Hunting Rare Human Variations using DNA Sudoku

描述(申请人提供)：在过去的几年里，我们经历了人类遗传学的范式转变。越来越多的证据突显了罕见的遗传变异在各种特征和疾病中的关键作用。研究罕见的变异是大海捞针的问题，因为为了捕捉变异并获得统计能力，必须对大量的队列进行测序。高通量测序的性能呈指数级增长，提供了足够的容量来分析大量的样本。然而，样品制备方案并不像测序能力那样规模化。为测序准备百分百到几千个样本的蛮力方法是繁琐的，而且成本很低。因此，下一个挑战是开发一种可扩展的技术，绕过样品制备的瓶颈。我们最近设计了一种名为DNA数独的测序策略，它具有应对这一挑战的巨大潜力。DNA数独的基础是根据组合模式将样本汇集在一起，作为一种多路复用的手段，这大大降低了大规模实验的成本。我们已经通过在一次测序运行中分析数万个细菌菌落来证明DNA数独的可行性。我们建议利用我们的概念验证研究的成功，并将DNA数独用于研究大型人类队列中罕见的遗传变异。作为一个测试案例，我们计划使用这一策略，通过对1000名种族匹配的个体进行风险基因座测序，来研究与犹太遗传病有关的罕见变异。这种积极主动的方法将第一次创建一个全面的风险等位基因目录，并可能立即产生临床意义。拟议项目的成功有可能产生深远的技术影响。它将为单基因和复杂疾病的广泛研究引入一种超经济高效的测序策略，克服基因组学中的一个关键障碍。DNA测序的未来发展将进一步增加对可伸缩多路复用方案的需求，使我们的策略具有长期的持久性，具有丰富的理论基础和广泛的应用。 与公共卫生相关：寻找在基因组中携带疾病等位基因的个体是大海捞针的问题。作为解决方案，我们建议开发一种创新和高效的DNA测序策略，该策略基于信号处理领域最近的突破，使人想起解决数独谜题。这一战略将被用来解决一个长期存在的问题--创建一个严重遗传病的全面风险等位基因目录，这将具有直接的临床意义，并可以防止毁灭性的病例。

DESCRIPTION (provided by applicant): In the past few years, we have experienced a paradigm shift in human genetics. Accumulating lines of evidence have highlighted the pivotal role of rare genetic variations in a wide variety of traits and diseases. Studying rare variations is a needle in a haystack problem, as large cohorts have to be sequenced in order to trap the variations and gain statistical power. The performance of high throughput sequencing is exponentially growing, providing sufficient capacity to profile an extensive number of specimens. However, sample preparation schemes do not scale as sequencing capacity. A brute force approach of preparing hundredths to thousands of specimens for sequencing is cumbersome and cost-prohibited. The next challenge, therefore, is to develop a scalable technique that circumvents the bottleneck in sample preparation. We have recently devised a sequencing strategy, called DNA Sudoku, which has a tremendous potential to address this challenge. DNA Sudoku is based on pooling the specimens according to combinatorial patterns as a means of multiplexing, which substantially reduces costs of large scale experiments. We have demonstrated the feasibility of DNA Sudoku by profiling tens of thousands of bacterial colonies in a single sequencing run. We propose to leverage the success of our proof-of-concept study and to adapt DNA Sudoku for the study of rare genetic variations in large human cohorts. As a test case, we plan to use the strategy to study rare variations that are implicated in Jewish genetic diseases by sequencing risk loci of a cohort of 1000 ethnically matched individuals. This proactive approach will create, for the first time, a comprehensive catalogue of risk alleles and can have immediate clinical implications. Success of the proposed project has the potential for a far-reaching technological impact. It will introduce an ultra cost-effective sequencing strategy for a wide-variety of studies on monogenic and complex diseases, overcoming a critical barrier in genomics. Future developments in DNA sequencing will further increase the requirement for scalable multiplexing schemes, rendering our strategy a long lasting one, with rich theoretical foundations and plurality of applications. PUBLIC HEALTH RELEVANCE: Finding individuals that carry disease alleles in their genome is a needle in a haystack problem. As a solution, we propose to develop an innovative and highly efficient DNA sequencing strategy that is based on recent breakthroughs in the field of signal processing and is reminiscent of solving Sudoku puzzles. The strategy will be used to address a long standing problem - creating a comprehensive catalogue of risk alleles for severe genetic diseases, which has immediate clinical implications and can prevent devastating cases.