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  1. Article ; Online: Prevalence of psychological distress, quality of life, and satisfaction among patients and family members following comprehensive genomic profiling testing

    Makoto Nishino / Maiko Fujimori / Takafumi Koyama / Makoto Hirata / Noriko Tanabe / Toshio Shimizu / Noboru Yamamoto / Yosuke Uchitomi

    PLoS ONE, Vol 18, Iss 5, p e

    Protocol of the Quality of life for Cancer genomics and Advanced Therapeutics (Q-CAT) study.

    2023  Volume 0283968

    Abstract: Precision medicine is rapidly changing the diagnostic and treatment spectrum of oncology. In May 2019, comprehensive genomic profiling (CGP) (somatic and/or germline) was approved for reimbursement in Japan. While the promise of novel and targeted ... ...

    Abstract Precision medicine is rapidly changing the diagnostic and treatment spectrum of oncology. In May 2019, comprehensive genomic profiling (CGP) (somatic and/or germline) was approved for reimbursement in Japan. While the promise of novel and targeted therapies has elevated hopes for the benefits of CGP, the lack of relevant genomic findings and/or limited access to relevant therapies remain important themes in this field. These challenges may also negatively influence the psychology of both cancer patients and their family members. However, few studies have reported longitudinal data on quality of life (QOL) with CGP. Here, we report the protocol of a prospective study, Q-CAT (QOL for Cancer genomics and Advanced Therapeutics among patients and their family members), which aims to explore the mental burden on patients and families arising from the implementation of CGP testing by collecting real-world longitudinal data using outcomes obtained with an electronic patient report, known as ePRO. This study has been registered with the Japan Registry of Clinical Trials (jRCT1030200039).
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Introducing AI to the molecular tumor board

    Ryuji Hamamoto / Takafumi Koyama / Nobuji Kouno / Tomohiro Yasuda / Shuntaro Yui / Kazuki Sudo / Makoto Hirata / Kuniko Sunami / Takashi Kubo / Ken Takasawa / Satoshi Takahashi / Hidenori Machino / Kazuma Kobayashi / Ken Asada / Masaaki Komatsu / Syuzo Kaneko / Yasushi Yatabe / Noboru Yamamoto

    Experimental Hematology & Oncology, Vol 11, Iss 1, Pp 1-

    one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information

    2022  Volume 23

    Abstract: Abstract Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year’s State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of ... ...

    Abstract Abstract Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year’s State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
    Keywords Molecular tumor board ; Precision medicine ; Artificial intelligence ; Next-generation sequencing ; Natural language processing ; Diseases of the blood and blood-forming organs ; RC633-647.5 ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
    Subject code 610
    Language English
    Publishing date 2022-10-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Clinical characteristics of advanced non-small cell lung cancer patients with EGFR exon 20 insertions

    Chie Morita / Tatsuya Yoshida / Masayuki Shirasawa / Ken Masuda / Yuji Matsumoto / Yuki Shinno / Shigehiro Yagishita / Yusuke Okuma / Yasushi Goto / Hidehito Horinouchi / Noboru Yamamoto / Noriko Motoi / Yasushi Yatabe / Yuichiro Ohe

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 7

    Abstract: Abstract Epidermal growth factor receptor (EGFR) exon 20 insertion mutations (Exon20ins) account for 4–12% of all EGFR mutations in non-small cell lung cancer (NSCLC) patients. Data on the differences in clinical characteristics between patients with ... ...

    Abstract Abstract Epidermal growth factor receptor (EGFR) exon 20 insertion mutations (Exon20ins) account for 4–12% of all EGFR mutations in non-small cell lung cancer (NSCLC) patients. Data on the differences in clinical characteristics between patients with Exon20ins and major mutations (M-mut) such as exon 19 deletion and L858R are limited. We retrospectively reviewed advanced NSCLC patients with EGFR mutations, who were treated with systemic therapy between January 2011 and December 2019. We identified 23 patients with Exon20ins and 534 patients with M-mut. In Exon20ins patients, the median age was 60 (range 27–88) years, and females and never-smokers were predominant. Clinical characteristics were similar in the two groups. In Exon20ins patients, 17 patients received platinum doublet as first-line therapy, and the overall response rate (ORR) and median progression-free survival (mPFS) were 11.8% and 8.9 months. Additionally, seven patients received conventional EGFR-tyrosine kinase inhibitors (TKIs), and eight patients anti-PD-1 antibodies in any-line therapy. ORR and mPFS of EGFR-TKIs and anti-PD-1 antibodies were 0%, 2.2 months and 25%, 3.1 months, respectively. Overall survival was significantly shorter in Exon20ins patients than in M-mut patients (29.3 vs. 43.4 months, p = 0.04). The clinical outcomes in Exon20ins patients were not satisfactory compared to M-mut patients.
    Keywords Medicine ; R ; Science ; Q
    Subject code 616 ; 610
    Language English
    Publishing date 2021-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Clinical Utility of Circulating Tumor DNA in Advanced Rare Cancers

    Hitomi Sumiyoshi Okuma / Kan Yonemori / Yuki Kojima / Maki Tanioka / Kazuki Sudo / Emi Noguchi / Susumu Hijioka / Keiko Wakakuwa / Ken Kato / Akihiro Hirakawa / Aya Kuchiba / Takashi Kubo / Hitoshi Ichikawa / Akihiko Yoshida / Yasushi Yatabe / Kenichi Nakamura / Hiroyuki Mano / Noboru Yamamoto / Yasuhiro Fujiwara

    Frontiers in Oncology, Vol

    2021  Volume 11

    Abstract: PurposePatients with advanced/relapsed rare cancers have few treatment options. Analysis of circulating tumor DNA in plasma may identify actionable genomic biomarkers using a non-invasive approach.Patients and MethodsRare cancer patients underwent ... ...

    Abstract PurposePatients with advanced/relapsed rare cancers have few treatment options. Analysis of circulating tumor DNA in plasma may identify actionable genomic biomarkers using a non-invasive approach.Patients and MethodsRare cancer patients underwent prospective plasma-based NGS testing. Tissue NGS to test concordance was also conducted. Plasma DNA alterations were assessed for incidence, functional impact, therapeutic implications, correlation to survival, and comparison with tissue NGS.ResultsNinety-eight patients were analyzed. Diseases included soft-tissue sarcoma, ovarian carcinoma, and others. Mean turn-around-time for results was 9.5 days. Seventy-six patients had detectable gene alterations in plasma, with a median of 2.8 alterations/patient. Sixty patients had a likely pathogenic alteration. Five received matched-therapy based on plasma NGS results. Two developed known resistance mutations while on targeted therapy. Patients with an alteration having VAF ≥5% had a significantly shorter survival compared to those of lower VAF. Tissue NGS results from eleven of 22 patients showed complete or partial concordance with plasma NGS.ConclusionPlasma NGS testing is less invasive and capable of identifying alterations in advanced rare cancers in a clinically meaningful timeframe. It should be further studied as a prospective enrollment assay in interventional studies for patients with rare advanced stage cancers.Clinical Registration[https://www.umin.ac.jp/ctr/index-j.htm], identifier UMIN000034394.
    Keywords rare cancer ; CtDNA (circulating tumor DNA) ; precision medicine ; soft tissue sarcoma ; targeted therapy ; Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282
    Subject code 610 ; 616
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Feasibility of genomic profiling with next-generation sequencing using specimens obtained by image-guided percutaneous needle biopsy

    Miyuki Sone / Yasuaki Arai / Shunsuke Sugawara / Takatoshi Kubo / Chihiro Itou / Tetsuya Hasegawa / Noriyuki Umakoshi / Noboru Yamamoto / Kumiko Sunami / Nobuyoshi Hiraoka / Takashi Kubo

    Upsala Journal of Medical Sciences, Vol 124, Iss 2, Pp 119-

    2019  Volume 124

    Abstract: Aims: The demand for specimen collection for genomic profiling is rapidly increasing in the era of personalized medicine. Percutaneous needle biopsy is recognized as minimally invasive, but the feasibility of comprehensive genomic analysis using next- ... ...

    Abstract Aims: The demand for specimen collection for genomic profiling is rapidly increasing in the era of personalized medicine. Percutaneous needle biopsy is recognized as minimally invasive, but the feasibility of comprehensive genomic analysis using next-generation sequencing (NGS) is not yet clear. The purpose of this study was to evaluate the feasibility of genomic analysis using NGS with specimens obtained by image-guided percutaneous needle biopsy with 18-G needles. Patients and methods: Forty-eight patients who participated in a clinical study of genomic profiling with NGS with the specimen obtained by image-guided needle biopsy were included. All biopsies were performed under local anesthesia, with imaging guidance, using an 18-G cutting needle. A retrospective chart review was performed to determine the rate of successful genomic analysis, technical success rate of biopsy procedure, adverse events, rate of success in pathological diagnosis, and cause of failed genomic analysis. Results: The success rate of genomic analysis was 79.2% (38/48). The causes of failure were unprocessed for DNA extraction due to insufficient specimen volume (6/10), insufficient DNA volume (2/10), and deteriorated DNA quality (2/10). The rate of successful genomic analysis excluding NGS analysis that failed for reasons unrelated to the biopsy procedures was 95.2% (40/42). Technical success of biopsy was achieved in all patients without severe adverse events. The rate of success in the pathological diagnosis was 97.9% (47/48). Conclusions: Image-guided needle biopsy specimens using an 18-G cutting needle yielded a successful NGS genomic analysis rate with no severe adverse events and could be an adoptable method for tissue sampling for NGS.
    Keywords Biopsy ; genomic analysis ; needle biopsy ; next-generation sequencing ; Medicine ; R
    Subject code 610
    Language English
    Publishing date 2019-04-01T00:00:00Z
    Publisher Upsala Medical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Evaluating Clinical Genome Sequence Analysis by Watson for Genomics

    Kota Itahashi / Shunsuke Kondo / Takashi Kubo / Yutaka Fujiwara / Mamoru Kato / Hitoshi Ichikawa / Takahiko Koyama / Reitaro Tokumasu / Jia Xu / Claudia S. Huettner / Vanessa V. Michelini / Laxmi Parida / Takashi Kohno / Noboru Yamamoto

    Frontiers in Medicine, Vol

    2018  Volume 5

    Abstract: Background: Oncologists increasingly rely on clinical genome sequencing to pursue effective, molecularly targeted therapies. This study assesses the validity and utility of the artificial intelligence Watson for Genomics (WfG) for analyzing clinical ... ...

    Abstract Background: Oncologists increasingly rely on clinical genome sequencing to pursue effective, molecularly targeted therapies. This study assesses the validity and utility of the artificial intelligence Watson for Genomics (WfG) for analyzing clinical sequencing results.Methods: This study identified patients with solid tumors who participated in in-house genome sequencing projects at a single cancer specialty hospital between April 2013 and October 2016. Targeted genome sequencing results of these patients' tumors, previously analyzed by multidisciplinary specialists at the hospital, were reanalyzed by WfG. This study measures the concordance between the two evaluations.Results: In 198 patients, in-house genome sequencing detected 785 gene mutations, 40 amplifications, and 22 fusions after eliminating single nucleotide polymorphisms. Breast cancer (n = 40) was the most frequent diagnosis in this analysis, followed by gastric cancer (n = 31), and lung cancer (n = 30). Frequently detected single nucleotide variants were found in TP53 (n = 107), BRCA2 (n = 24), and NOTCH2 (n = 23). MYC (n = 10) was the most frequently detected gene amplification, followed by ERBB2 (n = 9) and CCND1 (n = 6). Concordant pathogenic classifications (i.e., pathogenic, benign, or variant of unknown significance) between in-house specialists and WfG included 705 mutations (89.8%; 95% CI, 87.5%−91.8%), 39 amplifications (97.5%; 95% CI, 86.8–99.9%), and 17 fusions (77.3%; 95% CI, 54.6–92.2%). After about 12 months, reanalysis using a more recent version of WfG demonstrated a better concordance rate of 94.5% (95% CI, 92.7–96.0%) for gene mutations. Across the 249 gene alterations determined to be pathogenic by both methods, including mutations, amplifications, and fusions, WfG covered 84.6% (88 of 104) of all targeted therapies that experts proposed and offered an additional 225 therapeutic options.Conclusions: WfG was able to scour large volumes of data from scientific studies and databases to analyze in-house clinical genome sequencing ...
    Keywords clinical genome sequencing ; genome sequencing interpretation ; artificial intelligence ; watson for genomics ; precision medicine ; Medicine (General) ; R5-920
    Subject code 616 ; 610
    Language English
    Publishing date 2018-11-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Alveolar Soft Part Sarcoma

    Koichi Ogura / Yasuo Beppu / Hirokazu Chuman / Akihiko Yoshida / Noboru Yamamoto / Minako Sumi / Hirotaka Kawano / Akira Kawai

    Sarcoma, Vol

    A Single-Center 26-Patient Case Series and Review of the Literature

    2012  Volume 2012

    Keywords Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Oncology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing

    Mamoru Kato / Hiromi Nakamura / Momoko Nagai / Takashi Kubo / Asmaa Elzawahry / Yasushi Totoki / Yuko Tanabe / Eisaku Furukawa / Joe Miyamoto / Hiromi Sakamoto / Shingo Matsumoto / Kuniko Sunami / Yasuhito Arai / Yutaka Suzuki / Teruhiko Yoshida / Katsuya Tsuchihara / Kenji Tamura / Noboru Yamamoto / Hitoshi Ichikawa /
    Takashi Kohno / Tatsuhiro Shibata

    Genome Medicine, Vol 10, Iss 1, Pp 1-

    2018  Volume 11

    Abstract: Abstract Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, ... ...

    Abstract Abstract Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org.
    Keywords Medicine ; R ; Genetics ; QH426-470
    Language English
    Publishing date 2018-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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