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 language | English (US) |
---|---|
Pages (from-to) | 3-20 |
Number of pages | 18 |
Journal | Journal of Genetics |
Volume | 87 |
Issue number | 1 |
DOIs | |
State | Published - Apr 2008 |
Keywords
- Asia
- Complex disease
- HapMap
- Indian genome variation
- Pharmacogenomics
- Polymorphism
- SNP
ASJC Scopus subject areas
- Genetics
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In: Journal of Genetics, Vol. 87, No. 1, 04.2008, p. 3-20.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Genetic landscape of the people of India
T2 - A canvas for disease gene exploration
AU - Brahmachari, Samir K.
AU - Majumder, Partha P.
AU - Mukerji, Mitali
AU - Habib, Saman
AU - Dash, Debasis
AU - Ray, Kunal
AU - Bahl, Samira
AU - Singh, Lalji
AU - Sharma, Abhay
AU - Roychoudhury, Susanta
AU - Chandak, G. R.
AU - Thangaraj, K.
AU - Parmar, D.
AU - Sengupta, Shantanu
AU - Bharadwaj, Dwaipayan
AU - Rath, Srikanta K.
AU - Singh, Jagmohan
AU - Jha, Ganga Nath
AU - Virdi, Komal
AU - Rao, V. R.
AU - Sinha, Swapnil
AU - Singh, Ashok
AU - Mitra, Amit K.
AU - Mishra, Shrawan K.
AU - Pasha, Qadar
AU - Sivasubbu, Sridhar
AU - Pandey, Rajesh
AU - Baral, Aradhita
AU - Singh, Prashant K.
AU - Sharma, Amitabh
AU - Kumar, Jitender
AU - Stobdan, Tsering
AU - Bhasin, Yasha
AU - Chauhan, Chitra
AU - Hussain, Ashiq
AU - Sundaramoorthy, Elyanambi
AU - Singh, S. P.
AU - Bandyopadhyay, Arun
AU - Dasgupta, Krishanu
AU - Reddy, A. K.
AU - Spurgeon, Charles J.
AU - Idris, M. Mohd
AU - Khanna, Vinay
AU - Dhawan, Alok
AU - Anand, Mohini
AU - Shankar, R.
AU - Bharti, R. S.
AU - Singh, Madhu
AU - Singh, Arvind P.
AU - Khan, Anwar J.
AU - Shah, Parag P.
AU - Pant, A. B.
AU - Bharti, R. S.
AU - Kaur, Rupinder
AU - Bisht, Kamlesh K.
AU - Kumar, Ashok
AU - Rajamanickam, Victor
AU - Wilson, Eugene
AU - Thangadurai, Antony
AU - Jha, Pankaj K.
AU - Maulik, Mahua
AU - Makhija, Neelam
AU - Rahim, Abdur
AU - Sharma, Sangeeta
AU - Chopra, Rupali
AU - Rana, Pooja
AU - Chidambaram, M.
AU - Maitra, Arindam
AU - Chawla, Ruchi
AU - Soni, Suruchika
AU - Khurana, Preeti
AU - Khan, Mohamed Nadeem
AU - Sutar, Sushanta Das
AU - Tuteja, Amit
AU - Narayansamy, K.
AU - Shukla, Rachna
AU - Prakash, Swami
AU - Mahurkar, Swapna
AU - Mani, K. Radha
AU - Hemavathi, J.
AU - Bhaskar, Seema
AU - Khanna, Pankaj
AU - Ramalakshmi, G. S.
AU - Tripathi, Shalini Mani
AU - Thakur, Nikita
AU - Ghosh, Balaram
AU - Kukreti, Ritushree
AU - Madan, Taruna
AU - Verma, Ranjana
AU - Sudheer, G.
AU - Mahajan, Anubha
AU - Chavali, Sreenivas
AU - Tabassum, Rubina
AU - Grover, Sandeep
AU - Gupta, Meenal
AU - Batra, Jyotsna
AU - Kumar, Amrendra
AU - Nejatizadeh, Abdoulazim
AU - Vaid, Mudit
AU - Das, Swapan K.
AU - Sharma, Shilpy
AU - Sharma, Mamta
AU - Chatterjee, Rajshekhar
AU - Paul, Jinny A.
AU - Srivastava, Pragya
AU - Rajput, Charu
AU - Mittal, Uma
AU - Singh, Mridula
AU - Hariharan, Manoj
AU - Das, Sumantra
AU - Chaudhuri, Keya
AU - Sengupta, Mainak
AU - Acharya, Moulinath
AU - Bhattacharyya, Ashima
AU - Saha, Atreyee
AU - Biswas, Arindam
AU - Chaki, Moumita
AU - Gupta, Arnab
AU - Mukherjee, Saibal
AU - Mookherjee, Suddhasil
AU - Chattopadhyay, Ishita
AU - Banerjee, Taraswi
AU - Chakravorty, Meenakshi
AU - Misra, Chaitali
AU - Monadal, Gourish
AU - Sengupta, Shiladitya
AU - De, Dipanjana Dutta
AU - Bajaj, Swati
AU - Deb, Ishani
AU - Banerjee, Arunava
AU - Chowdhury, Rajdeep
AU - Banerjee, Debalina
AU - Kumar, Deepak
AU - Das, Sumit Ranjan
AU - Chandak, G. R.
AU - Tiwari, Shrish
AU - Bharadwaj, Anshu
AU - Chidambaram, M.
AU - Ahmed, Ikhlak
AU - Parveen, Sumera
AU - Singh, Nivedita
AU - Dasgupta, Dipayan
AU - Bisht, Siddharth Singh
AU - Khanna, Sangeeta
AU - Rajput, Rashmi
AU - Ghosh, Biswaroop
AU - Kumar, Naveen
AU - Chaurasia, Amit
AU - Abraham, James K.
AU - Sinha, Amit
AU - Sudheer, G.
AU - Scaria, Vinod
AU - Sethi, Tav Pritesh
AU - Mandal, Amit K.
AU - Mukhopadhyay, Arijit
N1 - 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.
PY - 2008/4
Y1 - 2008/4
N2 - 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.
AB - 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.
KW - Asia
KW - Complex disease
KW - HapMap
KW - Indian genome variation
KW - Pharmacogenomics
KW - Polymorphism
KW - SNP
UR - http://www.scopus.com/inward/record.url?scp=44149107150&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=44149107150&partnerID=8YFLogxK
U2 - 10.1007/s12041-008-0002-x
DO - 10.1007/s12041-008-0002-x
M3 - Article
C2 - 18560169
AN - SCOPUS:44149107150
SN - 0022-1333
VL - 87
SP - 3
EP - 20
JO - Journal of Genetics
JF - Journal of Genetics
IS - 1
ER -