Data Processing and Visualization for 1000 Genomes

描述：（由申请人提供）：国际千人基因组计划（1000 Genomes）旨在利用新一代测序技术的出现来编目常见的人类遗传变异。1000个基因组的宏伟目标和时间表将需要多个研究小组的高度协调合作。虽然我们的开发工作将涉及所有三个平台，但我们提案的主要部分将侧重于将SOLID数据优化整合到100个基因组数据生产管道中。我们的目标是确保平台的独特功能在数据处理过程中得到最大化，同时坚持在1000个基因组中建立的通用数据和分析标准。在目标1中，我们将开发用于监测数据质量的工具，部分侧重于检测实验偏差的工具，部分侧重于开发更好的质量指标。在目标2中，我们将开发通过使用递归使用比对和变异发现来检测遗传变异的工具。在目标3中，我们将进一步开发能够同时查看多个站点序列数据的客户端/服务器软件，以进行质量控制和变体检查。我们提案的交付成果是一系列独立的软件实用程序，这些实用程序可以集成到由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。该合作提案包括来自学术界（UCLA）、工业界（应用生物系统公司）和非营利研究机构（TGen）的团队。公共卫生相关性：本提案的目的是开发用于监测和解释千人基因组计划数据的工具。

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.