Abstract 5599: An introduction of a highly sensitive circulating tumor DNA monitoring system for minimal residual disease detection using a library of 1000 digital PCR probes
Authors: Nishizuka Satoshi S. , Hiraki Hayato , Abe Masakazu , Yashima-Abo Akiko , Iwaya Takeshi 
Published: April 2023

Background: Many patients undergo a next generation sequencing (NGS)-based cancer genome profiling (CGP) test, but it often does not aid in choosing an optimal therapeutic regimen. Therefore, the genomic information should be used for minimal residual disease (MRD) detection, which directly leads to improved post-treatment cancer patient management. Circulating tumor DNA (ctDNA) is a small fraction of DNA present in blood that carries somatic mutations in cancer patients. Our previous studies demonstrated the clinical validity of ctDNA as a tumor marker for MRD detection. However, the variant allele frequency (VAF; reflecting the fraction of somatic mutations) of ctDNA is less than 1%, at which stable detection is difficult for NGS. Instead of NGS, we have established a highly sensitive ctDNA monitoring system for MRD detection using an originally developed library of &gt;1000 digital PCR (dPCR) probes.

Patients and Methods: Using a Clinical Institutional Review Board approval from the Iwate Medical University Hospital, we initiated a dPCR assay system, called off-the-shelf (OTS)-Assay, in April 2022 under a partnership with Quantdetect, Inc (Tokyo, Japan). The OTS-Assay has three main components: OTS-Scan, OTS-Select, and OTS-Monitor. The OTS-Scan can provide an original CGP if a patient comes with no CGP results. The OTS-Select chooses matched somatic mutations from our dPCR probe library. The OTS-Monitor quantifies VAFs of ctDNA periodically in the patient plasma with a sensitivity of 0.05% VAF. There is no strict patient eligibility criteria other than the requirement of previous therapy for treatment of an advanced cancer.

Results: Between April and November 2022, 26 patients visited Iwate Medical University Hospital for the OTS-Assay. Twenty-five patients were referred from other Departments of Iwate Medical University Hospital. The primary cancer types include esophagus (n=21), colorectal (n=2), pancreas (n=2), and breast (n=1). Twenty patients had CGP results at their first visit. OTS-Select were used for 13 patients and picked an average of 11.4 mutations per patient. Among those, each of eight patients were immediately able to start ctDNA monitoring with one of the 1000 dPCR probes. As of November 2022, there are four patients who received OTS-Monitor more than one time. Any unexpected VAF increase of ctDNA has not been noted, although a substantial decrease of ctDNA VAF was found in one patient who received one cycle of chemotherapy.

Conclusion: The OTS-Assay is a practical introduction of our previous clinical research products based on a core technology, which uses an originally developed library of &gt;1000 dPCR probes. The potential of early and accurate MRD detection will improve post-treatment cancer patient management.

Citation Format: Satoshi S. Nishizuka, Hayato Hiraki, Masakazu Abe, Akiko Yashima-Abo, Takeshi Iwaya. An introduction of a highly sensitive circulating tumor DNA monitoring system for minimal residual disease detection using a library of 1000 digital PCR probes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5599.