A Genomewide Association Study of Skin Pigmentation in a South Asian Population

The American Journal of Human Genetics - Tập 81 - Trang 1119-1132 - 2007
Renee P. Stokowski1, P.V. Krishna Pant1, Tony Dadd2, Amelia Fereday2, David A. Hinds1, Carl Jarman2, Wendy Filsell2, Rebecca S. Ginger2, Martin R. Green2, Frans J. van der Ouderaa2, David R. Cox1
1From Perlegen Sciences, Mountain View, CA
2and Unilever Corporate Research, Bedford, United Kingdom

Tài liệu tham khảo

Armstrong, 1997, Sun exposure and skin cancer, Australas J Dermatol, 38, S1, 10.1111/j.1440-0960.1997.tb01000.x Palmer, 2000, Melanocortin-1 receptor polymorphisms and risk of melanoma: is the association explained solely by pigmentation phenotype?, Am J Hum Genet, 66, 176, 10.1086/302711 Rees, 2004, The genetics of sun sensitivity in humans, Am J Hum Genet, 75, 739, 10.1086/425285 Robbins, 1991 Branda, 1978, Skin color and nutrient photolysis: an evolutionary hypothesis, Science, 201, 625, 10.1126/science.675247 Chaplin, 2004, Geographic distribution of environmental factors influencing human skin coloration, Am J Phys Anthropol, 125, 292, 10.1002/ajpa.10263 Murray, 1934, Pigmentation, sunlight, and nutritional disease, Am Anthropol, 36, 438, 10.1525/aa.1934.36.3.02a00100 Clark, 1981, A twin study of skin reflectance, Ann Hum Biol, 8, 529, 10.1080/03014468100005371 Frisancho, 1981, Heritability and components of phenotypic expression in skin reflectance of Mestizos from the Peruvian lowlands, Am J Phys Anthropol, 55, 203, 10.1002/ajpa.1330550207 Harrison, 1964, Studies on the inheritance of human skin colour, Ann Hum Genet, 28, 27, 10.1111/j.1469-1809.1964.tb00457.x Izagirre, 2006, A scan for signatures of positive selection in candidate loci for skin pigmentation in humans, Mol Biol Evol, 23, 1697, 10.1093/molbev/msl030 Myles, 2007, Identifying genes underlying skin pigmentation differences among human populations, Hum Genet, 120, 613, 10.1007/s00439-006-0256-4 Norton, 2006, Genetic evidence for the convergent evolution of light skin in Europeans and East Asians, Mol Biol Evol, 24, 710, 10.1093/molbev/msl203 Relethford, 1997, Hemispheric difference in human skin color, Am J Phys Anthropol, 104, 449, 10.1002/(SICI)1096-8644(199712)104:4<449::AID-AJPA2>3.0.CO;2-N Bennett, 2003, The color loci of mice—a genetic century, Pigment Cell Res, 16, 333, 10.1034/j.1600-0749.2003.00067.x Sturm, 2001, Human pigmentation genes: identification, structure and consequences of polymorphic variation, Gene, 277, 49, 10.1016/S0378-1119(01)00694-1 Akey, 2001, Interaction between the melanocortin-1 receptor and P genes contributes to inter-individual variation in skin pigmentation phenotypes in a Tibetan population, Hum Genet, 108, 516, 10.1007/s004390100524 Bonilla, 2005, The 8818G allele of the agouti signaling protein (ASIP) gene is ancestral and is associated with darker skin color in African Americans, Hum Genet, 116, 402, 10.1007/s00439-004-1251-2 Graf, 2005, Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation variation, Hum Mutat, 25, 278, 10.1002/humu.20143 Graf, 2007, Promoter polymorphisms in the MATP (SLC45A2) gene are associated with normal human skin color variation, Hum Mutat, 28, 710, 10.1002/humu.20504 Hoggart, 2003, Control of confounding of genetic associations in stratified populations, Am J Hum Genet, 72, 1492, 10.1086/375613 Lamason, 2005, SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans, Science, 310, 1782, 10.1126/science.1116238 Naysmith, 2004, Quantitative measures of the effect of the melanocortin 1 receptor on human pigmentary status, J Invest Dermatol, 122, 423, 10.1046/j.0022-202X.2004.22221.x Shriver, 2003, Skin pigmentation, biogeographical ancestry and admixture mapping, Hum Genet, 112, 387, 10.1007/s00439-002-0896-y Soejima, 2007, Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2, Int J Legal Med, 121, 36, 10.1007/s00414-006-0112-z Yuasa, 2006, Distribution of the F374 allele of the SLC45A2 (MATP) gene and founder-haplotype analysis, Ann Hum Genet, 70, 802, 10.1111/j.1469-1809.2006.00261.x Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062 Venter, 2001, The sequence of the human genome, Science, 291, 1304, 10.1126/science.1058040 International HapMap Consortium, 2005, A haplotype map of the human genome, Nature, 437, 1299, 10.1038/nature04226 Hinds, 2005, Whole-genome patterns of common DNA variation in three human populations, Science, 307, 1072, 10.1126/science.1105436 Sachidanandam, 2001, A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms, Nature, 409, 928, 10.1038/35057149 Hinds, 2004, Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels, Hum Genomics, 1, 421, 10.1186/1479-7364-1-6-421 Hinds, 2004, Matching strategies for genetic association studies in structured populations, Am J Hum Genet, 74, 317, 10.1086/381716 Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945 Price, 2006, Principal components analysis corrects for stratification in genome-wide association studies, Nat Genet, 38, 904, 10.1038/ng1847 Patil, 2001, Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21, Science, 294, 1719, 10.1126/science.1065573 Bierut, 2007, Novel genes identified in a high-density genome wide association study for nicotine dependence, Hum Mol Genet, 16, 24, 10.1093/hmg/ddl441 Saccone, 2007, Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs, Hum Mol Genet, 16, 36, 10.1093/hmg/ddl438 Devlin, 1999, Genomic control for association studies, Biometrics, 55, 997, 10.1111/j.0006-341X.1999.00997.x Cordell, 2002, A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes, Am J Hum Genet, 70, 124, 10.1086/338007 Majumder, 1998, People of India: biological diversity and affinities, Evol Anthropol, 6, 100, 10.1002/(SICI)1520-6505(1998)6:3<100::AID-EVAN4>3.0.CO;2-I Barsh, 2003, What controls variation in human skin color?, PLoS Biol, 1, E27, 10.1371/journal.pbio.0000027 Rees, 2003, Genetics of hair and skin color, Annu Rev Genet, 37, 67, 10.1146/annurev.genet.37.110801.143233 Alaluf, 2002, The impact of epidermal melanin on objective measurements of human skin colour, Pigment Cell Res, 15, 119, 10.1034/j.1600-0749.2002.1o072.x Sengupta, 2004, DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies, Ann Hum Genet, 68, 574, 10.1046/j.1529-8817.2003.00126.x Pritchard, 1999, Use of unlinked genetic markers to detect population stratification in association studies, Am J Hum Genet, 65, 220, 10.1086/302449 Stein, 2002, The Generic Genome Browser: a building block for a model organism system database, Genome Res, 12, 1599, 10.1101/gr.403602 Patterson, 2006, Population structure and eigenanalysis, PLoS Genet, 2, e190, 10.1371/journal.pgen.0020190 Giebel, 1990, A frequent tyrosinase gene mutation in classic, tyrosinase-negative (type IA) oculocutaneous albinism, Proc Natl Acad Sci USA, 87, 3255, 10.1073/pnas.87.9.3255 Newton, 2001, Mutations in the human orthologue of the mouse underwhite gene (uw) underlie a new form of oculocutaneous albinism, OCA4, Am J Hum Genet, 69, 981, 10.1086/324340 Lao, 2007, Signatures of positive selection in genes associated with human skin pigmentation as revealed from analyses of single nucleotide polymorphisms, Ann Hum Genet, 71, 354, 10.1111/j.1469-1809.2006.00341.x Nakayama, 2002, Distinctive distribution of AIM1 polymorphism among major human populations with different skin color, J Hum Genet, 47, 92, 10.1007/s100380200007 Duffy, 2007, A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation, Am J Hum Genet, 80, 241, 10.1086/510885 Flanagan, 2000, Pleiotropic effects of the melanocortin 1 receptor (MC1R) gene on human pigmentation, Hum Mol Genet, 9, 2531, 10.1093/hmg/9.17.2531 Valverde, 1995, Variants of the melanocyte-stimulating hormone receptor gene are associated with red hair and fair skin in humans, Nat Genet, 11, 328, 10.1038/ng1195-328