Data Processing and Visualization for 1000 Genomes

1000 个基因组的数据处理和可视化

• 批准号: 7760707
• 负责人: David W Craig
• 金额: $ 71.8万
• 依托单位: TRANSLATIONAL GENOMICS RESEARCH INST
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-11 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7760707
• 关键词: Academia; Algorithms; Alleles; Apache Indians; Bite; Blood capillaries; Cataloging; Catalogs; Chemistry; Client; Collaborations; Color; Complex; Computer software; Data; Data Coordinating Center; Data Quality; Data Set; Detection; Development; Emulsions; Exons; Generations; Genetic Variation; Genome; Genomics; Genotype; Goals; Human Genetics; Image; Imagery; Individual; Industry; International; Libraries; Metric; Minor; Modeling; Monitor; Nature; Participant; Pattern; Phase; Principal Investigator; Process; Production; Quality Control; Reading; Recording of previous events; Recruitment Activity; Research; Research Institute; Research Personnel; Series; Site; Solid; Structure; System; Technology; TimeLine; Variant; base; capillary; computerized data processing; design; experience; genetic variant; meetings; next generation; novel; public health relevance; symposium; tool

DESCRIPTION: (provided by applicant): The International 1000 Genomes Project (1000 Genomes) aims to leverage the emergence of next generation sequencing technologies to catalogue common human genetic variability. The ambitious goals and timeline of 1000 Genomes will require highly coordinated collaboration by multiple research groups. While aspects of our development efforts will involve all three platforms, a major proportion of our proposal will focus on optimal integration of SOLID data into the 100 Genomes data production pipeline. Our goal is to insure that the unique capabilities of the platform are maximized during data processing, while adhering to common data and analytical standards established across the 1000 Genomes. In Aim 1, we will develop tools for monitoring data quality, focusing partly tools for detecting experimental biases and partly on developing better quality metrics. In Aim 2, we will develop tools for detection of genetic variation through the use of recursive use of alignment and variant discovery. In Aim 3, we will further develop client/server software capable of simultaneous viewing of sequence data across multiple sites for the purpose of quality control and variant inspection. The deliverable of our proposal is series of stand-alone software utilities that can be integrated into the software pipelines developed by the 1000 Genome DCC's and that fit within the collective analytical framework of 1000 genomes participants. This collaborative proposal includes teams from academia (UCLA), industry (Applied Biosystems) and non-profit research institutes (TGen). PUBLIC HEALTH RELEVANCE: The purpose of this proposal is to develop tools for monitoring and interpreting data from the 1000 Genomes Project.

描述：（由申请人提供）：国际1000个基因组项目（1000个基因组）旨在利用下一代测序技术的出现来分类常见的人类遗传变异性。 1000个基因组的雄心勃勃的目标和时间表将需要多个研究小组的高度协调协作。尽管我们开发工作的各个方面将涉及所有三个平台，但我们的大部分提案将重点侧重于将固体数据最佳整合到100个基因组数据生产管道中。我们的目标是确保在数据处理过程中最大化平台的独特功能，同时遵守1000个基因组建立的常见数据和分析标准。在AIM 1中，我们将开发用于监视数据质量的工具，重点是用于检测实验偏见的部分工具，并部分地放在开发更好的质量指标上。在AIM 2中，我们将通过使用递归使用对齐和变异发现来开发用于检测遗传变异的工具。在AIM 3中，我们将进一步开发能够同时查看跨多个站点的序列数据的客户/服务器软件，以进行质量控制和变体检查。我们的提案的可交付是一系列独立软件实用程序，可以集成到1000个基因组DCC开发的软件管道中，并且适合1000个基因组参与者的集体分析框架。该协作建议包括来自学术界（UCLA），行业（应用生物系统）和非营利研究机构（TGEN）的团队。公共卫生相关性：该提案的目的是开发用于监视和解释1000个基因组项目数据的工具。