CIF: Small: Collaborative Research: A General Theory of Group Testing for Genotyping

CIF：小型：协作研究：基因分型群体测试的一般理论

• 批准号: 1218764
• 负责人: Olgica Milenkovic
• 金额: $ 24.99万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-10-01 至 2016-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1218764&HistoricalAwards=false
• 关键词: CIF; Small; Collaborative; Research; General

Next generation high-throughput sequencing devices have brought the promise of personalized genotyping to the field of human genomics. Advances in personalized genotyping depend on developments of procedures for cost-efficient large-scale association studies. Such large-scale experiments and studies face a number of obstacles related to constraints imposed by bioengineering systems and test subjects, including a) the restriction that tests have to be performed with small samples of individuals? genetic material; b) the constraint that subjects have to be multiplexed, so that genetic sequences have to be barcoded; c) the fact that the outcomes of the tests are semi-quantitative; d) the reality that many tests have to be performed within groups of related individuals, thereby significantly increasing the cost of screening whole families; e) the fact that tests have to deal with the challenge of variant discovery and individuals that may exhibit different gene copy numbers. A natural way to overcome these and many other obstacles is to perform genotyping via group testing.The goals of this project include developing of a comprehensive, yet analytically or computationally tractable general theory of group testing for genotyping. The proposed theory will answer the unique challenges arising in genotyping by sequencing, although parts of the theory may find independent applications in areas as diverse as constrained multiple access channel analysis, fingerprinting and identification coding, and error-control coding. In particular, the investigators introduce several new models into the field of group testing, including subjects with different types and strengths, semi-quantitative testing, two-dimensional pooling, and Poisson probabilistic testing.

下一代高通量测序设备为人类基因组学领域带来了个性化基因分型的希望。个性化基因分型的进展取决于成本效益高的大规模关联研究程序的发展。这种大规模的实验和研究面临着许多与生物工程系统和测试对象所施加的限制有关的障碍，包括：a）必须用小样本个体进行测试的限制？遗传物质; B）受试者必须被多重化的限制，使得基因序列必须被条形码化; c）测试结果是半定量的事实; d）许多测试必须在相关个体的组内进行的现实，从而显著增加了筛查整个家庭的成本; e）测试必须应对变异发现和可能表现出不同基因拷贝数的个体的挑战。一个自然的方法来克服这些和许多其他障碍是通过组testing.The目标进行基因分型本项目包括开发一个全面的，但分析或计算易处理的一般理论的组测试基因分型。所提出的理论将回答独特的挑战，在基因分型测序，虽然理论的一部分可能会发现独立的应用领域不同的约束多路访问通道分析，指纹识别和识别编码，和错误控制编码。特别是，研究人员将几种新的模型引入到群体测试领域，包括不同类型和强度的受试者，半定量测试，二维池和泊松概率测试。