A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Joanna Hui Juan Tan, Zhihui Li, Mar Gonzalez Porta, Ramesh Rajaby, Weng Khong Lim, Ye An Tan, Rodrigo Toro Jimenez, Renyi Teo, Maxime Hebrard, Jack Ling Ow, Shimin Ang, Justin Jeyakani, Yap Seng Chong, Tock Han Lim, Liuh Ling Goh, Yih Chung Tham, Khai Pang Leong, Calvin Woon Loong Chin, Sonia Davila, Neerja Karnani, Ching-Yu Cheng, John Chambers, E. Shyong Tai, Jianjun Liu, Xueling Sim, Wing Kin Sung, Shyam Prabhakar (), Patrick Tan () and Nicolas Bertin ()
Additional contact information
Joanna Hui Juan Tan: Technology and Research
Zhihui Li: Technology and Research
Mar Gonzalez Porta: Technology and Research
Ramesh Rajaby: Technology and Research
Weng Khong Lim: Technology and Research
Ye An Tan: National University of Singapore and National University Health System
Rodrigo Toro Jimenez: Technology and Research
Renyi Teo: Technology and Research
Maxime Hebrard: Technology and Research
Jack Ling Ow: Technology and Research
Shimin Ang: Technology and Research
Justin Jeyakani: Technology and Research
Yap Seng Chong: National University of Singapore
Tock Han Lim: National Healthcare Group
Liuh Ling Goh: Tan Tock Seng Hospital
Yih Chung Tham: Singapore National Eye Centre
Khai Pang Leong: Tan Tock Seng Hospital
Calvin Woon Loong Chin: National Heart Centre Singapore
Sonia Davila: Duke-NUS Medical School
Neerja Karnani: Singapore Institute for Clinical Sciences
Ching-Yu Cheng: Singapore National Eye Centre
John Chambers: Lee Kong Chian School of Medicine
E. Shyong Tai: Duke-NUS Medical School
Jianjun Liu: Technology and Research (A*STAR)
Xueling Sim: National University of Singapore and National University Health System
Wing Kin Sung: Technology and Research
Shyam Prabhakar: Technology and Research
Patrick Tan: Technology and Research
Nicolas Bertin: Technology and Research

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-53620-8

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