Evan Charles Osmundson MD, PhD, Presenter: Nothing to Disclose

Aaron Newman PhD, Abstract Co-Author: Nothing to Disclose

Daniel Klass PhD, Abstract Co-Author: Nothing to Disclose

Scott Bratman MD, PhD, Abstract Co-Author: Nothing to Disclose

Li Zhou PhD, Abstract Co-Author: Nothing to Disclose

Jonathan Pai, Abstract Co-Author: Nothing to Disclose

Teri A. Longacre MD, Abstract Co-Author: Nothing to Disclose

Ash A. Alizadeh MD, PhD, Abstract Co-Author: Nothing to Disclose

Albert C. Koong MD, PhD, Abstract Co-Author: Nothing to Disclose

Maximilian Diehn MD, PhD, Abstract Co-Author: Research Consultant, Varian Medical Systems, Inc Research Grant, Varian Medical Systems, Inc

Novel biomarkers are needed for the reliable identification of patients likely to benefit from primary or adjuvant local therapy for pancreatic adenocarcinoma (PAC). We recently developed Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq), a novel next-generation sequencing (NGS) based technique that allows for the ultrasensitive and specific detection of circulating tumor DNA (ctDNA) in plasma. Our objective was to determine the feasibility of applying CAPP-Seq to patients undergoing therapy for PAC.

CAPP-Seq employs a hybrid capture technique, using a “selector” that is tailored to the cancer type of interest. A PAC-specific CAPP-Seq oligonucleotide selector was designed using a custom bioinformatics approach targeting recurrently mutated genomic regions in PAC from publically available whole exome sequencing data. Genomic DNA was extracted for genotyping from formalin fixed paraffin embedded (FFPE) specimens collected via fine needle aspirates (FNAs), core biopsies, or surgical resection. CAPP-Seq was used to identify tumor-specific mutations in these PACs. ctDNA levels were then quantitated from pre- and post-treatment blood samples collected from patients undergoing therapy for PAC at our institution.

The PAC-specific CAPP-Seq selector covered ~135 kb and targeted 979 genomic regions from 925 recurrently mutated genes. Although it comprised 96% of PACs. Adequate tumor genomic DNA (≥4ng) was extracted for CAPP-Seq genotyping from 95% of FFPE samples. Median sequencing depth of tumor DNA specimens (n=12) was ~1,600x. Based on the number of observed mutations detected (median=8), CAPP-Seq's expected detection limit in the plasma was estimated at ~0.002%. Finally, CAPP-Seq was used to quantitate ctDNA in pre- and post-treatment plasma samples.

CAPP-Seq is a promising method for the ultrasensitive and specific quantification of ctDNA in patients with PAC. Isolation of tumor DNA from PAC FNA specimens provides sufficient tumor DNA for genotyping using CAPP-Seq, with expected detection limits exceeding most currently available techniques. Ongoing analyses are exploring the prognostic and predictive utility of ctDNA analysis in PAC.

CAPP-Seq is an NGS-based method for ctDNA analysis that facilitates personalized detection and therapeutic monitoring of disease burden in cancer patients.

Osmundson, E, Newman, A, Klass, D, Bratman, S, Zhou, L, Pai, J, Longacre, T, Alizadeh, A, Koong, A, Diehn, M, Ultrasensitive Detection and Personalized Profiling of Circulating Tumor DNA in Patients with Pancreatic Adenocarcinoma.  Radiological Society of North America 2014 Scientific Assembly and Annual Meeting, - ,Chicago IL. http://archive.rsna.org/2014/14017064.html