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

Shukla, Anju and Girisha, KM (2017) India Allele Finder: a web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin. BMC Research Notes, 10. pp. 233-236. ISSN 1756-0500

[img] PDF
00002809.pdf - Published Version
Restricted to Registered users only

Download (859kB) | Request a copy

Abstract

Objective : We 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. Results :India 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.

Item Type: Article
Uncontrolled Keywords: Population genomics; India Variant annotation ;Whole exome sequencing.
Subjects: Medicine > KMC Manipal > Paediatrics
Depositing User: KMC Library
Date Deposited: 04 Jul 2017 08:57
Last Modified: 04 Jul 2017 08:57
URI: http://eprints.manipal.edu/id/eprint/149245

Actions (login required)

View Item View Item