Non invasive Cancer Detection with Next Generation Sequencing

Postdoc Fellow Ther Radiology
15 York St, New Haven, CT 06510-3221

The recent advent of next-generation, high-throughput DNA sequencing technologies presents an attractive approach to identify and enumerate rare sequence variants by oversampling multiple DNA molecules from a particular genomic region. We applied this to our advantage for detecting and quantifying small amounts of mutant tumor-derived DNA in the blood of patient’s with non-small cell lung cancer. A modified deep sequencing method was developed that demands redundancy within each clonal sequence to produce extremely high quality base-calls in short, mutation-prone regions of plasma DNA.  Amplification of both mutated and wild-type sequences was carried out by unbiased PCR in a single tube.  We found that mutant DNA could be accurately and reproducibly measured down to levels of approximately 1 in 5,000 molecules. Using multiplexed primers, the assay could simultaneously quantify multiple mutations from a given sample. Moreover, sample-specific barcoding allowed us to pool multiple samples, making the method more economical.  Using this approach, we were able to monitor changes in circulating tumor DNA levels in the context of treatment or disease progression in patients with non-small cell lung cancer.