The Indian Genome Variation Consortium: understanding population substructures, disease factors and drug response in the diverse Indian population

Saman Habib

(representing 35 researchers of the consortium)

Division of Molecular & Structural Biology,

 Central Drug Research Institute, Lucknow, India

The Indian Genome Variation Consortium (IGVC) formed by researchers of six constituent laboratories of the Council of Scientific and Industrial Research (CSIR) aims to generate a SNP database for the population of India with particular reference to genes associated with predisposition to complex disorders, variable drug responses and susceptibility to infectious disease. The Indian population comprises more than 4000 communities and several thousand endogamous groups and data generated under the consortium is also envisaged to answer questions related to ethnic diversity, founder populations and migrations. The project aims to generate SNP data for about 1000 genes and validate this in 15,000 individuals representative of the diverse spectrum of Indian subpopulations. In the initial phase, the consortium selected a discovery panel of 43 samples (DSNP panel) for SNP identification by DNA sequencing. The results from this panel were validated in a larger validation panel of ~1700 samples from 42 subpopulations primarily by DNA mass spectroscopy. Analysis of 463 SNPs (of which ~20% are novel) from 74 important disease and pharmacogenomic candidates, a 6Mb region on Chr22 has revealed interesting overlaps with the linguistic categorization of the Indian population. Genetic association between subpopulations classified in different linguistic groups has also been seen. Comparison of linkage patterns with HAPMAP population data shows distinct affinities between specific Indian subpopulations and two HAPMAP populations. Data generated under the consortium is also being used by researchers for their respective disease association and pharmacogenomic studies and is expected to result in improved understanding of disease predisposition and differential drug responses.