An integrated and diverse genomic medicine program for undiagnosed diseases

针对未确诊疾病的综合且多样化的基因组医学计划

• 批准号: 10376398
• 负责人: VANDANA SHASHI
• 金额: $ 14.99万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10376398
• 关键词: Bioinformatics; Candidate Disease Gene; Clinical; Custom; DNA Sequencing Facility; Data; Data Analyses; Data Storage and Retrieval; Diagnosis; Diagnostic; Disease; Effectiveness; Funding; Future; Genes; Genome; Genomic medicine; Genomics; Human Resources; Individual; Infrastructure; Laboratories; Link; Methods; Modeling; Output; Pathogenicity; Patients; Phenotype; Pilot Projects; Principal Investigator; Process; Publications; Reporting; Research; Resources; Running; Sequence Analysis; Site; Structure; Time; Variant; base; bioinformatics pipeline; bioinformatics tool; clinical research site; computer infrastructure; cost; cost efficient; exome; exome sequencing; family structure; file format; gene discovery; genetic variant; genome analysis; genome sequencing; genomic data; innovation; novel; programs; prospective; prototype; relative effectiveness; secondary analysis; variant of unknown significance

Abstract The full breadth of the clinical sites research based genomic analyses is resource intensive, requiring bioinformatics personnel and more expensively, a laboratory with computing infrastructure and storage capabilities. With the funding of the clinical sites of the UDN beyond 2022 being uncertain, exploring cost-efficient and at the same time effective strategies for genome analyses at the clinical sites is crucial to maintaining the scientific edge of the network. Our proposed project will evaluate an alternative pipeline for effectiveness and efficiency in the analysis of exome and genome sequencing data at the Duke/Columbia clinical site. We will customize a commercial platform to conform closely to our research pipeline. We will run this pipeline simultaneous to the sequencing core analyses and evaluate the relative effectiveness of this new analysis structure in determining pathogenic and likely pathogenic variants and novel candidate gene variants. If effective, such a paradigm might provide a less resource heavy approach to analyzing genomic data at the clinical sites. We believe that this pilot project will provide a paradigm for analyses of genomic data at the UDN clinical sites while maintaining most of the scientific rigor that has contributed to the diagnostic capabilities of the network and may offer a path forward for sustainability.

抽象的 基于临床站点的全部广度研究基因组分析是资源密集的， 需要生物信息学人员，更昂贵的是计算的实验室 基础架构和存储功能。在UDN的临床部位的资金中 在2022年以后，不确定，探索成本效益，同时有效 在临床部位进行基因组分析的策略对于维持科学的策略至关重要 网络的边缘。 我们提议的项目将评估替代管道的有效性和效率 杜克/哥伦比亚临床部位的外显子组和基因组测序数据的分析。我们 将定制一个商业平台，以符合我们的研究管道。我们将运行 该管道同时与测序核心分析并评估相对 这种新分析结构在确定致病性和可能致病性的有效性 变体和新型候选基因变体。如果有效，这样的范式可能会提供 在临床部位分析基因组数据的资源较少方法。 我们认为，该试点项目将为分析基因组数据的范例 UDN临床部位，同时维持大多数科学严谨性 网络的诊断功能，可能为可持续性提供前进的途径。