Human Pigmentation

Research into Normal Variation in:

  • Human Pigmentation: Inverstigating normal variation in human skin, hair and eye pigmentation.
  • Facial Features:¬†Inverstigating normal variation in human facial features from 3d photographs.
  • Dentition: Inverstigating normal variation in human dentition via dental casts.

Research into Human Perception:

  • Facial Perception: Studies involving human perception of facial variation.

Complex Disease Mapping

Carrie L. Pfaff is working on computer simulations of the admixture process to better understand the dynamics and the statistical power that will be present for mapping chonic diseases. Admixture mapping simulations provide a review of her project and a look at some recent results.

Ancestry Informative Marker (AIM) Resources

Verified and well-classified AIMs

All molecular and frequency information on the Ancestry Informative Markers that we have characterized have been submitted to dbSNP and are posted on the NCBI web site at NIH under the submitter handle PSU-ANTH. Click on the following link to be transfered to this site.

PSU-ANTH markers in dbSNP

Candidate AIMs: Allele frequencies from Akey et al. 2002

We have recently analyzed allele frequency data from the TSC on 26,000 SNPs. The first analysis of this data will be published in Genome Research in December 2002. Click on the link below to download the file with the allele frequencies and delta levels for the markers summarized in this work.

26,000 SNPs in 3 populations

Measuring European Population Stratification using Microarray Genotype Data

Bauchet M, McEvoy B, Pearson LN. , Quillen EE. , Sarkisian T, Hovhannesyan K, Deka R, Bradley DG, Shriver MD. 2007. American Journal of Human Genetics 80(May):948-956.

 

Admixture Map

Am J Hum Genet 1998 Dec;63(6):1839-51

Estimating African American admixture proportions by use of population-specific alleles.

Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, Allison DB, Deka R, Ferrell RE, Shriver MD Department of Human Genetics, Allegheny University of Health Sciences, Pittsburgh, Pennsylvania, USA.

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations.

PMID: 9837836, UI: 99057521