Software for the analysis of large-scale genotyping and sequencing studies

用于分析大规模基因分型和测序研究的软件

• 批准号: 8305019
• 负责人: Shaun M Purcell
• 金额: $ 33.56万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-27 至 2014-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8305019
• 关键词: Attention; Bioinformatics; Cataloging; Catalogs; Clinical Trials; Collection; Communities; Complex; Computer software; Coupling; Data; Data Analyses; Data Set; Data Storage and Retrieval; Development; Disease; Documentation; Ensure; Frequencies; Generations; Generic Drugs; Genes; Genetic; Genetic Determinism; Genetic Variation; Genome; Genomics; Genotype; Individual; Language; Lead; Mails; Maintenance; Maps; Medical; Memory; Methods; NIH Program Announcements; Observational Study; Ontology; Pathway interactions; Process; Research; Research Personnel; Resources; Risk; Sequence Analysis; Software Tools; Technology; Training; Variant; Work; base; design; epigenomics; exome; file format; genetic association; genome sequencing; genome wide association study; genome-wide analysis; insight; interest; interoperability; next generation; novel; parallel processing; population based; public health relevance; response; software development; tool; tool development; trait; wiki

DESCRIPTION (provided by applicant): The objective of this project is to develop software for the analysis of data from large- scale genotyping and sequencing genetic studies, building on the existing software package PLINK. PLINK, a software tool to manipulate and analyze whole-genome SNP datasets that has been actively developed over the past four years and has a wide base of users. The specific aims are to significantly upgrade core capacities, the interface, auxiliary resources and user-support: Core capacities: significantly adapt and upgrade data-storage capacities to handle a) order-of-magnitude larger datasets than can fit into memory and b) a more generic, unified representation of different types of genetic variation data and meta-information. Interface: extend the existing interface to provide a) a looser coupling between data storage and analysis components, via multiple interfaces in external languages, including standard bioinformatics tools such as R and Perl, and b) features designed to facilitate reproducible research and parallel processing. Auxiliary resources: package standard existing resources, including the functional annotation of variants, reference genome sequences and gene assemblies, pathways and ontologies, in a manner that allows seamless integration between genomic resources and user data. Support: create high-quality collection resources to support users, via online documentation and tutorials, including user-generated wiki pages, e-mail support and an annual training course. Particular attention will be paid to ensure interoperability with other major software, file-formats and resources that are generated by the broader genetics community. PUBLIC HEALTH RELEVANCE: This Project is to develop software for the analysis of large datasets from modern genetic studies. New high-throughput genotyping and sequencing technologies are capable of producing vast amounts of data, but there is a need for analytic tools that biomedical researchers can use. These studies have the potential to uncover genetic determinants for a large number of diseases and traits, which can be relevant for prediction of risk, and give insight into novel targets for treatments.

描述（由申请方提供）：本项目的目的是在现有软件包PLINK的基础上开发用于分析大规模基因分型和测序遗传学研究数据的软件。PLINK是一种用于操作和分析全基因组SNP数据集的软件工具，在过去四年中一直在积极开发，并拥有广泛的用户基础。核心能力：大幅度调整和升级数据存储能力，以处理a）数量级大于内存容量的数据集和B）更通用、统一地表示不同类型的遗传变异数据和元信息。接口：扩展现有接口，以提供a）通过外部语言的多个接口，包括标准生物信息学工具（如R和Perl），在数据存储和分析组件之间提供更松散的耦合，以及B）旨在促进可重复研究和并行处理的功能。辅助资源：以允许基因组资源和用户数据之间无缝集成的方式，打包标准现有资源，包括变体的功能注释、参考基因组序列和基因组装、途径和本体。支援：创建高质量的馆藏资源，通过在线文档和教程，包括用户生成的维基页面、电子邮件支持和年度培训课程，为用户提供支持。将特别注意确保与更广泛的遗传学界产生的其他主要软件、文件格式和资源的互操作性。 公共卫生相关性：该项目旨在开发用于分析现代遗传学研究大型数据集的软件。新的高通量基因分型和测序技术能够产生大量的数据，但生物医学研究人员需要可以使用的分析工具。这些研究有可能揭示大量疾病和特征的遗传决定因素，这些决定因素可能与风险预测相关，并为治疗提供新的靶点。