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

Jimmy F. Zhang, Francis James, Anju Shukla, Katta M. Girisha, Alex R. Paciorkowski

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Article number233
JournalBMC Research Notes
Volume10
Issue number1
DOIs
Publication statusPublished - 27-06-2017

Fingerprint

India
Alleles
Exome
Population
Nucleotides
Genes
Research Personnel
Metagenomics
Genomics
Genome
Databases
Research

All Science Journal Classification (ASJC) codes

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

@article{a7dcf4f0260b4a20a5706bf6fe4d5881,
title = "India Allele Finder: A web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin",
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.",
author = "Zhang, {Jimmy F.} and Francis James and Anju Shukla and Girisha, {Katta M.} and Paciorkowski, {Alex R.}",
year = "2017",
month = "6",
day = "27",
doi = "10.1186/s13104-017-2556-2",
language = "English",
volume = "10",
journal = "BMC Research Notes",
issn = "1756-0500",
publisher = "BioMed Central",
number = "1",

}

India Allele Finder : A web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin. / Zhang, Jimmy F.; James, Francis; Shukla, Anju; Girisha, Katta M.; Paciorkowski, Alex R.

In: BMC Research Notes, Vol. 10, No. 1, 233, 27.06.2017.

Research output: Contribution to journalArticle

TY - JOUR

T1 - India Allele Finder

T2 - A web-based annotation tool for identifying common alleles in next-generation sequencing data of Indian origin

AU - Zhang, Jimmy F.

AU - James, Francis

AU - Shukla, Anju

AU - Girisha, Katta M.

AU - Paciorkowski, Alex R.

PY - 2017/6/27

Y1 - 2017/6/27

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85021296255&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85021296255&partnerID=8YFLogxK

U2 - 10.1186/s13104-017-2556-2

DO - 10.1186/s13104-017-2556-2

M3 - Article

AN - SCOPUS:85021296255

VL - 10

JO - BMC Research Notes

JF - BMC Research Notes

SN - 1756-0500

IS - 1

M1 - 233

ER -