Targeted Comparative Gene Expression by Sequencing for Companion Diagnostics

描述（由申请人提供）：该项目的长期目标是开发一种使用下一代测序的癌症患者伴随诊断的高通量方法。它是一种与所有基因组测序平台兼容的前端方法，在第一步中预先选择基因并标记样品，以确保数据完整性并消除序列分析的复杂性。在第一阶段赠款中测试的技术可以开发成临床医生帮助预测药物如何影响特定患者的工具。 该方法将用于许多微小组织样本中许多基因的比较基因表达研究。长期目标将是在一次测序运行中量化10，000个样本中的1000个基因。样品可以是从患者的肿瘤中分离并直接测试的微量样品，或者可以是从肿瘤中生长的细胞（如果可能的话），并用许多不同的潜在药物或药物组合进行治疗。未来的一个重要应用将是对单个循环肿瘤细胞（CTC）进行转录分析，作为肿瘤细胞的非侵入性诊断。 癌症高危或复发性癌症患者。这可能是跟踪疾病进展的一种方法，例如，定义治疗过程中发生的分子变化。许多工作正在做，以完善从“液体”活检中分离活CTC的方法。我们也许能够与我们的技术合作，研究推定药物对单个CTC的影响。最近的数据显示，肿瘤的不同部位和类似的不同CTC在基因表达方面差异很大。对许多单个细胞的分析可能对于表征多样性和了解药物如何影响肿瘤内的亚群至关重要，然后预测哪些亚群并测试药物是否对特定患者有效。该项目有可能帮助改善临床实践，并有助于伴随诊断领域。 第一阶段SBIR资助的短期目标是验证为下一代测序准备样品的方法。它将在两个不同的细胞系中对18个基因进行验证。先前时间 课程实验提供的数据将与使用新技术获得的数据进行比较，结果将与标准的一次一个的表达分析方法进行比较。第一阶段拨款的成功完成将导致一项经过验证的技术，该技术可用于第二阶段，以扩大将用于实际患者样本的基因和样本数量。

DESCRIPTION (provided by applicant): The long range goal of this project is to develop a high throughput method for companion diagnostics for cancer patients using next generation sequencing. It is a front end method compatible with all genome sequencing platforms, which preselects genes and labels samples in the first step to assure data integrity and to eliminate complexities of sequence analysis. The technology being tested in this Phase I grant can be developed into a tool for clinicians to help predict how a drug affects particular patient. The method will be used for comparative gene expression studies for many genes in many tiny tissue samples. The long term goal will be to quantify 1000 genes in 10,000 samples in one sequencing run. The samples could be micro samples isolated from a patient's tumor and tested directly, or could be cells grown from a tumor (when this is possible) and treated with many different potential drugs or drug combinations. One important application in the future will be transcriptional analysis of single, circulating tumor cells (CTCs) as a non-invasive diagnostic for patients at high risk for cancer or with recurrent cancer. This could be an approach to follow disease progression, for example, to define molecular changes that occur with treatment. Much work is being done to perfect methods to isolate live CTCs from a "liquid" biopsy. We may be able to partner our technology to study the effects of putative drugs on individual CTCs. Recent data show that different parts of a tumor and similarly different CTCs vary widely in terms of gene expression. Analysis of many individual cells may be critical to characterize diversity and to understand how drugs affect subpopulations within a tumor, and then to predict which and test whether drugs will be effective for a particular patient. This project has the potential to hep improve clinical practice and contribute to the field of companion diagnostics. The short range goal of this Phase I SBIR grant is to validate the approach for preparing samples for next generation sequencing. It will be validated for 18 genes in two different cell lines. Previous time course experiments provide data that will be compared to data obtained using the new technology, and results will be compared with standard one-at-a-time methods of expression analysis. A successful completion of the Phase I grant will lead to a validated technology that can be used in Phase II to scale up the number of genes and samples that will be used on actual patient samples.