Dataset Information

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

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.

SUBMITTER: Basu Mallick C

PROVIDER: S-EPMC3820762 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Basu Mallick Chandana C Iliescu Florin Mircea FM Möls Märt M Hill Sarah S Tamang Rakesh R Chaubey Gyaneshwer G Goto Rie R Ho Simon Y W SY Gallego Romero Irene I Crivellaro Federica F Hudjashov Georgi G Rai Niraj N Metspalu Mait M Mascie-Taylor C G Nicholas CG Pitchappan Ramasamy R Singh Lalji L Mirazon-Lahr Marta M Thangaraj Kumarasamy K Villems Richard R Kivisild Toomas T

PLoS genetics 20131107 11

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 pigmen ...[more]

PMID: 24244186

Similar Datasets

Project description:BACKGROUND:The pathogenesis and cardiovascular impact of type 2 diabetes (T2D) may be different in South Asians compared with other ethnic groups. The phenotypic characterization of diabetic cardiomyopathy remains debated and little is known regarding differences in T2D-related cardiovascular remodeling across ethnicities. We aimed to characterize the differences in left ventricular (LV) diastolic and systolic function, LV structure, myocardial tissue characteristics and aortic stiffness between T2D patients and controls and to assess the differences in T2D-related cardiovascular remodeling between South Asians and Europeans. METHODS:T2D patients and controls of South Asian and European descent underwent 3 Tesla cardiovascular magnetic resonance imaging (CMR) and cardiac proton-magnetic resonance spectroscopy (1H-MRS). Differences in cardiovascular parameters between T2D patients and controls were examined using ANCOVA and were reported as mean (95% CI). Ethnic group comparisons in the association of T2D with cardiovascular remodeling were made by adding the interaction term between ethnicity and diabetes status to the model. RESULTS:A total of 131 individuals were included (54 South Asians [50.1?±?8.7 years, 33% men, 33 patients vs. 21 controls) and 77 Europeans (58.8?±?7.0 years, 56% men, 48 patients vs. 29 controls)]. The ratio of the transmitral early and late peak filling rate (E/A) was lower in T2D patients compared with controls, in South Asians [-?0.20 (-?0.36; -?0.03), P?=?0.021] and Europeans [-?0.20 (-?0.36; -?0.04), P?=?0.017], whereas global longitudinal strain and aortic pulse wave velocity were similar. South Asian T2D patients had a higher LV mass [+?22 g (15; 30), P?<?0.001] (P for interaction by ethnicity?=?0.005) with a lower extracellular volume fraction [-?1.9% (-?3.4; -?0.4), P?=?0.013] (P for interaction?=?0.114), whilst European T2D patients had a higher myocardial triglyceride content [+?0.59% (0.35; 0.84), P?=?0.001] (P for interaction?=?0.002) than their control group. CONCLUSIONS:Diabetic cardiomyopathy was characterized by impaired LV diastolic function in South Asians and Europeans. Increased LV mass was solely observed among South Asian T2D patients, whereas differences in myocardial triglyceride content between T2D patients and controls were only present in the European cohort. The diabetic cardiomyopathy phenotype may differ between subsets of T2D patients, for example across ethnicities, and tailored strategies for T2D management may be required.

Dataset Information

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Publications

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets