Skin pigmentation, biogeographical ancestry and admixture mapping

@article{Shriver2003SkinPB,
  title={Skin pigmentation, biogeographical ancestry and admixture mapping},
  author={Mark David Shriver and Esteban Juan Parra and Sonia Dios and Carolina Bonilla and Heather L. Norton and Celina Jovel and Carrie Lynn Pfaff and Cecily Jones and Aisha Massac and Neil Cameron and Archie Baron and Tabitha Jackson and George Argyropoulos and Li Jin and Clive J. Hoggart and Paul M. McKeigue and Rick A. Kittles},
  journal={Human Genetics},
  year={2003},
  volume={112},
  pages={387-399}
}
Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual. Ancestry estimates at both the subgroup and individual level can be directly instructive regarding the genetics of the phenotypes that differ qualitatively or in frequency between populations. These estimates can provide a compelling… 
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References

SHOWING 1-10 OF 55 REFERENCES
Estimating African American admixture proportions by use of population-specific alleles.
TLDR
Significant nonrandom association between two markers located 22 cM apart (FY-null and AT3) is detected, most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations, emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental population.
Ethnic-difference markers for use in mapping by admixture linkage disequilibrium.
TLDR
DNA-pooling technique was used to screen microsatellite and diallelic insertion/deletion markers for allele-frequency differences between putative representatives of the parental populations of the admixed Mexican American (MA) and African American (AA) populations, suggesting that EDMs with large interpopulation and small intrapopulation differences can be readily identified for MALD studies in both AA and MA populations.
Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations.
TLDR
A map of polymorphic markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats in African Americans, Hispanics, European Americans, and Asians is described, by choosing STR markers that have large differences in composite delta, log-likelihood ratios, and/or I*(2) for Mald.
Mapping by admixture linkage disequilibrium in human populations: limits and guidelines.
TLDR
This work has conducted analytic and computer simulations to quantify the effect of genetic, genomic, and population parameters that affect the amount and ascertainment of linkage disequilibrium in populations with a history of genetic admixture.
Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African‐American populations
We describe a novel method for analysis of marker genotype data from admixed populations, based on a hybrid of Bayesian and frequentist approaches in which the posterior distribution is generated by
Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture.
  • P. Mckeigue
  • Biology
    American journal of human genetics
  • 1998
TLDR
Simulations using a hidden Markov model suggest that, when admixture has occurred 2-10 generations earlier, a multipoint analysis using 2,000 biallelic markers, with f values of 30%, can extract 70%-90% of the ancestry information for each locus.
Quantitative genetics of human skin color
TLDR
Skin color has long been of interest to human geneticists and often used as an example of a human quantitative trait under relatively wellunderstood genetic control, but the evolutionary significance and mode of inheritance are still being debated.
Ancestral proportions and admixture dynamics in geographically defined African Americans living in South Carolina.
TLDR
The results of this study indicate, in accordance with previous historical, cultural, and anthropological evidence, a very low level of European admixture in the Gullah Sea Islanders, and a continuous gene flow model of admixture could explain the observed pattern of genetic structure.
Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28
TLDR
A high-density SNP map of the Xq25–Xq28 region is constructed and male genotypes and haplotypes across this region for LD are analysed, suggesting that LD is not a monotonic function of the distance between markers, but is more a property of the particular location in the human genome.
Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci.
  • R. Chakraborty, K. Weiss
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1988
TLDR
It is shown that substantial disequilibrium remains today under widely applicable situations, which can be detected without requiring inordinately close linkage between trait and marker loci.
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