title: Clinical utility of circulating tumor DNA for molecular assessment in pancreatic cancer.
abstract: Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. The genomic landscape of the PDAC genome features four frequently mutated genes (KRAS, CDKN2A, TP53, and SMAD4) and dozens of candidate driver genes altered at low frequency, including potential clinical targets. Circulating cell-free DNA (cfDNA) is a promising resource to detect and monitor molecular characteristics of tumors. In the present study, we determined the mutational status of KRAS in plasma cfDNA using multiplex picoliter-droplet digital PCR in 259 patients with PDAC. We constructed a novel modified SureSelect-KAPA-Illumina platform and an original panel of 60 genes. We then performed targeted deep sequencing of cfDNA and matched germline DNA samples in 48 patients who had ≥1% mutant allele frequencies of KRAS in plasma cfDNA. Importantly, potentially targetable somatic mutations were identified in 14 of 48 patients (29.2%) examined by targeted deep sequencing of cfDNA. We also analyzed somatic copy number alterations based on the targeted sequencing data using our in-house algorithm, and potentially targetable amplifications were detected. Assessment of mutations and copy number alterations in plasma cfDNA may provide a prognostic and diagnostic tool to assist decisions regarding optimal therapeutic strategies for PDAC patients.
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Erina
authors.initials: E
authors.lastname: Takai
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Totoki
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Nakamura
authors.affiliation: Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan.
authors.forename: Chigusa
authors.initials: C
authors.lastname: Morizane
authors.affiliation: Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo 1040045, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nara
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Natsuko
authors.initials: N
authors.lastname: Hama
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Masami
authors.initials: M
authors.lastname: Suzuki
authors.affiliation: Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Eisaku
authors.initials: E
authors.lastname: Furukawa
authors.affiliation: Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Mamoru
authors.initials: M
authors.lastname: Kato
authors.affiliation: Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan.|Division of Genome Biology, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Hayashi
authors.affiliation: Division of Genome Biology, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kohno
authors.affiliation: Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Ueno
authors.affiliation: Hepatobiliary and Pancreatic Surgery Division, National Cancer Center Hospital, Tokyo 1040045, Japan.
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Shimada
authors.affiliation: Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 1040045, Japan.
authors.forename: Takuji
authors.initials: T
authors.lastname: Okusaka
authors.affiliation: Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Nakagama
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.|Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan.
authors.forename: Tatsuhiro
authors.initials: T
authors.lastname: Shibata
authors.affiliation: Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 1040045, Japan.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Yachida
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D021441:Carcinoma, Pancreatic Ductal / Q000097:blood / Q000235:genetics; D004273:DNA, Neoplasm / Q000097:blood / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation; D010190:Pancreatic Neoplasms / Q000097:blood / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics*
chemical_list: D004273:DNA, Neoplasm; C117307:KRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras)