Center for Big Data in Translational Genomics

转化基因组学大数据中心

• 批准号: 9064924
• 负责人: DAVID H HAUSSLER
• 金额: $ 44.13万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-29 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9064924
• 关键词: Benchmarking; Big Data; Bioinformatics; Breeding; California; Communities; Complex; Computer Systems; Computer software; Data; Data Set; Development; Diagnosis; Disease; Ecosystem; European; Funding; Gene Expression Profile; Genetic Variation; Genome; Genomics; Genotype; Goals; Health; Health Sciences; Human; Individual; Institutes; Institution; International; Malignant Neoplasms; Ontario; Oregon; Pathway interactions; Phenotype; Provider; Research; Research Infrastructure; Research Project Grants; San Francisco; Scientist; Solutions; System; Translational Research; Universities; anticancer research; base; cancer genome; cancer genomics; clinical practice; data modeling; design; genome analysis; leukemia; malignant breast neoplasm; open source; programs; public health relevance; tool

DESCRIPTION (provided by applicant): The Center for Big Data in Translational Genomics is a multi-institution partnership coordinated by the University of California at Santa Cruz to create scalable infrastructure for the broad application of genomics in biomedicine. Our U.S. partners include UC San Francisco, UC Berkeley, Oregon Health Science University, Caltech, and several major big data companies. International partners include the European Bioinformatics Institute, the Sanger Centre, the Ontario Institute for Cancer Research and a computer systems provider. The Center will make software solutions interoperable through the development of standard Application Programming Interfaces (APIs) and tools at multiple levels, from raw sequence data to genetic variation and functional data, through to systems, pathways and phenotypes. The overriding goal is to create implementations capable of handling genomics datasets that are orders of magnitude larger than those that can now be handled. The APIs and all academic reference implementations will be open source, while several major corporate partners not funded by the project will provide proprietary implementations, creating a competitive ecosystem of interoperable big data genomics software. All-comers extensive benchmarking will be performed on all implementations within and external to our center to identify best-of-breed and results made broadly available. Design will be in part driven by the needs of a diverse set of separately funded specific biomedical projects that will serve as pilots. These include the Pan-Cancer whole genome analysis project of the International Cancer Genomics Consortium to analyze 2,000 cancer genomes, the UK10K project to analyze 10,000 personal genomes, the UCSF-led I-SPY2 adaptive breast cancer trial, and the omics-guided leukemia therapy project BeatAML at Oregon Health Sciences University.

描述（由申请人提供）：转化基因组学大数据中心是一个由加州大学圣克鲁斯分校协调的多机构合作伙伴关系，旨在创建 可扩展的基础设施，用于基因组学在生物医学中的广泛应用。我们的美国合作伙伴包括加州大学旧金山分校、加州大学伯克利分校、俄勒冈健康科学大学、加州理工学院以及几家主要的大数据公司。国际合作伙伴包括欧洲生物信息学研究所、桑格中心、安大略癌症研究所和计算机系统提供商。该中心将通过开发标准应用程序编程接口（API）和多个级别的工具，使软件解决方案具有互操作性，从原始序列数据到遗传变异和功能数据，再到系统、途径和表型。最重要的目标是创建能够处理比现在可以处理的数据集大几个数量级的基因组数据集的实现。 API 和所有学术参考实现都将是开源的，而不受该项目资助的几个主要企业合作伙伴将提供专有的实现，从而创建一个具有竞争力的可互操作大数据基因组学软件生态系统。将对我们中心内外的所有实施进行广泛的基准测试，以确定最佳品种和广泛提供的结果。设计将部分由一系列单独资助的特定生物医学项目的需求驱动，这些项目将作为试点。 其中包括国际癌症基因组学联盟的泛癌症全基因组分析项目（分析2000个癌症基因组）、UK10K项目（分析10000个个人基因组）、加州大学旧金山分校（UCSF）领导的I-SPY2适应性乳腺癌试验以及组学引导的白血病治疗俄勒冈健康科学大学的 BeatAML 项目。