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.

摘要 基于基因组分析的临床站点研究的全部广度是资源密集型的， 需要生物信息学人员，更昂贵的是，需要一个实验室， 基础设施和存储能力。在UDN临床研究中心的资助下， 2022年以后的不确定性，探索成本效益，同时有效 在临床地点进行基因组分析的策略对于保持科学的 网络的边缘。 我们建议的项目将评估替代管道的有效性和效率， 在杜克/哥伦比亚临床研究中心对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，以密切符合我们的研究管道。我们将运行 该管道同时对测序岩心进行分析和评价， 这种新的分析结构在确定致病性和可能致病性方面的有效性 变体和新的候选基因变体。如果有效的话，这种模式可能会提供一个 在临床站点分析基因组数据的资源较少的方法。 我们相信，这一试点项目将提供一个范例，分析基因组数据在 UDN临床网站，同时保持了大部分的科学严谨性，有助于 网络的诊断能力，并可能提供一条可持续发展的道路。