Projects

Tianqi (Kiki) Chen

Previous studies in our group showed multiple features from cell free DNA (cfDNA) that could be used as potential biomarkers for early cancer detection in various cancers like CRC and NSCLC. These features include DNA fragmentation, methylation (5mC) and hydroxymethylation (5hmC). In this project, we aim to analyze the cell free RNA (cfRNA) together with cfDNA from the same patient. We combine the features from cfRNA e.g. isoforms and differential gene expression with features from cfDNA to build a more powerful model for early cancer detection. 

cfRNA and cfDNA were extracted from the same blood draw from the patient. The cancer types in the project include colorectal cancer (CRC) and pancreatic neuroendocrine tumor (pNET). We observed distinct patterns of isoform and differential gene expressions between healthy controls (N=34) and cancer patients of either CRC (N=39) or pNET (N=19). More samples are expected for further validation.