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利用下一代测序技术为癌症患者开发一种高通量的伴随诊断方法。它是一种兼容所有基因组测序平台的前端方法，在第一步预先选择基因和标记样本，保证数据的完整性，消除序列分析的复杂性。在第一阶段拨款中测试的技术可以发展成为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。长期目标是在一次测序中对10000个样本中的1000个基因进行量化。这些样本可以是从患者肿瘤中分离出来的微样本，并直接进行测试，也可以是从肿瘤中生长出来的细胞（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。未来一个重要的应用将是对单个循环肿瘤细胞（ctc）的转录分析，作为一种非侵入性诊断

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.