Skip to main content
SpringerLink
Log in

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

  • Review Article
  • Published:
Human Genetics Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Ahsan A, Charu R, Pasha MAQ, Norboo T, Afrin F, Baig MA (2004) eNOS allelic variants at the same locus associate with HAPE and adaptation. Thorax 59:1000–1002

    Article  PubMed  CAS  Google Scholar 

  • Allchin B, Allchin R (1982) The rise of civilization in India and Pakistan. Cambridge University Press, Cambridge

    Google Scholar 

  • Bahl S, Virdi K, Mittal U, Sachdeva MP, Kalla AK, Holmes SE, O’Hearn E, Margolis RL, Jain S, Srivastava AK, Mukerji M (2005) Evidence of a common founder for SCA12 in the Indian population. Ann Hum Genet (in press)

  • Bamshad MJ, Watkins WS, Dixon ME, Jorde LB, Rao BB, Naidu JM, Prasad BV, Rasanayagam A, Hammer MF (1998) Female gene flow stratifies Hindu castes. Nature 395:651–652

    Article  PubMed  CAS  Google Scholar 

  • Bamshad M, Kivisild T, Watkins WS, Dixon ME, Ricker CE, Rao BB, Naidu JM, Prasad BV, Reddy PG, Rasanayagam A, Papiha SS, Villems R, Redd AJ, Hammer MF, Nguyen SV, Carroll ML, Batzer MA, Jorde LB (2001) Genetic evidence on the origins of caste populations. Genome Res 11:994–10004

    Article  PubMed  CAS  Google Scholar 

  • Basu A, Mukherjee N, Roy S, Sengupta S, Banerjee S, Chakraborty M, Dey B, Roy M, Roy B, Bhattacharyya NP, Roychoudhury S, Majumder PP (2003) Ethnic India: a genomic view, with special reference to peopling and structure. Genome Res 13:2277–2290

    Article  PubMed  CAS  Google Scholar 

  • Basu A, Chaudhuri P, Majumder PP (2005) Identification of polymorphic motifs using probabilistic search algorithms. Genome Res 15:67–77

    Article  PubMed  CAS  Google Scholar 

  • Batra J, Niphadkar PV, Sharma SK, Ghosh B (2005) Uteroglobin-related protein 1(UGRP1) gene polymorphisms and atopic asthma in the Indian population. Int Arch Allergy Immunol 136:1–6. Epub 2004 December 08

    Google Scholar 

  • Batra J, Sharma M, Chatterjee R, Sharma S, Mabalirajan U, Ghosh B (2005) Chemokine receptor 5 (CCR5) D32 deletion and atopic asthma in India. Thorax 60:85

    PubMed  CAS  Google Scholar 

  • Bhasin MK, Walter H, Danker-Hopfe (1994) People of India: an investigation of biological variability in ecological ethnoeconomic and linguistic groups. Kamla-Raj Enterprises, Delhi

    Google Scholar 

  • Bhattacharyya NP, Basu P, Das M, Pramanik S, Banerjee R, Roy B, Roychoudhury S, Majumder PP (1999) Negligible male gene flow across ethnic boundaries in India, revealed by analysis of Y-chromosomal DNA polymorphisms. Genome Res 9:711–719

    PubMed  CAS  Google Scholar 

  • Bittles AH (2002) Endogamy, consanguinity and community genetics. J Genet 81:91–98

    Article  PubMed  CAS  Google Scholar 

  • Bittles AH, Neel JV (1994) The costs of human inbreeding and their implications for variations at the DNA level. Nat Genet 8:117–121

    Article  PubMed  CAS  Google Scholar 

  • Cann RL (2001) Genetic clues to dispersal in human populations: retracing the past from the present. Science 291:1742–1748

    Article  PubMed  CAS  Google Scholar 

  • Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton, NJ, pp 208–213

    Google Scholar 

  • Chandak GR, Sridevi MU, Vas CJ, Panikker DM, Singh L (2002) Apolipoprotein E and presenilin-1 allelic variation and Alzheimer’s disease in India. Hum Biol 74:683–693

    Article  PubMed  CAS  Google Scholar 

  • Choudhry S, Mukerji M, Srivastava AK, Jain S, Brahmachari SK (2001) CAG repeat instability at SCA2 locus: anchoring CAA interruptions and linked single nucleotide polymorphisms. Hum Mol Genet 10:2437–2446

    Article  PubMed  CAS  Google Scholar 

  • Fredman D, Munns G, Rios D, Sjoholm F, Siegfried M, Lenhard B, Lehvaslaiho H, Brookes AJ (2004) HGVbase: a curated resource describing human DNA variation and phenotype relationships. Nucleic Acids Res 32:D516–D519

    Article  PubMed  CAS  Google Scholar 

  • Gadgil M, Guha R (1992) The fissure land: an ecological history of India. Oxford University Press, New Delhi

    Google Scholar 

  • Gadgil M, Joshi NV, Prasad UV, Manoharan S, Patil S (eds) (1998) In the Indian human heritage. Universities Press, Hyderabad, pp 100–129

    Google Scholar 

  • Guha BS (1935) The racial affinities of the people of India; in census of India, 1931, Part III—Ethnographical. Government of India Press, Simla

    Google Scholar 

  • Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y (2002) JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res 30:158–162

    Article  PubMed  CAS  Google Scholar 

  • Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas P (2002) The celera discovery system. Nucleic Acids Res 30:129–136

    Article  PubMed  CAS  Google Scholar 

  • Kivisild T, Rootsi S, Metspalu M, Mastana S, Kaldma K, Parik J, Metspalu E, Adojaan M, Tolk HV, Stepanov V, Golge M, Usanga E, Papiha SS, Cinnioglu C, King R, Cavalli-Sforza L, Underhill PA, Villems R (2003) The genetic heritage of the earliest settlers persists both in Indian tribal and caste populations. Am J Hum Genet 72:313–332

    Article  PubMed  CAS  Google Scholar 

  • Kukreti R, C BR, Das SK, De M, Talukder G, Vaz F, Verma IC, Brahmachari SK (2002) Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human beta-globin locus control region (LCR) in Indian population. Am J Hematol 69:77–79

    Article  PubMed  CAS  Google Scholar 

  • Mahajan A, Chavali S, Kabra M, Chowdhury MR, Bharadwaj D (2004) Molecular characterization of hemophilia B in North Indian families: identification of novel and recurrent molecular events in the factor IX gene. Haematologica 89:1498–1503

    PubMed  CAS  Google Scholar 

  • Majumder PP (1998) People of India: biological diversity and affinities. Evol Anthrop 6:100–110

    Article  Google Scholar 

  • Majumder PP (2001) Ethnic populations of India as seen from an evolutionary perspective. J Biosci 26:533–545

    Article  PubMed  CAS  Google Scholar 

  • Majumder PP, Roy B, Banerjee S, Chakraborty M, Dey B, Mukherjee N, Roy M, Thakurta PG, Sil SK (1999) Human-specific insertion/deletion polymorphisms in Indian populations and their possible evolutionary implications. Eur J Hum Genet 7:435–446

    Article  PubMed  CAS  Google Scholar 

  • Malhotra KC (1978) Morphological composition of the people of India. J Hum Evol 7:45–63

    Article  Google Scholar 

  • Malhotra KC, Vasulu TS (1993) Structure of human populations in India. In: Majumdar PP (ed) Human population genetics: a centennial tribute to JBS Haldane. Plenum Press, New York, pp 207–233

    Google Scholar 

  • Mishra S (1992) The age of the Acheulian in India: new evidence. Curr Anthropol 33:325

    Article  Google Scholar 

  • Misra VN (1992) Stone age in India: an ecological perspective. Man Env 14:17–64

    Google Scholar 

  • Misra VN (2001) Prehistoric human colonization of India. J Biosci 26:491–531

    Article  PubMed  CAS  Google Scholar 

  • Mittal U, Srivastava AK, Jain S, Jain S, Mukerji M (2005) Founder haplotype for Machado-Joseph disease in the Indian population: novel insights from history and polymorphism studies. Arch Neurol 62:637–640

    Article  PubMed  Google Scholar 

  • Mountain JL, Hebert JM, Bhattacharyya S, Underhill PA, Ottolenghi C, Gadgil M, Cavalli-Sforza LL (1995) Demographic history of India and mtDNA-sequence diversity. Am J Hum Genet 56:979–992

    PubMed  CAS  Google Scholar 

  • Mukherjee N, Nebel A, Oppenheim A, Majumder PP (2001) High-resolution analysis of Y-chromosomal polymorphisms reveals signatures of population movements from Central Asia and West Asia into India. J Genet 80:125–135

    Article  PubMed  CAS  Google Scholar 

  • Mukherjee S, Mukhopadhyay A, Banerjee D, Chandak GR, Ray K (2004) Molecular pathology of haemophilia B: identification of five novel mutations including a LINE 1 insertion in Indian patients. Haemophilia 10:259–263

    Article  PubMed  CAS  Google Scholar 

  • Nagarkatti R, Ghosh B (2002) Identification of single-nucleotide and repeat polymorphisms in two candidate genes, interleukin 4 receptor (IL4RA) and signal transducer and activator of transcription protein 6 (STAT6), for Th2 mediated diseases. J Hum Genet 47(12):684–687

    Article  PubMed  CAS  Google Scholar 

  • Nagarkatti R, Rao C-B, Rishi JP, Chetiwal R, Shandilya V, Vijayan V, Kumar R, Pemde HK, Sharma SK, Sharma S, Singh AB, Gangal SV, Ghosh B (2002) Association of IFNG gene polymorphism with asthma in the Indian population. J Allergy Clin Immunol 110:410–412

    Article  PubMed  CAS  Google Scholar 

  • Nagarkatti R, C BR, Vijayan V, Sharma SK, Ghosh B (2004a) Signal transducer and activator of transcription 6 haplotypes and asthma in the Indian population. Am J Respir Cell Mol Biol 31:317–321. Epub 2004 April 22

    Google Scholar 

  • Nagarkatti R, Kumar R, Sharma SK, Ghosh B (2004b) Association of IL4 gene polymorphisms with asthma in North Indians. Int Arch Allergy Immunol 134:206–212. Epub 2004 June 01

    Google Scholar 

  • Pasha MAQ, Khan AP, Kumar R, Ram RB, Grover SK, Srivastava KK, Selvamurthy W, Brahmachari SK (2002) Variations in angiotensin-converting enzyme gene insertion/deletion polymorphism in Indian populations of different ethnic origins. J Biosci 27:67–70

    Article  PubMed  CAS  Google Scholar 

  • Pramanik S, Basu P, Gangopadhaya PK, Sinha KK, Jha DK, Sinha S, Das SK, Maity BK, Mukherjee SC, Roychoudhuri S, Majumder PP, Bhattacharyya NP (2000) Analysis of CAG and CCG repeats in Huntingtin gene among HD patients and normal populations of India. Eur J Hum Genet 8:678–682

    Article  PubMed  CAS  Google Scholar 

  • Rajput C, Makhijani K, Norboo T, Afrin F, Sharma M, Pasha ST, Pasha MAQ (2005) CYP11B2 gene polymorphisms and hypertension in highlanders accustomed to high salt intake. J Hypertens 23:79–86

    Article  PubMed  CAS  Google Scholar 

  • Ramana GV, Chandak GR, Singh L (2000) Sickle cell gene haplotypes in Relli and Thurpu Kapu populations of Andhra Pradesh. Hum Biol 72:535–540

    PubMed  CAS  Google Scholar 

  • Ramana GV, Su B, Jin L, Singh L, Wang N, Underhill P, Chakraborty R (2001) Y-chromosome SNP haplotypes suggest evidence of gene flow among caste, tribe, and the migrant Siddi populations of Andhra Pradesh, South India. Eur J Hum Genet 9:695–700

    Article  PubMed  CAS  Google Scholar 

  • Rao PSS (1984) Inbreeding in India: concepts and consequences. In: Lukacs JR (ed) The people of South Asia. Plenum Press, New York, pp 239–268

    Google Scholar 

  • Roy B, Majumder PP, Dey B, Chakraborty M, Banerjee S, Roy M, Mukherjee N, Sil SK (2001) Ethnic differences in distributions of GSTM1 and GSTT1 homozygous “null” genotypes in India. Hum Biol 73:443–450

    Article  PubMed  CAS  Google Scholar 

  • Roy S, Thakur Mahadik C, Majumder PP (2003) Mitochondrial DNA variation in ranked caste groups of Maharashtra (India) and its implication on genetic relationships and origins. Ann Hum Biol 30:443–454

    Article  PubMed  Google Scholar 

  • Roychoudhury S, Roy S, Basu A, Banerjee R, Vishwanathan H, Usha Rani MV, Sil SK, Mitra M, Majumder PP (2001) Genomic structures and population histories of linguistically distinct tribal groups of India. Hum Genet 109:339–350

    Article  PubMed  CAS  Google Scholar 

  • Saleem Q, Choudhry S, Mukerji M, Bashyam L, Padma MV, Chakravarthy A, Maheshwari MC, Jain S, Brahmachari SK (2000) Molecular analysis of autosomal dominant hereditary ataxias in the Indian population: high frequency of SCA2 and evidence for a common founder mutation. Hum Genet 106:179–187

    Article  PubMed  CAS  Google Scholar 

  • Saleem Q, Muthane U, Verma IC, Brahmachari SK, Jain S (2002) Expanding colonies and expanding repeats. Lancet 359:895–896

    Article  PubMed  Google Scholar 

  • Saleem Q, Roy S, Murgood U, Saxena R, Verma IC, Anand A, Muthane U, Jain S, Brahmachari SK (2003) Molecular analysis of Huntington’s disease and linked polymorphisms in the Indian population. Acta Neurol Scand 108:281–286

    Article  PubMed  CAS  Google Scholar 

  • Sankalia HD (1974) Prehistory and protohistory of India and Pakistan. Deccan College, Poona

    Google Scholar 

  • Sengupta S, Farheen S, Mukherjee N, Dey B, Mukhopadhyay B, Sil SK, Prabhakaran N, Ramesh A, Edwin D, Usha Rani MV, Mitra M, Mahadik CT, Singh S, Sehgal SC, Majumder PP (2004) DNA sequence variation and haplotype structure of the ICAM1 and TNF genes in 12 ethnic groups of India reveal patterns of importance in designing association studies. Ann Hum Genet 68:574–587

    Article  PubMed  CAS  Google Scholar 

  • Sharma S, Ghosh B (2004) Association of an intragenic microsatellite marker in the CC16 gene with asthma in the Indian population. J Hum Genet 49:677–683. Epub 2004 November 12

    Google Scholar 

  • Sharma S, Nagarkatti R, B-Rao C, Niphadkar PV, Vijayan V, Sharma SK, Ghosh B (2004) A three locus haplotype, A_16_C, in Fc epsilon RI beta gene confers higher risk for atopic asthma. Clin Genet 66:417–425

    Article  PubMed  CAS  Google Scholar 

  • Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311

    Article  PubMed  CAS  Google Scholar 

  • Singh KS (2002) People of India: introduction national series. Anthropological Survey of India-Oxford University Press, Delhi

    Google Scholar 

  • Tapadar P, Ghosh S, Majumder PP (2000) Haplotyping in pedigrees via a genetic algorithm. Hum Hered 50:43–56

    Article  PubMed  CAS  Google Scholar 

  • Thangaraj K, Ramana GV, Singh L (1999) Y-chromosome and mitochondrial DNA polymorphisms in Indian populations. Electrophoresis 20:1743–1747

    Article  PubMed  CAS  Google Scholar 

  • Thangaraj K, Joshi MB, Reddy AG, Gupta NJ, Chakravarty B, Singh L (2002) CAG repeat expansion in the androgen receptor gene is not associated with male infertility in Indian populations. J Androl 23:815–818

    PubMed  CAS  Google Scholar 

  • The International HapMap Consortium (2003) The international HapMap Project. Nature 426:789–796

    Google Scholar 

  • Verma R, Chauhan C, Saleem Q, Gandhi C, Jain S, Brahmachari SK (2004) A nonsense mutation in the synaptogyrin 1 gene in a family with schizophrenia. Biol Psychiatry 55:196–199

    Article  PubMed  CAS  Google Scholar 

  • Verma R, Mukerji M, Grover D, Rao CB, Das SK, Kubendran S, Jain S, Brahmachari SK (2005) MLC1 gene is associated with schizophrenia and bipolar disorder in Southern India. Biol Psychiatry (in press)

Download references

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).

Author information

Authors and Affiliations

    Consortia

    The Indian Genome Variation Consortium

    Electronic supplementary material

    Appendix

    Appendix

      Box 1 The Indian Genome Variation database consortium
    Full size table

    Rights and permissions

    Reprints and permissions

    About this article

    Cite this article

    The Indian Genome Variation Consortium. The Indian Genome Variation database (IGVdb): a project overview. Hum Genet 118, 1–11 (2005). https://doi.org/10.1007/s00439-005-0009-9

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

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

    Keywords

    Search

    Navigation