Dataset Information

Characterising private and shared signatures of positive selection in 37 Asian populations.

ABSTRACT: The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

SUBMITTER: Liu X

PROVIDER: S-EPMC5386408 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Characterising private and shared signatures of positive selection in 37 Asian populations.

Liu Xuanyao X Lu Dongsheng D Saw Woei-Yuh WY Shaw Philip J PJ Wangkumhang Pongsakorn P Ngamphiw Chumpol C Fucharoen Suthat S Lert-Itthiporn Worachart W Chin-Inmanu Kwanrutai K Chau Tran Nguyen Bich TN Anders Katie K Kasturiratne Anuradhani A de Silva H Janaka HJ Katsuya Tomohiro T Kimura Ryosuke R Nabika Toru T Ohkubo Takayoshi T Tabara Yasuharu Y Takeuchi Fumihiko F Yamamoto Ken K Yokota Mitsuhiro M Mamatyusupu Dolikun D Yang Wenjun W Chung Yeun-Jun YJ Jin Li L Hoh Boon-Peng BP Wickremasinghe Ananda R AR Ong RickTwee-Hee RH Khor Chiea-Chuen CC Dunstan Sarah J SJ Simmons Cameron C Tongsima Sissades S Suriyaphol Prapat P Kato Norihiro N Xu Shuhua S Teo Yik-Ying YY

European journal of human genetics : EJHG 20170118 4

The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 1 ...[more]

PMID: 28098149

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Project description:BackgroundCurrently, there is very limited knowledge about the genes involved in normal pigmentation variation in East Asian populations. We carried out a genome-wide scan of signatures of positive selection using the 1000 Genomes Phase I dataset, in order to identify pigmentation genes showing putative signatures of selective sweeps in East Asia. We applied a broad range of methods to detect signatures of selection including: 1) Tests designed to identify deviations of the Site Frequency Spectrum (SFS) from neutral expectations (Tajima's D, Fay and Wu's H and Fu and Li's D* and F*), 2) Tests focused on the identification of high-frequency haplotypes with extended linkage disequilibrium (iHS and Rsb) and 3) Tests based on genetic differentiation between populations (LSBL). Based on the results obtained from a genome wide analysis of 25 kb windows, we constructed an empirical distribution for each statistic across all windows, and identified pigmentation genes that are outliers in the distribution.ResultsOur tests identified twenty genes that are relevant for pigmentation biology. Of these, eight genes (ATRN, EDAR, KLHL7, MITF, OCA2, TH, TMEM33 and TRPM1,) were extreme outliers (top 0.1% of the empirical distribution) for at least one statistic, and twelve genes (ADAM17, BNC2, CTSD, DCT, EGFR, LYST, MC1R, MLPH, OPRM1, PDIA6, PMEL (SILV) and TYRP1) were in the top 1% of the empirical distribution for at least one statistic. Additionally, eight of these genes (BNC2, EGFR, LYST, MC1R, OCA2, OPRM1, PMEL (SILV) and TYRP1) have been associated with pigmentary traits in association studies.ConclusionsWe identified a number of putative pigmentation genes showing extremely unusual patterns of genetic variation in East Asia. Most of these genes are outliers for different tests and/or different populations, and have already been described in previous scans for positive selection, providing strong support to the hypothesis that recent selective sweeps left a signature in these regions. However, it will be necessary to carry out association and functional studies to demonstrate the implication of these genes in normal pigmentation variation.

Dataset Information

Characterising private and shared signatures of positive selection in 37 Asian populations.

Publications

Characterising private and shared signatures of positive selection in 37 Asian populations.

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