ArticleNature communications2023
South Asian medical cohorts reveal strong founder effects and high rates of homozygosity.
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Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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33citing papers in PubMed, 1 pooled it
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Human genetic diversity across South Asian populations: A systematic review and meta-analysis.Medicine · 2025Pooled it
- Founder mutations in movement disorders: global distribution, molecular mechanisms, and clinical consequences-a scoping review.Neurogenetics · 2026Article
- Whole-Exome Sequencing in a Consanguinity-Enriched South Indian Retinitis Pigmentosa Cohort: Diagnostic Yield and Molecular Spectrum.Ophthalmology science · 2026Article
- Allele frequencies at recessive disease genes are mainly determined by pleiotropic effects in heterozygotes.Genetics · 2026Article
- Validated Polygenic Risk Scores Complement Monogenic Testing in South Asian Patients With Familial Hypercholesterolemia.JACC. Asia · 2026Article
- Assembling unmapped reads reveals hidden variation in South Asian genomes.Nature communications · 2026Article
- Genome-wide rare copy number variations potentially associated with drug resistance in epilepsy.Scientific reports · 2026Article
- A Novel Bi-Allelic Mutation in the Paired Box 7 Gene Causing Congenital Myopathy 19 in an Indian Family.Annals of Indian Academy of Neurology · 2026Article
- The OurHealth Study: A digital genomic cohort for cardiometabolic risk mechanisms in US South Asians.NPJ digital medicine · 2026Review
- Integrated Approach to Diagnosing Limb-Girdle Muscular Dystrophies in Resource-Limited Settings.Human mutation · 2026Article
- Obstructive Cholestasis in IL12RB1 Deficiency: A Case Report of an Unusual Hepatobiliary Presentation in Mendelian Susceptibility to Mycobacterial Disease.Case reports in pediatrics · 2026Article
- Compound Heterozygous ATM Variants Cause Adolescent-Onset Cerebellar and Extrapyramidal Disease Without Telangiectasia in a Consanguineous Pakistani Family.Genetics research · 2026Article
- Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes.bioRxiv : the preprint server for biology · 2025Article
- Genetic analysis of two bladder exstrophy populations of South Asian and North American origin.Journal of pediatric urology · 2025Article
- Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes.bioRxiv : the preprint server for biology · 2025Article
- Inbreeding and deleterious variation in South Asian populations.Scientific reports · 2025Article
- Article
- The impact of genetic ancestry on survival outcomes in pediatric rhabdomyosarcoma: A report from the Children's Oncology Group.HGG advances · 2025Observational
- Article
- South Asians and cardiometabolic health: A framework for comprehensive care for the individual, community, and population - An American society for preventive cardiology clinical practice statement.American journal of preventive cardiology · 2025Article
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Authors and funding
68 authors.
Jeffrey D Wall *Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA. jeffwall.genetics@gmail.com.ORCID 0000-0001-5066-1235
J Fah Sathirapongsasuti *MedGenome Inc., Foster City, CA, 94404, USA.
Ravi Gupta *MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Asif Rasheed *Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Radha Venkatesan *Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India.ORCID 0000-0002-4281-0250
Saurabh BelsareInstitute for Human Genetics, University of California, San Francisco, CA, 94143, USA.ORCID 0000-0002-8148-1867
Ramesh MenonMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Sameer PhalkeMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Anuradha MittalThermo Fisher Scientific, Santa Clara, CA, 95051, USA.
John FangThermo Fisher Scientific, Santa Clara, CA, 95051, USA.ORCID 0000-0003-2372-0839
Deepak TanneeruMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Manjari DeshmukhMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Akshi BassiMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.ORCID 0000-0002-4443-1430
Jacqueline RobinsonInstitute for Human Genetics, University of California, San Francisco, CA, 94143, USA.ORCID 0000-0002-5556-815X
Ruchi ChaudharyMedGenome Inc., Foster City, CA, 94404, USA.
Sakthivel MuruganMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Zameer Ul-AsarCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Imran SaleemCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Unzila IshtiaqCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Areej FatimaCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Saqib Shafi SheikhPunjab Institute of Cardiology, Lahore, Pakistan.
Shahid HameedPunjab Institute of Cardiology, Lahore, Pakistan.
Mohammad IshaqKarachi Institute of Heart Diseases, Karachi, Pakistan.
Syed Zahed RasheedKarachi Institute of Heart Diseases, Karachi, Pakistan.
Fazal-Ur-Rehman MemonRed Crescent Institute of Cardiology, Hyderabad, Pakistan.
Anjum JalalFaisalabad Institute of Cardiology, Faisalabad, Pakistan.
Shahid AbbasFaisalabad Institute of Cardiology, Faisalabad, Pakistan.
Philippe FrossardCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.
Christian FuchsbergerDepartment of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
Lukas ForerInstitute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.ORCID 0000-0003-2139-7329
Sebastian SchoenherrInstitute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
Qixin BeiDepartment of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
Tushar BhangaleDepartment of Human Genetics, Genentech, South San Francisco, CA, 94080, USA.
Jennifer TomProduct Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA.
Santosh Gopi Krishna GaddeNarayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.
Priya B VNarayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.
Naveen Kumar NaikNarayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.
Minxian WangProgram 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 KwokInstitute for Human Genetics, University of California, San Francisco, CA, 94143, USA.ORCID 0000-0002-5087-3059
Amit V KheraHarvard Medical School, Boston, MA, 02115, USA.ORCID 0000-0001-6535-5839
B R LakshmiMDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India.
Adam S ButterworthBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.ORCID 0000-0002-6915-9015
Rajiv ChowdhuryBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
John DaneshBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Emanuele di AngelantonioBritish Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Aliya NaheedInitiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh.
Vinay GoyalAll India Institute of Medical Sciences (AIIMS), New Delhi, India.
Rukmini M KandadaiNizams Institute of Medical Sciences (NIMS), Hyderabad, India.
Hrishikesh KumarInstitute of Neurosciences Kolkata, Kolkata, India.
Rupam BorgohainNizams Institute of Medical Sciences (NIMS), Hyderabad, India.
Adreesh MukherjeeBangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.
Pettarusp M WadiaJaslok Hospital and Research Centre, Mumbai, India.
Ravi YadavNational Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.
Soaham DesaiShree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India.ORCID 0000-0003-0378-1888
Niraj KumarAll India Institute of Medical Sciences, Rishikesh, India.ORCID 0000-0002-5863-2532
Atanu BiswasBangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.
Pramod Kumar PalNational Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India.
Uday B MuthaneParkinson and Ageing Research Foundation, Bengaluru, India.
Shymal K DasBangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India.
Vedam L RamprasadMedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India.
Prashanth L KukkleAll India Institute of Medical Sciences, Rishikesh, India.ORCID 0000-0002-4610-947X
Somasekar SeshagiriGenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
Sekar KathiresanProgram in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
Arkasubhra GhoshNarayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India.
V MohanMadras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India.ORCID 0000-0001-5038-6210
Danish SaleheenCenter for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan.ORCID 0000-0001-6193-020X
Eric W StawiskiMedGenome Inc., Foster City, CA, 94404, USA.ORCID 0000-0002-9387-6719
Andrew S PetersonMedGenome Inc., Foster City, CA, 94404, USA. peterson.andrew@genomeasia100k.org.
Funding
Center for Common Disease GeneticsUM1HG008895 · NHGRI · BROAD INSTITUTE, INC. · PI DALY, MARK JOSEPH, GABRIEL, STACEY · 2016 to 2020
$111.2MEnabling improved applicability and transferability of polygenic scores across populationsU01HG011719 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI Alicia Martin · 2021 to 2026
$5.5MLeveraging consanguinity and homozygosity to identify novel recessive variantsR01HG010689 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALEHEEN, DANISH, TORGERSON, DARA · 2019 to 2022
$2.4MPolygenic prediction of common, complex diseasesK08HG010155 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI KHERA, AMIT VIKRAM · 2018 to 2021
$1.1MNHGRI NIH HHS K08 HG010155NHGRI NIH HHS R01 HG010689NHGRI NIH HHS U01 HG011719NHGRI NIH HHS UM1 HG008895
Abstract
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.
Indexed as
Founder EffectSouth Asian PeopleBangladeshHomozygoteHumansIndiaPakistan
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