The Indian Genome Variation database (IGVdb): A project overview

Samir K. Brahmachari; Lalji Singh; Abhay Sharma; Mitali Mukerji; Kunal Ray; Susanta Roychoudhury; G. R. Chandak; K. Thangaraj; Saman Habib; D. Parmar; Partha P. Majumder; Shantanu Sengupta; Dwaipayan Bharadwaj; Debasis Dash; Srikanta K. Rath; R. Shankar; Jagmohan Singh; Komal Virdi; Samira Bahl; V. R. Rao; Swapnil Sinha; Ashok Singh; Amit Mitra; Shrawan K. Mishra; B. R K Shukla; Qadar Pasha; Souvik Maiti; Amitabh Sharma; Jitender Kumar; Aarif Ahsan; Tsering Stobdan; Chitra Chauhan; Saurabh Malhotra; Ajay Vidhani; S. Siva; Aradhita Baral; Rajesh Pandey; Ravishankar Roy; Mridula Singh; S. P. Singh; Nitin Maurya; Arun Bandyopadhyay; Ganga Nath Jha; Somnath Dutta; Gautam Ghosh; Tufan Naiya; Manoj Jain; J. P. Srivatava; J. R. Gupta; Vinay Khanna; Alok Dhawan; Mohini Anand; R. S. Bharti; Madhu Singh; Arvind P. Singh; Anwar J. Khan; Kamlesh Kumar Bisht; Ashok Kumar; Balaram Ghosh; Swapan Kumar Das; Taruna Madan; Chitra Chauhan; Ranjana Verma; Uma Mittal; Anubha Mahajan; Sreenivas Chavali; Rubina Tabassum; Vijaya Banerjee; Jyotsna Batra; Rana Nagarkatti; Shilpy Sharma; Mamta Sharma; Rajshekhar Chatterjee; Jinny A. Paul; Pragya Srivastava; Rupali Chopra; Ankur Saxena; Charu Rajput; Prashant Kumar Singh; Mudit Vaid; Sumantra Das; Keya Chaudhuri; Rukhsana Chowdhury; Arijit Mukhopadhyay; 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; Ishani Deb; Arunava Banerjee

doi:10.1007/s00439-005-0009-9

The Indian Genome Variation database (IGVdb): A project overview

Samir K. Brahmachari, Lalji Singh, Abhay Sharma, Mitali Mukerji, Kunal Ray, Susanta Roychoudhury, G. R. Chandak, K. Thangaraj, Saman Habib, D. Parmar, Partha P. Majumder, Shantanu Sengupta, Dwaipayan Bharadwaj, Debasis Dash, Srikanta K. Rath, R. Shankar, Jagmohan Singh, Komal Virdi, Samira Bahl, V. R. RaoSwapnil Sinha, Ashok Singh, Amit Mitra, Shrawan K. Mishra, B. R K Shukla, Qadar Pasha, Souvik Maiti, Amitabh Sharma, Jitender Kumar, Aarif Ahsan, Tsering Stobdan, Chitra Chauhan, Saurabh Malhotra, Ajay Vidhani, S. Siva, Aradhita Baral, Rajesh Pandey, Ravishankar Roy, Mridula Singh, S. P. Singh, Nitin Maurya, Arun Bandyopadhyay, Ganga Nath Jha, Somnath Dutta, Gautam Ghosh, Tufan Naiya, Manoj Jain, J. P. Srivatava, J. R. Gupta, Vinay Khanna, Alok Dhawan, Mohini Anand, R. S. Bharti, Madhu Singh, Arvind P. Singh, Anwar J. Khan, Kamlesh Kumar Bisht, Ashok Kumar, Balaram Ghosh, Swapan Kumar Das, Taruna Madan, Chitra Chauhan, Ranjana Verma, Uma Mittal, Anubha Mahajan, Sreenivas Chavali, Rubina Tabassum, Vijaya Banerjee, Jyotsna Batra, Rana Nagarkatti, Shilpy Sharma, Mamta Sharma, Rajshekhar Chatterjee, Jinny A. Paul, Pragya Srivastava, Rupali Chopra, Ankur Saxena, Charu Rajput, Prashant Kumar Singh, Mudit Vaid, Sumantra Das, Keya Chaudhuri, Rukhsana Chowdhury, Arijit Mukhopadhyay, 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, Ishani Deb, Arunava Banerjee

Neuroscience

Research output: Contribution to journal › Review article › peer-review

111 Scopus citations

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	https://doi.org/10.1007/s00439-005-0009-9
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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10.1007/s00439-005-0009-9

Cite this

Brahmachari, S. K., Singh, L., Sharma, A., Mukerji, M., Ray, K., Roychoudhury, S., Chandak, G. R., Thangaraj, K., Habib, S., Parmar, D., Majumder, P. P., Sengupta, S., Bharadwaj, D., Dash, D., Rath, S. K., Shankar, R., Singh, J., Virdi, K., Bahl, S., ... Banerjee, A. (2005). The Indian Genome Variation database (IGVdb): A project overview. Human genetics, 118(1), 1-11. https://doi.org/10.1007/s00439-005-0009-9

Brahmachari, SK, Singh, L, Sharma, A, Mukerji, M, Ray, K, Roychoudhury, S, Chandak, GR, Thangaraj, K, Habib, S, Parmar, D, Majumder, PP, Sengupta, S, Bharadwaj, D, Dash, D, Rath, SK, Shankar, R, Singh, J, Virdi, K, Bahl, S, Rao, VR, Sinha, S, Singh, A, Mitra, A, Mishra, SK, Shukla, BRK, Pasha, Q, Maiti, S, Sharma, A, Kumar, J, Ahsan, A, Stobdan, T, Chauhan, C, Malhotra, S, Vidhani, A, Siva, S, Baral, A, Pandey, R, Roy, R, Singh, M, Singh, SP, Maurya, N, Bandyopadhyay, A, Jha, GN, Dutta, S, Ghosh, G, Naiya, T, Jain, M, Srivatava, JP, Gupta, JR, Khanna, V, Dhawan, A, Anand, M, Bharti, RS, Singh, M, Singh, AP, Khan, AJ, Bisht, KK, Kumar, A, Ghosh, B, Das, SK, Madan, T, Chauhan, C, Verma, R, Mittal, U, Mahajan, A, Chavali, S, Tabassum, R, Banerjee, V, Batra, J, Nagarkatti, R, Sharma, S, Sharma, M, Chatterjee, R, Paul, JA, Srivastava, P, Chopra, R, Saxena, A, Rajput, C, Singh, PK, Vaid, M, Das, S, Chaudhuri, K, Chowdhury, R, Mukhopadhyay, A, Acharya, M, Bhattacharyya, A, Saha, A, Biswas, A, Chaki, M, Gupta, A, Mukherjee, S, Mookherjee, S, Chattopadhyay, I, Banerjee, T, Chakravorty, M, Misra, C, Monadal, G, Sengupta, S, Deb, I & Banerjee, A 2005, 'The Indian Genome Variation database (IGVdb): A project overview', Human genetics, vol. 118, no. 1, pp. 1-11. https://doi.org/10.1007/s00439-005-0009-9

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title = "The Indian Genome Variation database (IGVdb): A project overview",

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.",

keywords = "Ethnicity, Genetic structure, Indian genome variation database, Indian population, Repeat polymorphism, Single nucleotide polymorphism",

author = "Brahmachari, {Samir K.} and Lalji Singh and Abhay Sharma and Mitali Mukerji and Kunal Ray and Susanta Roychoudhury and Chandak, {G. R.} and K. Thangaraj and Saman Habib and D. Parmar and Majumder, {Partha P.} and Shantanu Sengupta and Dwaipayan Bharadwaj and Debasis Dash and Rath, {Srikanta K.} and R. Shankar and Jagmohan Singh and Komal Virdi and Samira Bahl and Rao, {V. R.} and Swapnil Sinha and Ashok Singh and Amit Mitra and Mishra, {Shrawan K.} and Shukla, {B. R K} and Qadar Pasha and Souvik Maiti and Amitabh Sharma and Jitender Kumar and Aarif Ahsan and Tsering Stobdan and Chitra Chauhan and Saurabh Malhotra and Ajay Vidhani and S. Siva and Aradhita Baral and Rajesh Pandey and Ravishankar Roy and Mridula Singh and Singh, {S. P.} and Nitin Maurya and Arun Bandyopadhyay and Jha, {Ganga Nath} and Somnath Dutta and Gautam Ghosh and Tufan Naiya and Manoj Jain and Srivatava, {J. P.} and Gupta, {J. R.} and Vinay Khanna and Alok Dhawan and Mohini Anand and Bharti, {R. S.} and Madhu Singh and Singh, {Arvind P.} and Khan, {Anwar J.} and Bisht, {Kamlesh Kumar} and Ashok Kumar and Balaram Ghosh and Das, {Swapan Kumar} and Taruna Madan and Chitra Chauhan and Ranjana Verma and Uma Mittal and Anubha Mahajan and Sreenivas Chavali and Rubina Tabassum and Vijaya Banerjee and Jyotsna Batra and Rana Nagarkatti and Shilpy Sharma and Mamta Sharma and Rajshekhar Chatterjee and Paul, {Jinny A.} and Pragya Srivastava and Rupali Chopra and Ankur Saxena and Charu Rajput and Singh, {Prashant Kumar} and Mudit Vaid and Sumantra Das and Keya Chaudhuri and Rukhsana Chowdhury and Arijit Mukhopadhyay and Moulinath Acharya and Ashima Bhattacharyya and Atreyee Saha and Arindam Biswas and Moumita Chaki and Arnab Gupta and Saibal Mukherjee and Suddhasil Mookherjee and Ishita Chattopadhyay and Taraswi Banerjee and Meenakshi Chakravorty and Chaitali Misra and Gourish Monadal and Shiladitya Sengupta and Ishani Deb and Arunava Banerjee",

note = "Funding Information: Acknowledgements This work was supported by grants from the Council of Scientific and Industrial Research (CSIR), Government of India for the project {\textquoteleft}{\textquoteleft}Predictive medicine using repeat and single nucleotide polymorphisms{\textquoteright}{\textquoteright} (CMM0016). 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.",

year = "2005",

month = nov,

doi = "10.1007/s00439-005-0009-9",

language = "English (US)",

volume = "118",

pages = "1--11",

journal = "Human Genetics",

issn = "0340-6717",

publisher = "Springer Verlag",

number = "1",

}

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: 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). 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.

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

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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 -

The Indian Genome Variation database (IGVdb): A project overview

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Keywords

ASJC Scopus subject areas

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