The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent
Publication Date
November 07, 2013
Journal
PLOS Genetics
Authors
Chandana Basu Mallick, Florin Mircea Iliescu, Märt Möls, Sarah Hill, et al
Volume
9
Issue
11
Pages
e1003912
DOI
https://dx.plos.org/10.1371/journal.pgen.1003912
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1003912
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24244186
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820762
Europe PMC
http://europepmc.org/abstract/MED/24244186
Web of Science
000330369000014
Scopus
84888227090
Mendeley
http://www.mendeley.com/research/light-skin-allele-slc24a5-south-asians-europeans-shares-identity-descent
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{"title"=>"The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent", "type"=>"journal", "authors"=>[{"first_name"=>"Chandana", "last_name"=>"Basu Mallick", "scopus_author_id"=>"55938312400"}, {"first_name"=>"Florin Mircea", "last_name"=>"Iliescu", "scopus_author_id"=>"55937396000"}, {"first_name"=>"Märt", "last_name"=>"Möls", "scopus_author_id"=>"6602364118"}, {"first_name"=>"Sarah", "last_name"=>"Hill", "scopus_author_id"=>"56729786400"}, {"first_name"=>"Rakesh", "last_name"=>"Tamang", "scopus_author_id"=>"26532059600"}, {"first_name"=>"Gyaneshwer", "last_name"=>"Chaubey", "scopus_author_id"=>"57199506601"}, {"first_name"=>"Rie", "last_name"=>"Goto", "scopus_author_id"=>"24773126600"}, {"first_name"=>"Simon Y.W.", "last_name"=>"Ho", "scopus_author_id"=>"7403716888"}, {"first_name"=>"Irene", "last_name"=>"Gallego Romero", "scopus_author_id"=>"23111689800"}, {"first_name"=>"Federica", "last_name"=>"Crivellaro", "scopus_author_id"=>"19638325100"}, {"first_name"=>"Georgi", "last_name"=>"Hudjashov", "scopus_author_id"=>"8937651700"}, {"first_name"=>"Niraj", "last_name"=>"Rai", "scopus_author_id"=>"55777761600"}, {"first_name"=>"Mait", "last_name"=>"Metspalu", "scopus_author_id"=>"8937652900"}, {"first_name"=>"C. G.Nicholas", "last_name"=>"Mascie-Taylor", "scopus_author_id"=>"57197146583"}, {"first_name"=>"Ramasamy", "last_name"=>"Pitchappan", "scopus_author_id"=>"6701316953"}, {"first_name"=>"Lalji", "last_name"=>"Singh", "scopus_author_id"=>"55628587703"}, {"first_name"=>"Marta", "last_name"=>"Mirazon-Lahr", "scopus_author_id"=>"6603894491"}, {"first_name"=>"Kumarasamy", "last_name"=>"Thangaraj", "scopus_author_id"=>"6603011487"}, {"first_name"=>"Richard", "last_name"=>"Villems", "scopus_author_id"=>"7004629464"}, {"first_name"=>"Toomas", "last_name"=>"Kivisild", "scopus_author_id"=>"55804366500"}], "year"=>2013, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84888227090", "doi"=>"10.1371/journal.pgen.1003912", "pui"=>"370341814", "pmid"=>"24244186", "scopus"=>"2-s2.0-84888227090", "issn"=>"15537390", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)"}, "id"=>"2463b89d-5f40-3d28-b7ae-8ea95d0c2875", "abstract"=>"Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.", "link"=>"http://www.mendeley.com/research/light-skin-allele-slc24a5-south-asians-europeans-shares-identity-descent", "reader_count"=>94, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Librarian"=>2, "Student > Doctoral Student"=>2, "Researcher"=>20, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>9, "Student > Master"=>11, "Other"=>5, "Student > Bachelor"=>10, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>4, "Librarian"=>2, "Student > Doctoral Student"=>2, "Researcher"=>20, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1272031"], "description"=>"<p>Exons of the gene are shown in yellow, introns in blue and 5′ flanking region in pink. The black lines underneath the gene show the regions resequenced in this study (total of 11741 bp) spanning 25674 bp. rs1426654 is the functional SNP located in the third exon.</p>", "links"=>[], "tags"=>["48409019"], "article_id"=>844309, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003912.g003", "stats"=>{"downloads"=>7, "page_views"=>105, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_of_the_human_SLC24A5_gene_Chromosome_15q21_1_48409019_to_48434692_/844309", "title"=>"The structure of the human <i>SLC24A5</i> gene (Chromosome 15q21.1, 48409019 to 48434692).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-07 03:43:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1272030"], "description"=>"<p>The map has been drawn based on rs1426654-A allele frequencies of 2763 subjects obtained from published datasets (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912#pgen.1003912.s012\" target=\"_blank\">Table S7</a>) and 1446 individuals from the present study (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912#pgen.1003912.s010\" target=\"_blank\">Table S5</a>). Red dots correspond to the sampling locations.</p>", "links"=>[], "tags"=>["illustrating", "geospatial", "snp", "rs1426654-a", "allele"], "article_id"=>844308, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003912.g002", "stats"=>{"downloads"=>3, "page_views"=>132, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Isofrequency_map_illustrating_the_geospatial_distribution_of_SNP_rs1426654_A_allele_across_the_world_/844308", "title"=>"Isofrequency map illustrating the geospatial distribution of SNP rs1426654-A allele across the world.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-07 03:43:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1272038", "https://ndownloader.figshare.com/files/1272039", "https://ndownloader.figshare.com/files/1272040", "https://ndownloader.figshare.com/files/1272041", "https://ndownloader.figshare.com/files/1272042", "https://ndownloader.figshare.com/files/1272043", "https://ndownloader.figshare.com/files/1272044", "https://ndownloader.figshare.com/files/1272045", "https://ndownloader.figshare.com/files/1272046", "https://ndownloader.figshare.com/files/1272047", "https://ndownloader.figshare.com/files/1272048", "https://ndownloader.figshare.com/files/1272049", "https://ndownloader.figshare.com/files/1272050", "https://ndownloader.figshare.com/files/1272051", "https://ndownloader.figshare.com/files/1272052", "https://ndownloader.figshare.com/files/1272053", "https://ndownloader.figshare.com/files/1272054", "https://ndownloader.figshare.com/files/1272055", "https://ndownloader.figshare.com/files/1272056", "https://ndownloader.figshare.com/files/1272057"], "description"=>"<div><p>Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of <i>SLC24A5</i> accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of <i>SLC24A5</i> in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.</p></div>", "links"=>[], "tags"=>["allele", "asians", "europeans", "shares", "descent"], "article_id"=>844316, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003912.s001", "https://dx.doi.org/10.1371/journal.pgen.1003912.s002", "https://dx.doi.org/10.1371/journal.pgen.1003912.s003", "https://dx.doi.org/10.1371/journal.pgen.1003912.s004", "https://dx.doi.org/10.1371/journal.pgen.1003912.s005", "https://dx.doi.org/10.1371/journal.pgen.1003912.s006", "https://dx.doi.org/10.1371/journal.pgen.1003912.s007", "https://dx.doi.org/10.1371/journal.pgen.1003912.s008", "https://dx.doi.org/10.1371/journal.pgen.1003912.s009", "https://dx.doi.org/10.1371/journal.pgen.1003912.s010", "https://dx.doi.org/10.1371/journal.pgen.1003912.s011", "https://dx.doi.org/10.1371/journal.pgen.1003912.s012", "https://dx.doi.org/10.1371/journal.pgen.1003912.s013", "https://dx.doi.org/10.1371/journal.pgen.1003912.s014", "https://dx.doi.org/10.1371/journal.pgen.1003912.s015", "https://dx.doi.org/10.1371/journal.pgen.1003912.s016", "https://dx.doi.org/10.1371/journal.pgen.1003912.s017", "https://dx.doi.org/10.1371/journal.pgen.1003912.s018", "https://dx.doi.org/10.1371/journal.pgen.1003912.s019", "https://dx.doi.org/10.1371/journal.pgen.1003912.s020"], "stats"=>{"downloads"=>41, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Light_Skin_Allele_of_SLC24A5_in_South_Asians_and_Europeans_Shares_Identity_by_Descent/844316", "title"=>"The Light Skin Allele of <i>SLC24A5</i> in South Asians and Europeans Shares Identity by Descent", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-11-07 03:43:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1272033"], "description"=>"<p>The upper triangle of the matrix (green) shows average pairwise differences between populations (PiXY). The average number of pairwise differences (PiX) within each population is shown along the diagonal (orange). The lower triangle of the matrix (blue) shows differences between populations based on Nei's distance, i.e., corrected average pairwise differences (PiXY−(PiX+PiY)/2).</p>", "links"=>[], "tags"=>["intra-", "inter-population", "pairwise", "differences"], "article_id"=>844311, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003912.g004", "stats"=>{"downloads"=>2, "page_views"=>83, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_showing_the_intra_and_inter_population_variation_measured_by_average_pairwise_sequence_differences_of_the_SLC24A5_gene_/844311", "title"=>"Heat map showing the intra- and inter-population variation measured by average pairwise sequence differences of the <i>SLC24A5</i> gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-07 03:43:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1272034"], "description"=>"<p>Global range of human skin pigmentation assessed by the melanin index (MI).</p>", "links"=>[], "tags"=>["pigmentation", "melanin"], "article_id"=>844312, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003912.t001", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_range_of_human_skin_pigmentation_assessed_by_the_melanin_index_MI_/844312", "title"=>"Global range of human skin pigmentation assessed by the melanin index (MI).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-07 03:43:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/1272028"], "description"=>"<p>(A) Distribution of melanin index (MI) in 1228 individuals of Cohort A. The two dotted black lines represent approximately 10% thresholds for the low (MI<38) and high (MI>50) MI groups, which were used to assess genotype-phenotype association using a logistic regression model. (B) Distribution of mean melanin index for the genotypes of rs1426654. The mean melanin indices for each genotype, as obtained separetely for males and females are shown together with their 95% confidence intervals, as estimated by multiple imputation model (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003912#pgen.1003912.s008\" target=\"_blank\">Table S3A</a>).</p>", "links"=>[], "tags"=>["rs1426654", "genotypes", "melanin"], "article_id"=>844307, "categories"=>["Biological Sciences", "Science Policy", "Ecology", "Earth and Environmental Sciences"], "users"=>["Chandana Basu Mallick", "Florin Mircea Iliescu", "Märt Möls", "Sarah Hill", "Rakesh Tamang", "Gyaneshwer Chaubey", "Rie Goto", "Simon Y. W. Ho", "Irene Gallego Romero", "Federica Crivellaro", "Georgi Hudjashov", "Niraj Rai", "Mait Metspalu", "C. G. Nicholas Mascie-Taylor", "Ramasamy Pitchappan", "Lalji Singh", "Marta Mirazon-Lahr", "Kumarasamy Thangaraj", "Richard Villems", "Toomas Kivisild"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003912.g001", "stats"=>{"downloads"=>6, "page_views"=>130, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_of_rs1426654_genotypes_with_melanin_index_/844307", "title"=>"Association of rs1426654 genotypes with melanin index.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-07 03:43:59"}

PMC Usage Stats | Further Information

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Relative Metric

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