ASHG 2010: Pigmentation genetics

Selected abstracts from the 2010 meeting of the American Society of Human Genetics.

Pigmentation in Britain: Regional patterns and genotype-phenotype correspondence. E. C. Røyrvik1, W. F. Bodmer1,2 1) Clinical Pharmacology, University of Oxford, Oxford, United Kingdom; 2) Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom.

Large differences in external pigmentation are some of the most striking features in human populations, and some of the most notable of these differences are found in hair and eye color in Northwest Europe. These phenotypes are genetically determined, and many associated genetic variants have been identified. To investigate to what extent pigmentation phenotype is predictable from genotype, we have genotyped 2842 locally rooted individuals from different regions of Britain for a subset of these variants, and use their frequencies to estimate hair and eye color in these areas. The results are compared to observed frequencies from two large mid-19th and early 20th century surveys of 9470 British people from the same or adjacent areas.¬ The SNPs used include rs12913832 - a major determinant of brown versus non-brown eye color, and major variants of MC1R that cause red hair. Pairwise comparisons of color categories in the current and 19th/early 20th century local populations were conducted to investigate differences, either diachronic or geographical, between them. There are significant differences between different areas of Britain in terms of pigmentation. North Wales has a significantly higher proportion of dark eyes than the rest of the island, although South Wales also has a comparatively high count. Red hair is approximately equally frequent in all regions; the other main hair shades show a tendency to separate Wales and Southwest England from other areas at a significant level, in particular from East England. We find good general accord between the observed and estimated color frequencies in any given area. Small but regular underestimates of the observed values by the estimated values are likely due to the contribution to any given color category of alleles that are unknown or have a lesser effect, or to uncertainties in effect size of known variants. Our results indicate that average regional hair and eye color have remained relatively stable in Britain over the past century, and support that it is possible to predict normal pigmentation phenotypes from genotype data.

Alleles from SNPs at the SLC24A5 and SLC45A2 genes are associated with the presence of freckles and eye, hair and skin pigmentation in Brazil. C. T. Mendes-Junior1, N. C. A. Fracasso2, L. R. Zanão1, C. C. F. Andrade2, M. S. Silva1, L. A. Marano2, C. E. V. Wiezel2, E. A. Donadi3, A. L. Simões2 1) Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto-SP, Brazil; 2) Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900, Ribeirão Preto-SP, Brazil; 3) Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14048-900, Ribeirão Preto-SP, Brazil.

SNPs from the SLC24A5 (solute carrier family 24, member 5) and SLC45A2 (solute carrier family 45, member 2) genes have been associated with variation in eye, hair, and skin pigmentation across worldwide populations. Protein products of both genes are involved in cross-membrane transport, and their expression in melanocytes are required to regulate melanogenesis and for melanosome maturation. The present study aimed at verifying the influence of the genetic diversity of such genes in the presence of freckles and determination of eye, hair, and skin pigmentation in a highly admixed population sample. The determination of eye, hair, and skin pigmentation of unknown samples found in crime scenes would be of great value for forensic caseworks. To achieve that goal, a SNP from the SLC24A5 gene [rs1426654 G>A (Ala111Thr)] and five SNPs spread across the SLC45A2 gene [rs732740 (intron 1 T>C), rs3776549 (intron 2 G>A), rs250417 (intron 4 G>C), rs16891982 (exon 5 G>C; Leu374Phe), and rs35394 (intron 5 A>G)] were evaluated in 150 unrelated individuals from the Ribeirão Preto area, a city located at the Northwestern region of the São Paulo State, Southeastern Brazil. DNA was extracted by a salting-out procedure and SNPs were genotyped either by PCR-RFLP or Allele-Specific PCR, followed by Polyacrylamide Gel Electrophoresis (PAGE). Even though SNP rs732740 was monomorphic (considering the 99% threshold), alleles from every remaining SNPs presented statistically significant associations with at least one of the four considered morphological features. It is noteworthy that most of the observed associations concerns SNPs rs1426654 (Ala111Thr) and rs16891982 (Leu374Phe), both of them located at the peptide-coding region of SLC24A5 and SLC45A2, respectively. For instance, alleles 111Thr (rs1426654) and 374Phe (rs16891982) were observed in association with fair pigmentation features (like pale skin, green/blue eyes, and/or blond hair), while alleles 111Ala 374Leu are associated with dark pigmentation. The present results corroborate previous findings and emphasize the role played by SNPs at SLC24A5 and SLC45A2 in the determination of pigmentation aspects of human populations. FINANCIAL SUPPORT: This study was supported by CNPq/Brazil (Grant 478843/2009-7).

Genes regulating skin color in Koreans: The Health Twin Study. M. Han1, J. Sung1, Y. M. Song2, K. Lee3, M. Lee1, D. H. Lee1 1) Seoul National University, Seoul, Korea; 2) Department of Family Medicine, Samsung Medical Center, SungKyunKwan University School of Medicine; 3) Department of Family Medicine, Busan Paik Hospital, School of Medicine, Inje University.

Variations in human skin color are but only inborn, not also adaptive traits that correlate closely with the sun’s ultraviolet (UV) radiation. The skin’s pigment is Melanin that protects peoples from the many harmful effects of ultraviolet (UV) rays. But it is very diverse with individual life style besides race. Recently genetic studies have identified a subset of genes influencing the extent of skin pigmentation; MATP, IRF4, TYR, OCA2, and MC1R were associated with skin colors in a Genome-wide association studies (GWAS) in Europian population. But little is known about the genetic regulators in skin pigmentation difference in Asian family-based population. Specific aims of the study was 1) to test whether there are genetic influences on the skin colors of both ultraviolet light(UV)-exposed (cheek) and UV-unexposed (arm, flank) in Asians, and 2) to identify the genes which are responsible for the degree of skin pigmentation in both body areas. A total of 1440 individuals of Korean twins and their families (543 men and 897 women aged from 17 to 80 years, mean age: 44.1 ± 0.4) join this study. The skin surface pigmentation, were measured using MPA 5, Courage-Khazaka electronic. The average skin pigmentation in cheek, arm and flank were 166.01±55.5, 155.48±49.3 and 134.07±51.9. Pearson correlation coefficients between skin brightness on the cheek and arm, the flank and arm, the flank and cheek are respectively 0.62 , 0.47 and 0.35. The heritabilities of skin pigmentation were 0.55 (p = 6.63e-39) for cheek and 0.66 (p = 3.02e-67)for arm, 0.58 (p = 1.00e-44) for flank area. Genome-wide association test was conducted with Affymetrix GeneChip version 6 (with 541,000 effective SNP markers), using FBAT. We identified rs7956106(12, p12.3,) rs12117410(1,-p31.1), rs11162211(1,-p31.1) SNPs associated with the skin pigmentation on the cheek , rs17016276(1,-q32.2), rs2501892(1,+q32.2), rs1542140(1,-q32.3) SNPs on the arm, and rs8060157(16, q12.1), rs9940645(16, +q12.1), SNPs on the flank. While these genes await replication or further validation, we concluded that different sets of genes may regulate the skin pigmentation according to the UV exposure status.

Evidence of selection in the pigmentation genes SLC24A5 in Europeans, East Africans, and Southwest and Central Asians and SLC45A2 in East Asians and Native Americans. M. P. Donnelly, W. C. Speed, A. J. Pakstis, J. R. Kidd, K. K. Kidd Department of Genetics, Yale University School of Medicine, New Haven, CT.

Skin pigmentation is one of the most recognizable human phenotypes and tends to vary on a latitudinal cline, even within Europe. The derived alleles of missense SNPs in SLC24A5 (rs1426654) and SLC45A2 (rs16891982) have both been implicated in light skin pigmentation among Europeans. We have collected data for these markers from 4474 individuals in 107 population samples. The derived alleles of both SNPs were observed at high frequencies throughout Europe, though the derived allele of rs16891982 is found at lower frequencies in Southern Europe. The derived allele of rs1426654 was also found at moderate to high frequencies 2 to 100% in East Africa, Southwest Asia, and Central Asia, whereas the derived allele of rs16891982 was seen at frequencies of 0 to 58% in these populations. At SLC24A5 a single allele of a 13-SNP (including rs1426654) haplotype covering ~146 kb accounts for ~95% of the chromosomes in Europe. At SLC45A2, we saw no significant LD around rs16891982. Using the REHH test, we found strong evidence of selection for the derived allele of rs1426654 in Europe as well as East Africa, Southwest Asia, and Central Asia where it had not previously been seen and were able to confirm the evidence of selection in East Africa using nHS. We saw no or very weak evidence of selection for rs1689192 using REHH or nHS among European and nearby populations. We did find previously unidentified evidence of selection in East Asians and Native Americans at a SNP about 15 kb upstream of SLC45A2. The allele showing evidence of selection at this SNP is found at high to moderate frequencies throughout the world except in Europe where it is virtually absent. Given its location it is likely part of or in LD with an upstream regulatory element upon which selection is/was acting. Taken together these results suggest several conclusions about the evolution of skin pigmentation in humans. First two SNPs shown to play a role in pigmentation in a region of the world can show different distribution patterns Second, it suggests that light skin among Europeans evolved both by means of natural selection and neutral factors. Finally, the evidence of selection in the upstream region of SLC45A2 in East Asians and Native Americans, suggests that though light skin pigmentation likely evolved separately in regions where light skin pigmentation is predominant, the evolution at some genes may have occurred independently through different variants. Funded in part by NIH Grant GM57672.

Contrasting patterns of sequence variation in pigmentation and neutral loci indicate population-level effects of selection. H. Norton1, M. Hammer2 1) ARL-Biotech, Univ Arizona, Tucson, AZ; 2) Department of Ecology and Evolutionary Biology.

While demographic processes affect all regions of the genome in a similar manner, selection should preferentially affect levels of diversity and the site frequency spectrum (SFS) in genic regions relative to neutral regions. Here we compare patterns of variation in ten pigmentation candidate loci to a neutral dataset comprised of 61 loci located in regions of high recombination and far from genes. Both the genic and neutral loci were sequenced in the same panel of 72 African (Biaka, Mandenka, and San) and 80 Non-African (Han Chinese, French Basque, and PNG Highlander) chromosomes. As expected, mean levels of diversity are significantly lower in genic relative to neutral regions (?genic = 0.00072; ?neutral = 0.00113; p < 0.01). Because it is often assumed that pigmentation loci have been affected by purifying selection within Africa and by positive directional selection outside of Africa, we compared the SFS of pigmentation and neutral loci in these regions. We observe a trend towards an excess of rare or singleton alleles (exhibited as negative Tajima’s D and Fu and Li’s D values) consistent with either purifying or directional selection in the genic regions. However, as a class pigmentation loci do not significantly differ from the neutral loci in either Africans (TDpigmentation = -0.80, TDneutral = -0.82, p = 0.92; FLDpigmentation = -1.08, FLDneutral =-1.03 p = 0.90) or non-Africans (TDpigmentation = -0.38, TDneutral = -0.04, p = 0.16; FLDpigmentation = -1.00, FLDneutral =-0.60 p = 0.36). At the population level, only the French Basque showed a significant difference between pigmentation loci and the neutral regions for Tajima’s D (TDpigmentation = -0.30, TDneutral = 0.35, p < 0.05). However, despite the failure of pigmentation loci as class to appear distinct from neutral loci, several individual loci stood out from the neutral regions in population-level comparisons. The gene MATP exhibits an excess of high frequency derived alleles in the French Basque (FWH = -4.11, p < 0.01) consistent with expectations under positive directional selection, while the gene MITF exhibits an excess of rare alleles in the Mandenka population (TD = -1.46, p < 0.05) indicating a role for purifying selection. These results suggest that while selection pressure on pigmentation loci may differ between Africans and non-Africans, the effects of selection on individual genes may have varied among populations within broader geographic regions. Genome Wide Scan of Malignant Melanoma Identifies Additional Pigmentation Gene Influencing Risk. C. I. Amos1, J. E. Lee2, W. V. Chen1, E. Pugh3, K. F. Doheny3, C. C. Laurie4, L.-E. Wang1, Q. Wei1 1) Dept Epidemiology, MD Anderson Cancer Ctr, Houston, TX; 2) Dept Surgery, MD Anderson Cancer Ctr, Houston, TX; 3) Center for Inherited Disease Research, 333 Cassell Drive, Suite 2000, Baltimore, MD; 4) Department of Biostatistics, Box 359461, University of Washington, Seattle, WA.

Malignant melanoma causes 75% of skin-cancer related death and siblings of cases have an approximately 4-fold higher melanoma risk, suggesting the importance of genetic factors in its etiology. We therefore conducted a genome-wide association analysis of melanoma using samples and data from 1781 melanoma cases from M.D. Anderson Cancer Center and 1050 age and sex-matched healthy controls. Samples were anlyzed using an Omni 1M Quad V1-0_B SNP chip and standard quality control filters were applied with assistance from the GENEVA coordinating center including removing SNPs and samples with low call rates (<95% and < 90% respectively), and removing non-Caucasians and genetic outliers. After filtering, 818237 SNPs had minor allele frequency >0.01, passed the Hardy-Weinberg Disequilibrium test (p> 10-5) and were retained for analyses. Analyses were conducted using logistic regression in PLINK. Results identify known causal regions such as MC1R (rs4785751, p=3.4 x 10-10) and CDK2NA region (rs1889680, p=4.89 x 10-7). However, in addition one SNP in HERC2 reaches genome wide significance (rs12913832, p=7.9 x 10-8) and several additional interesting candidate loci are highly suggestive: DACH1 (rs17613530, 5.7 x 10-6) and CSMD1 (rs2617055, p= 5.9 x 10-6). HERC2 influences hair and eye pigmentation (iris color), and skin sensitivity to sun and freckling. We are further investigating the effects of these SNPs according to skin pigmentation type and history of sunburns. These results further expand knowledge about the role of skin pigmentation in determining risk for sporadic melanoma.

Gene mapping study of constitutive skin color in a genetically isolated population. H.-J. Kim1,4, SH. Paik2, H.-Y. Son3, SB. Lee1,4, YS. Ju3,4, JH. Yeon2, SJ. Jo2, J.-S. Seo1,3,4, OS. Kwon2,6, J.-I. Kim3,4,5 1) Department of Biomedical Sciences, Seoul National University Graduate School; 2) Departments of Dermatology, Seoul National University College of Medicine; 3) Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine; 4) Genomic Medicine Institute (GMI), Medical Research Center, Seoul National University; 5) Psoma Therapeutics, Inc., Seoul; 6) Laboratory of Cutaneous Aging and Hair Research, Institute of Dermatological Science, Seoul National University.

To elucidate the responsible genes governing constitutive skin color, we measured the extent of skin pigmentation in buttock, the sun-unexposed area for the life time, and conducted a gene mapping study on skin color in genetically isolated population composed of 344 individuals from 59 families who live in Dashbalbar, Dornod Province, Mongolia. Through the linkage analysis of 1039 short tandem repeat (STR) microsatellite markers, we found novel genomic region regulating constitutive skin color on 11q24.2 with an LOD score of 3.39. Moreover, we found other five candidate regions controlling intrinsic skin color. To test further association in regions of linkage, we selected chromosome 11, 17, and 6 (maximum LOD score > 2.5), and in each chromosome, high linkage peak regions (LOD score >1.5) were analyzed. On linkage region of chromosome 11, we identified 19 significant SNPs (p < 9.29 × 10-6). Further we found two (p =9.74 × 10-7) and one (p=2.00×10-6) significant SNPs on linkage regions of chromosome 17 and chromosome 6, respectively. In that the strongest locus of linkage on 11q24.2 harbors and significant SNP is located adjacent to ST3GAL4, we suggest ST3GAL4 as the novel candidate gene responsible for controlling constitutive skin color. Taken together with our linkage analysis and association study, other candidate genes are DRD2, MPZL3, BRIP1 and ZBTB17.