III: Small: Collaborative Research: Reconstruction of Haplotype Spectra from High-Throughput Sequencing Data

III：小：合作研究：从高通量测序数据重建单倍型谱

• 批准号: 0916948
• 负责人: Ion Mandoiu
• 金额: $ 27.53万
• 依托单位: University of Connecticut
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0916948&HistoricalAwards=false
• 关键词: III; Small; Collaborative; Research; Reconstruction

Recent advances in high-throughput sequencing (HTS) technologies provide opportunities to study genome structure, function, and evolution at an unprecedented scale, and are profoundly transforming genomic research. However, fully realizing the potential of HTS technologies requires sophisticated data analysis methods. This research project is aimed at developing efficient computational methods for reconstructing the full spectrum of haplotype sequences from HTS data. Working in collaboration with molecular biologists from the University of Connecticut Health Center and the Centers for Disease Control, the investigators will develop methods enabling three novel applications of HTS, namely (a) reconstruction of diploid genome sequences, including complete haplotype sequences of each CNV copy, (b) reconstruction of alternative splicing isoform sequences and their frequencies, and (c) reconstruction of viral quasispecies sequences and their frequencies. Major outcomes of the project will include the development of a comprehensive analytical toolkit for these problems, and high-quality open source software implementations that will be made available free of charge to the research community. The project will provide opportunities for participation of undergraduate and graduate students in bioinformatics research at UCONN and Georgia State University, and will especially encourage participation of women and underrepresented groups.

高通量测序（HTS）技术的最新进展为以前所未有的规模研究基因组结构、功能和进化提供了机会，并正在深刻地改变基因组研究。然而，充分实现HTS技术的潜力需要复杂的数据分析方法。 该研究项目旨在开发高效的计算方法，用于从HTS数据重建全谱单倍型序列。 研究人员将与康涅狄格大学健康中心和疾病控制中心的分子生物学家合作，开发实现HTS三种新应用的方法，即（a）重建二倍体基因组序列，包括每个CNV拷贝的完整单体型序列，（B）重建选择性剪接异构体序列及其频率，以及（c）病毒准种序列及其频率的重建。该项目的主要成果将包括为这些问题开发一个全面的分析工具包，以及免费向研究界提供高质量的开放源码软件。 该项目将为康州大学和格鲁吉亚州立大学的本科生和研究生提供参与生物信息学研究的机会，并将特别鼓励妇女和代表性不足的群体参与。