Year: 2026
Type: preprint
Study design: Observational Study
Abstract: India, the most populous country, remains significantly underrepresented in the global genomics landscape. Previous efforts to catalog Indian genetic diversity were limited in scale, scope, and representation. Here, we present the GenomeIndia dataset, comprising whole genome sequences of 9,768 healthy individuals from 83 populations spanning the ethnolinguistic and biogeographic spectrum of India. We identify 129.93 million high-confidence biallelic variants, 44.03 million of which are previously unreported in global databases. In contrast to large populations that show steady population growth and internal homogeneity, we observe low effective population sizes, significant genetic drift, and profound homozygosity in small tribal groups, likely shaped by antiquity, isolation, and endogamy. We report multiple population-specific pharmacogenomic and deleterious variants, necessitating the integration of local genetic architecture and the inclusion of underrepresented South Asian genomes in global reference resources. Finally, we highlight the limited transferability of Eurocentric polygenic scores to Indian populations, and present an imputation panel that outperforms existing resources for both rare and common variants. Together, our work fills a significant gap in the equity of global human genomics, and paves way for precision medicine strategies that will benefit a quarter of the world population.
Source: medRxiv
Authors: Krithika Subramanian, Chandrika Bhattacharyya, Pratheusa Machha, Ankit Mukherjee, Devashish Tripathi, Shreya Chakraborty, Sauma Suvra Majumdar, Shouvanik Sengupta, Priyanka Singh, Vinay More, Shreya Bari, MS Sreelekshmi, Eric Macwan, Debasrija Mondal, Arghya Dey, Haya Afreen, Siddhi P Jani, Payel Mukherjee, Neha Singh, Tiyasha De, Pooja Sharma, Bharathram Upilli, Arindam Maitra, Kuldeep Singh, Praveen Sharma, Nanaocha Sharma, Sunil K. Raghav, Punit Prasad, E. V. Soniya, Abdul Jaleel, M Radhakrishna Pillai, Shijulal Nelson Sathi, Madhvi Joshi, Chaitanya Joshi, Mayurika Lahiri, Santosh Dixit, L. S. Shashidhara, Nachimuthu Senthil Kumar, H. Lalhruaitluanga, Lal Nundanga, Venkataram Shivakumar, Ganesan Venkatasubramanian, Naren P. Rao, Mohd Ashraf Ganie, Imtiyaz Ahmad Wani, Ganganath Jha, Ashwin Dalal, Murali Dharan Bashyam, Pritish Kumar Varadwaj, BS Sanjeev, Yogesh Simmhan, Chirag Jain, Arun Kumar, Durai Sundar, Ishaan Gupta, Pankaj Yadav, Manikandan Narayanan, Karthik Raman, Padinjat Raghu, Radhakrishnan Sabarinathan, Sridhar Sivasubbu, Vinod Scaria, Prathima Arvind, Suman K Paine, Tulasi Nagabandi, Khader Valli Rupanagudi, Himanshu Sinha, Nidhan K. Biswas, Shweta Ramdas, Karthik Bharadwaj Tallapaka, Vijayalakshmi Ravindranath, Yadati Narahari, Kumarasamy Thangaraj, Divya Tej Sowpati, Mohammed Faruq, Bratati Kahali, Analabha Basu
Institutions: Manipal Academy of Higher Education, National Institute of Biomedical Genomics, Centre for Cellular and Molecular Biology, Institute of Genomics and Integrative Biology, Regional Centre for Biotechnology, Indian Institute of Science Bangalore, All India Institute of Medical Sciences Jodhpur, Institute of Bio-Resources and Sustainable Development, Institute of Life Sciences, Rajiv Gandhi Centre for Biotechnology, Gujarat Biotechnology Research Centre, Indian Institute of Science Education and Research Pune, National Centre for Biological Sciences, Mizoram University, National Institute of Mental Health and Neurosciences, Sher-i-Kashmir Institute of Medical Sciences, Vinoba Bhave University, Centre for DNA Fingerprinting and Diagnostics, Indian Institute of Information Technology Allahabad, Indian Institute of Technology Delhi, Indian Institute of Technology Jodhpur, Indian Institute of Technology Madras, Academy of Scientific and Innovative Research
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
Award: G3047375522
OpenAlex ID: W7140179399