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Feasibility and utility of a panel testing for 114 cancer-associated genes in a clinical setting: A hospital-based study.

ABSTRACT: Next-generation sequencing (NGS) of tumor tissue (ie, clinical sequencing) can guide clinical management by providing information about actionable gene aberrations that have diagnostic and therapeutic significance. Here, we undertook a hospital-based prospective study (TOP-GEAR project, 2nd stage) to investigate the feasibility and utility of NGS-based analysis of 114 cancer-associated genes (the NCC Oncopanel test). We examined 230 cases (comprising more than 30 tumor types) of advanced solid tumors, all of which were matched with nontumor samples. Gene profiling data were obtained for 187 cases (81.3%), 111 (59.4%) of which harbored actionable gene aberrations according to the Clinical Practice Guidelines for Next Generation Sequencing in Cancer Diagnosis and Treatment (Edition 1.0) issued by 3 major Japanese cancer-related societies. Twenty-five (13.3%) cases have since received molecular-targeted therapy according to their gene aberrations. These results indicate the utility of tumor-profiling multiplex gene panel testing in a clinical setting in Japan. This study is registered with UMIN Clinical Trials Registry (UMIN 000011141).

SUBMITTER: Sunami K

PROVIDER: S-EPMC6447843 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Feasibility and utility of a panel testing for 114 cancer-associated genes in a clinical setting: A hospital-based study.

Sunami Kuniko K Ichikawa Hitoshi H Kubo Takashi T Kato Mamoru M Fujiwara Yutaka Y Shimomura Akihiko A Koyama Takafumi T Kakishima Hiroki H Kitami Mayuko M Matsushita Hiromichi H Furukawa Eisaku E Narushima Daichi D Nagai Momoko M Taniguchi Hirokazu H Motoi Noriko N Sekine Shigeki S Maeshima Akiko A Mori Taisuke T Watanabe Reiko R Yoshida Masayuki M Yoshida Akihiko A Yoshida Hiroshi H Satomi Kaishi K Sukeda Aoi A Hashimoto Taiki T Shimizu Toshio T Iwasa Satoru S Yonemori Kan K Kato Ken K Morizane Chigusa C Ogawa Chitose C Tanabe Noriko N Sugano Kokichi K Hiraoka Nobuyoshi N Tamura Kenji K Yoshida Teruhiko T Fujiwara Yasuhiro Y Ochiai Atsushi A Yamamoto Noboru N Kohno Takashi T

Cancer science 20190402 4

Next-generation sequencing (NGS) of tumor tissue (ie, clinical sequencing) can guide clinical management by providing information about actionable gene aberrations that have diagnostic and therapeutic significance. Here, we undertook a hospital-based prospective study (TOP-GEAR project, 2nd stage) to investigate the feasibility and utility of NGS-based analysis of 114 cancer-associated genes (the NCC Oncopanel test). We examined 230 cases (comprising more than 30 tumor types) of advanced solid t ...[more]

PMID: 30742731

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Project description:ObjectiveTo investigate the diagnostic yield of clinical whole-genome sequencing (WGS) in prenatally diagnosed non-immune hydrops fetalis (NIHF).MethodsThis was a retrospective study of 23 fetuses with prenatally diagnosed NIHF, negative for trisomies and copy-number variants, referred for analysis by WGS with an in-silico panel of 281 genes associated with hydrops fetalis. Due to identification of a high proportion of causative variants in the HRAS gene in the main cohort, Sanger sequencing of HRAS was performed in a replication cohort, consisting of 24 additional fetuses with NIHF that were negative for trisomies and copy-number variants and had not undergone WGS.ResultsOf the 23 fetuses in the main cohort, a molecular diagnosis was achieved in 12 (52.2%). Pathogenic or likely pathogenic variants were identified in seven genes: HRAS (n = 5), RIT1 (n = 2), FOXP3 (n = 1), GLB1 (n = 1), MAP2K1 (n = 1), PTPN11 (n = 1) and RASA1 (n = 1). The inheritance pattern of the 12 causative variants was autosomal dominant in 10 cases (HRAS, MAP2K1, PTPN11, RASA1, RIT1), autosomal recessive in one (GLB1) and X-linked recessive in one (FOXP3). Of the 24 fetuses in the replication cohort, a pathogenic variant in HRAS was identified in one, resulting in an overall frequency of causative HRAS variants of 12.8% (6/47) in our two cohorts.ConclusionsWe demonstrate a diagnostic yield of 52% with clinical WGS in NIHF using an in-silico panel of 281 genes. However, the high diagnostic yield may be attributed to the small sample size and possible over-representation of severe phenotypes in the included fetuses. Bearing in mind that chromosomal abnormalities were excluded in our cohorts, a detection rate of up to 75% is possible in prenatally diagnosed NIHF when WGS analysis includes calling of chromosomal aberrations. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Dataset Information

Feasibility and utility of a panel testing for 114 cancer-associated genes in a clinical setting: A hospital-based study.

Publications

Feasibility and utility of a panel testing for 114 cancer-associated genes in a clinical setting: A hospital-based study.

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