used to correct for spurious effects of population stratification in tests of association.
Authors Purcell S, Sham P
References http://pngu.mgh.harvard.edu/~purcell/lpop/

 

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* Description retrieved from http://linkage.rockefeller.edu/soft/