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

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.

SUBMITTER: Wall JD

PROVIDER: S-EPMC10250394 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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

Wall Jeffrey D JD Sathirapongsasuti J Fah JF Gupta Ravi R Rasheed Asif A Venkatesan Radha R Belsare Saurabh S Menon Ramesh R Phalke Sameer S Mittal Anuradha A Fang John J Tanneeru Deepak D Deshmukh Manjari M Bassi Akshi A Robinson Jacqueline J Chaudhary Ruchi R Murugan Sakthivel S Ul-Asar Zameer Z Saleem Imran I Ishtiaq Unzila U Fatima Areej A Sheikh Saqib Shafi SS Hameed Shahid S Ishaq Mohammad M Rasheed Syed Zahed SZ Memon Fazal-Ur-Rehman FU Jalal Anjum A Abbas Shahid S Frossard Philippe P Fuchsberger Christian C Forer Lukas L Schoenherr Sebastian S Bei Qixin Q Bhangale Tushar T Tom Jennifer J Gadde Santosh Gopi Krishna SGK B V Priya P Naik Naveen Kumar NK Wang Minxian M Kwok Pui-Yan PY Khera Amit V AV Lakshmi B R BR Butterworth Adam S AS Chowdhury Rajiv R Danesh John J di Angelantonio Emanuele E Naheed Aliya A Goyal Vinay V Kandadai Rukmini M RM Kumar Hrishikesh H Borgohain Rupam R Mukherjee Adreesh A Wadia Pettarusp M PM Yadav Ravi R Desai Soaham S Kumar Niraj N Biswas Atanu A Pal Pramod Kumar PK Muthane Uday B UB Das Shymal K SK Ramprasad Vedam L VL Kukkle Prashanth L PL Seshagiri Somasekar S Kathiresan Sekar S Ghosh Arkasubhra A Mohan V V Saleheen Danish D Stawiski Eric W EW Peterson Andrew S AS

Nature communications 20230608 1

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 ...[more]

PMID: 37291107

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Project description:ObjectivesThe medical field is facing a clinician-scientist shortage. Medical schools could foster the clinician-scientist workforce by offering students research opportunities. Most medical schools offer elective research programmes. Subsequently, a subset of doctors graduates without any research experience. Mandatory research projects may be more sufficient to develop clinician-scientist, but take more supervision and curricular time. There is limited insight in the scientific outcomes of mandatory research experiences. This study aims to examine publication rates of a mandatory research experience, identify factors associated with publication, and includes postgraduate research engagement.Design and settingProspective follow-up study involving 10 cohorts of medical students' mandatory research projects from Leiden University Medical Center.ParticipantsAll medical students who conducted their research project between 2008 and 2018 (n=2329) were included.Main outcome measurePublication rates were defined as peer-reviewed scientific publications, including research papers, reviews, and published meeting abstracts. Postgraduate research engagement was defined as research participation and dissemination of research at scientific conferences or in journals.ResultsIn total, 644 (27.7%) of all mandatory research experiences resulted in publication, with students mainly as first (n=984, 42.5%) or second author (n=587, 25.3%) and above world average citation impact (mean normalised journal score 1.29, mean normalised citation score 1.23). Students who conducted their research in an academic centre (adjusted OR 2.82; 95% CI 2.10 to 3.77), extended their research (adjusted OR 1.73; 95% CI 1.35 to 2.20), were involved in an excellency track (adjusted OR 2.08; 95% CI 1.44 to 3.01), or conducted clinical (adjusted OR 2.08; 95% CI 1.15 to 3.74) or laboratory (adjusted OR 2.16; 95% CI 1.16 to 4.01) research published their research more often. Later as junior doctors, this group significantly more often disseminate their research results at scientific conferences (adjusted OR 1.89; 95% CI 1.11 to 3.23) or in journals (adjusted OR 1.98; 95% CI 1.14 to 3.43).ConclusionsOur findings suggest that a significant subset of hands-on mandatory research projects with flexible learning pathways result in tangible research output with proper impact and that such successful experiences can be considered as diving board towards a research-oriented career.

Dataset Information

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

Publications

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

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