PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data.
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DOI：
10.1186/s13023-021-01916-z
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发表时间：
2021-08-18
影响因子：
3.7
通讯作者：
Sobreira N
中科院分区：
文献类型：
--
作者：
Wohler E;Martin R;Griffith S;Rodrigues EDS;Antonescu C;Posey JE;Coban-Akdemir Z;Jhangiani SN;Doheny KF;Lupski JR;Valle D;Hamosh A;Sobreira N
随着全外显子组 (ES) 和基因组测序 (GS) 作为疾病基因发现工具的出现，罕见变异过滤、优先级排序和数据共享已成为寻找可能导致疾病表型的疾病基因和变异的重要组成部分。对 ES 和 GS 中分别识别的数千至数百万个变异进行计算存储、数据操作和生物信息学解释是一项具有挑战性的任务。为了帮助实现这一目标，我们构建了 PhenoDB、GeneMatcher 和 VariantMatcher。 PhenoDB 是一个可访问、免费提供的基于网络的平台，允许用户存储、共享、分析和解释患者的 ES/GS 数据表型和变异。 GeneMatcher 作为一种基于网络的工具可供所有利益相关者使用，旨在将全球各地对相同基因、变异或表型感兴趣的个人（研究人员、临床医生、医疗保健提供者和患者）联系起来。最后，VariantMatcher 的开发是为了使公众能够共享作为多种疾病基因发现项目的一部分而测序的个体的变异水平数据和表型信息。在这里，我们提供 PhenoDB 和 GeneMatcher 应用程序和实现的更新，并介绍 VariantMatcher。这些工具都促进了全球数据共享和数据分析，并提高了我们将基因与表型性状联系起来的能力。这些平台的进一步开发将扩大变异分析、解释、新疾病基因发现，并促进人类基因组的功能注释，以实现临床基因组学实施和精准医学计划。在线版本包含可在 10.1186/s13023-021-01916-z 获取的补充材料。
With the advent of whole exome (ES) and genome sequencing (GS) as tools for disease gene discovery, rare variant filtering, prioritization and data sharing have become essential components of the search for disease genes and variants potentially contributing to disease phenotypes. The computational storage, data manipulation, and bioinformatic interpretation of thousands to millions of variants identified in ES and GS, respectively, is a challenging task. To aid in that endeavor, we constructed PhenoDB, GeneMatcher and VariantMatcher. PhenoDB is an accessible, freely available, web-based platform that allows users to store, share, analyze and interpret their patients’ phenotypes and variants from ES/GS data. GeneMatcher is accessible to all stakeholders as a web-based tool developed to connect individuals (researchers, clinicians, health care providers and patients) around the globe with interest in the same gene(s), variant(s) or phenotype(s). Finally, VariantMatcher was developed to enable public sharing of variant-level data and phenotypic information from individuals sequenced as part of multiple disease gene discovery projects. Here we provide updates on PhenoDB and GeneMatcher applications and implementation and introduce VariantMatcher. Each of these tools has facilitated worldwide data sharing and data analysis and improved our ability to connect genes to phenotypic traits. Further development of these platforms will expand variant analysis, interpretation, novel disease-gene discovery and facilitate functional annotation of the human genome for clinical genomics implementation and the precision medicine initiative. The online version contains supplementary material available at 10.1186/s13023-021-01916-z.
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DOI：
10.1038/gim.2013.73
发表时间：
2013-07
期刊：
Genetics in medicine : official journal of the American College of Medical Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
14.9
作者：
Buniello, Annalisa;MacArthur, Jacqueline A. L.;Parkinson, Helen
通讯作者：
Parkinson, Helen
影响因子：
64.8
作者：
Karczewski, Konrad J;Francioli, Laurent C;MacArthur, Daniel G
通讯作者：
MacArthur, Daniel G
影响因子：
3.9
作者：
Sobreira N;Schiettecatte F;Boehm C;Valle D;Hamosh A
通讯作者：
Hamosh A