Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Degang Wu; Jinzhuang Dou; Xiaoran Chai; Claire Bellis; Andreas Wilm; Chih Chuan Shih; Wendy Wei Jia Soon; Nicolas Bertin; Clarabelle Bitong Lin; Chiea Chuen Khor; Michael Degiorgio; Shanshan Cheng; Li Bao; Neerja Karnani; William Ying Khee Hwang; Sonia Davila; Patrick Tan; Asim Shabbir; Angela Moh; Eng-King Tan; Jia Nee Foo; Liuh Ling Goh; Khai Pang Leong; Roger Foo; Carolyn Su Ping Lam; Arthur Mark Richards; Ching-Yu Cheng; Tin Aung; Tien Yin Wong; Huck Hui Ng; Jianjun Liu; Chaolong Wang; Matthew Andrew Ackers-Johnson; Edita Aliwarga; Kenneth Hon Kim Ban; Denis Bertrand; John Chambers; Dana Leng Hui Chan; Cheryl Xue Li Chan; Miao Li Chee; Miao Ling Chee; Pauline Chen; Yunxin Chen; Elaine Guo Yan Chew; Wen Jie Chew; Lynn Hui Yun Chiam; Jenny Pek Ching Chong; Ivan Chua; Stuart Cook; Wei Dai; Rajkumar Dorajoo; Chuan-Sheng Foo; Rick Siow Mong Goh; Axel Hillmer; Ishak Irwan; Fazlur Jaufeerally; Asif Javed; Justin Jeyakani; John Tat Hung Koh; Jia Yu Koh; Pavitra Krishnaswamy; Jyn Ling Kuan; Neelam Kumari; Ai Shan Lee; Seow Eng Lee; Sheldon Lee; Yen Ling Lee; See Ting Leong; Zheng Li; Peter Yiqing Li; Jun Xian Liew; Oi Wah Liew; Su Chi Lim; Weng Khong Lim; Chia Wei Lim; Tingsen Benson Lim; Choon Kiat Lim; Seet Yoong Loh; Au Wing Lok; Calvin W.L. Chin; Shivani Majithia; Sebastian Maurer-Stroh; Wee Yang Meah; Shi Qi Mok; Niranjan Nargarajan; Pauline Ng; Sarah Ng; Zhenyuan Ng; Jessica Yan Xia Ng; Ebonne Ng; Shi Ling Ng; Simon Nusinovici; Chin Thing Ong; Bangfen Pan; Vincent Pedergnana; Stanley Poh; Shyam Prabhakar; Kumar Prakash; Ivy Quek; Charumathi Sabanayagam; Wei Qiang See; Yee Yen Sia; Xueling Sim; Wey Cheng Sim; Jimmy So; Dinna K.N. Soon; E. Shyong Tai; Nicholas Tan; Louis C.S. Tan; Hong Chang Tan; Wilson Lek Wen Tan; Moses Tandiono; Amanda Tay; Sahil Thakur; Yih Chung Tham; Zenia Tiang; Grace Li-Xian Toh; Pi Kuang Tsai; Lavanya Veeravalli; Chandra Verma; Ling Wang; Min Rui Wang; Wing-Cheong Wong; Zhicheng Xie; Khung Keong Yeo; Liang Zhang; Weiwei Zhai; Yi Zhao

doi:10.1016/j.cell.2019.09.019

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Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Journal article

Open access

Peer reviewed

Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore

Degang Wu, Jinzhuang Dou, Xiaoran Chai, Claire Bellis, Andreas Wilm, Chih Chuan Shih, Wendy Wei Jia Soon, Nicolas Bertin, Clarabelle Bitong Lin, Chiea Chuen Khor, …

Cell, Vol.179(3), pp.736-749.e15

10/2019

DOI: https://doi.org/10.1016/j.cell.2019.09.019

PMID: 31626772

Abstract

Asian populations

GWAS

admixture

demographic history

genetic diversity

imputation

natural selection

population structure

precision medicine

whole-genome sequencing

Asians

Female

Singapore

Whole Genome Sequencing

Genetics, Population

Genome, Human

Genotype

Humans

Malaysia

Male

Polymorphism, Single Nucleotide

Selection, Genetic

Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, we found 98.3 million SNPs and small insertions or deletions, over half of which are novel. Population structure analysis demonstrated great representation of Asian genetic diversity by three ethnicities in Singapore and revealed a Malay-related novel ancestry component. Furthermore, demographic inference suggested that Malays split from Chinese ∼24,800 years ago and experienced significant admixture with East Asians ∼1,700 years ago, coinciding with the Austronesian expansion. Additionally, we identified 20 candidate loci for natural selection, 14 of which harbored robust associations with complex traits and diseases. Finally, we show that our data can substantially improve genotype imputation in diverse Asian and Oceanian populations. These results highlight the value of our data as a resource to empower human genetics discovery across broad geographic regions.

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Title: Large-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore
Creators - without role: Degang Wu - Huazhong University of Science and Technology
Jinzhuang Dou - Agency for Science, Technology and Research
Xiaoran Chai - Agency for Science, Technology and Research
Claire Bellis - Queensland University of Technology
Andreas Wilm - Agency for Science, Technology and Research
Chih Chuan Shih - Agency for Science, Technology and Research
Wendy Wei Jia Soon - Agency for Science, Technology and Research
Nicolas Bertin - Genome Institute of Singapore
Clarabelle Bitong Lin - Agency for Science, Technology and Research
Chiea Chuen Khor - Agency for Science, Technology and Research
Michael Degiorgio - Florida Atlantic University
Shanshan Cheng - Huazhong University of Science and Technology
Li Bao - Huazhong University of Science and Technology
Neerja Karnani - Singapore Institute for Clinical Sciences
William Ying Khee Hwang - National Cancer Centre Singapore
Sonia Davila - SingHealth
Patrick Tan - National University Cancer Institute, Singapore
Asim Shabbir - National University Health System
Angela Moh - Khoo Teck Puat Hospital
Eng-King Tan - Duke-NUS Medical School
Jia Nee Foo - Nanyang Technological University
Liuh Ling Goh - Tan Tock Seng Hospital
Khai Pang Leong - Tan Tock Seng Hospital
Roger Foo - National University Heart Centre Singapore
Carolyn Su Ping Lam - National Heart Centre Singapore
Arthur Mark Richards - University of Otago
Ching-Yu Cheng - Singapore Eye Research Institute
Tin Aung - Singapore National Eye Center
Tien Yin Wong - Singapore Eye Research Institute
Huck Hui Ng - Genome Institute of Singapore
Jianjun Liu - National University of Singapore
Chaolong Wang - Agency for Science, Technology and Research
Matthew Andrew Ackers-Johnson
Edita Aliwarga
Kenneth Hon Kim Ban
Denis Bertrand
John Chambers
Dana Leng Hui Chan
Cheryl Xue Li Chan
Miao Li Chee
Miao Ling Chee
Pauline Chen
Yunxin Chen
Elaine Guo Yan Chew
Wen Jie Chew
Lynn Hui Yun Chiam
Jenny Pek Ching Chong
Ivan Chua
Stuart Cook
Wei Dai
Rajkumar Dorajoo
Chuan-Sheng Foo
Rick Siow Mong Goh
Axel Hillmer
Ishak Irwan
Fazlur Jaufeerally
Asif Javed
Justin Jeyakani
John Tat Hung Koh
Jia Yu Koh
Pavitra Krishnaswamy
Jyn Ling Kuan
Neelam Kumari
Ai Shan Lee
Seow Eng Lee
Sheldon Lee
Yen Ling Lee
See Ting Leong
Zheng Li
Peter Yiqing Li
Jun Xian Liew
Oi Wah Liew
Su Chi Lim
Weng Khong Lim
Chia Wei Lim
Tingsen Benson Lim
Choon Kiat Lim
Seet Yoong Loh
Au Wing Lok
Calvin W.L. Chin
Shivani Majithia
Sebastian Maurer-Stroh
Wee Yang Meah
Shi Qi Mok
Niranjan Nargarajan
Pauline Ng
Sarah Ng
Zhenyuan Ng
Jessica Yan Xia Ng
Ebonne Ng
Shi Ling Ng
Simon Nusinovici
Chin Thing Ong
Bangfen Pan
Vincent Pedergnana - Université de Montpellier, Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle - MIVEGEC
Stanley Poh
Shyam Prabhakar
Kumar Prakash
Ivy Quek
Charumathi Sabanayagam
Wei Qiang See
Yee Yen Sia
Xueling Sim
Wey Cheng Sim
Jimmy So
Dinna K.N. Soon
E. Shyong Tai
Nicholas Tan
Louis C.S. Tan
Hong Chang Tan
Wilson Lek Wen Tan
Moses Tandiono
Amanda Tay
Sahil Thakur
Yih Chung Tham
Zenia Tiang
Grace Li-Xian Toh
Pi Kuang Tsai
Lavanya Veeravalli
Chandra Verma
Ling Wang
Min Rui Wang
Wing-Cheong Wong
Zhicheng Xie
Khung Keong Yeo
Liang Zhang
Weiwei Zhai
Yi Zhao
Publication Details: Cell, Vol.179(3), pp.736-749.e15
Identifiers: 9942009309311
Academic Unit: Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle - MIVEGEC
Language: English
Resource Type: Journal article
Local Fields: hal-03692183