Streamlined Template Preparation for Advanced Sequencing Methods

项目概述/摘要：虽然人类基因组序列在2002年基本完成，但对DNA序列数据的生产仍有巨大的需求。特别是，致癌组织内的基因组被认为与正常基因组有很大差异，无论是遗传突变还是由疾病引起的突变。NCI最近设定了一个目标，对来自不同个体的恶性肿瘤的12500个基因组进行测序，以便更多地了解该疾病的分子基础。为了经济有效地实现这一目标，将需要新的DNA测序技术。我们建议使用合成测序（SBS）方法作为原型仪器的基础，该仪器将能够有效地测序来自高度突变的肿瘤组织的基因组。充分优化后，我们的系统应该能够产生至少与当今最先进的电泳系统一样长的读取长度。这可能成为癌症基因组的一个关键参数，这些基因组经历了足够复杂的突变，这将使短重测序数据的准确组装变得困难。在这个第一阶段的SBIR项目中，我们建议开发一种样品制备方法，该方法将简化SBS步骤，使该过程对长样本读取更具鲁棒性，并且可以在数十万或数百万个样本上实现。I期里程碑的成功完成以及随后的II期和III期项目的完成将导致超高通量系统的开发，该系统可以生产具有成本效益的高密度芯片，用于与先进的DNA测序仪器相结合。最终，这种下一代样品制备和测序技术可以比现有系统更便宜、更快地产生几个数量级的DNA序列，可以帮助研究人员更深入地了解癌症的分子机制，并使个性化治疗的承诺成为现实。项目描述：最终，为复杂生物体基因组提供非常廉价的详细DNA序列信息的能力，将加速整个生物学的发现，并为药物基因组学提供基础。药物基因组学是治疗学的一种新范式，在这种范式中，药物是根据个体基因型而不仅仅是观察到的症状来处方的。一种可以廉价地对特定肿瘤内的DNA进行测序的系统将帮助癌症研究人员了解与各种癌症相关的突变，并有助于开发更有效的治疗方法。由于一个人的基因组序列永远不会改变，未来很可能每个人都将在出生时对他们的基因组进行测序，以电子方式记录下来，并在他们的一生中使用通量来定制他们的医疗保健。

DESCRIPTION (provided by applicant): Project Summary/Abstract: Although the sequence of the human genome was substantially completed in 2002, there is still a huge need for the production of DNA sequence data. In particular, the genome within carcinogenic tissues is believed to vary widely from a normal genome, both in inherited mutations and those caused by the disease. The NCI has recently set a goal of sequencing 12,500 genomes from malignant tumors of different individuals in order to learn more about the molecular basis of the disease. To cost effectively reach this goal, new technologies for DNA sequencing will be required. We propose to use the sequencing by synthesis (SBS) method as the basis for a prototype instrument which will be capable of effectively sequencing genomes from highly mutated tumor tissues. When fully optimized, our system should be able to produce read lengths which are at least as long as today's state-of-the-art electrophoresis-based systems. This may become a critical parameter for cancer genomes which have undergone sufficiently complex mutations that will make accurate assembly of short re- sequencing data difficult. In this Phase I SBIR project, we propose to develop the sample preparation approach which will simplify the SBS steps and make the process more robust for long sample reads and could be implemented on hundreds of thousands or millions of samples. Successful accomplishment of the Phase I milestones and completion of a subsequent Phase II and Phase III projects will result in the development of an ultra-high throughput system which can produce cost-effective high-density chips for use in conjunction with advanced DNA sequencing instruments. Ultimately, this next generation of sample preparation and sequencing technologies, which can produce DNA sequence several orders of magnitude cheaper and faster than existing systems, can help give researchers more insight into the molecular mechanisms of cancer and make the promise of individualized treatments a reality. Project Narrative: Ultimately, the ability to produce very inexpensive detailed DNA sequence information for complex organisms genomes will both lead to accelerated discoveries throughout biology and provide the basis for Pharmacogenomics, a new paradigm in therapeutics wherein medicines are prescribed based on individual genotypes rather than just observed symptoms. A system which could inexpensively sequence the DNA within a specific tumor will help cancer researchers understand the mutations associated with various types of cancers and help lead to more effective treatments. Since one's genomic sequence never changes, it is likely in the future that everyone will have their genomes sequenced at birth, recorded electronically and used throughput their lifetime to customize their healthcare.