IGVBrowser-a genomic variation resource from diverse Indian populations

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

Medical genetics and genomic medicine in India: current status and opportunities ahead

“…Overall there are more than 4000 anthropologically distinct groups and 22 languages with various dialects in this diverse nation (Majumdar ; Narang et al. ; Tamang et al. ).…”

“…This forms an important database for design of further studies of multifactorial as well as single gene disorders (Narang et al. ). The geographical & linguistic disparity is further complicated by the caste system and religious boundaries, which are associated with high degree of endogamy, although recent reports have indicated some degree of admixture (Tripathi et al.…”

“…Sequencing of the first Indian genome and establishment of the Indian Genome Variation Consortium have been notable landmarks achieved by these scientific groups which are likely to further genetic research in the field of both complex and Mendelian genetics (Narang et al. ). Besides playing pivotal role in scientific research, many national funding organizations have also been instrumental in the establishment of DNA based diagnostics and medical genetics centers since last three decades.…”

“…The majority of the modern Indian population is an admixture of two large genetically divergent and heterogeneous population groups that mixed in ancient times (about 1200-3500 BC), known as Ancestral North Indians (ANI) or the Caucasoids and Ancestral South Indians (ASI) or the Australoids. Overall there are more than 4000 anthropologically distinct groups and 22 languages with various dialects in this diverse nation (Majumdar 2010;Narang et al 2010;Tamang et al 2012). Genetic studies for classifying the population into subgroups and identifying the origins have been at the best incomplete due to the vast population and extreme complexity.…”

Genetic counseling education at the undergraduate level: An outreach initiative to promote professional recruitment and support workforce development

“…Much of the modern Indian population is a genetic admixture of two large, divergent populations; Ancestral North Indians and Ancestral South Indians (Moorjani et al, 2013). There are more than 4,500 anthropologically defined groups (Majumdar, 2010; Narang, Roy, Chaurasia, Mukhopadhyay, & Mukerji, 2010). Consanguinity as well as endogamous marriages are prevalent in certain communities (Aggarwal & Phadke, 2015; Bittles, 2002).…”