India Allele Finder: a web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin

Abstract

ObjectiveWe built India Allele Finder, an online searchable database and command line tool, that gives researchers access to variant frequencies of Indian Telugu individuals, using publicly available fastq data from the 1000 Genomes Project. Access to appropriate population-based genomic variant annotation can accelerate the interpretation of genomic sequencing data. In particular, exome analysis of individuals of Indian descent will identify population variants not reflected in European exomes, complicating genomic analysis for such individuals.ResultsIndia Allele Finder offers improved ease-of-use to investigators seeking to identify and annotate sequencing data from Indian populations. We describe the use of India Allele Finder to identify common population variants in a disease quartet whole exome dataset, reducing the number of candidate single nucleotide variants from 84 to 7. India Allele Finder is freely available to investigators to annotate genomic sequencing data from Indian populations. Use of India Allele Finder allows efficient identification of population variants in genomic sequencing data, and is an example of a population-specific annotation tool that simplifies analysis and encourages international collaboration in genomics research.

Ophthalmic genetics practice and research in India: Vision in 2020

“…Among the initial studies, Indian Genomic Variation Consortium, reported the SNPs associated with CYP1B1 gene, important in glaucoma, and showed its association with ethnic diversity distribution in the country (Indian Genome Variation Consortium, 2008). India Allele Finder, curated and presented data from the 1,000 genome browser (Zhang, James, Shukla, Girisha, & Paciorkowski, 2017). Among the multiple forums for rare diseases in India, organizations such as the Organization for Rare Diseases in India, ORDI, have developed a platform for all information regarding rare diseases in India, catering to the patients.…”

“…Consortium, 2008). India Allele Finder, curated and presented data from the 1,000 genome browser (Zhang, James, Shukla, Girisha, & Paciorkowski, 2017). Among the multiple forums for rare diseases in India, organizations such as the Organization for Rare Diseases in India, ORDI, have developed a platform for all information regarding rare diseases in India, catering to the patients.…”