IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes

Abstract

With the advent of next-generation sequencing, large-scale initiatives for mining whole genomes and exomes have been employed to better understand global or population-level genetic architecture. India encompasses more than 17% of the world population with extensive genetic diversity, but is under-represented in the global sequencing datasets. This gave us the impetus to perform and analyze the whole genome sequencing of 1029 healthy Indian individuals under the pilot phase of the ‘IndiGen’ program. We generated a compendium of 55,898,122 single allelic genetic variants from geographically distinct Indian genomes and calculated the allele frequency, allele count, allele number, along with the number of heterozygous or homozygous individuals. In the present study, these variants were systematically annotated using publicly available population databases and can be accessed through a browsable online database named as ‘IndiGenomes’ http://clingen.igib.res.in/indigen/. The IndiGenomes database will help clinicians and researchers in exploring the genetic component underlying medical conditions. Till date, this is the most comprehensive genetic variant resource for the Indian population and is made freely available for academic utility. The resource has also been accessed extensively by the worldwide community since it's launch.

Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency

“…However, India is underrepresented in global genome studies despite encompassing 17% of the world population. The diverse anthropologically distinct populations in India result in a high prevalence of recessive alleles (Jain et al, 2021). In India, the practice of marriage within small communities is quite common, giving rise to inbreeding.…”

Pharmacogenomic Landscape of Covid-19 Therapies From Indian Population Genomes

“…The genetic variants and their allele frequencies in the cosmopolitan Indian population were obtained from Variant Calling Format of 1029 whole genome sequences of unrelated Indian individuals, sequenced across India as a part of IndiGen [ 16 ] study. The participants of the IndiGen study spread across most states in India [ 16 ]. The variants are annotated according to the GRCh38 human reference genome and genotype information of 55,898,112 genetic variations consisting of SNVs and indels.…”

“…In the last 5 years, several large-scale national genomic sequencing initiatives have been established with the aim of advancing genomic medicine and generating population-specific evidence for its wider adoption in clinical practice [ 15 ]. Recently, India has initiated its own national genome sequencing initiative, the IndiGen Project, which in its first phase has successfully sequenced over 1029 Indian whole genomes belonging to diverse ethnic groups in India [ 16 ]. The IndiGen dataset along with the South Asian subpopulations included in the 1000 Genomes project (n = 489) collectively represent one of the most comprehensive genomic representations of the geographic and ethnic diversity of the Indian population available as of today.…”

A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early‐onset monogenic disorders in Indians

“…The current representation of the Indians in the available variant databases or data sets is illustrated in Table 2. We would like to emphasize the term “Asians” is a geographic descriptor for ethnically diverse Chinese, Indian and South‐Eastern populations and often the second most populous country is not included in the studies on “Asians.” IndiGenomes (Jain et al, 2020), a recent addition and Singapore Genome Project (Wu et al, 2019) are the currently available large data sets for Indians. These data sets are far from capturing the complete spectrum of genomic variation of the Indian population.…”