Abstract
Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.
Original language | English (US) |
---|---|
Pages (from-to) | 1-11 |
Number of pages | 11 |
Journal | Human genetics |
Volume | 118 |
Issue number | 1 |
DOIs | |
State | Published - Nov 2005 |
Keywords
- Ethnicity
- Genetic structure
- Indian genome variation database
- Indian population
- Repeat polymorphism
- Single nucleotide polymorphism
ASJC Scopus subject areas
- Genetics
- Genetics(clinical)
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The Indian Genome Variation database (IGVdb) : A project overview. / Brahmachari, Samir K.; Singh, Lalji; Sharma, Abhay; Mukerji, Mitali; Ray, Kunal; Roychoudhury, Susanta; Chandak, G. R.; Thangaraj, K.; Habib, Saman; Parmar, D.; Majumder, Partha P.; Sengupta, Shantanu; Bharadwaj, Dwaipayan; Dash, Debasis; Rath, Srikanta K.; Shankar, R.; Singh, Jagmohan; Virdi, Komal; Bahl, Samira; Rao, V. R.; Sinha, Swapnil; Singh, Ashok; Mitra, Amit; Mishra, Shrawan K.; Shukla, B. R K; Pasha, Qadar; Maiti, Souvik; Sharma, Amitabh; Kumar, Jitender; Ahsan, Aarif; Stobdan, Tsering; Chauhan, Chitra; Malhotra, Saurabh; Vidhani, Ajay; Siva, S.; Baral, Aradhita; Pandey, Rajesh; Roy, Ravishankar; Singh, Mridula; Singh, S. P.; Maurya, Nitin; Bandyopadhyay, Arun; Jha, Ganga Nath; Dutta, Somnath; Ghosh, Gautam; Naiya, Tufan; Jain, Manoj; Srivatava, J. P.; Gupta, J. R.; Khanna, Vinay; Dhawan, Alok; Anand, Mohini; Bharti, R. S.; Singh, Madhu; Singh, Arvind P.; Khan, Anwar J.; Bisht, Kamlesh Kumar; Kumar, Ashok; Ghosh, Balaram; Das, Swapan Kumar; Madan, Taruna; Chauhan, Chitra; Verma, Ranjana; Mittal, Uma; Mahajan, Anubha; Chavali, Sreenivas; Tabassum, Rubina; Banerjee, Vijaya; Batra, Jyotsna; Nagarkatti, Rana; Sharma, Shilpy; Sharma, Mamta; Chatterjee, Rajshekhar; Paul, Jinny A.; Srivastava, Pragya; Chopra, Rupali; Saxena, Ankur; Rajput, Charu; Singh, Prashant Kumar; Vaid, Mudit; Das, Sumantra; Chaudhuri, Keya; Chowdhury, Rukhsana; Mukhopadhyay, Arijit; Acharya, Moulinath; Bhattacharyya, Ashima; Saha, Atreyee; Biswas, Arindam; Chaki, Moumita; Gupta, Arnab; Mukherjee, Saibal; Mookherjee, Suddhasil; Chattopadhyay, Ishita; Banerjee, Taraswi; Chakravorty, Meenakshi; Misra, Chaitali; Monadal, Gourish; Sengupta, Shiladitya; Deb, Ishani; Banerjee, Arunava.
In: Human genetics, Vol. 118, No. 1, 11.2005, p. 1-11.Research output: Contribution to journal › Review article › peer-review
}
TY - JOUR
T1 - The Indian Genome Variation database (IGVdb)
T2 - A project overview
AU - Brahmachari, Samir K.
AU - Singh, Lalji
AU - Sharma, Abhay
AU - Mukerji, Mitali
AU - Ray, Kunal
AU - Roychoudhury, Susanta
AU - Chandak, G. R.
AU - Thangaraj, K.
AU - Habib, Saman
AU - Parmar, D.
AU - Majumder, Partha P.
AU - Sengupta, Shantanu
AU - Bharadwaj, Dwaipayan
AU - Dash, Debasis
AU - Rath, Srikanta K.
AU - Shankar, R.
AU - Singh, Jagmohan
AU - Virdi, Komal
AU - Bahl, Samira
AU - Rao, V. R.
AU - Sinha, Swapnil
AU - Singh, Ashok
AU - Mitra, Amit
AU - Mishra, Shrawan K.
AU - Shukla, B. R K
AU - Pasha, Qadar
AU - Maiti, Souvik
AU - Sharma, Amitabh
AU - Kumar, Jitender
AU - Ahsan, Aarif
AU - Stobdan, Tsering
AU - Chauhan, Chitra
AU - Malhotra, Saurabh
AU - Vidhani, Ajay
AU - Siva, S.
AU - Baral, Aradhita
AU - Pandey, Rajesh
AU - Roy, Ravishankar
AU - Singh, Mridula
AU - Singh, S. P.
AU - Maurya, Nitin
AU - Bandyopadhyay, Arun
AU - Jha, Ganga Nath
AU - Dutta, Somnath
AU - Ghosh, Gautam
AU - Naiya, Tufan
AU - Jain, Manoj
AU - Srivatava, J. P.
AU - Gupta, J. R.
AU - Khanna, Vinay
AU - Dhawan, Alok
AU - Anand, Mohini
AU - Bharti, R. S.
AU - Singh, Madhu
AU - Singh, Arvind P.
AU - Khan, Anwar J.
AU - Bisht, Kamlesh Kumar
AU - Kumar, Ashok
AU - Ghosh, Balaram
AU - Das, Swapan Kumar
AU - Madan, Taruna
AU - Chauhan, Chitra
AU - Verma, Ranjana
AU - Mittal, Uma
AU - Mahajan, Anubha
AU - Chavali, Sreenivas
AU - Tabassum, Rubina
AU - Banerjee, Vijaya
AU - Batra, Jyotsna
AU - Nagarkatti, Rana
AU - Sharma, Shilpy
AU - Sharma, Mamta
AU - Chatterjee, Rajshekhar
AU - Paul, Jinny A.
AU - Srivastava, Pragya
AU - Chopra, Rupali
AU - Saxena, Ankur
AU - Rajput, Charu
AU - Singh, Prashant Kumar
AU - Vaid, Mudit
AU - Das, Sumantra
AU - Chaudhuri, Keya
AU - Chowdhury, Rukhsana
AU - Mukhopadhyay, Arijit
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 - Deb, Ishani
AU - Banerjee, Arunava
N1 - Funding Information: Abstract Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacoge-nomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, Funding Information: The IGV initiative is a network program on predictive medicine that focuses on repeats and single nucleotide polymorphisms, initiated in 2003 and tenured for 5 years, by six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India. The laboratories include Institute of Genomics and Integrative Biology (IGIB), Delhi, Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Indian Institute of Chemical Biology (IICB), Kolkata, Central Drug Research Institute (CDRI), Lucknow, Industrial Toxicological Research Centre (ITRC), Lucknow and Institute of Microbial technology (IMTECH), Chandigarh (Box 1). These laboratories are involved in studies related to asthma, diabetes, neuropsychiatric disorders, cancer, coronary artery disease, clot disorders, high altitude disorders, retinitis pigmentosa, predisposition to malaria as well as other infectious diseases and drug metabolism. The consortium deemed it pertinent to understand the inherent genetic variability of the subpopulations as a first step towards identifying susceptible biomarkers for any disease or understanding drug response in different subpopulations. This consortium, therefore, aims at providing information on variations in the subpopulations representing the entire country. These variations would be useful for investigators for specific candidate gene studies conducted in any part of the country. Funding Information: Apart from the CSIR laboratories, a key participant in the project is the Indian Statistical Institute (ISI), Kolkata, which will help us in the analysis of our data. The institute has an established expertise in human genetic variation data analysis (Tapadar et al. 2000; Basu et al. 2005). The project also involves active participation of the Anthropological Survey of India (Singh 2002) that has helped in the identification of the various Indian subpopulations. In addition to the institutional facility, the project also has collaborations with The Centre for Genomic Application (TCGA), established through the support of Department of Science and Technology (DST), CSIR with The Chatterjee Group (TCG) for high throughput sequencing and genotyping and Silic-oGene Informatics Private Limited along with Lab-Vantage, India for development of a comprehensive platform for IGV database management, analysis and portal development. Funding Information: Acknowledgements This work was supported by grants from the Council of Scientific and Industrial Research (CSIR), Government of India for the project ‘‘Predictive medicine using repeat and single nucleotide polymorphisms’’ (CMM0016).
PY - 2005/11
Y1 - 2005/11
N2 - Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.
AB - Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.
KW - Ethnicity
KW - Genetic structure
KW - Indian genome variation database
KW - Indian population
KW - Repeat polymorphism
KW - Single nucleotide polymorphism
UR - http://www.scopus.com/inward/record.url?scp=28044436937&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=28044436937&partnerID=8YFLogxK
U2 - 10.1007/s00439-005-0009-9
DO - 10.1007/s00439-005-0009-9
M3 - Review article
C2 - 16133172
AN - SCOPUS:28044436937
VL - 118
SP - 1
EP - 11
JO - Human Genetics
JF - Human Genetics
SN - 0340-6717
IS - 1
ER -