Towards the clinical implementation of tumor RNA sequencing
Mentor Name: Olena Vaske
RNA sequence (RNA-seq) datasets have been shown to be useful for the identification of overexpressed genes (gene expression outliers) in individual tumor and similar tumors. Comparative RNA sequencing analysis is the comparison of genomic data from multiple tumor samples to determine similarities and differences between cancers that may not have been otherwise apparent. This comparison could be vital to furthering treatment and bettering patient outcomes. The Treehouse Childhood Cancer Initiative (Treehouse) has taken this approach to analyze tumor samples from pediatric patients; as of now, the methods are being used in a research setting. Treehouse has shown in published case studies that this approach can identify new treatments and refine diagnoses for rare tumors. The next step is a broader investigation of the clinical utility of comparative RNA sequencing in a clinical trial. use RNA-seq to identify molecular targets for treatment by looking at gene expression outliers. This setup and validation of creating a clinical-grade pediatric oncology diagnostic lab and the full procedure are in early phases. Translating the research-grade assay into a clinical-grade assay will happen in several stages. The project being proposed will focus on developing and validating RNA- seq. library preparation and identifying gene expression outliers within different data sets. This project will further the establishment of a novel pediatric oncology clinical diagnostic lab that specializes in genomic analysis of cancer. A new venture of the Vaske lab will bring the research setting to a clinical grade. The goal is for the Vaske lab to be able to receive tumor samples, extract RNA, build sequencing libraries, and use RNA-seq to identify molecular targets for treatment by looking at gene expression outliers. This setup and validation of creating a clinical-grade pediatric oncology diagnostic lab and the full procedure are in early phases. Translating the research-grade assay into a clinical-grade assay will happen in several stages. The project being proposed will focus on developing and validating RNA- seq. library preparation and identifying gene expression outliers within different data sets. This project will further the establishment of a novel pediatric oncology clinical diagnostic lab that specializes in genomic analysis of cancer.
