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Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (Edition 1.0).

ABSTRACT: In Japan, the social (medical) health-care system is on the way to being developed to advance personalized medicine through the implementation of cancer genomic medicine, known as "cancer clinical sequencing," which uses a next-generation sequencer. However, no Japanese guidance for cancer genomic testing exists. Gene panel testing can be carried out to help determine patient treatment, confirm diagnosis, and evaluate prognostic predictions of patients with mainly solid cancers for whom no standard treatment is available. This guidance describes how to utilize gene panel testing according to the type of cancer: childhood cancer, rare cancer, carcinoma of unknown primary, and other cancers. The level of evidence classification for unified use in Japan is also detailed. This guidance establishes the basic principles of the quality control of specimens, requirements of medical institutions, informed consent, handling of data during the postanalysis stage, and treatment options based on the evidence level. In Japan, gene panel testing for cancer treatment and diagnosis is recommended to comply with this guidance. This is a collaborative work of the Japanese Society of Medical Oncology, Japan Society of Clinical Oncology, and the Japanese Cancer Association.

SUBMITTER: Sunami K

PROVIDER: S-EPMC6125473 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (Edition 1.0).

Sunami Kuniko K Takahashi Hideaki H Tsuchihara Katsuya K Takeda Masayuki M Suzuki Tatsuya T Naito Yoichi Y Sakai Kazuko K Dosaka-Akita Hirotoshi H Ishioka Chikashi C Kodera Yasuhiro Y Muto Manabu M Wakai Toshifumi T Yamazaki Kentaro K Yasui Wataru W Bando Hideaki H Fujimoto Yumi Y Fukuoka Shota S Harano Kenichi K Kawazoe Akihito A Kimura Gen G Koganemaru Shigehiro S Kogawa Takahiro T Kotani Daisuke D Kuboki Yasutoshi Y Matsumoto Hiroshi H Matsumoto Shingo S Mishima Saori S Nakamura Yoshiaki Y Sawada Kentaro K Shingaki Sumito S Shitara Kohei K Umemoto Kumiko K Umemura Shigeki S Yasuda Kayo K Yoshino Takayuki T Yamamoto Noboru N Nishio Kazuto K

Cancer science 20180901 9

In Japan, the social (medical) health-care system is on the way to being developed to advance personalized medicine through the implementation of cancer genomic medicine, known as "cancer clinical sequencing," which uses a next-generation sequencer. However, no Japanese guidance for cancer genomic testing exists. Gene panel testing can be carried out to help determine patient treatment, confirm diagnosis, and evaluate prognostic predictions of patients with mainly solid cancers for whom no stand ...[more]

PMID: 30187675

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Project description:Abstract Background Metagenomic next-generation sequencing (mNGS) of CSF can identify nearly all pathogens in a single test. We previously validated a CSF mNGS assay in a licensed clinical laboratory. To date, the utility of mNGS for infectious disease diagnosis has been described in case reports and small case series, but not in a large-scale clinical trial. Methods The PDAID (“Precision Diagnosis of Acute Infectious Diseases”) study was a 1-year nationwide prospective study across 8 tertiary care hospitals to evaluate the performance and utility of a clinical metagenomic sequencing assay for diagnosis of meningitis, encephalitis, or myelitis from cerebrospinal fluid (CSF) (ClinicalTrials.gov number NCT02910037). We recruited acutely ill hospitalized inpatients lacking a diagnosis at the time of enrollment. CSF samples were processed and analyzed by mNGS testing within 1 week of receipt in the clinical microbiology laboratory, with sequencing results reported in the patient medical record and used to make contemporaneous treatment decisions. Weekly clinical microbial sequencing boards were convened to discuss mNGS results with treating physicians, and clinical impact evaluated by surveys, chart review, and direct clinician feedback. Results A total of 204 patients were enrolled. Patients were severely ill (ICU 48%, average length of stay 26 days, overall 30-day mortality 7.4%). Fifty-nine neurologic infections were diagnosed in 57 patients (27.9%). mNGS identified 15 (25.4%) infections that were missed by all conventional microbiological tests, including emerging and/or uncommon pathogens such as St. Louis encephalitis virus, hepatitis E virus acquired by lung transplant, and Nocardia farcinica. Twelve of the 15 mNGS-only diagnoses (80%) had clinical impact, with 9 of 15 (60%) guiding appropriate treatment. For diagnosis of infections by direct detection CSF testing, mNGS had 79.1% sensitivity and 98.8% specificity, versus 65.1% sensitivity and 99.4% specificity by conventional testing. Conclusion A significant proportion of neurologic infections are missed despite extensive diagnostic testing performed in tertiary care hospitals. Clinical metagenomic CSF testing was found to be useful in increasing the number of diagnosed neurologic infections and providing actionable information for physicians. Disclosures All authors: No reported disclosures.

Dataset Information

Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (Edition 1.0).

Publications

Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (Edition 1.0).

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