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Eur J Hum Genet. 2017 Apr;25(4):499-508. doi: 10.1038/ejhg.2016.181. Epub 2017 Jan 18.

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

Author information

1
NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.
2
Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
3
Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
4
Life Sciences Institute, National University of Singapore, Singapore, Singapore.
5
National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand.
6
Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.
7
Faculty of Science, Molecular Medicine Graduate Programme, Mahidol University, Bangkok, Thailand.
8
Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
9
Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam.
10
Nuffield Department of Clinical Medicine, Centre for Tropical Medicine, University of Oxford, Oxford, UK.
11
Department of Public Health, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
12
Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
13
Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan.
14
Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan.
15
Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan.
16
Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan.
17
Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
18
Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan.
19
Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan.
20
Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.
21
College of the Life Sciences and Technology, Xinjiang University, Urumqi, China.
22
Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, YinchuanChina.
23
Department of Microbiology, Integrated Research Center for Genome Polymorphism, The Catholic University Medical College, Seoul, Korea.
24
State Key Laboratory of Genetic Engineering and Ministry of Education (MOE), Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
25
Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia.
26
Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.
27
The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
28
Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia.
29
Institute of Personalized Genomics and Gene Therapy (IPGG), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
30
School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.
31
Collaborative Innovation Center of Genetics and Development, Shanghai, China.
32
Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.

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.

PMID:
28098149
PMCID:
PMC5386408
DOI:
10.1038/ejhg.2016.181
[Indexed for MEDLINE]
Free PMC Article

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