The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)

Using admixture mapping to identify genetic linkages with variation in human facial shape


1Department of Anthropology, Pennsylvania State University, 2Centre for the Processing of Speech & Images, Katholic University of Leuven, 3Department of Genetics, Stanford University, 4HudsonAlpha Institute

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Using a dataset of 594 individuals from three populations with genetic ancestry contributions primarily from European and West African parental populations, we tested 72 SNPs in 45 selection-nominated candidate genes that are known to be involved in Mendelian craniofacial dysmorphologies as well as 68 ancestry informative markers with no known involvement with craniofacial variation for association with normal variation in facial shape. A dense mesh of over 7,000 high-density landmarks was placed on three-dimensional images of adult faces taken with the 3dMDface imaging system. Principal Component (PC) scores were then calculated as a representation of normal morphological variation across the surface of a face. A subset of the top PCs that showed significant associations with West African genetic ancestry was selected for the association study.

The program ADMIXMAP was used to test for admixture linkages between these 140 SNPs and facial shape variation. Sex, height, weight and BMI were included as covariates to control for the effects of body size on face shape morphology. After applying a correction for multiple testing, four SNPs were found to be significantly associated with facial variation. Two of these SNPs were located in craniofacial candidate genes, suggesting a role for these genes in determining normal facial variation. Interestingly, two of the AIMs, which are not located in candidate genes, were also significant. This suggests that these SNPs may be in admixture linkage disequilibrium with variants in the region that may have a previously unknown role with craniofacial variation.

This study was funded by the National Institute for Justice, Grant 2008-DN-BX-K125; National Science Foundation, DDIG #0851815, Wenner-Gren Foundation Dissertation Fieldwork Grant #7967.

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