Functional annotation of genomic variants in studies of late-onset Alzheimer's disease
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease
复制标题
晚期阿尔茨海默病研究中基因组变异的功能注释
DOI：
10.1093/bioinformatics/bty177
复制
发表时间：
2018-08-15
期刊：
影响因子：
5.8
通讯作者：
Bush, William S.
中科院分区：
文献类型：
--
作者：
Butkiewicz, Mariusz;Blue, Elizabeth E.;Bush, William S.
动机：基因组变异的注释是基于序列的基因组分析中越来越重要和复杂的部分。变异功能的计算预测通常被纳入罕见变异的基因分析中，尽管迄今为止大多数研究使用有限的信息来评估变异功能，这些信息通常与所研究的疾病无关。在这项工作中，我们概述了阿尔茨海默病测序项目的注释过程，说明包括组织特异性转录本集和基因调控信息来源的影响，并评估改变基因组构建对注释过程的潜在影响。虽然这些因素只影响总变异注释的一小部分（类似于5%），但它们影响大部分基因的潜在分析（类似于25%）。可用性和实施：通过NIAGADS GenomicsDB可获得个体变异注释，网址为www.example.com。注释也可在www.example.com批量下载，处理软件可在www.example.com：wsb36@case.edu补充信息：补充数据可在生物信息学在线获得。
Motivation: Annotation of genomic variants is an increasingly important and complex part of the analysis of sequence-based genomic analyses. Computational predictions of variant function are routinely incorporated into gene-based analyses of rare-variants, though to date most studies use limited information for assessing variant function that is often agnostic of the disease being studied.Results: In this work, we outline an annotation process motivated by the Alzheimer's Disease Sequencing Project, illustrate the impact of including tissue-specific transcript sets and sources of gene regulatory information and assess the potential impact of changing genomic builds on the annotation process. While these factors only impact a small proportion of total variant annotations (similar to 5%), they influence the potential analysis of a large fraction of genes (similar to 25%).Availability and implementation: Individual variant annotations are available via the NIAGADS GenomicsDB, at https://www.niagads.org/genomics/tools-and-software/databases/genomics-database. Annotations are also available for bulk download at https://www.niagads.org/datasets.Annotation processing software is available at http://www.icompbio.net/resources/software-and-downloads/.Contact: wsb36@case.eduSupplementary information: Supplementary data are available at Bioinformatics online.