IGVBrowser-a genomic variation resource from diverse Indian populations

A Narang,A Chaurasia,R D Roy,M Mukerji,D Dash,A Mukhopadhyay

doi:10.1093/database/baq022

Abstract

The Indian Genome Variation Consortium (IGVC) project, an initiative of the Council for Scientific and Industrial Research, has been the first large-scale comprehensive study of the Indian population. One of the major aims of the project is to study and catalog the variations in nearly thousand candidate genes related to diseases and drug response for predictive marker discovery, founder identification and also to address questions related to ethnic diversity, migrations, extent and relatedness with other world population. The Phase I of the project aimed at providing a set of reference populations that would represent the entire genetic spectrum of India in terms of language, ethnicity and geography and Phase II in providing variation data on candidate genes and genome wide neutral markers on these reference set of populations. We report here development of the IGVBrowser that provides allele and genotype frequency data generated in the IGVC project. The database harbors 4229 SNPs from more than 900 candidate genes in contrasting Indian populations. Analysis shows that most of the markers are from genic regions. Further, a large fraction of genes are implicated in cardiovascular, metabolic, cancer and immune system-related diseases. Thus, the IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology. Additionally, it also houses data on ∼50 000 (Affy 50 K array) genome wide neutral markers in these reference populations. In IGVBrowser one can analyze and compare genomic variations in Indian population with those reported in HapMap along with annotation information from various primary data sources.Database URL: http://igvbrowser.igib.res.in

Highlights

Indian population representing one-sixth of the world population has been the global melting pot of human diversity. It has all the world’s major linguistic groups and the populations have been shaped by different waves of migrations and admixture [1, 2]
The Indian Genome Variation Consortium (IGVC) project, an initiative of the Council for Scientific and Industrial Research (CSIR)—was set up to develop a database of genomic variations in Indian population for predictive marker discovery in complex diseases such as diabetes, asthma, neuropsychiatric, infectious and cardiovascular disorders, response to drugs, etc
The Phase I of the project was conducted to determine the extent of genetic differentiation in India. Toward this genotype data of 405 SNPs from 75 genes and 4.2 Mb contiguous chromosome 22 regions were studied in 55 contrasting populations [4, 5]. These populations were identified from 4 major linguistic groups namely, Austro-Asiatic (AA), Tibeto-Burman (TB), Indo-European (IE) and Dravidian(DR) spanning 6 geographical regions of habitat (N, north; NE, north-east; W, west; E, east; S, south; C, central) and different ethnic groups

Summary

Database tool

The Indian Genome Variation Consortium (IGVC) project, an initiative of the Council for Scientific and Industrial Research, has been the first large-scale comprehensive study of the Indian population. The Phase I of the project aimed at providing a set of reference populations that would represent the entire genetic spectrum of India in terms of language, ethnicity and geography and Phase II in providing variation data on candidate genes and genome wide neutral markers on these reference set of populations. The IGVC data provide a basal level variation data in Indian population to study genetic diseases and pharmacology. It houses data on 50 000 (Affy 50 K array) genome wide neutral markers in these reference populations. In IGVBrowser one can analyze and compare genomic variations in Indian population with those reported in HapMap along with annotation information from various primary data sources

Introduction

Data Source and Organization

Future directions