Data Studio

Li Ka Shing Learning Center (LKSC)
Rm 209

DATE: October 11, 2017
TIME: 1:30 - 3:00 pm
TITLE: Utilizing platelet RNAseq for early detection of kidney cancer
INVESTIGATOR:

Viola Chen, Medical Fellow, and Alice FanAssistant Professor

Medicine-Oncology, Stanford

 

Summary:

A simple and reliable blood test for early stage kidney cancer could save many lives.  Based on evidence that circulating blood contains a cancer signature, this project is planning experimental design and analysis for a pilot study to investigate whether RNA sequencing of blood platelets can identify kidney cancer. The first step to achieve this goal is to identify genes whose expression in platelets changes in the early stage of kidney cancer.  To serve as a biomarker, a gene must also have predictable expression levels in people that do not have kidney cancer so that a diagnostic classification rule can be developed. Leveraging data and results from the background reading, this consultation will discuss issues such as the use of paired samples before and after removal of a kidney tumor as well as the pros and cons of some classification algorithms.

Suggested readings:

Lisa M. Chung et al.  Differential expression analysis for paired RNA-seq data. BMC Bioinformatics 2013; 14:110.

Myron G. Best et al. RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics. Cancer Cell 2015; 28:666-676.

Myron G. Best et al. Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets. Cancer Cell 2017; 32:238-252.e9.