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4 results on '"Manjari Deshmukh"'

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

Author

Jeffrey D. Wall, J. Fah Sathirapongsasuti, Ravi Gupta, Asif Rasheed, Radha Venkatesan, Saurabh Belsare, Ramesh Menon, Sameer Phalke, Anuradha Mittal, John Fang, Deepak Tanneeru, Manjari Deshmukh, Akshi Bassi, Jacqueline Robinson, Ruchi Chaudhary, Sakthivel Murugan, Zameer ul-Asar, Imran Saleem, Unzila Ishtiaq, Areej Fatima, Saqib Shafi Sheikh, Shahid Hameed, Mohammad Ishaq, Syed Zahed Rasheed, Fazal-ur-Rehman Memon, Anjum Jalal, Shahid Abbas, Philippe Frossard, Christian Fuchsberger, Lukas Forer, Sebastian Schoenherr, Qixin Bei, Tushar Bhangale, Jennifer Tom, Santosh Gopi Krishna Gadde, Priya B V, Naveen Kumar Naik, Minxian Wang, Pui-Yan Kwok, Amit V. Khera, B. R. Lakshmi, Adam S. Butterworth, Rajiv Chowdhury, John Danesh, Emanuele di Angelantonio, Aliya Naheed, Vinay Goyal, Rukmini M. Kandadai, Hrishikesh Kumar, Rupam Borgohain, Adreesh Mukherjee, Pettarusp M. Wadia, Ravi Yadav, Soaham Desai, Niraj Kumar, Atanu Biswas, Pramod Kumar Pal, Uday B. Muthane, Shymal K. Das, Vedam L. Ramprasad, Prashanth L. Kukkle, Somasekar Seshagiri, Sekar Kathiresan, Arkasubhra Ghosh, V. Mohan, Danish Saleheen, Eric W. Stawiski, and Andrew S. Peterson

Subjects
Science
Abstract

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.

Published
2023
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2. Validation of a Genome-Wide Polygenic Score for Coronary Artery Disease in South Asians

Author

Minxian Wang, Aliya Naheed, Muralidhar Kanchi, Manjari Deshmukh, Aniketh Vijay Balegadde, Adam S. Butterworth, Sanika Apte, Praveena Lakshmipathy, Oshin Mathew, Ravi Gupta, Alben Sigamani, Emanuele Di Angelantonio, Rajiv Chowdhury, Ajit S. Mullasari, Ramesh Menon, Rajeev Gupta, Karthikeyan Rajendran, Rajesh Thachathodiyl, Michael Inouye, Amit Khera, Sakthivel Murugan, Mark Chaffin, Aniruddh P. Patel, Hisham Ahamed, Sumathi Sundaram, Krishnan Swaminathan, John Danesh, Sekar Kathiresan, Andrew S. Peterson, Krishna Kumar Sharma, Christina S. Devanboo, Ramprasad Vedam, Sanghamitra Mishra, Deepak Tanneeru, Sam Santhosh, Thomas Alexander, Butterworth, Adam [0000-0002-6915-9015], Danesh, John [0000-0003-1158-6791], Di Angelantonio, Emanuele [0000-0001-8776-6719], Inouye, Michael [0000-0001-9413-6520], and Apollo - University of Cambridge Repository

Subjects
Adult, Male, Multifactorial Inheritance, medicine.medical_specialty, South asia, India, Coronary Artery Disease, 030204 cardiovascular system & hematology, Dna variants, Genome, Coronary artery disease, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, South Asian, Humans, Medicine, Genomic medicine, polygenic score, 030212 general & internal medicine, Aged, Bangladesh, business.industry, Middle Aged, medicine.disease, genomic medicine, Case-Control Studies, Female, Cardiology and Cardiovascular Medicine, business, Genome-Wide Association Study
Abstract

BACKGROUND: Genome-wide polygenic scores (GPS) integrate information from many common DNA variants into a single number. Because rates of coronary artery disease (CAD) are substantially higher among South Asians, a GPS to identify high-risk individuals may be particularly useful in this population. OBJECTIVES: This analysis used summary statistics from a prior genome-wide association study to derive a new GPSCAD for South Asians. METHODS: This GPSCAD was validated in 7,244 South Asian UK Biobank participants and tested in 491 individuals from a case-control study in Bangladesh. Next, a static ancestry and GPSCAD reference distribution was built using whole-genome sequencing from 1,522 Indian individuals, and a framework was tested for projecting individuals onto this static ancestry and GPSCAD reference distribution using 1,800 CAD cases and 1,163 control subjects newly recruited in India. RESULTS: The GPSCAD, containing 6,630,150 common DNA variants, had an odds ratio (OR) per SD of 1.58 in South Asian UK Biobank participants and 1.60 in the Bangladeshi study (p

Published
2020
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3. The GenomeAsia 100K Project enables genetic discoveries across Asia

Author

Manjari Deshmukh, Stephan C. Schuster, Jong Il Kim, Venkatesan Radha, Partha P. Majumder, Herawati Sudoyo, Somasekar Seshagiri, John C. Chambers, Kok-Gan Chan, R. Rand Allingham, Vladimir Kharkov, Arkasubhra Ghosh, Ravi Gupta, Changhoon Kim, Keith C. Cheng, Lukas Forer, Thiramsett Sattibabu, Qixin Bei, Jeremy Stinson, Murray P. Cox, J. Stephen Lansing, Joseph Guillory, Akshi Bassi, Purushothaman Natarajan, Vadim Stepanov, George Koki, Markus S. Schröder, Ramesh Menon, Santosh Gopi Krishna Gadde, Elena S. Gusareva, Nidhan K. Biswas, Analabha Basu, Christian Fuchsberger, Michael A. Hauser, Santiago-Turla, Sandhya Nair, Mahesh Pratapneni, Sivasankar Malaichamy, Sebastian Schoenherr, Jonathan S. Friedlaender, Seik-Soon Khor, Jeong-Sun Seo, Aakrosh Ratan, Vivek Gopalan, Jeffrey D. Wall, Madasamy Parani, Tatiana M. Karafet, Viswanathan Mohan, Rikky W. Purbojati, Steffen Durinck, Anjali Verma, Kushal Suryamohan, Vedam L. Ramprasad, Badrul Munir Md-Zain, Phalkek Sameer, Andrew S. Peterson, Jong-Yeon Shin, Hie Lim Kim, Eric Stawiski, Joyner T. George, Michael F. Hammer, Katsushi Tokunaga, Jiani Li, Khai C. Ang, Sam Santhosh, Jennifer Tom, Syed Qasim Mehdi, Belong Cho, Tushar Bhangale, Asian School of the Environment, Lee Kong Chian School of Medicine (LKCMedicine), and Complexity Institute

Subjects
Asia, Genotype, Population structure, Population, Datasets as Topic, Disease, Article, 03 medical and health sciences, 0302 clinical medicine, Asian People, Genetic variation, Humans, Medicine [Science], education, Alleles, 030304 developmental biology, Genetic association, 0303 health sciences, education.field_of_study, Multidisciplinary, Genome, Human, Geography, Evolutionary biology, Genetic Discoveries, 030217 neurology & neurosurgery, Imputation (genetics), Founder effect, Reference genome, Genome-Wide Association Study
Abstract

The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity of individuals in genomic datasets and led to reduced medical relevance for a large proportion of the world’s population. Population-specific reference genome datasets as well as genome-wide association studies in diverse populations are needed to address this issue. Here we describe the pilot phase of the GenomeAsia 100K Project. This includes a whole-genome sequencing reference dataset from 1,739 individuals of 219 population groups and 64 countries across Asia. We catalogue genetic variation, population structure, disease associations and founder effects. We also explore the use of this dataset in imputation, to facilitate genetic studies in populations across Asia and worldwide., Using whole-genome sequencing data from 1,739 individuals, the GenomeAsia 100K Project catalogues genetic variation, population structure and disease associations to facilitate genetic studies in Asian populations and increase representation in genetics studies worldwide.

Published
2019

4. Identification of African-Specific Admixture between Modern and Archaic Humans

Author

Jeffrey D. Wall, Aakrosh Ratan, Eric Stawiski, Hie Lim Kim, Changhoon Kim, Ravi Gupta, Kushal Suryamohan, Elena S. Gusareva, Rikky Wenang Purbojati, Tushar Bhangale, Vadim Stepanov, Vladimir Kharkov, Markus S. Schrӧder, Vedam Ramprasad, Jennifer Tom, Steffen Durinck, Qixin Bei, Jiani Li, Joseph Guillory, Samir Phalke, Analabha Basu, Jeremy Stinson, Sandhya Nair, Sivasankar Malaichamy, Nidhan K. Biswas, John C. Chambers, Keith C. Cheng, Joyner T. George, Seik Soon Khor, Jong-Il Kim, Belong Cho, Ramesh Menon, Thiramsetti Sattibabu, Akshi Bassi, Manjari Deshmukh, Anjali Verma, Vivek Gopalan, Jong-Yeon Shin, Mahesh Pratapneni, Sam Santhosh, Katsushi Tokunaga, Badrul M. Md-Zain, Kok Gan Chan, Madasamy Parani, Purushothaman Natarajan, Michael Hauser, R. Rand Allingham, Cecilia Santiago-Turla, Arkasubhra Ghosh, Santosh Gopi Krishna Gadde, Christian Fuchsberger, Lukas Forer, Sebastian Shoenherr, Herawati Sudoyo, J. Stephen Lansing, Jonathan Friedlaender, George Koki, Murray P. Cox, Michael Hammer, Tatiana Karafet, Khai C. Ang, Syed Q. Mehdi, Venkatesan Radha, Viswanathan Mohan, Partha P. Majumder, Sekar Seshagiri, Jeong-Sun Seo, Stephan Schuster, and Andrew S. Peterson

Subjects
Neanderthal, Black People, Archaic humans, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, biology.animal, Genetics, Animals, Humans, Denisovan, Genetics (clinical), 030304 developmental biology, Neanderthals, 0303 health sciences, biology, Fossils, Genome, Human, Hominidae, Gene Pool, biology.organism_classification, Homo floresiensis, Geography, Genetics, Population, Evolutionary biology, Identification (biology), Gene pool, 030217 neurology & neurosurgery, Reference genome
Abstract

Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.

Published
2019

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