Zhang Jimmy F, James Francis, Shukla Anju, Girisha Katta M, Paciorkowski Alex R
Center for Neurotherapeutics Development, University of Rochester Medical Center, Rochester, NY, USA.
Rochester Institute of Technology, Rochester, NY, USA.
BMC Res Notes. 2017 Jun 27;10(1):233. doi: 10.1186/s13104-017-2556-2.
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.
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.
我们构建了印度等位基因查找工具（India Allele Finder），这是一个在线可搜索数据库和命令行工具，它利用千人基因组计划中公开可用的fastq数据，让研究人员能够获取印度泰卢固族个体的变异频率。获取基于适当人群的基因组变异注释可以加速基因组测序数据的解读。特别是，对印度裔个体的外显子组分析会发现欧洲外显子组中未体现的人群变异，这会使此类个体的基因组分析变得复杂。
印度等位基因查找工具为试图识别和注释来自印度人群的测序数据的研究人员提供了更高的易用性。我们描述了使用印度等位基因查找工具在一个疾病四重奏全外显子组数据集中识别常见人群变异的情况，将候选单核苷酸变异的数量从84个减少到了7个。研究人员可免费使用印度等位基因查找工具来注释来自印度人群的基因组测序数据。使用印度等位基因查找工具能够高效识别基因组测序数据中的人群变异，它是一个特定人群注释工具的范例，该工具简化了分析并鼓励在基因组研究中开展国际合作。
