Genetic landscape of the people of India: A canvas for disease gene exploration

Samir K. Brahmachari, Partha P. Majumder, Mitali Mukerji, Saman Habib, Debasis Dash, Kunal Ray, Samira Bahl, Lalji Singh, Abhay Sharma, Susanta Roychoudhury, G. R. Chandak, K. Thangaraj, D. Parmar, Shantanu Sengupta, Dwaipayan Bharadwaj, Srikanta K. Rath, Jagmohan Singh, Ganga Nath Jha, Komal Virdi, V. R. RaoSwapnil Sinha, Ashok Singh, Amit K. Mitra, Shrawan K. Mishra, Qadar Pasha, Sridhar Sivasubbu, Rajesh Pandey, Aradhita Baral, Prashant K. Singh, Amitabh Sharma, Jitender Kumar, Tsering Stobdan, Yasha Bhasin, Chitra Chauhan, Ashiq Hussain, Elyanambi Sundaramoorthy, S. P. Singh, Arun Bandyopadhyay, Krishanu Dasgupta, A. K. Reddy, Charles J. Spurgeon, M. Mohd Idris, Vinay Khanna, Alok Dhawan, Mohini Anand, R. Shankar, R. S. Bharti, Madhu Singh, Arvind P. Singh, Anwar J. Khan, Parag P. Shah, A. B. Pant, R. S. Bharti, Rupinder Kaur, Kamlesh K. Bisht, Ashok Kumar, Victor Rajamanickam, Eugene Wilson, Antony Thangadurai, Pankaj K. Jha, Mahua Maulik, Neelam Makhija, Abdur Rahim, Sangeeta Sharma, Rupali Chopra, Pooja Rana, M. Chidambaram, Arindam Maitra, Ruchi Chawla, Suruchika Soni, Preeti Khurana, Mohamed Nadeem Khan, Sushanta Das Sutar, Amit Tuteja, K. Narayansamy, Rachna Shukla, Swami Prakash, Swapna Mahurkar, K. Radha Mani, J. Hemavathi, Seema Bhaskar, Pankaj Khanna, G. S. Ramalakshmi, Shalini Mani Tripathi, Nikita Thakur, Balaram Ghosh, Ritushree Kukreti, Taruna Madan, Ranjana Verma, G. Sudheer, Anubha Mahajan, Sreenivas Chavali, Rubina Tabassum, Sandeep Grover, Meenal Gupta, Jyotsna Batra, Amrendra Kumar, Abdoulazim Nejatizadeh, Mudit Vaid, Swapan K. Das, Shilpy Sharma, Mamta Sharma, Rajshekhar Chatterjee, Jinny A. Paul, Pragya Srivastava, Charu Rajput, Uma Mittal, Mridula Singh, Manoj Hariharan, Sumantra Das, Keya Chaudhuri, Mainak Sengupta, Moulinath Acharya, Ashima Bhattacharyya, Atreyee Saha, Arindam Biswas, Moumita Chaki, Arnab Gupta, Saibal Mukherjee, Suddhasil Mookherjee, Ishita Chattopadhyay, Taraswi Banerjee, Meenakshi Chakravorty, Chaitali Misra, Gourish Monadal, Shiladitya Sengupta, Dipanjana Dutta De, Swati Bajaj, Ishani Deb, Arunava Banerjee, Rajdeep Chowdhury, Debalina Banerjee, Deepak Kumar, Sumit Ranjan Das, G. R. Chandak, Shrish Tiwari, Anshu Bharadwaj, M. Chidambaram, Ikhlak Ahmed, Sumera Parveen, Nivedita Singh, Dipayan Dasgupta, Siddharth Singh Bisht, Sangeeta Khanna, Rashmi Rajput, Biswaroop Ghosh, Naveen Kumar, Amit Chaurasia, James K. Abraham, Amit Sinha, G. Sudheer, Vinod Scaria, Tav Pritesh Sethi, Amit K. Mandal, Arijit Mukhopadhyay

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Abstract

Analyses of frequency profiles of markers on disease or drug-response related genes in diverse populations are important for the dissection of common diseases. We report the results of analyses of data on 405 SNPs from 75 such genes and a 5.2 Mb chromosome, 22 genomic region in 1871 individuals from diverse 55 endogamous Indian populations. These include 32 large (> 10 million individuals) and 23 isolated populations, representing a large fraction of the people of India. We observe high levels of genetic divergence between groups of populations that cluster largely on the basis of ethnicity and language. Indian populations not only overlap with the diversity of HapMap populations, but also contain population groups that are genetically distinct. These data and results are useful for addressing stratification and study design issues in complex traits especially for heterogeneous populations.

Original languageEnglish (US)
Pages (from-to)3-20
Number of pages18
JournalJournal of Genetics
Volume87
Issue number1
DOIs
StatePublished - Apr 2008

Bibliographical note

Funding Information:
Financial support from Council of Scientific and Industrial Research (CSIR) Government of India, Task Force Project on ‘Predictive Medicine using repeat and single nucleotide polymorphisms’ (CMM0016); Department of Science and Technology (DST) for the TCGA facility and Department of Biotechnology (DBT) for ‘Programme support on Functional Genomics to IGIB’ is duly acknowledged. Consortium members would like to acknowledge the help of a large number of anthropologists and other members for help in community engagement and sample collection - Profs. P. K. Das and Jagannath Das, Dept. of Anthropology, Utkal University, Bhubaneshwar, Orissa; Thakur Prasad Murmu, Sunil Baraik, Ranchi; Prof. Jebon Singh, Dept. of Anthropology, Manipur University, Imphal; Dr A. V. Arakeri, Anthropological Survey of India (ASI), Udaipur; Dr F. A. Kulirani (ASI), Shillong; Dr B. N. Sarkar (ASI), Kolkata; Dr B. R. K. Shukla, Dept. of Anthropology, Lucknow University, Lucknow; Prof. Pradeep K. Singh, Dept. of Anthropology. Ranchi College, Jharkhand; Biren Ha-jong, Tura, Meghalaya; V. S. Upadhye and his team in LABINDIA, Shekhar Ranjan Ghoshal, Western Railways, Mumbai; Mr Rajesh Bhandari, Sundernagar; Devi Singh and Karan Thakur, Chambi village, Himachal; Nitin Maurya, Leena Kalla, Delhi University; Rana Nagarkatti, Kamya Mehla, Tej P. Singh, S. Siva, Aarif Ahsan, Karamjit Singh Dolt, Chitra Chauhan, Mridula Singh, Dr Sou-vik Maiti, Inder Singh, Ravishankar Roy (IGIB); V. Prasad Kolla, V. N. S. Prathyusha, Inder Deo Mali (CCMB), Bipin C. Mishra, J. P. Srivastava, R. K Gupta (CDRI); Somnath Dutta, and Siddiq Sarkar (IICB), clinicians Drs. Saurabh Malhotra and Ajay Vidhani. For HTSSS implementation we would like to acknowledge Ranjan Basu, Biswajit Das, Shuvankar Mukherjee, Jhuma Mukherjee, De-basish Saha (Silicogene); Pallab Banerjee, Bijoyesh Saha, Anirban Chatterjee, S. R. Moquim, Navneet Kwarta, Manish Kumar, De-bkumar Sinha (Labvantage Asia) and Raghunath Chatterjee (IICB) for help in informatics support. Administrative support from Dr Rekha Chaturvedi, T. V. Joshua, V. P. Bharadwaj, Ajit Singh, He-mant Kulkarni, P. Bansal, (IGIB) and Arpita Sengupta and Pabitra Patnaik (TCGA) is duly acknowledged. Critical prereviewing and comments on the drafts of the manuscript from Dr Satyajit Rath, National Institute of Immunology, Delhi; Prof. Irfan Habib, Aligarh Muslim University and Prof. Vani Brahmachari, Ambedkar Centre for Biomedical Research, Delhi University are acknowledged. Authors also thank Dr Ashis K. Saha and Department of Geography, Delhi University, for help in map preparation and Drs R. A. Mashelkar, V. S. Ramamurthy, M. K. Bhan, G. Padmanabhan, V. C. Vora for support and encouragement. Authors are indebted to Myles Axton, Alan Packer and the anonymous referees of Nature Genetics for their constructive suggestions and several rounds of reviewing of the manuscript. But for their efforts, the manuscript would not be in the present form.

Keywords

  • Asia
  • Complex disease
  • HapMap
  • Indian genome variation
  • Pharmacogenomics
  • Polymorphism
  • SNP

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