Research & Publications
Extensive Research Description
Genomic profiling of cancer is gradually becoming central theme for cancer research, clinical trials and drug development programs.As spotlight changes towards personalized medicine, recurrent genomic profiling of tumor is imperative for administration of therapy, patient selection in clinical trials,and monitoring the therapy response. To meet the challenges of cost effective, high-throughput personalized medicine, we developed two novel methods for measuring tumor–derived DNA and RNA fragments in circulation. First method called “Ultrasensitive error suppressed deep sequencing” can detect traces of tumor–specific mutations in a background of abundant normal DNA in plasma. The assay uses highly multiplexed PCR to amplify mutation prone target regions, and then identifies rare variants by oversampling thousands of amplified copies using next-generation sequencing. We designed novel molecular and computational strategies to optimize detection sensitivity by suppressing noise from PCR misincorporations and sequencer errors. Importantly, the assay does not require patient-specific optimization, because it simultaneously samples the majority of mutations that are commonly found in patients with a specific type of cancer. A more recently developed second method, termed “META RNA profiling” is aimed for high-throughput RNA quantitation. This method is capable of simultaneously measuring up to 96 microRNAs or messenger RNAs from up to 96 samples, rapidly and at a very low cost per-sample. The method can be applied to RNAs derived from a variety of sources. Long term goal is to use these technologies to investigate potential clinical applications for which nucleic acid biomarkers are better suited than conventional serum protein markers.
Drug Resistance, Microbial; Molecular Diagnostic Techniques; Early Detection of Cancer
Public Health Interests
Cancer; Genetics, Genomics, Epigenetics; Infectious Diseases