INDICO: the development of a resource for epigenomic study of Indians undergoing socioeconomic transition

INDICO brings together the expertise and experience of clinicians, scientists, and young researchers involved in diabetes research from all over the country (Supplementary Figure 1), that will lead to capacity building for high-end genetic, epigenetic, and proteomic studies in India in terms of sample repository, infrastructure, and skilled manpower. The resources developed by INDICO can bestow: (1) GWAS to discover genes associated with T2D and related metabolic traits, (2) Effect of lifestyle transitions by re-sampling from the same areas at regular intervals, (3) Gene expression profiling of different tissues to identify differentially expressed genes in T2D, (4) Deep re-sequencing to discover rare variants with high penetrance, (5) Proteomic and metabolite studies to develop pre-diagnostic markers for T2D and related traits, (6) Metagenomics to understand the difference in gut micro-biota in T2D and normal individuals, and (7) Exchange of knowledge and experiences across the globe to counter disease burden.

Moreover, the consortium is also actively engaged in identification of novel genes and pathways for T2D through different strategies including in silico candidate gene prioritization, in silico function prediction and in vitro functional analyses (Sharma et al. 2010). The consortium monitors the effects of urbanization on a population-in-transition by re-sampling at regular intervals from the same geographical locations. The time range of sample collection (2003–2011) coincides with the rapid increase in the Gross Domestic Product (GDP) growth of the Indian economy (World Development Indicator 2011). We have already observed an apparent clinical shift in the major biochemical parameters (lipid profile & Hb1Ac) in congruence with the rise in GDP (Fig. 2) indicating an epidemiological transition in progress. This gives us an unprecedented opportunity to probe the correlation, if any, between genetic and epigenetic changes in the genome and rapid changes in lifestyle.

The INDICO bio-repository opens up new avenues to initiate large-scale studies that can unravel new risk factors and pre-diagnostic markers at the genetic, epigenetic, metabolite, and proteomic levels for T2D, its associated and related traits. DNA repository will serve as a valuable resource to understand the synergistic role of genetic and epigenetic factors in the pathogenesis of T2D through large-scale studies. Our previous candidate gene studies which identified a couple of novel putative T2D genes, (Tabassum et al. 2008, 2010) suggest that exploration of genetic factors in Indian population can lead to better understanding of T2D. This huge DNA repository also provides opportunity to discover rare variants for T2D that will be a testimony for the “mosaic model” (Sharma et al. 2005) which propose that T2D results from interactions among large number of rare alleles, smaller number of common alleles and the environment. Recently we have completed the genotyping of the first type 2 diabetes GWAS in Indian population using the 610 Quad chips. We expect this GWAS to not only reveal novel loci for T2D but also serve as a dataset for GWA analysis for large number of anthropometric and quantitative metabolic traits such as BMI, blood pressure, plasma glucose, lipids, etc.

Apart from this, the whole genome genotyping data of the 1,250 controls which are well characterized can also be used as control dataset for number of other complex disorders such as type 1 diabetes, chronic pancreatitis, hypertension, polycystic kidney disorder etc. Proteome analysis at different pre-disease and disease states can lead to the identification of protein and metabolic biomarkers that may be predictive of the disease manifestation. Differential gene expression and methylation profiles would be a key to mechanistically dissecting the development of the disease and identifying novel drug targets. To aid this, the tissue repository will allow tissue specific epigenetic and gene expression studies for T2D. Moreover, the superimposition of GWAS data with these exhaustive epigenetic and proteomics profiling will help us understand the correlation between the genome, proteome and epigenome, thus revealing example of gene environment interaction. This will be crucial in developing a complete picture of the disease leading to better treatment and healthcare policy.

The consortium deemed the resource fabrication pertinent to divulge the risk factors accountable for the high vulnerability of Indians to T2D by identifying pre-diagnostic markers at genetic, epigenetic, metabolite and proteomic levels for managing T2D and other related life style disorders. We also hope that INDICO will eventually be of value to not just the diabetes research community but would be able to contribute towards an improved understanding, diagnosis and prevention of numerous complex human disorders.