Hunting Rare Human Variations using DNA Sudoku

描述（由申请人提供）：在过去的几年里，我们经历了人类遗传学的范式转变。越来越多的证据强调了罕见的遗传变异在各种性状和疾病中的关键作用。研究罕见的变异是大海捞针的问题，因为为了捕获变异并获得统计功效，必须对大型队列进行测序。高通量测序的性能呈指数增长，提供足够的能力来分析大量的标本。然而，样品制备方案不能与测序能力成比例。制备百分之一到数千个样本用于测序的蛮力方法是繁琐的并且成本高昂。因此，下一个挑战是开发一种可扩展的技术，以绕过样品制备中的瓶颈。我们最近设计了一种名为DNA Sudoku的测序策略，它具有解决这一挑战的巨大潜力。DNA数独是基于根据组合模式汇集样本作为复用的手段，这大大降低了大规模实验的成本。我们已经证明了DNA数独的可行性，通过分析成千上万的细菌菌落在一个单一的测序运行。我们建议利用我们的概念验证研究的成功，并调整DNA数独用于大型人类队列中罕见遗传变异的研究。作为一个测试案例，我们计划使用该策略通过对1000名种族匹配个体的风险基因座进行测序来研究与犹太人遗传疾病有关的罕见变异。这种积极主动的方法将首次创建一个全面的风险等位基因目录，并可立即产生临床意义。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各种研究引入一种超成本效益的测序策略，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扩展的多路复用方案的需求，使我们的策略成为一个持久的策略，具有丰富的理论基础和多种应用。 公共卫生相关性：寻找基因组中携带疾病等位基因的个体是大海捞针的问题。作为一种解决方案，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的最新突破，并让人想起解决数独难题。该战略将用于解决一个长期存在的问题-为严重遗传疾病创建一个全面的风险等位基因目录，这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.