South Asian medical cohorts reveal strong founder effects and high rates of homozygosity
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Published:2023-06-08
Issue:1
Volume:14
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Wall Jeffrey D.ORCID, Sathirapongsasuti J. Fah, Gupta Ravi, Rasheed Asif, Venkatesan RadhaORCID, Belsare SaurabhORCID, Menon Ramesh, Phalke Sameer, Mittal Anuradha, Fang JohnORCID, Tanneeru Deepak, Deshmukh Manjari, Bassi AkshiORCID, Robinson JacquelineORCID, Chaudhary Ruchi, Murugan Sakthivel, ul-Asar Zameer, Saleem Imran, Ishtiaq Unzila, Fatima Areej, Sheikh Saqib Shafi, Hameed Shahid, Ishaq Mohammad, Rasheed Syed Zahed, Memon Fazal-ur-Rehman, Jalal Anjum, Abbas Shahid, Frossard Philippe, Fuchsberger Christian, Forer LukasORCID, Schoenherr Sebastian, Bei Qixin, Bhangale Tushar, Tom Jennifer, Gadde Santosh Gopi Krishna, B V Priya, Naik Naveen Kumar, Wang MinxianORCID, Kwok Pui-YanORCID, Khera Amit V.ORCID, Lakshmi B. R., Butterworth Adam S.ORCID, Chowdhury Rajiv, Danesh John, di Angelantonio Emanuele, Naheed Aliya, Goyal Vinay, Kandadai Rukmini M., Kumar Hrishikesh, Borgohain Rupam, Mukherjee Adreesh, Wadia Pettarusp M., Yadav Ravi, Desai SoahamORCID, Kumar NirajORCID, Biswas Atanu, Pal Pramod Kumar, Muthane Uday B., Das Shymal K., Ramprasad Vedam L., Kukkle Prashanth L.ORCID, Seshagiri Somasekar, Kathiresan Sekar, Ghosh Arkasubhra, Mohan V.ORCID, Saleheen DanishORCID, Stawiski Eric W.ORCID, Peterson Andrew S.
Abstract
AbstractThe benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
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