Dataset Information

Identification of a novel locus associated with skin colour in African-admixed populations.

ABSTRACT: Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ?1?×?10-5 were followed up in 373 African Americans. Fourteen single nucleotide polymorphisms were replicated, of which nine were associated with skin colour at genome-wide significance in a meta-analysis across the two studies. These results validated the association of two previously known skin pigmentation genes, SLC24A5 (minimum p?=?2.62?×?10-14, rs1426654) and SLC45A2 (minimum p?=?9.71?×?10-10, rs16891982), and revealed the intergenic region of BEND7 and PRPF18 as a novel locus associated with this trait (minimum p?=?4.58?×?10-9, rs6602666). The most significant variant within this region is common among African-descent populations but not among Europeans or Native Americans. Our findings support the advantages of analyzing African-admixed populations to discover new genes influencing skin pigmentation.

SUBMITTER: Hernandez-Pacheco N

PROVIDER: S-EPMC5353593 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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Identification of a novel locus associated with skin colour in African-admixed populations.

Hernandez-Pacheco Natalia N Flores Carlos C Alonso Santos S Eng Celeste C Mak Angel C Y AC Hunstman Scott S Hu Donglei D White Marquitta J MJ Oh Sam S SS Meade Kelley K Farber Harold J HJ Avila Pedro C PC Serebrisky Denise D Thyne Shannon M SM Brigino-Buenaventura Emerita E Rodriguez-Cintron William W Sen Saunak S Kumar Rajesh R Lenoir Michael M Rodriguez-Santana Jose R JR Burchard Esteban G EG Pino-Yanes Maria M

Scientific reports 20170316

Skin pigmentation is a complex trait that varies largely among populations. Most genome-wide association studies of this trait have been performed in Europeans and Asians. We aimed to uncover genes influencing skin colour in African-admixed individuals. We performed a genome-wide association study of melanin levels in 285 Hispanic/Latino individuals from Puerto Rico, analyzing 14 million genetic variants. A total of 82 variants with p-value ≤1 × 10<sup>-5</sup> were followed up in 373 African Am ...[more]

PMID: 28300201

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Project description:Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.

Dataset Information

Identification of a novel locus associated with skin colour in African-admixed populations.

Publications

Identification of a novel locus associated with skin colour in African-admixed populations.

Similar Datasets

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