Clinical implementation of a comprehensive targeted amplicon sequencing system for cancer in Japan.

Abstract

e13115 Background: The development of clinical sequence systems in hospitals is a critical issue in Japan, especially for medical oncology, as multiplex gene profiling enables precision medicine for cancer. We have launched an in-house clinical sequencing system,“CLHURC” to perform exhaustive targeted exome sequencing for patients with all types of cancer, as an outpatient service. We have analyzed the clinical utility of this system. Methods: Genomic DNA was extracted from tumor tissues and peripheral blood sera of 81 patients with different stages of cancer, during April-December 2016. The top five types of primary cancer were pancreas (16%), colorectal (16%), breast (10%), stomach (9%), and lung (6%). We performed a targeted amplicon exome sequencing for 160 cancer-related genes. The sequencing data was analyzed using an original bioinformatics pipeline within three days, and we identified cancer-specific somatic gene alterations such as SNV (Single Nucleotide Variation), Ins (Insertion)/Del (Deletion), and CNV (Copy Number Variation). The primary endpoints were the detection rates of potential actionable and druggable genes. The secondary endpoints were the detection rates of incidental germline variants and the period from initial visit to elucidation of the results to the patients. Results: Actionable and druggable gene alterations were detected in 90% (73/81) and 51% (41/81) of the subjects, respectively. Druggable gene alterations were frequently detected in BRCA1/2 (11/41), PIK3CA (9/41), AKT1/2 (6/41), TSC1 (5/41), and PTEN (5/41). Surprisingly, incidental germline variants were detected in 31% (25/81) of the patients, and were found in BRCA1/2 (5/25), APC (5/25), and TSC1(3/25), among others. The median period of examination was 21 days (10-66 days). Twelve out of the 81 patients (15%) were treated with therapeutic agents, based on the results of our clinical sequencing. Conclusions: We have established a robust in-house clinical sequencing system, “CLHURC,” and have initiated the development of precision medicine for cancer in Japan. Our novel clinical sequencing system could improve individualized medicine against cancer throughout Japan and Asia.