Targeted Comparative Gene Expression by Sequencing for Companion Diagnostics

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 predicthow 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