Replies to post #73095 on DNAprint Genomics (DNAG)

[johnnyfiber]

Nature Genetics
Published online: 21 October 2007 | doi:10.1038/ng.2007.13


Genetic determinants of hair, eye and skin pigmentation in Europeans
Patrick Sulem1, Daniel F Gudbjartsson1, Simon N Stacey1, Agnar Helgason1, Thorunn Rafnar1, Kristinn P Magnusson1, Andrei Manolescu1, Ari Karason1, Arnar Palsson1, Gudmar Thorleifsson1, Margret Jakobsdottir1, Stacy Steinberg1, Snæbjörn Pálsson1, Fridbert Jonasson2, Bardur Sigurgeirsson3, Kristin Thorisdottir3,4, Rafn Ragnarsson4, Kristrun R Benediktsdottir5, Katja K Aben6, Lambertus A Kiemeney7,8, Jon H Olafsson3, Jeffrey Gulcher1, Augie Kong1, Unnur Thorsteinsdottir1 & Kari Stefansson1


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AbstractHair, skin and eye colors are highly heritable and visible traits in humans. We carried out a genome-wide association scan for variants associated with hair and eye pigmentation, skin sensitivity to sun and freckling among 2,986 Icelanders. We then tested the most closely associated SNPs from six regions—four not previously implicated in the normal variation of human pigmentation—and replicated their association in a second sample of 2,718 Icelanders and a sample of 1,214 Dutch. The SNPs from all six regions met the criteria for genome-wide significance. A variant in SLC24A4 is associated with eye and hair color, a variant near KITLG is associated with hair color, two coding variants in TYR are associated with eye color and freckles, and a variant on 6p25.3 is associated with freckles. The fifth region provided refinements to a previously reported association in OCA2, and the sixth encompasses previously described variants in MC1R.

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Department of Urology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands.

http://npg.nature.com/ng/journal/vaop/ncurrent/full/ng.2007.13.html#B19

[johnnyfiber]

A Genomewide Single-NucleotidePolymorphism Panel for Mexican American Admixture Mapping
Author(s) Chao Tian, David A. Hinds, Russell Shigeta, Sharon G. Adler, Annette Lee, Madeleine V. Pahl, Gabriel Silva, John W. Belmont, Robert L. Hanson, William C. Knowler, Peter K. Gregersen, Dennis G. Ballinger, and Michael F. Seldin
Identifiers The American Journal of Human Genetics, volume 80 (2007), page 000
DOI: 10.1086/513522

Availability This site: PS | HTML | PDF (316.2k)
Copyright © 2007, The American Society of Human Genetics.
Abstract For admixture mapping studies in Mexican Americans (MAM), we define a genomewide single-nucleotidepolymorphism (SNP) panel that can distinguish between chromosomal segments of Amerindian (AMI) or European (EUR) ancestry. These studies used genotypes for >400,000 SNPs, defined in EUR and both Pima and Mayan AMI, to define a set of ancestry-informative markers (AIMs). The use of two AMI populations was necessary to remove a subset of SNPs that distinguished genotypes of only one AMI subgroup from EUR genotypes. The AIMs set contained 8,144 SNPs separated by a minimum of 50 kb with only three intermarker intervals >1 Mb and had EUR/AMI FST values >0.30 (mean FST=0.48) and Mayan/Pima FST values <0.05 (mean FST<0.01). Analysis of a subset of these SNP AIMs suggested that this panel may also distinguish ancestry between EUR and other disparate AMI groups, including Quechuan from South America. We show, using realistic simulation parameters that are based on our analyses of MAM genotyping results, that this panel of SNP AIMs provides good power for detecting disease-associated chromosomal segments for genes with modest ethnicity risk ratios. A reduced set of 5,287 SNP AIMs captured almost the same admixture mapping information, but smaller SNP sets showed substantial drop-off in admixture mapping information and power. The results will enable studies of type 2 diabetes, rheumatoid arthritis, and other diseases among which epidemiological studies suggest differences in the distribution of ancestry-associated susceptibility.

http://www.journals.uchicago.edu/cgi-bin/resolve?id=doi:10.1086/513522&erFrom=-6401546418201314829Guest