A Highly Sensitive Digital Droplet PCR Assay for Analysis of Circulating Tumor DNA in Pancreatic Adenocarcinoma

Hareena conducting lab bench work




Assistant Professor Of Medicine At The Hospital Of The University Of Pennsylvania

Project Summary

This summer, I worked in Erica Carpenter’s lab (Circulating Tumor Material laboratory) in the Perelman Center for Advanced Medicine on a project funded by PURM under the guidance of Mark O’Hara and Erica Carpenter. The goal of my project was to assess feasibility of a non-invasive blood plasma assay to detect KRAS mutations (a type of mutation frequently found in pancreatic cancers) in circulating tumor DNA for monitoring disease progression and outcome for diagnostic value for pancreatic cancer patients compared to less reliable biomarkers from blood serum. 

This project required me to aid in collecting blood from pancreatic cancer patients from the hematology-oncology clinic and process it by centrifuging it (spinning it at a high speed) to isolate blood plasma or serum from the red and white blood cells. Then, I banked this plasma for later analysis.

To start the analysis of this blood, a cell-free DNA (cfDNA) extraction was performed, a procedure that isolates the DNA that is found circulating in the bloodstream from the blood. Then, the Qubit technology was used to quantify the amount of double stranded DNA. Finally, we conducted digital droplet PCR, which creates millions of tiny droplet with the DNA, and then performed a RainDance analysis to detect KRAS mutations and variants in the patients’ blood.

I learned a lot through this experience. Besides blood collection, plasma extraction, banking, cfDNA extraction, Qubit, digital PCR, and RainDance, I created a presentation of recent relevant abstracts relating to circulating tumor material. I also performed cell culture for pancreatic cancer cell lines. Furthermore, I learned how to work with research data and input information into the Research Electronic Data Capture database (REDCap), work efficiently in a team, effectively synthesize scientific information, create a scientific presentation and poster that will undoubtedly help me further in my academic and scientific career.

I also shadowed in the clinic every week throughout my PURM experience. I shadowed doctors specializing in gastrointestinal cancers, lung cancer, and genitourinary cancers. This was a very rewarding experience as I got to interact with patients and see the real world implications of our research. It was truly amazing to see the research from the broad patient and therapy level down up to the specific DNA and genetic mutations.

I learned many skills this summer, from science to teamwork to patient interaction that will stay with me throughout my academic career. I am excited to continue to work in the Carpenter lab in the school year.