South Asian medical cohorts reveal strong founder effects and high rates of homozygosity.

Humans Asian People / genetics Bangladesh Founder Effect Homozygote India Pakistan South Asian People

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
08 06 2023
Historique:
received: 08 09 2021
accepted: 15 05 2023
medline: 12 6 2023
pubmed: 9 6 2023
entrez: 8 6 2023
Statut: epublish

Résumé

The 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.

Identifiants

DOI: 10.1038/s41467-023-38766-1 PMID: 37291107 PMC: PMC10250394
pubmed: 37291107
doi: 10.1038/s41467-023-38766-1
pii: 10.1038/s41467-023-38766-1
pmc: PMC10250394
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3377

Subventions

Organisme : NHGRI NIH HHS
ID : R01 HG010689
Pays : United States
Organisme : NHGRI NIH HHS
ID : K08 HG010155
Pays : United States
Organisme : NHGRI NIH HHS
ID : U01 HG011719
Pays : United States
Organisme : NHGRI NIH HHS
ID : UM1 HG008895
Pays : United States

Informations de copyright

© 2023. The Author(s).

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Auteurs

Jeffrey D Wall (JD)

Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA. jeffwall.genetics@gmail.com.
Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA. jeffwall.genetics@gmail.com.
ORCID: 0000-0001-5066-1235

J Fah Sathirapongsasuti (JF)

MedGenome Inc., Foster City, CA, 94404, USA.
GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.

Ravi Gupta (R)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Asif Rasheed (A)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Radha Venkatesan (R)

Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India.
ORCID: 0000-0002-4281-0250

Saurabh Belsare (S)

Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
ORCID: 0000-0002-8148-1867

Ramesh Menon (R)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Sameer Phalke (S)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Anuradha Mittal (A)

Thermo Fisher Scientific, Santa Clara, CA, 95051, USA.

John Fang (J)

Thermo Fisher Scientific, Santa Clara, CA, 95051, USA.
ORCID: 0000-0003-2372-0839

Deepak Tanneeru (D)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Manjari Deshmukh (M)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Akshi Bassi (A)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
ORCID: 0000-0002-4443-1430

Jacqueline Robinson (J)

Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
ORCID: 0000-0002-5556-815X

Ruchi Chaudhary (R)

MedGenome Inc., Foster City, CA, 94404, USA.

Sakthivel Murugan (S)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Zameer Ul-Asar (Z)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Imran Saleem (I)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Unzila Ishtiaq (U)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Areej Fatima (A)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Saqib Shafi Sheikh (SS)

Punjab Institute of Cardiology, Lahore, Pakistan.

Shahid Hameed (S)

Punjab Institute of Cardiology, Lahore, Pakistan.

Mohammad Ishaq (M)

Karachi Institute of Heart Diseases, Karachi, Pakistan.

Syed Zahed Rasheed (SZ)

Karachi Institute of Heart Diseases, Karachi, Pakistan.

Fazal-Ur-Rehman Memon (FU)

Red Crescent Institute of Cardiology, Hyderabad, Pakistan.

Anjum Jalal (A)

Faisalabad Institute of Cardiology, Faisalabad, Pakistan.

Shahid Abbas (S)

Faisalabad Institute of Cardiology, Faisalabad, Pakistan.

Philippe Frossard (P)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.

Christian Fuchsberger (C)

Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
Institute for Biomedicine, Eurac Research, Bolzano, Italy.
Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.

Lukas Forer (L)

Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
ORCID: 0000-0003-2139-7329

Sebastian Schoenherr (S)

Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.

Qixin Bei (Q)

Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.

Tushar Bhangale (T)

Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA.

Jennifer Tom (J)

Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA.

Santosh Gopi Krishna Gadde (SGK)

Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.

Priya B V (P)

Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.

Naveen Kumar Naik (NK)

Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.

Minxian Wang (M)

Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
ORCID: 0000-0002-3753-508X

Pui-Yan Kwok (PY)

Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA.
Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
ORCID: 0000-0002-5087-3059

Amit V Khera (AV)

Harvard Medical School, Boston, MA, 02115, USA.
Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA.
Verve Therapeutics, Cambridge, MA, 02139, USA.
ORCID: 0000-0001-6535-5839

B R Lakshmi (BR)

MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India.

Adam S Butterworth (AS)

British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK.
Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
ORCID: 0000-0002-6915-9015

Rajiv Chowdhury (R)

British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

John Danesh (J)

British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK.
Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK.

Emanuele di Angelantonio (E)

British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK.
Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.

Aliya Naheed (A)

Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh.

Vinay Goyal (V)

All India Institute of Medical Sciences (AIIMS), New Delhi, India.
Medanta Hospital, New Delhi, India.
Medanta, The Medicity, Gurgaon, India.

Rukmini M Kandadai (RM)

Nizams Institute of Medical Sciences (NIMS), Hyderabad, India.

Hrishikesh Kumar (H)

Institute of Neurosciences Kolkata, Kolkata, India.

Rupam Borgohain (R)

Nizams Institute of Medical Sciences (NIMS), Hyderabad, India.

Adreesh Mukherjee (A)

Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.

Pettarusp M Wadia (PM)

Jaslok Hospital and Research Centre, Mumbai, India.

Ravi Yadav (R)

National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.

Soaham Desai (S)

Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India.
ORCID: 0000-0003-0378-1888

Niraj Kumar (N)

All India Institute of Medical Sciences, Rishikesh, India.
ORCID: 0000-0002-5863-2532

Atanu Biswas (A)

Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.

Pramod Kumar Pal (PK)

National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.

Uday B Muthane (UB)

Parkinson and Ageing Research Foundation, Bengaluru, India.

Shymal K Das (SK)

Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.

Vedam L Ramprasad (VL)

MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.

Prashanth L Kukkle (PL)

All India Institute of Medical Sciences, Rishikesh, India.
Manipal Hospital, Miller Road, Bengaluru, India.
Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India.
ORCID: 0000-0002-4610-947X

Somasekar Seshagiri (S)

GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.

Sekar Kathiresan (S)

Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Verve Therapeutics, Cambridge, MA, 02139, USA.
Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.

Arkasubhra Ghosh (A)

Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.

V Mohan (V)

Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India.
ORCID: 0000-0001-5038-6210

Danish Saleheen (D)

Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA.
ORCID: 0000-0001-6193-020X

Eric W Stawiski (EW)

MedGenome Inc., Foster City, CA, 94404, USA.
GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
Caribou Biosciences, Berkeley, CA, 94710, USA.
ORCID: 0000-0002-9387-6719

Andrew S Peterson (AS)

MedGenome Inc., Foster City, CA, 94404, USA. peterson.andrew@genomeasia100k.org.
GenomeAsia 100K Foundation, Foster City, CA, 94404, USA. peterson.andrew@genomeasia100k.org.
Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA. peterson.andrew@genomeasia100k.org.
Broadwing Bio, South San Francisco, CA, 94080, USA. peterson.andrew@genomeasia100k.org.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Personnes › Asiatiques › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Régions géographiques › Asie › Asie de l'Ouest › Asie du Sud › Bangladesh › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Phénomènes génétiques › Effet fondateur › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Phénomènes génétiques › Génotype › Homozygote › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Régions géographiques › Asie › Asie de l'Ouest › Asie du Sud › Inde › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Régions géographiques › Asie › Asie de l'Ouest › Asie du Sud › Pakistan › South Asian medical cohorts reveal strong...
questionsmedicales.fr › Personnes › Asiatiques › Populations d'Asie de l'Ouest › Populations d'Asie du Sud › South Asian medical cohorts reveal strong...