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

项目描述（由申请人提供）：本项目的目标是在现有的PLINK软件包的基础上，开发用于分析大规模基因分型和测序基因研究数据的软件。PLINK是一种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，拥有广泛的用户基础。具体目标是显著升级核心能力、接口、辅助资源和用户支持：核心能力：显著适应和升级数据存储能力，以处理a)比内存能容纳的大数量级的数据集，b)不同类型的遗传变异数据和元信息的更通用、统一的表示。接口：扩展现有接口，以提供a)数据存储和分析组件之间更松散的耦合，通过外部语言的多个接口，包括标准的生物信息学工具，如R和Perl，以及b)旨在促进可重复研究和并行处理的功能。辅助资源：打包标准现有资源，包括变体、参考基因组序列和基因组装、途径和本体的功能注释，以实现基因组资源和用户数据之间的无缝集成。支持：通过在线文档和教程，包括用户生成的wiki页面、电子邮件支持和年度培训课程，创建高质量的收藏资源来支持用户。将特别注意确保与其他主要软件、文件格式和由更广泛的遗传学社区产生的资源的互操作性。

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.