GeneMatcher, VariantMatcher and PhenoDB, implementation of new features and connections

GeneMatcher、VariantMatcher 和 PhenoDB，新功能和连接的实现

• 批准号: 10605159
• 负责人: Nara Sobreira
• 金额: $ 58.14万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-07 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10605159
• 关键词: Affect; Bioinformatics; Code; Collaborations; Communities; Consent; Country; DNA Sequence Analysis; Data; Data Analyses; Databases; Development; Disease; Education; Educational workshop; Electronic Mail; Family; Frequencies; Genes; Genetics and Medicine; Genome; Genomic medicine; Genomics; Genotype; Human; Individual; Internet; Java; Learning Module; Link; Maps; Metadata; Methods; Mitochondrial DNA; Molecular; Notification; Orthologous Gene; Patients; Phenotype; Proteins; Publications; Pythons; Rare Diseases; Research Personnel; Resources; Single Nucleotide Polymorphism; Source Code; Stream; Students; Variant; Visualization; Work; analysis pipeline; data integration; data sharing; exome sequencing; gene discovery; genome sequencing; genomic data; improved; insertion/deletion mutation; interest; lectures; member; model organism; novel; online resource; phenome; phenotypic data; programs; public database; search engine; sharing platform; therapy development; tool; tool development; user-friendly; web-based tool

Project Summary/Abstract The interpretation of thousands to millions of variants identified in whole exome and genome sequencing (WES/WGS), respectively, is a challenging task and requires variant frequency together with phenotype information that are not available in most public databases. The development of tools that enable data sharing of genomic data together with phenotypic features is essential for rare disease gene discovery. In 2013 we created GeneMatcher (10,574 users in 93 countries, cited in >380 publications), the first and most used web- based tool to connect individuals (researchers, clinicians, patients, etc) around the globe with interest in the same genes, variants or phenotypes. In 2019, we developed VariantMatcher (625 users in 43 countries, 428 queried variants, 61 matched variants), to share variant-level and phenotypic data from WES/WGS. To enable variant prioritization for investigators around the world, we developed PhenoDB (> 143 unique downloads of source code, 1,828 users from 65 countries). This freely available, web-based tool allows users naïve to bioinformatics to store, share, analyze and interpret patient phenotypes and sequence variants from WES/WGS. Users currently store in one instance of PhenoDB extensive phenotypic data (described with 3,646 terms mapped to HPO) from 37,712 individuals in 9,711 families with an average of 6.8 features/affected individual, describing > 2,282 diseases. Annotated WES/WGS variants are available for 7,724 individuals from 4,446 families. PhenoDB facilitates data sharing and analysis access world-wide. As of 1 December 2020, 6,151 sequenced individuals in PhenoDB were consented and submitted for phenotypic and genotypic matching through VariantMatcher. However, the ongoing development of new sequencing methods, analysis pipelines and data sharing platforms requires development of novel functions in our highly utilized resources and integration with other newly created platforms to ensure that thousands of investigators can perform state of the art analysis of genomic and phenotypic data to better interpret candidate variants. There is a critical need to maintain and improve tools that allow genomic and phenotypic data integration and sharing. To fill this need, we will leverage input from users of PhenoDB, GeneMatcher and VariantMatcher, collaborations with creators of tools and platforms with complementary functions, and our evolving expertise in sequencing analysis and gene discovery to improve our community resources. To this end, we will: 1. Implement new functions in GeneMatcher, VariantMatcher and PhenoDB to enable additional types of queries, variant filtering and prioritization pipelines. 2. Connect GeneMatcher and VariantMatcher with other, community-wide data sharing tools and integrate PhenoDB with other workflow platforms. 3. Expand our PhenoDB Genomic Education program.

项目摘要/摘要 在整个外显子组和基因组测序中鉴定的数千种变体的解释 （WES/WGS）分别是一项挑战任务，需要变异频率与表型一起 大多数公共数据库中无法使用的信息。开发启用数据共享的工具 基因组数据以及表型特征的含量对于罕见疾病基因发现至关重要。在2013年我们 创建了GeneMatcher（在93个国家 /地区的10,574个用户，在> 380个出版物中引用），这是第一个也是最常用的Web- 基于对全球的个人（研究人员，临床医生，患者等）连接个人的工具 相同的基因，变体或表型。在2019年，我们开发了变体（43个国家 /地区的625位用户，428个用户 查询变体，61个匹配的变体），共享WES/WGS的变体级别和表型数据。启用 我们为世界各地的调查人员的变体优先级排序，我们开发了PhenoDB（> 143个独特的下载 源代码，来自65个国家 /地区的1,828位用户）。这种免费的基于网络的免费工具使用户幼稚 生物信息学以存储，共享，分析和解释WES/WGS的患者表型和序列变体。 用户目前存储在PenodB广泛的表型数据的一个实例中（描述了3,646个术语 从9,711个家庭中的37,712个人映射到HPO），平均功能/受影响的个体， 描述> 2,282种疾病。带注释的WES/WGS变体可用于4,446的7,724个人 家庭。 PENODB收藏夹数据共享和分析在全球范围内访问。截至2020年12月1日，6,151 同意的phenoDB中的测序个体进行表型和基因型匹配 通过VariantMatcher。但是，新测序方法的持续开发，分析管道 数据共享平台需要在我们高度利用的资源和 与其他新创建的平台集成，以确保成千上万的调查人员可以执行状态 基因组和表型数据的艺术分析，以更好地解释候选变异。迫切需要 维护和改进允许基因组和表型数据集成和共享的工具。为了满足这一需求，我们 将利用PhenoDB，GeneMatcher和VariantMatcher的用户的投入，与创建者的合作 具有完整功能的工具和平台，以及我们在测序分析和基因方面的进化专业知识 发现以改善我们的社区资源。为此，我们将： 1。在GeneMatcher，VariantMatcher和PenodB中实现新功能，以启用其他类型的 查询，变体过滤和优先级管道。 2。将GeneMatcher和VariantMatcher与其他社区范围的数据共享工具和 与其他工作流平台集成的PhenoDB。 3。扩展我们的PenoDB基因组教育计划。