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将个性化基因分型的希望带入了人类基因组学领域。个性化基因分型的进展取决于为具有成本效益的大规模关联研究程序的发展。如此大规模的实验和研究面临着许多与生物工程系统和测试受试者施加的限制有关的障碍，包括a）必须对小个人样本进行测试的限制？遗传物质； b）必须将受试者多路复用的约束，因此必须对遗传序列进行条形码； c）测试结果是半定量的事实； D）必须在相关个人组中进行许多测试，从而大大增加筛查整个家庭的成本； e）测试必须应对变异发现的挑战和可能表现出不同基因拷贝数的个人的挑战。克服这些障碍和许多其他障碍的一种自然方法是通过小组测试进行基因分型。该项目的目标包括开发综合的，但在分析或计算上可以探讨基因分型的小组测试的一般理论。提出的理论将通过测序回答基因分型中产生的独特挑战，尽管该理论的一部分可能会在像受约束多个访问渠道分析，指纹识别和识别编码以及错误控制的领域中找到独立的应用。特别是，研究人员将几个新模型引入了小组测试领域，包括具有不同类型和优势的受试者，半定量测试，二维合并和泊松概率测试。