A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, with little known about SV diversity in other ancestries, particularly from Asia. Here, we present a WGS catalogue of 73,035 SVs from 8392 Singaporeans of East Asian, Southeast Asian and South Asian ancestries, of which ~65% (47,770 SVs) are novel. We show that Asian populations can be stratified by their global SV patterns and identified 42,239 novel SVs that are specific to Asian populations. 52% of these novel SVs are restricted to one of the three major ancestry groups studied (Indian, Chinese or Malay). We uncovered SVs affecting major clinically actionable loci. Lastly, by identifying SVs in linkage disequilibrium with single-nucleotide variants, we demonstrate the utility of our SV catalogue in the fine-mapping of Asian GWAS variants and identification of potential causative variants. These results augment our knowledge of structural variation across human populations, thereby reducing current ancestry biases in global references of genetic variation afflicting equity, diversity and inclusion in genetic research.

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Journal
Nature Communications
Published
2024-11-04
DOI
https://doi.org/10.1038/s41467-024-53620-8
Citations
5
Primary Topic
Genetic Associations and Epidemiology
Type
article
Field-Weighted Citation Impact
2.75

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article

A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Justin Jeyakani, Paul Eillot, Rob M. van Dam, Patrick Tan et al.
5 citations
Nature Communications
Genetic Associations and Epidemiology
2.75
article

A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Justin Jeyakani, Paul Eillot, Rob M. van Dam, Patrick Tan, Hong Kiat Ng, Miao Ling Chee, Xueling Sim, Charumathi Sabanayagam, Yap Seng Chong, Johan G. Eriksson, Pi Kuang Tsai, Chia Wei Lim, Wing‐Kin Sung, Theresia Handayani Mina, Khung Keong Yeo, Li-xian Grace Toh, John C. Chambers, Tin Aung, Wen Jie Chew, Shyam Prabhakar, Chee Jian Pua, Ching‐Yu Cheng, Wey Ching Sim, Raghavan Lavanya, Sonia Dávila, E Shyong Tai, Calvin Chin, Khai Pang Leong, Maxime Hebrard, Dorrain Yanwen Low, Eng Sing Lee, Liuh Ling Goh, Darwin Tay, Jin Fang Chai, Peter D. Gluckman, Hengtong Li, Kok Hian Tan, Nilanjana Sadhu, Elio Ríboli, Joanna Tan, Stuart A. Cook, Weng Khong Lim, Tien Yin Wong, Yung Seng Lee, Fabian Yap, Joanne Ngeow, Neerja Karnani, Yih Chung Tham, Nicolas Bertin, Jack Ling Ow, Shimin Ang, Chengxi Yang, Ramesh Rajaby, Jianjun Liu, Xiaoyan Wang, Zhihui Li, Jimmy Lee, Ye An Tan, Miao Li Chee, Mar Gonzalez Porta, Rodrigo Toro Jimenez, Tock Han Lim, Yik Ying Teo, Pritesh Rajesh Jain, Renyi Teo
article en
5 citations

Abstract

Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, with little known about SV diversity in other ancestries, particularly from Asia. Here, we present a WGS catalogue of 73,035 SVs from 8392 Singaporeans of East Asian, Southeast Asian and South Asian ancestries, of which ~65% (47,770 SVs) are novel. We show that Asian populations can be stratified by their global SV patterns and identified 42,239 novel SVs that are specific to Asian populations. 52% of these novel SVs are restricted to one of the three major ancestry groups studied (Indian, Chinese or Malay). We uncovered SVs affecting major clinically actionable loci. Lastly, by identifying SVs in linkage disequilibrium with single-nucleotide variants, we demonstrate the utility of our SV catalogue in the fine-mapping of Asian GWAS variants and identification of potential causative variants. These results augment our knowledge of structural variation across human populations, thereby reducing current ancestry biases in global references of genetic variation afflicting equity, diversity and inclusion in genetic research.

Nature CommunicationsVol. 15(1)
Agency for Science, Technology and Research (SG), Qatar Airways (Qatar) (QA), Milken Institute (US), Harvard University (US), Bunkyo University (JP), University of Auckland (NZ), SingHealth (SG), National University of Singapore (SG), Nanyang Technological University (SG), Chinese University of Hong Kong (HK), Singapore National Eye Center (SG), Tan Tock Seng Hospital (SG), SingHealth Duke-NUS Academic Medical Centre (SG), Singapore Institute for Clinical Sciences (SG), National University Cancer Institute, Singapore (SG), Nanyang Academy of Fine Arts (SG), KK Women's and Children's Hospital (SG), Singapore Eye Research Institute (SG), Duke-NUS Medical School (SG), Sidra Medical and Research Center (QA), National Cancer Centre Singapore (SG), Institute of Mental Health (SG), National University Hospital (SG), National Heart Centre Singapore (SG), Bioinformatics Institute (SG), National University Health System (SG), A*STAR Graduate Academy (SG), Imperial College London (GB), Genome Institute of Singapore (SG)
Lee Foundation, Duke-NUS Medical School, Tanoto Foundation, National Research Foundation, Agency for Science, Technology and Research, National University of Singapore, Singapore Institute for Clinical Sciences, National Research Foundation Singapore, Singapore Eye Research Institute, Nanyang Technological University, Ministerio de Economía y Competitividad, National University Health System, Medical Research Council, National Medical Research Council, Lee Kong Chian School of Medicine, Nanyang Technological University, Biomedical Research Council
Reduced inequalities
Openalex Percentile: Top 9%
Genetic Associations and Epidemiology
2.75
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