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Metellus P, Camilla C, Bialecki E, Beaufils N, Vellutini C, Pellegrino E, Tomasini P, Ahluwalia MS, Mansouri A, Nanni I, Ouafik L. The landscape of cancer-associated transcript fusions in adult brain tumors: a longitudinal assessment in 140 patients with cerebral gliomas and brain metastases. Front Oncol 2024; 14:1382394. [PMID: 39087020 PMCID: PMC11288828 DOI: 10.3389/fonc.2024.1382394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
Background Oncogenic fusions of neurotrophic receptor tyrosine kinase NTRK1, NTRK2, or NTRK3 genes have been found in different types of solid tumors. The treatment of patients with TRK fusion cancer with a first-generation TRK inhibitor (such as larotrectinib or entrectinib) is associated with high response rates (>75%), regardless of tumor histology and presence of metastases. Due to the efficacy of TRK inhibitor therapy of larotrectinib and entrectinib, it is clinically important to identify patients accurately and efficiently with TRK fusion cancer. In this retrospective study, we provide unique data on the incidence of oncogenic NTRK gene fusions in patients with brain metastases (BM) and gliomas. Methods 140 samples fixed and paraffin-embedded tissue (FFPE) of adult patients (59 of gliomas [17 of WHO grade II, 20 of WHO grade III and 22 glioblastomas] and 81 of brain metastasis (BM) of different primary tumors) are analyzed. Identification of NTRK gene fusions is performed using next-generation sequencing (NGS) technology using Focus RNA assay kit (Thermo Fisher Scientific). Results We identified an ETV6 (5)::NTRK3 (15) fusion event using targeted next-generation sequencing (NGS) in one of 59 glioma patient with oligodendroglioma-grade II, IDH-mutated and 1p19q co-deleted at incidence of 1.69%. Five additional patients harboring TMPRSS (2)::ERG (4) were identified in pancreatic carcinoma brain metastasis (BM), prostatic carcinoma BM, endometrium BM and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted. A FGFR3 (17)::TACC3 (11) fusion was identified in one carcinoma breast BM. Aberrant splicing to produce EGFR exons 2-7 skipping mRNA, and MET exon 14 skipping mRNA were identified in glioblastoma and pancreas carcinoma BM, respectively. Conclusions This study provides data on the incidence of NTRK gene fusions in brain tumors, which could strongly support the relevance of innovative clinical trials with specific targeted therapies (larotrectinib, entrectinib) in this population of patients. FGFR3 (17)::TACC3 (11) rearrangement was detected in breast carcinoma BM with the possibility of using some specific targeted therapies and TMPRSS (2)::ERG (4) rearrangements occur in a subset of patients with, prostatic carcinoma BM, endometrium BM, and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted, where there are yet no approved ERG-directed therapies.
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Affiliation(s)
- Philippe Metellus
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Ramsay Santé, Hôpital Privé Clairval, Département de Neurochirurgie, Marseille, France
| | - Clara Camilla
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Emilie Bialecki
- Ramsay Santé, Hôpital Privé Clairval, Département de Neurochirurgie, Marseille, France
| | - Nathalie Beaufils
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Christine Vellutini
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
| | - Eric Pellegrino
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - Pascale Tomasini
- Aix Marseille Univ, APHM, Oncologie multidisciplinaire et innovations thérapeutiques, Marseille, France
- Aix-Marseille Univ, Centre national de Recherche Scientifique (CNRS), Inserm, CRCM, Marseille, France
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL, United States
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Alireza Mansouri
- Department of Neurosurgery, Penn State Cancer Institute, Hershey, PA, United States
| | - Isabelle Nanni
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
| | - L’Houcine Ouafik
- Aix Marseille Univ, Centre national de Recherche Scientifique (CNRS), INP, Inst Neurophysiopathol, Marseille, France
- Aix Marseille Univ, APHM, CHU Timone, Service d’OncoBiologie, Marseille, France
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2
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Gray JE, Markovets A, Reungwetwattana T, Majem M, Nogami N, Peled N, Lee JS, Cho BC, Chewaskulyong B, John T, Han JY, Sebastian M, Todd A, Rukazenkov Y, Barrett C, Chmielecki J, Lee SM, Ramalingam SS, Hartmaier R. Longitudinal Analyses of Circulating Tumor DNA for the Detection of EGFR Mutation-Positive Advanced NSCLC Progression During Treatment: Data From FLAURA and AURA3. J Thorac Oncol 2024:S1556-0864(24)00676-2. [PMID: 39029876 DOI: 10.1016/j.jtho.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024]
Abstract
INTRODUCTION EGFR tyrosine kinase inhibitor (EGFR-TKI)-sensitizing and -resistance mutations may be detected in plasma through circulating tumor DNA (ctDNA). Circulating tumor DNA level changes reflect alterations in tumor burden and could be a dynamic indicator of treatment effect. This analysis aimed to determine whether longitudinal EGFR-mutation ctDNA testing could detect progressive disease (PD) before radiologic detection. METHODS This was a retrospective, exploratory ctDNA analysis in two phase 3 trials (FLAURA, NCT02296125; AURA3, NCT02151981). Patients had treatment-naïve (FLAURA) or EGFR-TKI pre-treated (AURA3) advanced NSCLC with EGFR mutations and on-study PD (RECIST [Response Evaluation Criteria in Solid Tumors]), with a baseline ctDNA result and EGFR-mutation ctDNA monitoring beyond Cycle 3 Day 1. Patients received osimertinib versus comparator EGFR-TKIs (FLAURA) or chemotherapy (AURA3). Outcomes included time from ctDNA PD to RECIST PD and the first subsequent treatment (FLAURA only). RESULTS Circulating tumor DNA PD preceded or co-occurred with RECIST-defined PD in 93 out of 146 patients (64%) in FLAURA and 82 out of 146 patients (56%) in AURA3. Median time from ctDNA PD to RECIST-defined PD (mo) was 3.4 and 2.6 in the osimertinib and comparator EGFR-TKI arms (FLAURA) and 2.8 and 1.5 in the osimertinib and chemotherapy arms (AURA3). In FLAURA, the median time from ctDNA PD to the first subsequent treatment (mo) was 6.0 and 4.7 in the osimertinib (n = 51) and comparator EGFR-TKI arms (n = 70). CONCLUSIONS Among patients with EGFR mutation-positive advanced NSCLC receiving EGFR-TKI or chemotherapy with ctDNA data and RECIST-defined PD, ctDNA PD preceded/co-occurred with RECIST-defined PD in approximately 60% of cases. Longitudinal ctDNA monitoring may detect PD before radiologic PD.
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Affiliation(s)
- Jhanelle E Gray
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Aleksandra Markovets
- Oncology Data Science, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Margarita Majem
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Naoyuki Nogami
- Department of Thoracic Oncology, National Hospital Organization Shikoku Cancer Center, Minamiumemoto-machi, Matsuyama, Japan
| | - Nir Peled
- Department of Oncology, The Institute of Oncology, Shaare Zedek Cancer Center & Ben-Gurion University, Jerusalem, Israel
| | - Jong-Seok Lee
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Tom John
- Department of Medical Oncology, Austin Health, Melbourne, Australia
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea
| | - Martin Sebastian
- Goethe University Frankfurt, University Hospital, Hematology/Medical Oncology, Frankfurt, Germany
| | - Alexander Todd
- Oncology Biometrics, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Carl Barrett
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Juliann Chmielecki
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
| | - Siow Ming Lee
- Department of Oncology, University College London Hospitals and UCL Cancer Institute, Paul O'Gorman Building, London, United Kingdom
| | - Suresh S Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Winship Cancer Institute, Atlanta, Georgia, USA
| | - Ryan Hartmaier
- Translational Medicines, Research and Early Development, Oncology R&D, AstraZeneca, Boston, Massachusetts, USA
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3
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Sakaguchi T, Iketani A, Esumi S, Esumi M, Suzuki Y, Ito K, Fujiwara K, Nishii Y, Katsuta K, Yasui H, Taguchi O, Hataji O. The Current Achievements of Multi-Gene Panel Tests in Clinical Settings for Patients with Non-Small-Cell Lung Cancer. Cancers (Basel) 2024; 16:1670. [PMID: 38730622 PMCID: PMC11083571 DOI: 10.3390/cancers16091670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Some multi-gene panel tests have been implemented in clinical settings to guide targeted therapy in non-small-cell lung cancer (NSCLC) in Japan. The current performance of multi-gene panel tests under the condition that the Oncomine Dx Target Test (ODxTT) and Amoy Dx® Pan Lung Cancer PCR panel (AmoyDx-multi) are available remains relatively unknown. We retrospectively reviewed consecutive patients with NSCLC, whose FFPE samples were considered for genetic testing. We assessed the submission rates, the success rates, and the driver oncogene detection rates of multi-gene panel tests. A total of 225 patients were histologically newly diagnosed with NSCLC or diagnosed with a recurrence of NSCLC without a previous multi-gene panel test at our institution. Among the 225 patients, the FFPE samples of 212 patients (94.2%) were submitted for multi-gene panel testing, including 191 samples (84.9%) for the ODxTT and 21 samples (9.3%) for the AmoyDx-multi. Among the 212 samples submitted to multi-gene panel tests, the success rate was 99.5% (211/212). The detection rate of driver oncogene alterations for all histologies was 52.4% (111/212), and that for adenocarcinoma was 69.7% (106/152). A favorable submission rate and success rate of multi-gene panel tests were shown, along with a favorable detection rate in recent clinical settings.
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Affiliation(s)
- Tadashi Sakaguchi
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Akemi Iketani
- Pathology Department, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Seiya Esumi
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Maki Esumi
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Yuta Suzuki
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Kentaro Ito
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Kentaro Fujiwara
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Yoichi Nishii
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Koji Katsuta
- Pathology Department, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Hiroki Yasui
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Osamu Taguchi
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
| | - Osamu Hataji
- Department of Respiratory Medicine, Matsusaka Municipal Hospital, 1550, Tonomachi, Matsusaka 515-0073, Mie, Japan
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Konkwo C, Chowdhury S, Vilarinho S. Genetics of liver disease in adults. Hepatol Commun 2024; 8:e0408. [PMID: 38551385 PMCID: PMC10984672 DOI: 10.1097/hc9.0000000000000408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Chronic liver disease stands as a significant global health problem with an estimated 2 million annual deaths across the globe. Combining the use of next-generation sequencing technologies with evolving knowledge in the interpretation of genetic variation across the human genome is propelling our understanding, diagnosis, and management of both rare and common liver diseases. Here, we review the contribution of risk and protective alleles to common forms of liver disease, the rising number of monogenic diseases affecting the liver, and the role of somatic genetic variants in the onset and progression of oncological and non-oncological liver diseases. The incorporation of genomic information in the diagnosis and management of patients with liver disease is driving the beginning of a new era of genomics-informed clinical hepatology practice, facilitating personalized medicine, and improving patient care.
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Affiliation(s)
- Chigoziri Konkwo
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shanin Chowdhury
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Silvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
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5
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Sakamoto T, Matsubara T, Takahama T, Yokoyama T, Nakamura A, Tokito T, Okamoto T, Akamatsu H, Oki M, Sato Y, Tobino K, Ikeda S, Mori M, Mimura C, Maeno K, Miura S, Harada T, Nishimura K, Hiraoka M, Kenmotsu H, Fujimoto J, Shimokawa M, Yamamoto N, Nakagawa K. Biomarker Testing in Patients With Unresectable Advanced or Recurrent Non-Small Cell Lung Cancer. JAMA Netw Open 2023; 6:e2347700. [PMID: 38100106 PMCID: PMC10724778 DOI: 10.1001/jamanetworkopen.2023.47700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Importance Biomarker testing for driver mutations is essential for selecting appropriate non-small cell lung cancer (NSCLC) treatment but is insufficient. Objective To investigate the status of biomarker testing and drug therapy for NSCLC in Japan for identifying problems in treatment. Design, Setting, and Participants The REVEAL cohort study included retrospective data collection and prospective follow-up from 29 institutions across Japan. Of 1500 patients diagnosed with advanced or recurrent NSCLC between January 1 and March 18, 2021, 1479 were eligible. Cases recognized at the wrong clinical stage (n = 12), diagnosed outside the study period (n = 6), not treated according to eligibility criteria before recurrence (n = 2), and with deficient consent acquisition procedure (n = 1) were excluded. Main Outcomes and Measures The primary end point was the biomarker testing status. Treatment-related factors were examined. Results Among the 1479 patients included in the analysis, the median age was 72 (range, 30-95) years; 1013 (68.5%) were men; 1161 (78.5%) had an Eastern Cooperative Oncology Group performance status 0 or 1; 1097 (74.2%) were current or past smokers; and 947 (64.0%) had adenocarcinoma. Biomarker status was confirmed in 1273 patients (86.1%). Multigene testing was performed in 705 cases (47.7%); single-gene testing, in 847 (57.3%); and both, in 279 (18.9%). Biomarker testing was performed for EGFR in 1245 cases (84.2%); ALK, in 1165 (78.8%); ROS1, in 1077 (72.8%); BRAF, in 803 (54.3%); and MET, in 805 (54.4%). Positivity rates among 898 adenocarcinoma cases included 305 (34.0%) for EGFR, 29 (3.2%) for ALK, 19 (2.1%) for ROS1, 11 (1.2%) for BRAF, and 14 (1.6%) for MET. Positivity rates among 375 nonadenocarcinoma cases were 14 (3.7%) for EGFR, 6 (1.6%) for ALK, 1 (0.3%) for ROS1, 3 (0.8%) for BRAF, and 8 (2.1%) for MET. Poor physical status, squamous cell carcinoma, and other comorbidities were associated with hampered multigene testing. Targeted therapy was received as first-line treatment by 263 of 278 cases (94.6%) positive for EGFR, 25 of 32 (78.1%) positive for ALK, 15 of 24 (62.5%) positive for ROS1, 9 of 12 (75.0%) positive for BRAF, and 12 of 19 (63.2%) positive for MET. Median overall survival of patients with positive findings for driver gene alteration and who received targeted therapy was 24.3 (95% CI, not reported) months; with positive findings for driver gene alteration and who did not receive targeted therapy, 15.2 (95% CI, 7.7 to not reported) months; and with negative findings for driver gene alteration, 11.0 (95% CI, 10.0-12.5) months. Multigene testing for nonadenocarcinomas and adenocarcinomas accounted for 705 (47.7%) of all NSCLC cases. Conclusions and Relevance These findings suggest that multigene testing has not been sufficiently implemented in Japan and should be considered prospectively, even in nonadenocarcinomas, to avoid missing rare driver gene alterations.
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Affiliation(s)
- Tomohiro Sakamoto
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Taichi Matsubara
- Department of Thoracic Surgery, Kitakyushu Municipal Medical Center, Kitakyushu, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Toshihide Yokoyama
- Department of Respiratory Medicine, Kurashiki Central Hospital, Kurashiki, Japan
| | - Atsushi Nakamura
- Department of Pulmonary Medicine, Sendai Kousei Hospital, Sendai, Japan
| | - Takaaki Tokito
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Tatsuro Okamoto
- Department of Thoracic Oncology, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Hiroaki Akamatsu
- Department of Internal Medicine III, Wakayama Medical University, Wakayama, Japan
| | - Masahide Oki
- Department of Respiratory Medicine, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yuki Sato
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Kazunori Tobino
- Department of Respiratory Medicine, Iizuka Hospital, Iizuka, Japan
| | - Satoshi Ikeda
- Department of Respiratory Medicine, Kanagawa Cardiovascular and Respiratory Center, Yokohama, Japan
| | - Masahide Mori
- Department of Thoracic Oncology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka City, Japan
| | - Chihiro Mimura
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ken Maeno
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Satoru Miura
- Department of Internal Medicine, Niigata Cancer Center Hospital, Niigata, Japan
| | - Toshiyuki Harada
- Center for Respiratory Diseases, Japan Community Health Care Organization Hokkaido Hospital, Sapporo, Japan
| | | | - Manabu Hiraoka
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Limited, Tokyo, Japan
| | | | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Mototsugu Shimokawa
- Department of Biostatistics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Nobuyuki Yamamoto
- Department of Internal Medicine III, Wakayama Medical University, Wakayama, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
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Kajita Y, Teranishi S, Sawazumi T, Watanabe H, Nagaoka S, Tanaka A, Suzukawa Y, Motobayashi Y, Hirose T, Maeda C, Seki K, Tashiro K, Kobayashi N, Yamamoto M, Kudo M, Inayama Y, Kaneko T. Comparison of the slow-pull and aspiration methods of endobronchial ultrasound-guided transbronchial needle aspiration for next-generation sequencing-compatible tissue collection in non-small cell lung cancer. Cancer Med 2023; 12:19512-19522. [PMID: 37732488 PMCID: PMC10587950 DOI: 10.1002/cam4.6561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/07/2023] [Accepted: 09/09/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Personalized treatment for non-small cell lung cancer (NSCLC) has advanced rapidly, and elucidating the genetic changes that trigger this disease is crucial for appropriate treatment selection. Both slow-pull and aspiration methods of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) are accepted methods for collecting samples suitable for next-generation sequencing (NGS) to examine driver gene mutations and translocations in NSCLC. Here, we aimed to determine which of these two methods is superior for obtaining higher-quality samples from patients with NSCLC. METHODS Seventy-one patients diagnosed with NSCLC via EBUS-TBNA using the slow-pull or aspiration (20-mL negative pressure) methods between July 2019 and September 2022 were included. A total of 203 tissue samples from the 71 patients were fixed in formalin, embedded in paraffin, and mounted on slides. The presence of tissue cores, degree of blood contamination, and number of tumor cells were compared between the groups. The success rate of NGS, using Oncomine Dx Target Test Multi-CDx, was also compared between the groups. RESULTS The slow-pull method was associated with a higher yield of tissue cores, lower degree of blood contamination, and higher number of tumor cells than the aspiration method. The success rate of the NGS was also significantly higher for the slow-pull group (95%) than for the aspiration group (68%). CONCLUSION Overall, these findings suggest that the slow-pull method is a superior technique for EBUS-TBNA to obtain high-quality tissue samples for NGS. The slow-pull method may contribute to the identification of driver gene mutations and translocations and facilitate personalized treatment of NSCLC.
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Affiliation(s)
- Yukihito Kajita
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Shuhei Teranishi
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Tomoe Sawazumi
- Division of PathologyYokohama City University Medical CenterYokohamaJapan
| | - Haruka Watanabe
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Satoshi Nagaoka
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Anna Tanaka
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Yuichirou Suzukawa
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Yuto Motobayashi
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Tomofumi Hirose
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Chihiro Maeda
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Kenichi Seki
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Ken Tashiro
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Nobuaki Kobayashi
- Department of PulmonologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Masaki Yamamoto
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Makoto Kudo
- Respiratory Disease CenterYokohama City University Medical CenterYokohamaJapan
| | - Yoshiaki Inayama
- Division of PathologyYokohama City University Medical CenterYokohamaJapan
| | - Takeshi Kaneko
- Department of PulmonologyYokohama City University Graduate School of MedicineYokohamaJapan
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7
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Zhao S, Zhuang W, Han B, Song Z, Guo W, Luo F, Wu L, Hu Y, Wang H, Dong X, Jiang D, Wang M, Miao L, Wang Q, Zhang J, Fu Z, Huang Y, Xu C, Hu L, Li L, Hu R, Yang Y, Li M, Yang X, Zhang L, Huang Y, Fang W. Phase 1b trial of anti-EGFR antibody JMT101 and Osimertinib in EGFR exon 20 insertion-positive non-small-cell lung cancer. Nat Commun 2023; 14:3468. [PMID: 37308490 DOI: 10.1038/s41467-023-39139-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 05/31/2023] [Indexed: 06/14/2023] Open
Abstract
EGFR exon 20 insertion (20ins)-positive non-small-cell lung cancer (NSCLC) is an uncommon disease with limited therapeutic options and dismal prognosis. Here we report the activity, tolerability, potential mechanisms of response and resistance for dual targeting EGFR 20ins with JMT101 (anti-EGFR monoclonal antibody) plus osimertinib from preclinical models and an open label, multi-center phase 1b trial (NCT04448379). Primary endpoint of the trial is tolerability. Secondary endpoints include objective response rate, duration of response, disease control rate, progression free survival, overall survival, the pharmacokinetic profile of JMT101, occurrence of anti-drug antibodies and correlation between biomarkers and clinical outcomes. A total of 121 patients are enrolled to receive JMT101 plus osimertinib 160 mg. The most common adverse events are rash (76.9%) and diarrhea (63.6%). The confirmed objective response rate is 36.4%. Median progression-free survival is 8.2 months. Median duration of response is unreached. Subgroup analyses were performed by clinicopathological features and prior treatments. In patients with platinum-refractory diseases (n = 53), confirmed objective response rate is 34.0%, median progression-free survival is 9.2 months and median duration of response is 13.3 months. Responses are observed in distinct 20ins variants and intracranial lesions. Intracranial disease control rate is 87.5%. Confirmed intracranial objective response rate is 25%.
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Affiliation(s)
- Shen Zhao
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wu Zhuang
- Department of Thoracic Oncology, Fujian Cancer Hospital, Fuzhou, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai, China
| | - Zhengbo Song
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Wei Guo
- Department of Respiratory Medicine, Shanxi Provincial Cancer Hospital, Taiyuan, China
| | - Feng Luo
- Lung Cancer Center, West China School of Medicine and West China Hospital, Sichuan University, Chengdu, China
| | - Lin Wu
- Department of Thoracic Medicine, Hunan Cancer Hospital, Changsha, China
| | - Yi Hu
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing, China
| | - Huijuan Wang
- Department of Medical Oncology, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Da Jiang
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University and Hebei Tumor Hospital, Shijiazhuang, China
| | - Mingxia Wang
- Department of Clinical Pharmacology, The Fourth Hospital of Hebei Medical University and Hebei Tumor Hospital, Shijiazhuang, China
| | - Liyun Miao
- Department of Respiratory and Critical Care Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qian Wang
- Department of Respiratory Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Junping Zhang
- Department of Medical Oncology, Shanxi Bethune Hospital, Taiyuan, China
| | - Zhenming Fu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yihua Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Longyu Hu
- HaploX Biotechnology Co,. Ltd., Shenzhen, China
| | - Lei Li
- Clinical Science Division, CSPC Pharmaceutical Group Co., Ltd, Shijiazhuang, China
| | - Rong Hu
- Clinical Science Division, CSPC Pharmaceutical Group Co., Ltd, Shijiazhuang, China
| | - Yang Yang
- Clinical Science Division, CSPC Pharmaceutical Group Co., Ltd, Shijiazhuang, China
| | - Mengke Li
- Clinical Science Division, CSPC Pharmaceutical Group Co., Ltd, Shijiazhuang, China
| | - Xiugao Yang
- Clinical Science Division, CSPC Pharmaceutical Group Co., Ltd, Shijiazhuang, China.
| | - Li Zhang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yan Huang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Wenfeng Fang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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8
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Morita-Tanaka S, Miyagawa-Hayashino A, Yamada T, Matsui Y, Morimoto K, Hiranuma O, Masuzawa N, Yoshimura A, Iwasaku M, Tokuda S, Kaneko Y, Kim YH, Konishi E, Takayama K. Significance of localized expression of full-length growth differentiation factor-15 in cachexia of advanced non-small cell lung cancer. Support Care Cancer 2023; 31:308. [PMID: 37115357 DOI: 10.1007/s00520-023-07771-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/18/2023] [Indexed: 04/29/2023]
Abstract
PURPOSE Growth differentiation factor-15 (GDF-15) is one of the key cachexia-inducing factors. Clinical trials on therapies targeting GDF-15 for cancer and cancer cachexia are underway. While the role of circulating GDF-15 in cachexia has been clarified, the effects of GDF-15 expression within cancer cells remain to be fully elucidated. Hence, the objective of this study was to investigate the expression of GDF-15 in advanced lung cancer tissues and to understand its role in cachexia. METHODS We retrospectively examined the expression level of full-length GDF-15 in advanced non-small cell lung cancer tissues and analyzed the relationship between the staining intensity and clinical data in 53 samples. RESULTS We found that 52.8% of the total samples were GDF-15 positive, and GDF-15 expression significantly correlated with improved C-reactive protein/albumin ratio (p = 0.008). It did not correlate with the existence of cancer cachexia and overall survival (p = 0.43). CONCLUSION Our findings show that GDF-15 expression significantly correlated with improved C-reactive protein/albumin ratio, but not the existence of cancer cachexia in advanced NSCLC patients.
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Affiliation(s)
- Satomi Morita-Tanaka
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Aya Miyagawa-Hayashino
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tadaaki Yamada
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Yohei Matsui
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenji Morimoto
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Osamu Hiranuma
- Department of Respiratory Medicine, Otsu City Hospital, Otsu, Japan
| | - Naoko Masuzawa
- Department of Surgical Pathology, Otsu City Hospital, Otsu, Japan
| | - Akihiro Yoshimura
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahiro Iwasaku
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsaku Tokuda
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiko Kaneko
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Young Hak Kim
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eiichi Konishi
- Department of Surgical Pathology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koichi Takayama
- Department of Respiratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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9
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Liu X, Zhang J, Hua K. Intelligent Genetic Decoding System Based on Nucleic Acid Isothermal Amplification for Non-Small Cell Lung Cancer Diagnosis. MICROMACHINES 2023; 14:647. [PMID: 36985054 PMCID: PMC10051770 DOI: 10.3390/mi14030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/26/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a major cause of cancer-related deaths around the world. Targeting the sensitized epidermal growth factor receptor (EGFR) caused by gene mutation through the tyrosine kinase inhibitor is an effective therapeutic strategy for NSCLC. Hence, the individualized therapeutic strategy has highlighted the demand for a simple, fast, and intelligent strategy for the genetic decoding of EGFR to cater to the popularization of precision medicine. In this research, a one-pot assay for EGFR identification is established by combining a loop-mediated isothermal amplification and amplification refractory mutation system. By optimizing the component and condition of the nucleic acid amplification system, a sensitive and specific distinguishability is achieved for tracing target variant (60 copies, 0.1%) identification under a strong interferential background within 40 min. Moreover, complex operation and time-consuming data processing, as well as the aerosol contamination, are avoided owing to the whole process for intelligent genetic decoding being performed in a sealed tube. As a demonstration, L858R, the primary point mutation for the sensitization of EGFR, has been accurately decoded using this assay with highly heterogeneous cancerous tissue. In addition, this method can be easily extended for other genetic information decoding using a tailor-made primer set. Thus, we propose that this straightforward strategy may serve as a promising tool for NSCLC diagnosis in clinical practice.
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Affiliation(s)
- Xiaonan Liu
- College of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jiaxing Zhang
- College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Kai Hua
- College of Life Sciences, Northwest University, Xi’an 710069, China
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10
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Behnke A, Cayre A, De Maglio G, Giannini G, Habran L, Tarsitano M, Chetta M, Cappellen D, Lespagnol A, Le Naoures C, Massazza G, Destro A, Bonzheim I, Rau A, Battmann A, Kah B, Watkin E, Hummel M. FACILITATE: A real-world, multicenter, prospective study investigating the utility of a rapid, fully automated real-time PCR assay versus local reference methods for detecting epidermal growth factor receptor variants in NSCLC. Pathol Oncol Res 2023; 29:1610707. [PMID: 36798672 PMCID: PMC9927408 DOI: 10.3389/pore.2023.1610707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023]
Abstract
Accurate testing for epidermal growth factor receptor (EGFR) variants is essential for informing treatment decisions in non-small cell lung cancer (NSCLC). Automated diagnostic workflows may allow more streamlined initiation of targeted treatments, where appropriate, while comprehensive variant analysis is ongoing. FACILITATE, a real-world, prospective, multicenter, European study, evaluated performance and analytical turnaround time of the Idylla™ EGFR Mutation Test compared with local reference methods. Sixteen sites obtained formalin-fixed paraffin-embedded biopsy samples with ≥ 10% neoplastic cells from patients with NSCLC. Consecutive 5 μm sections from patient samples were tested for clinically relevant NSCLC-associated EGFR variants using the Idylla™ EGFR Mutation Test and local reference methods; performance (concordance) and analytical turnaround time were compared. Between January 2019 and November 2020, 1,474 parallel analyses were conducted. Overall percentage agreement was 97.7% [n = 1,418; 95% confidence interval (CI): 96.8-98.3], positive agreement, 87.4% (n = 182; 95% CI: 81.8-91.4) and negative agreement, 99.2% (n = 1,236; 95% CI: 98.5-99.6). There were 38 (2.6%) discordant cases. Ninety percent of results were returned with an analytical turnaround time of within 1 week using the Idylla™ EGFR Mutation Test versus ∼22 days using reference methods. The Idylla™ EGFR Mutation Test performed well versus local methods and had shorter analytical turnaround time. The Idylla™ EGFR Mutation Test can thus support application of personalized medicine in NSCLC.
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Affiliation(s)
- Anke Behnke
- Charité-Universitätsmedizin Berlin, Institute of Pathology and Berlin Institute of Health, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anne Cayre
- Département de Pathologie, Centre Jean-Perrin, Clermont-Ferrand, France
| | - Giovanna De Maglio
- Azienda Sanitaria Universitaria Friuli Centrale, Pathology Department, Santa Maria della Misericordia Hospital, Udine, Italy
| | - Giuseppe Giannini
- Department Molecular Medicine, Università di Roma La Sapienza, Rome, Italy
| | - Lionel Habran
- Anatomopathology Department, CHU Liège, Liège, Belgium
| | - Marina Tarsitano
- Di Laboratorio, A.O.R.N. Cardarelli, Medical Genetics Laboratory, and Ospedale Antonio Cardarelli, U.O.C. di Genetica Medica, Naples, Italy
| | - Massimiliano Chetta
- Di Laboratorio, A.O.R.N. Cardarelli, Medical Genetics Laboratory, and Ospedale Antonio Cardarelli, U.O.C. di Genetica Medica, Naples, Italy
| | - David Cappellen
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac, France
| | - Alexandra Lespagnol
- CHU de Rennes, Laboratoire de Génétique Somatique des Cancers, Rennes, France
| | - Cecile Le Naoures
- CHU de Rennes, Service d’Anatomie et Cytologie Pathologiques, Rennes, France
| | - Gabriella Massazza
- Dipartimento Medicina di Laboratorio Anatomia Patologica, ASST Papa Giovanni XXIII, Bergamo, BG, Italy
| | - Annarita Destro
- Pathology Department, Humanitas Clinical and Research Center—IRCCS, Milan, Italy
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Achim Rau
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Achim Battmann
- Institut für Pathologie und Zytodiagnostik am Krankenhaus Nordwest, Frankfurt, Germany
| | - Bettina Kah
- Institut für Hämatopathologie Hamburg, Hamburg, Germany
| | | | - Michael Hummel
- Charité-Universitätsmedizin Berlin, Institute of Pathology and Berlin Institute of Health, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Michael Hummel,
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11
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Cifuentes C, Lombana M, Vargas H, Laguado P, Ruiz-Patiño A, Rojas L, Navarro U, Vargas C, Ricaurte L, Arrieta O, Zatarain-Barron L, Zapata L, González G, Ortiz C, Bernal L, Restrepo JG, Viola L, Grosso F, Zapata R, Mantilla W, Carranza H, Bustillo I, Llinas N, Duarte R, Rodríguez J, Archila P, Ávila J, Bermúdez M, Gámez T, Sotelo C, Otero J, Forero E, Lema M, Limpias C, Ordóñez-Reyes C, Mejía S, Rolfo C, Rosell R, Cardona AF. Application of Comprehensive Genomic Profiling-Based Next-Generation Sequencing Assay to Improve Cancer Care in a Developing Country. Cancer Control 2023; 30:10732748231175256. [PMID: 37148308 PMCID: PMC10164853 DOI: 10.1177/10732748231175256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
PURPOSE Identifying actionable oncogenic mutations have changed the therapeutic landscape in different types of tumors. This study investigated the utility of comprehensive genomic profiling (CGP), a hybrid capture-based next-generation sequencing (NGS) assay, in clinical practice in a developing country. METHODS In this retrospective cohort study, CGP was performed on clinical samples from patients with different solid tumors recruited between December 2016 and November 2020, using hybrid capture-based genomic profiling, at the individual treating physicians' request in the clinical care for therapy decisions. Kaplan-Meier survival curves were estimated to characterize the time-to-event variables. RESULTS Patients median age was 61 years (range: 14-87 years), and 64.7% were female. The most common histological diagnosis was lung primary tumors, with 90 patients corresponding to 52.9% of the samples (95% CI 45.4-60.4%). Actionable mutations with FDA-approved medications for specific alterations correspondent to tumoral histology were identified in 58 cases (46.4%), whereas other alterations were detected in 47 different samples (37.6%). The median overall survival was 15.5 months (95% CI 11.7 months-NR). Patients who were subjected to genomic evaluation at diagnosis reached a median overall survival of 18.3 months (95% CI 14.9 months-NR) compared to 14.1 months (95% CI 11.1 months-NR) in patients who obtained genomic evaluation after tumor progression and during standard treatment (P = .7). CONCLUSION CGP of different types of tumors identifies clinically relevant genomic alterations that have benefited from targeted therapy and improve cancer care in a developing country to guide personalized treatment to beneficial outcomes of cancer patients.
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Affiliation(s)
- Claudia Cifuentes
- Clinical Oncology Department, Hospital Universitario Mayor de Mederi, Bogotá, Colombia
| | - Milton Lombana
- Hematology and Oncology Department, Clínica de Occidente, Cali, Colombia
| | - Henry Vargas
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - Paola Laguado
- Clinical Research Institute, Clínica del Country, Bogotá Colombia
| | - Alejandro Ruiz-Patiño
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Leonardo Rojas
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Uriel Navarro
- Clinical Oncology Department, Clínica General del Norte, Barranquilla, Colombia
| | - Carlos Vargas
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | | | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Institute (INCan), México City, México
| | | | - Leandro Zapata
- Oncology Department, San Vicente Fundación, Medellín, Colombia
| | - Guido González
- Centro Integral del Cáncer, Clínica de Occidente, Cali, Colombia
| | - Carlos Ortiz
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Laura Bernal
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
- Clinical Oncology Department, Clínica Marly, Bogotá, Colombia
| | - Juan G Restrepo
- Oncology Department, Fundación Valle de Lili, Cali, Colombia
| | - Lucia Viola
- Thoracic Oncology Unit, Fundación Neumológica Colombiana, Bogotá, Colombia
| | - Fabio Grosso
- Oncology Department, Medical Plus, Bogotá, Colombia
| | - Ricardo Zapata
- Oncology Department, Clínica Cardio-VID, Medellín, Colombia
| | - William Mantilla
- Hematology and Oncology Department, Fundación Cardio Infantil, Bogotá, Colombia
| | - Hernán Carranza
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Clinical Oncology Department, Clínica del Country, Bogotá, Colombia
| | - Iván Bustillo
- Oncology Department, Clínica Porto Azul, Barranquilla, Colombia
| | - Néstor Llinas
- Oncology Department, Clínica Vida, Medellín, Colombia
| | - Ricardo Duarte
- Oncology Department, Clínica Colsanitas, Bogotá, Colombia
| | - July Rodríguez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Pilar Archila
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Jenny Ávila
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Maritza Bermúdez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Tatiana Gámez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Carolina Sotelo
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Jorge Otero
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Elkin Forero
- Clinical Oncology Department, Hospital Universitario Mayor de Mederi, Bogotá, Colombia
| | - Mauricio Lema
- Hematology and Oncology Department, Clínica Astorga, Medellín, Colombia
| | | | - Camila Ordóñez-Reyes
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
| | - Sergio Mejía
- Clinical Oncology Department, San Vicente Fundación, Medellín, Colombia
| | - Christian Rolfo
- Thoracic Oncology Center, Icahn School of Medicine at Mount Sinai Tisch Cáncer Center, Mount Sinai Hospital System, New York, NY, US
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G), Universidad el Bosque, Bogotá, Colombia
- Direction of Research, Science and Education, Luis Carlos Sarmiento Angulo Cancer Treatment and Research Center (CTIC), Bogotá, Colombia
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12
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Buglioni A, Caffes PL, Hessler MG, Mansfield AS, Lo YC. Clinical Utility Validation of an Automated Ultrarapid Gene Fusion Assay for NSCLC. JTO Clin Res Rep 2022; 3:100434. [PMID: 36536899 PMCID: PMC9758522 DOI: 10.1016/j.jtocrr.2022.100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/13/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Gene rearrangements are frequent oncologic drivers in NSCLC, and many are suitable for treatment with Food and Drug Administration-approved or experimental targeted therapies. We evaluated the accuracy, specimen acceptance profile, and limits of detection of a rapid fusion assay (Idylla GeneFusion Assay), a commercially available ultrarapid molecular assay, for its clinical utility. Methods A collection of 97 specimens which had previously undergone next-generation sequencing testing were analyzed using the rapid fusion assay. Accuracy was evaluated by sensitivity and specificity compared with the next-generation sequencing results. The performance characteristics were tested by using a variety of different clinically relevant specimen types. Limits of detection were assessed by evaluating different input of tumor percentage and material amount. Results The rapid fusion assay was found to have 100% sensitivity in detecting fusions of ALK, ROS1, RET, NTRK1, and MET exon 14 skipping and 83% sensitivity for NTRK2/3 fusions. There were 100% specificity in detecting fusions of ROS1, RET, NTRK2/3, and MET exon 14 skipping and 98% specificity for ALK. Testing was successful with formalin-fixed paraffin-embedded biopsy and surgical tissues, cell blocks from fine-needle aspiration and pleural fluid (down to 5% tumor content, 18 mm2 tissue scraped), cytology smears (≥300 cells), and previously extracted RNA (minimal 20 ng). Conclusions The rapid fusion assay is quick, accurate, and versatile, allowing reliable detection of ALK, ROS1, RET fusions, and MET exon 14 skipping in NSCLC, and NTRK fusions. Rapid molecular testing may expedite treatment with appropriate targeted therapies.
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Affiliation(s)
- Alessia Buglioni
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia L. Caffes
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mark G. Hessler
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Ying-Chun Lo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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13
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Real-World Clinical Outcomes after Genomic Profiling of Circulating Tumor DNA in Patients with Previously Treated Advanced Non-Small Cell Lung Cancer. Curr Oncol 2022; 29:4811-4826. [PMID: 35877242 PMCID: PMC9318660 DOI: 10.3390/curroncol29070382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Comprehensive genomic profiling for advanced non-small cell lung cancer (NSCLC) can identify patients for molecularly targeted therapies that improve clinical outcomes. We analyzed data from 3084 patients (median age 65 years, 72.9% with adenocarcinoma) with advanced NSCLC registered in a real-world healthcare claims database (GuardantINFORMTM, Guardant Health) who underwent next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) testing (Guardant360®, Guardant Health) after first-line therapy (28.0% with agents targeted against genomic alterations). ctDNA was detected in 2771 samples (89.9%), of which 41.9% harbored actionable alterations, most commonly EGFR (epidermal growth factor receptor) mutations (29.7%). Actionable alterations were detected in 26.7% of patients (534/2001) previously treated with non-targeted agents. Emerging potentially targetable mutations were found in 40.1% (309/770) of patients previously treated with targeted therapies. Among patients with qualifying alterations detected by ctDNA testing, the time to treatment discontinuation (median 8.8 vs. 4.2 months; hazard ratio 1.97, p < 0.001) and overall survival (median 36.1 vs. 16.6 months; hazard ratio 2.08, p < 0.001) were longer for those who received matched second-line therapy versus unmatched second-line therapy. In real-world practice, results of a blood-based NGS assay prior to second-line treatment inform therapeutic decisions that can improve clinical outcomes for patients with advanced NSCLC.
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14
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Ke L, Shen J, Feng J, Chen J, Shen S, Li S, Kuang M, Liang L, Lu C, Li D, He Q, Peng B, Hua Y. Somatic Mutation Profiles Revealed by Next Generation Sequencing (NGS) in 39 Chinese Hepatocellular Carcinoma Patients. Front Mol Biosci 2022; 8:800679. [PMID: 35118119 PMCID: PMC8804344 DOI: 10.3389/fmolb.2021.800679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
The features and significance of somatic mutation profiles in hepatocellular carcinoma (HCC) have not been completely elucidated to date. In this study, 39 tumor specimens from HCC patients were collected for gene variation analysis by next-generation sequencing (NGS), and a correlation analysis between mutated genes and clinical characteristics was also conducted. The results were compared with genome data from cBioPortal database. Our study found that T > G/A > C transversions (Tv) and C > T/G > A transitions (Ti) were dominant. The sequence variations of TP53, MUC16, MUC12, MUC4 and others, and the copy number variations (CNVs) of FGF3, TERT, and SOX2 were found to be more frequent in our cohort than in cBioPortal datasets, and they were highly enriched in pathways in cancer and participated in complex biological regulatory processes. The TP53 mutation was the key mutation (76.9%, 30/39), and the most common amino acid alteration and mutation types were p.R249S (23.5%) and missense mutation (82.3%) in the TP53 variation. Furthermore, TP53 had more co-mutations with MUC17, NBPF10, and AHNAK2. However, there were no significant differences in clinical characteristics between HCC patients with mutant TP53 and wild-type TP53, and the overall survival rate between treatment via precision medication guided by NGS and that via empirical medication (logrank p = 0.181). Therefore, the role of NGS in the guidance of personalized targeted therapy, solely based on NGS, may be limited. Multi-center, large sample, prospective studies are needed to further verify these results.
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Affiliation(s)
- Lixin Ke
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianming Shen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jikun Feng
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jialin Chen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shunli Shen
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaoqiang Li
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ming Kuang
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lijian Liang
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Cuncun Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dongming Li
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Qiang He
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Baogang Peng
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
| | - Yunpeng Hua
- Hepatobiliary and Pancreatic Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yunpeng Hua, ; Baogang Peng, ; Qiang He, ; Dongming Li,
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15
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Takeda T, Yamada T, Tanimura K, Nakano T, Ishida M, Tachibana Y, Shiotsu S, Horiuchi S, Hibino M, Okada A, Chihara Y, Takayama K. Prognostic Markers of Survival among Japanese Patients with Anaplastic Lymphoma Kinase-Positive Non-Small-Cell Lung Cancer Receiving First-Line Alectinib. Diagnostics (Basel) 2021; 11:diagnostics11122170. [PMID: 34943412 PMCID: PMC8699991 DOI: 10.3390/diagnostics11122170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
The prognoses of patients with non-small-cell lung cancer (NSCLC) harboring anaplastic lymphoma kinase (ALK) gene rearrangement have dramatically improved with the use of ALK tyrosine kinase inhibitors. Although immunological and nutritional markers have been investigated to predict outcomes in patients with several cancers, their usefulness in targeted therapies is scarce, and their significance has never been reported in patients receiving first-line treatment with alectinib. Meanwhile, neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio (PLR) has been investigated during crizotinib treatment. This multicenter retrospective study evaluated 42 consecutive Japanese patients with ALK-positive NSCLC who received first-line treatment with alectinib. Immunological and nutritional markers were evaluated at baseline and 3 weeks after alectinib introduction, and their significance in predicting progression-free survival (PFS) was explored. PFS duration was significantly associated with baseline PLR (hazard ratio (HR): 2.49, p = 0.0473), systemic immune-inflammation index (SII; HR: 2.65, p = 0.0337), prognostic nutrition index (PNI; HR: 4.15, p = 0.00185), and the 3-week values for SII (HR: 2.85, p = 0.0473) and PNI (HR: 3.04, p = 0.0125). Immunological and nutritional markers could be useful in predicting the outcomes of first-line treatment with alectinib. Since PLR and SII consist of platelet counts, platelet count could be an important constituent of these markers.
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Affiliation(s)
- Takayuki Takeda
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daini Hospital, Kyoto 602-8026, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Keiko Tanimura
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daini Hospital, Kyoto 602-8026, Japan
| | - Takayuki Nakano
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daini Hospital, Kyoto 602-8026, Japan
| | - Masaki Ishida
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Yusuke Tachibana
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto 605-0981, Japan
| | - Shinsuke Shiotsu
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto 605-0981, Japan
| | - Shigeto Horiuchi
- Department of Respiratory Medicine, Shonan Fujisawa Tokushukai Hospital, Fujisawa 251-0041, Japan
| | - Makoto Hibino
- Department of Respiratory Medicine, Shonan Fujisawa Tokushukai Hospital, Fujisawa 251-0041, Japan
| | - Asuka Okada
- Department of Respiratory Medicine, Saiseikai Suita Hospital, Suita 564-0013, Japan
| | - Yusuke Chihara
- Department of Respiratory Medicine, Uji-Tokushukai Medical Center, Uji 611-0041, Japan
| | - Koichi Takayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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16
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Zhao S, Zhang Z, Zhan J, Zhao X, Chen X, Xiao L, Wu K, Ma Y, Li M, Yang Y, Fang W, Zhao H, Zhang L. Utility of comprehensive genomic profiling in directing treatment and improving patient outcomes in advanced non-small cell lung cancer. BMC Med 2021; 19:223. [PMID: 34592968 PMCID: PMC8485523 DOI: 10.1186/s12916-021-02089-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/06/2021] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND With the identification of new targetable drivers and the recent emergence of novel targeted drugs, using comprehensive genomic profiling in lieu of the routine testing for classic drivers in the clinical care for advanced NSCLC has been increasingly advocated. However, the key assumption justifying this practice, that comprehensive genomic profiling could lead to effective anticancer therapies and improve patient outcomes, remains unproved. METHODS Comprehensive genomic profiling was prospectively applied in 1564 advanced NSCLC patients to identify potentially actionable genomic alterations. Patients were assigned to genotype-matched targeted therapies or nonmatched therapies based on the profiling results. Its utility in directing treatments was determined by the proportion of patients receiving genotype-matched targeted therapies and the proportion of patients being enrolled into genotype-matched clinical trials. Its impacts on patient outcomes were assessed by comparing progression-free survival (PFS) and overall survival (OS) between patients who received a genotype-matched and nonmatched therapy. RESULTS From October 2016 to October 2019, tumor genomic profiles were established in 1166 patients, leading to a matched targeted therapy in 37.7% (n = 440) and a genotype-matched trial enrollment in 20.9% of patients (n = 244). Potentially actionable alterations were detected in 781 patients (67.0%). For these patients, a genomic profiling-directed matched therapy significantly improved PFS (9.0 months vs 4.9 months, P < 0.001) and OS (3.9 years vs 2.5 years, P < 0.001) compared with a nonmatched therapy. Excluding patients with standard targeted therapies, genomic profiling led to a matched targeted therapy in 16.7% (n = 24) and a matched trial enrollment in 11.2% (n = 16) of patients. No PFS (4.7 months vs 4.6 months, P = 0.530) or OS (1.9 years vs 2.4 years, P = 0.238) benefit was observed with the use of genotype-matched targeted therapies in this population. CONCLUSIONS Comprehensive genomic profiling is of clinical utility in assisting treatment selection, facilitating clinical trial enrollment, and improving patient outcomes in advanced NSCLC. However, for patients carrying alterations without standard-of-care targeted drugs, the interpretation of genomic profiling results should be careful given the low likelihood of benefit from the investigational or off-label use of targeted therapies in this population in the current treatment landscape. TRIAL REGISTRATION ChiCTR1900027582 (retrospectively registered on 19 November 2019).
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Affiliation(s)
- Shen Zhao
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Zhonghan Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jianhua Zhan
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | | | - Xinru Chen
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | | | - Kui Wu
- BGI-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuxiang Ma
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Clinical Research, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Mengzhen Li
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Yunpeng Yang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wenfeng Fang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Hongyun Zhao
- State Key Laboratory of Oncology in South China, Guangzhou, China.
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
- Department of Clinical Research, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China.
| | - Li Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China.
- State Key Laboratory of Oncology in South China, Guangzhou, China.
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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17
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Imamura Y, Tanaka K, Kiyota N, Hayashi H, Ota I, Arai A, Iwae S, Minami S, Yane K, Yamazaki T, Nagatani Y, Toyoda M, Takahama T, Sakai K, Nishio K, Otsuki N, Nibu KI, Minami H. Docetaxel plus cisplatin in recurrent and/or metastatic non-squamous-cell head and neck cancer: a multicenter phase II trial. Med Oncol 2021; 38:128. [PMID: 34550483 DOI: 10.1007/s12032-021-01581-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023]
Abstract
The clinical utility of systemic therapy and genomic profiling in non-squamous-cell head and neck cancer (NSCHNC) has not been fully elucidated. This phase II trial evaluated the efficacy and safety of docetaxel and cisplatin combination in the first-line setting. Eligibility criteria were recurrent and/or metastatic NSCHNC; progressive disease within the last 6 months; no prior systemic therapy; and ECOG performance status of 0-1. Patients received docetaxel (75 mg/m2 on day 1) and cisplatin (75 mg/m2 on day 1), repeated every 21 days for 6 cycles. The primary endpoint was confirmed objective response rate (ORR). The secondary endpoints included progression-free survival (PFS), overall survival (OS), and adverse events. Next-generation sequencing (NGS) was performed using the Ion AmpliSeq Cancer Hotspot Panel v2. Twenty-three patients were enrolled from November 2012 to October 2016, of whom 8 were male. Median age was 57 years. Ninety-six percent of cases were metastatic. Among 22 evaluable patients, confirmed ORR was 45% (95% confidential interval 24-68%). With a median follow-up period of 18.8 months, median PFS and OS were 6.7 and 20.1 months, respectively. Grade 3/4 adverse events included febrile neutropenia (39%) and anemia (22%). No treatment-related deaths were observed. NGS analysis revealed potential treatment targets, including ERBB2, KIT, and ALK. The docetaxel and cisplatin combination regimen can be considered a new treatment option in recurrent and/or metastatic NSCHNC, although primary prophylaxis for febrile neutropenia should be considered. Diverse genomic alterations may lead novel treatment options.This trial was registered with the UMIN Clinical Trials Registry as UMIN000008333 on [September 1st, 2012].
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Affiliation(s)
- Yoshinori Imamura
- Department of Medical Oncology and Hematology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kaoru Tanaka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Naomi Kiyota
- Department of Medical Oncology and Hematology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan. .,Cancer Center, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan.
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Ichiro Ota
- Department of Otolaryngology-Head and Neck Surgery, Nara Medical University, 840 Shijo-Cho, Kashihara, Nara, 634-8521, Japan
| | - Akihito Arai
- Department of Otolaryngology, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto, 602-8566, Japan
| | - Shigemichi Iwae
- Department of Head and Neck Surgery, Hyogo Cancer Center, 13-70 Kitaoujicho, Akashi, Hyogo, 673-8588, Japan
| | - Shujiro Minami
- Department of Otolaryngology, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
| | - Katsunari Yane
- Department of Otolaryngology, Kindai University Nara Hospital, 1248-1 Otoda-cho, Ikoma, Nara, 630-0293, Japan
| | - Tomoko Yamazaki
- Division of Head and Neck Medical Oncology, Miyagi Cancer Center, 47-1 Nodayama, Medeshimashiode, Natori, Miyagi, 981-1293, Japan
| | - Yoshiaki Nagatani
- Department of Medical Oncology and Hematology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Masanori Toyoda
- Department of Medical Oncology and Hematology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Takayuki Takahama
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Naoki Otsuki
- Department of Otolaryngology-Head and Neck Surgery, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Ken-Ichi Nibu
- Department of Otolaryngology-Head and Neck Surgery, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Hironobu Minami
- Department of Medical Oncology and Hematology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan.,Cancer Center, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan
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18
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Current Status of Next-Generation Sequencing-Based Cancer Genome Profiling Tests in Japan and Prospects for Liquid Biopsy. Life (Basel) 2021; 11:life11080796. [PMID: 34440540 PMCID: PMC8399872 DOI: 10.3390/life11080796] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/01/2021] [Accepted: 08/03/2021] [Indexed: 12/15/2022] Open
Abstract
Next-generation sequencing-based comprehensive genome profiling (CGP) testing, OncoGuide NCC Oncopanel System, and FoundationOne CDx Cancer Genomic Profile have been covered by the Japanese national health insurance system since June 2019. Because CGP was initially developed to enroll patients into an early-phase clinical trial for solid tumors, its approved indications have been limited to patients who have completed the standard chemotherapy treatment. Approximately 14,000 cases have been registered with the Center for Cancer Genomics and Advanced Therapeutics as of March 2021. Measuring the drug access rate is not enough due to patients' deteriorating condition during CGP analysis and due to the limited number of ongoing clinical trials available, although tumor-agnostic therapies, such as the use of pembrolizumab in high microsatellite-instable solid tumors and in conditions with a high tumor mutational burden (≥10 mut/Mb) as well as the use of entrectinib and larotrectinib in NTRK fusion-positive tumors have been approved in Japan. Moreover, since this analysis is performed using DNA derived from tumor tissue, it is difficult to perform CGP in cases in which an insufficient amount of tissue exists. Thus, noninvasive blood-based assays have been developed, and CGP panels using circulating tumor DNA from blood were approved in March 2021. However, cost, timing, and the number of tests allowed by the health system have not yet been determined. Therefore, in this review, we outline the current status and issues of CGP testing using tumor tissues as well as the expectations and limitations of liquid biopsy for use in Japanese clinical practice.
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19
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Kim IA, Hur JY, Kim HJ, Park JH, Hwang JJ, Lee SA, Lee SE, Kim WS, Lee KY. Targeted Next-Generation Sequencing Analysis for Recurrence in Early-Stage Lung Adenocarcinoma. Ann Surg Oncol 2021; 28:3983-3993. [PMID: 33140254 PMCID: PMC8184531 DOI: 10.1245/s10434-020-09276-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 10/07/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Despite surgical resection, early lung adenocarcinoma has a recurrence rate of 20-50%. No clear predictive markers for recurrence of early lung adenocarcinoma are available. Targeted next-generation sequencing (NGS) is rarely used to identify recurrence-related genes. We aimed to identify genetic alterations that can predict recurrence, by comparing the molecular profiles of patient groups with and without recurrence. METHODS Tissues from 230 patients with resected stage I-II lung adenocarcinoma (median follow-up: 49 months) were analyzed via targeted NGS for 207 cancer-related genes. The recurrence-free survival according to the number and type of mutation was estimated using the Kaplan-Meier method. Independent predictive biomarkers related to recurrence were identified using the Cox proportional hazards model. RESULTS Recurrence was observed in 64 patients (27.8%). In multivariate analysis adjusted for age, sex, smoking history, stage, surgical mode, and visceral pleural invasion, the CTNNB1 mutation and fusion genes (ALK, ROS1, RET) were negative prognostic factors for recurrence in early-stage lung adenocarcinoma (HR 4.47, p = 0.001; HR 2.73, p = 0.009). EGFR mutation was a favorable factor (HR 0.51, p = 0.016), but the CTNNB1/EGFR co-mutations were negative predictors (HR 19.2, p < 0.001). TP53 mutation was a negative predictor compared with EGFR mutation for recurrence (HR 5.24, p = 0.02). CONCLUSIONS Targeted NGS can provide valuable information to predict recurrence and identify patients at high recurrence risk, facilitating selection of the treatment strategy among close monitoring and adjuvant-targeted therapy. Larger datasets are required to validate these findings.
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Affiliation(s)
- In Ae Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Hee Joung Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
| | | | - Jae Joon Hwang
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Thoracic Surgery, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Song Am Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Thoracic Surgery, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Seung Eun Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Wan Seop Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
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20
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Fukui T, Sakai K, Sasaki J, Kakegawa MI, Igawa S, Mitsufuji H, Takeda M, Takahama T, Nakagawa K, Nishio K, Naoki K. Implementation of clinical sequencing for molecular profiling in patients with advanced cancer. Cancer Biomark 2021; 31:119-126. [PMID: 33896820 DOI: 10.3233/cbm-200781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND The advancement of cancer genomics has allowed for multiplex gene assays using next-generation sequencing (NGS) to be practically implemented, however, a clinical practice system remains to be established. OBJECTIVE We evaluated the feasibility of clinical sequencing using NGS-based multiplex gene assays between cooperating medical institutions in patients with advanced cancers. METHODS In this observational study, DNA and RNA samples prepared from existing tumor tissues were subjected to comprehensive genomic profiling using targeted sequencing. RESULTS From January 2017 to March 2019, 36 samples from 33 patients were assessed. Of all patients, 27 (82%) had lung cancer, with the median age of 50 years (range 38-83). Multiplex gene panel tests were successfully carried out on 35/36 (97%) samples. Potentially actionable gene alterations were identified in 10/30 (33%) samples (3 HER2, 2 KRAS, 2 ALK, 1 PIK3CA, 1 RET, and 1 CDKN2A). In the 6 samples examined for resistant mechanisms, ALK I1171N mutation and MET copy number gain were detected in 2 patients with ALK rearrangement-positive lung cancer. CONCLUSIONS Clinical sequencing using NGS-based multiplex gene assays between collaborating domestic medical institutions was feasible, with a success rate of > 97%. Overall, clinical sequencing benefits therapeutic decision-making in patients with advanced cancer.
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Affiliation(s)
- Tomoya Fukui
- Department of Respiratory Medicine, Kitasato University School of Medicine, Kanagawa, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Jiichiro Sasaki
- Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Kanagawa, Japan
| | | | - Satoshi Igawa
- Department of Respiratory Medicine, Kitasato University School of Medicine, Kanagawa, Japan
| | - Hisashi Mitsufuji
- Fundamental Nursing, Kitasato University School of Nursing, Kanagawa, Japan
| | - Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Katsuhiko Naoki
- Department of Respiratory Medicine, Kitasato University School of Medicine, Kanagawa, Japan
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21
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Mutation Profile Assessed by Next-Generation Sequencing (NGS) of Circulating Tumor DNA (ctDNA) in Chinese Lung Adenocarcinoma Patients: Analysis of Real-World Data. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8817898. [PMID: 33997043 PMCID: PMC8116141 DOI: 10.1155/2021/8817898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 04/25/2021] [Indexed: 12/09/2022]
Abstract
Background Genomic testing gives guidance to the treatment options in lung adenocarcinoma patients, but some patients are unable to obtain tissue samples due to lesion location or intolerance. Cell-free circulating tumor DNA (ctDNA) tested in plasma or pleural effusion is an advanced access to solve the problem. Our study descriptively identified the genetic variations of advanced Chinese lung adenocarcinoma patients and analyzed the overall survival of patients with EGFR mutations. Methods A total of 152 patients' plasma samples were included, and gene mutations were detected by NGS using an Illumina Miseq tabletop sequencer. Results Frequencies of altered were EGFR 46.05%, ALK 7.24%, KRAS 6.58%, PIK3CA 6.58%, PTEN 2.63%, HER2 1.97%, MET 1.97%, BRAF 1.32%, NF1 1.32%, and ROS1 0.66%. We identified 48 cases with double or triple driver gene mutations. Multiple mutations were more frequently observed in EGFR and PIK3CA genes. Patients harboring coexistent mutations with an EGFR mutation tended to have a shorter overall survival than those with exclusively EGFR mutations. Conclusion EGFR, ALK, and KRAS were common driver gene in Chinese patients with stage IV lung adenocarcinoma. Multiple mutations were detected in the ctDNA samples and involve more EGFR and PIK3CA mutations. The existence of coexisting gene mutations may have adverse effects on the prognosis of patients with EGFR mutation. The unknown mutations discovered by NGS may provide new targets for gene targeting therapy, and ctDNA test by NGS is an effective method for making appropriate treatment choices.
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22
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Takeda M, Takahama T, Sakai K, Shimizu S, Watanabe S, Kawakami H, Tanaka K, Sato C, Hayashi H, Nonagase Y, Yonesaka K, Takegawa N, Okuno T, Yoshida T, Fumita S, Suzuki S, Haratani K, Saigoh K, Ito A, Mitsudomi T, Handa H, Fukuoka K, Nakagawa K, Nishio K. Clinical Application of the FoundationOne CDx Assay to Therapeutic Decision-Making for Patients with Advanced Solid Tumors. Oncologist 2021; 26:e588-e596. [PMID: 33325566 PMCID: PMC8018334 DOI: 10.1002/onco.13639] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Implementation of personalized medicine requires the accessibility of tumor molecular profiling in order to allow prioritization of appropriate targeted therapies for individual patients. Our aim was to study the role of comprehensive genomic profiling assays that may inform treatment recommendations for patients with solid tumors. MATERIALS AND METHODS We performed a prospective study to evaluate the feasibility of application of the FoundationOne CDx panel-which detects substitutions, insertions and deletions, and copy number alterations in 324 genes, select gene rearrangements, and genomic signatures including microsatellite instability and tumor mutation burden (TMB)-to patients with advanced or recurrent solid tumors before its approval in Japan. RESULTS A total of 181 samples were processed for genomic testing between September 2018 and June 2019, with data being successfully obtained for 175 of these samples, yielding a success rate of 96.7%. The median turnaround time was 41 days (range, 21-126 days). The most common known or likely pathogenic variants were TP53 mutations (n = 113), PIK3CA mutations (n = 33), APC mutations (n = 32), and KRAS mutations (n = 29). Among the 153 patients assessed for TMB, the median TMB was 4 mutations/Mb, and tumors with a high TMB (≥10 mutations/Mb) were more prevalent for lung cancer (11/32) than for other solid tumor types (9/121, Fisher's exact test p < .01). No clear trend toward increased efficacy for immune checkpoint inhibitor (ICI) monotherapy or ICI combination chemotherapy in patients with a high programmed cell death-ligand 1 tumor proportion score or a high TMB was apparent. Among the 174 patients found to harbor known or likely pathogenic actionable alterations, 24 individuals (14%) received matched targeted therapy. CONCLUSION The FoundationOne CDx assay was performed with formalin-fixed, paraffin-embedded tumor specimens with a success rate of >95%. Such testing may inform the matching of patients with cancer with investigational or approved targeted drugs. IMPLICATIONS FOR PRACTICE This prospective cohort study was initiated to investigate the feasibility and utility of clinical application of FoundationOne CDx. A total of 181 samples were processed for genomic testing between September 2018 and June 2019, with data being successfully obtained for 175 of these samples, yielding a success rate of 96.7%, and 24 individuals (14%) received matched targeted therapy.
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Affiliation(s)
- Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Shigeki Shimizu
- Department of Pathology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Satomi Watanabe
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Hisato Kawakami
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kaoru Tanaka
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Chihiro Sato
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Yoshikane Nonagase
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kimio Yonesaka
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Naoki Takegawa
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Tatsuya Okuno
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Takeshi Yoshida
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Soichi Fumita
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Shinichiro Suzuki
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Koji Haratani
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kazumasa Saigoh
- Clinical Genetics, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Akihiko Ito
- Department of Pathology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Hisashi Handa
- Research Institute for Informatics, Kindai UniversityHigashi‐OsakaOsakaJapan
- Research Institute for Science and Technology, Kindai UniversityHigashi‐OsakaOsakaJapan
- Faculty of Science and Engineering, Kindai UniversityHigashi‐OsakaOsakaJapan
| | - Kazuya Fukuoka
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of MedicineOsaka‐SayamaOsakaJapan
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23
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Saito Y, Takahashi N, Matsui A, Michiyuki S, Yamauchi Y, Shimizu Y, Hoshi E, Sakao Y, Kawamura M. Comparative study of the loop-mediated isothermal amplification method and the QIAGEN therascreen PCR kit for the detection of EGFR mutations in non-small cell lung cancer. J Thorac Dis 2021; 13:743-753. [PMID: 33717546 PMCID: PMC7947485 DOI: 10.21037/jtd-20-2642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background Epidermal growth factor receptor (EGFR) mutations are important biomarkers in the treatment of patients with advanced or metastatic diseases. The therascreen EGFR Rotor-Gene Q (RGQ) PCR Kit® (Qiagen, Inc.) is an approved diagnostic test for EGFR mutations in non-small cell lung cancer (NSCLC). This study aims to investigate the diagnostic capability of a loop-mediated isothermal amplification (LAMP) assay as an accurate, efficient, and cost-effective alternative to the therascreen assay. Methods EGFR mutations were investigated by LAMP and therascreen assays using tissue samples that were surgically resected or biopsied from 117 consecutive patients with NSCLC tumors. The EGFR status from the LAMP assay was compared with that of the therascreen assay. Next-generation sequencing (NGS) was performed to confirm EGFR status of tumors that did not match in both assays. To establish an optimal LAMP AUC value, receiver operating characteristics (ROC) curve analysis was performed within tumors with exon 19 deletion or L858R point mutation. Results Of the 117 tumors assayed, 45 tumors with EGFR mutations and 68 tumors with EGFR wild type were matched in both assays, four tumors having mismatched EGFR statuses. NGS further confirmed that two of the four discordant tumors had the same EGFR status that was determined by the LAMP assay. The AUC values were 0.973 (95% CI: 0.929–1.00) in exon 19 deletion, and 0.952 (95% CI: 0.885–1.00) in L858R point mutation. In exon 19 deletion, sensitivity, specificity, and accuracy were 89.3%, 98.9%, and 96.6%, respectively, and 94.7%, 95.9%, and 95.7%, respectively, in L858R using AUC value of 0.222. Conclusions The LAMP assay compared favorably with the therascreen assay and has potential as an effective, simple, rapid, and low-cost diagnostic alternative. Based on these results, a liquid biopsy LAMP system should be developed for point-of-care testing of oncogenes in the near future.
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Affiliation(s)
- Yuichi Saito
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan.,Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Nobumasa Takahashi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Satoru Michiyuki
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Tochigi, Japan
| | - Yoshikane Yamauchi
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Eishin Hoshi
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Yukinori Sakao
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Masafumi Kawamura
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
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24
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Hayashi H, Takiguchi Y, Minami H, Akiyoshi K, Segawa Y, Ueda H, Iwamoto Y, Kondoh C, Matsumoto K, Takahashi S, Yasui H, Sawa T, Onozawa Y, Chiba Y, Togashi Y, Fujita Y, Sakai K, Tomida S, Nishio K, Nakagawa K. Site-Specific and Targeted Therapy Based on Molecular Profiling by Next-Generation Sequencing for Cancer of Unknown Primary Site: A Nonrandomized Phase 2 Clinical Trial. JAMA Oncol 2020; 6:1931-1938. [PMID: 33057591 DOI: 10.1001/jamaoncol.2020.4643] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Importance Although profiling of gene expression and gene alterations by next-generation sequencing (NGS) to predict the primary tumor site and guide molecularly targeted therapy might be expected to improve clinical outcomes for cancer of unknown primary site (CUP), to our knowledge, no clinical trial has previously evaluated this approach. Objective To assess the clinical use of site-specific treatment, including molecularly targeted therapy based on NGS results, for patients with CUP. Design, Setting, and Participants This phase 2 clinical trial was conducted at 19 institutions in Japan and enrolled 111 previously untreated patients with the unfavorable subset of CUP between March 2015 and January 2018, with 97 patients being included in the efficacy analysis. Eligibility criteria included a diagnosis of unfavorable CUP after mandatory examinations, including pathological evaluation by immunohistochemistry, chest-abdomen-pelvis computed tomography scans, and a positron emission tomography scan. Interventions RNA and DNA sequencing for selected genes was performed simultaneously to evaluate gene expression and gene alterations, respectively. A newly established algorithm was applied to predict tumor origin based on these data. Patients received site-specific therapy, including molecularly targeted therapy, according to the predicted site and detected gene alterations. Main Outcomes And Measures The primary end point was 1-year survival probability. Secondary end points included progression-free survival (PFS), overall survival (OS), objective response rate, safety, efficacy according to predicted site, and frequency of gene alterations. Results Of 97 participants, 49 (50.5%) were women and the median (range) age was 64 (21-81) years. The cancer types most commonly predicted were lung (21 [21%]), liver (15 [15%]), kidney (15 [15%]), and colorectal (12 [12%]) cancer. The most frequent gene alterations were in TP53 (45 [46.4%]), KRAS (19 [19.6%]), and CDKN2A (18 [18.6%]). The 1-year survival probability, median OS, and median PFS were 53.1% (95% CI, 42.6%-62.5%), 13.7 months (95% CI, 9.3-19.7 months), and 5.2 months (95% CI, 3.3-7.1 months), respectively. Targetable EGFR mutations in tumor specimens were detected in 5 patients with predicted non-small-cell lung cancer (5.2%), 4 of whom were treated with afatinib; 2 of these patients achieved a durable PFS of longer than 6 months. Conclusions and Relevance This study's findings suggest that site-specific treatment, including molecularly targeted therapy based on profiling gene expression and gene alterations by NGS, can contribute to treating patients with the unfavorable subset of CUP. Trial Registration UMIN Identifier: UMIN000016794.
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Affiliation(s)
- Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Yuichi Takiguchi
- Department of Medical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kohei Akiyoshi
- Department of Medical Oncology, Osaka City General Hospital, Osaka, Japan
| | - Yoshihiko Segawa
- Department of Medical Oncology, International Medical Center, Saitama Medical University, Hidaka, Japan
| | - Hiroki Ueda
- Third Department of Internal Medicine, Wakayama Medical University, Wakayama, Japan
| | - Yasuo Iwamoto
- Department of Medical Oncology, Hiroshima City Hospital Organization, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan
| | - Chihiro Kondoh
- Department of Medical Oncology, Toranomon Hospital, Tokyo, Japan
| | - Koji Matsumoto
- Medical Oncology Division, Hyogo Cancer Center, Akashi, Japan
| | - Shin Takahashi
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Hisateru Yasui
- Department of Medical Oncology, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Toshiyuki Sawa
- Department of Respiratory Medicine and Medical Oncology, Gifu Municipal Hospital, Gifu, Japan
| | - Yusuke Onozawa
- Division of Clinical Oncology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yasutaka Chiba
- Clinical Research Center, Kindai University Hospital, Osaka-Sayama, Japan
| | | | - Yoshihiko Fujita
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
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25
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Wei J, Rybczynska AA, Meng P, Terpstra M, Saber A, Sietzema J, Timens W, Schuuring E, Hiltermann TJN, Groen HJM, van der Wekken AJ, van den Berg A, Kok K. An All-In-One Transcriptome-Based Assay to Identify Therapy-Guiding Genomic Aberrations in Nonsmall Cell Lung Cancer Patients. Cancers (Basel) 2020; 12:cancers12102843. [PMID: 33019710 PMCID: PMC7650834 DOI: 10.3390/cancers12102843] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/22/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
The number of genomic aberrations known to be relevant in making therapeutic decisions for non-small cell lung cancer patients has increased in the past decade. Multiple molecular tests are required to reliably establish the presence of these aberrations, which is challenging because available tissue specimens are generally small. To optimize diagnostic testing, we developed a transcriptome-based next-generation sequencing (NGS) assay based on single primed enrichment technology. We interrogated 11 cell lines, two patient-derived frozen biopsies, nine pleural effusion, and 29 formalin-fixed paraffin-embedded (FFPE) samples. All clinical samples were selected based on previously identified mutations at the DNA level in EGFR, KRAS, ALK, PIK3CA, BRAF, AKT1, MET, NRAS, or ROS1 at the DNA level, or fusion genes at the chromosome level, or by aberrant protein expression of ALK, ROS1, RET, and NTRK1. A successful analysis is dependent on the number of unique reads and the RNA quality, as indicated by the DV200 value. In 27 out of 51 samples with >50 K unique reads and a DV200 >30, all 19 single nucleotide variants (SNVs)/small insertions and deletions (INDELs), three MET exon 14 skipping events, and 13 fusion gene transcripts were detected at the RNA level, giving a test accuracy of 100%. In summary, this lung-cancer-specific all-in-one transcriptome-based assay for the simultaneous detection of mutations and fusion genes is highly sensitive.
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Affiliation(s)
- Jiacong Wei
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (J.W.); (A.A.R.); (M.T.)
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100029, China
| | - Anna A. Rybczynska
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (J.W.); (A.A.R.); (M.T.)
| | - Pei Meng
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
- Department of Pathology, Collaborative and Creative Centre, Shantou University Medical College, Shantou 515063, Guangdong, China
| | - Martijn Terpstra
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (J.W.); (A.A.R.); (M.T.)
| | - Ali Saber
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
| | - Jantine Sietzema
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.); (A.J.v.d.W.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.); (A.J.v.d.W.)
| | - Anthonie J. van der Wekken
- Department of Pulmonary Diseases, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (T.J.N.H.); (H.J.M.G.); (A.J.v.d.W.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (P.M.); (A.S.); (J.S.); (W.T.); (E.S.); (A.v.d.B.)
| | - Klaas Kok
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700RB Groningen, The Netherlands; (J.W.); (A.A.R.); (M.T.)
- Correspondence: ; Tel.: +31-655256364/+31-503617100
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26
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Characteristics and response to crizotinib in lung cancer patients with MET amplification detected by next-generation sequencing. Lung Cancer 2020; 149:17-22. [PMID: 32949827 DOI: 10.1016/j.lungcan.2020.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 06/23/2020] [Accepted: 08/30/2020] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Mesenchymal-epithelial transition (MET) amplification is a rare gene alteration in lung cancer. The aim of this study was to investigate the clinical characteristics of MET amplification in lung cancer and the response to crizotinib by subsets of patients with MET amplification detected by next-generation sequencing (NGS). PATIENTS AND METHODS We collected NGS sequencing data for patients with MET amplification in our institution from January 2018 to April 2019. The efficacy of crizotinib in MET amplification was retrospectively analyzed. RESULTS A total of 2694 patients received NGS tests, 3.27 % (82/2507) of patients had primary MET amplification, and acquired MET amplification accounted for 16.04 % (30/187) of re-biopsy patients. Only 19 patients received monotherapy with crizotinib. In survival analysis, ten patients with copy number greater than 4 (CN > 4) had longer median PFS (mPFS) (4.76 months; 95 %CI: 1.67-7.85 months) compared with other nine patients (CN ≤ 4) (2.10 months; 95 %CI: 1.53-2.68 months; P = 0.063), but failed to get a statistical significance. No significant differences were observed between median PFS (mPFS) of the patients with primary and acquired MET amplification (4.04 months vs 2.76 months; P = 0.310). CONCLUSIONS Primary and acquired MET amplification were detected in 3.27 % and 16.04 % of lung cancer patients, respectively. Patients with CN > 4 seemed to have longer PFS after crizotinib treatment. No significant differences in PFS were observed between patients with primary and acquired MET amplification.
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27
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The 2020 update of the recommendations of the Austrian working group on lung pathology and oncology for the diagnostic workup of non-small cell lung cancer with focus on predictive biomarkers. MEMO-MAGAZINE OF EUROPEAN MEDICAL ONCOLOGY 2020. [DOI: 10.1007/s12254-019-00565-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Yamamoto Y, Kanai M, Kou T, Sugiyama A, Nakamura E, Miyake H, Yamada T, Nishigaki M, Kondo T, Murakami H, Torishima M, Matsumoto S, Kosugi S, Muto M. Clinical significance of TP53 variants as possible secondary findings in tumor-only next-generation sequencing. J Hum Genet 2019; 65:125-132. [PMID: 31628423 PMCID: PMC6917569 DOI: 10.1038/s10038-019-0681-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022]
Abstract
In tumor-only next-generation sequencing (NGS), identified variants have the potential to be secondary findings (SFs), but they require verification through additional germline testing. In the present study, 194 patients with advanced cancer who underwent tumor-only NGS between April 2015 and March 2018 were enrolled, and the incidences of possible and true SFs were evaluated. Among them, 120 patients (61.9%) harbored at least one possible SF. TP53 was the most frequent gene in which 97 variants were found in 91 patients (49.5%). Nine patients provided informed consent to undergo additional germline testing, and a total of 14 variants (BRCA1, n = 1; BRCA2, n = 2; PTEN, n = 2; RB1, n = 1; SMAD4, n = 1; STK11, n = 1; TP53, n = 6) were analyzed. Three variants (BRCA1, n = 1; BRCA2, n = 2) were confirmed to be SFs, whereas TP53 variants were confirmed to be somatic variants. To confirm the low prevalence of SFs in TP53, we analyzed 24 patients with TP53 variants who underwent a paired tumor–normal NGS assay. As expected, all TP53 variants were confirmed to be somatic variants. A total of 30 patients were tested for germline variants in TP53, but none of them resulted in true SFs, suggesting the low prevalence of SFs in this gene. Therefore, the significance of additional germline testing for TP53 variants appears to be relatively low in daily clinical practice using a tumor-only NGS assay, unless patients have any relevant medical or family history.
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Affiliation(s)
- Yoshihiro Yamamoto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Kanai
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Tadayuki Kou
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Aiko Sugiyama
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eijiro Nakamura
- DSK Project, Medical Innovation Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidehiko Miyake
- Faculty of Core Research, Natural Science Division, Ochanomizu University, Tokyo, Japan.,Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | - Takahiro Yamada
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan.,Department of Medical Ethics and Medical Genetics, Kyoto University School of Public Health, Kyoto, Japan
| | - Masakazu Nishigaki
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan.,Department of Human Health Sciences, School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Kondo
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | - Hiromi Murakami
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | | | - Shigemi Matsumoto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Kosugi
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan.,Department of Medical Ethics and Medical Genetics, Kyoto University School of Public Health, Kyoto, Japan
| | - Manabu Muto
- Department of Medical Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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29
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A comparative study of curated contents by knowledge-based curation system in cancer clinical sequencing. Sci Rep 2019; 9:11340. [PMID: 31383922 PMCID: PMC6683116 DOI: 10.1038/s41598-019-47673-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 07/22/2019] [Indexed: 01/08/2023] Open
Abstract
Medical oncologists are challenged to personalize medicine with scientific evidence, drug approvals, and treatment guidelines based on sequencing of clinical samples using next generation sequencer (NGS). Knowledge-based curation systems have the potential to help address this challenge. We report here the results of examining the level of evidence regarding treatment approval and clinical trials between recommendations made by Watson for Genomics (WfG), QIAGEN Clinical Insight Interpret (QCII), and Oncomine knowledge-based reporter (OKR). The tumor samples obtained from the solid cancer patients between May to June 2018 at Kindai University Hospital. The formalin-fixed paraffin-embedded tumor samples (n = 31) were sequenced using Oncomine Comprehensive Assay v3. Variants including copy number alteration and gene fusions identified by the Ion reporter software were used commonly on three curation systems. Curation process of data were provided for 25 solid cancers using three curation systems independently. Concordance and distribution of curated evidence levels of variants were analyzed. As a result of sequencing analysis, nonsynonymous mutation (n = 58), gene fusion (n = 2) or copy number variants (n = 12) were detected in 25 cases, and subsequently subjected to knowledge-based curation systems (WfG, OKR, and QCII). The number of curated information in any systems was 51/72 variants. Concordance of evidence levels was 65.3% between WfG and OKR, 56.9% between WfG and QCII, and 66.7% between OKR and QCII. WfG provided great number of clinical trials for the variants. The annotation of resistance information was also observed. Larger differences were observed in clinical trial matching which could be due to differences in the filtering process among three curation systems. This study demonstrates knowledge-based curation systems (WfG, OKR, and QCII) could be helpful tool for solid cancer treatment decision making. Difference in non-concordant evidence levels was observed between three curation systems, especially in the information of clinical trials. This point will be improved by standardized filtering procedure and enriched database of clinical trials in Japan.
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30
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Takeda M, Sakai K, Nishio K, Nakagawa K. Successful long-term treatment of non-small cell lung cancer positive for RET rearrangement with pemetrexed. Onco Targets Ther 2019; 12:5355-5358. [PMID: 31360064 PMCID: PMC6625745 DOI: 10.2147/ott.s211582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/21/2019] [Indexed: 11/23/2022] Open
Abstract
The discovery of RET rearrangement in non–small cell lung cancer (NSCLC) has prompted development of molecularly targeted therapy for such tumors, with several clinical trials being under way to evaluate the therapeutic effects of multitargeted tyrosine kinase inhibitors. The sensitivity of RET fusion–positive NSCLC to cytotoxic chemotherapy has remained unclear, however. We here report a case of NSCLC positive for the CCDC6-RET fusion gene that benefited from treatment with pemetrexed over a period of 30 months, suggesting that thymidylate synthase–targeted drugs such as pemetrexed may show efficacy for NSCLC harboring RET fusions.
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Affiliation(s)
- Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
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31
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Takeda M, Sakai K, Takahama T, Fukuoka K, Nakagawa K, Nishio K. New Era for Next-Generation Sequencing in Japan. Cancers (Basel) 2019; 11:cancers11060742. [PMID: 31142054 PMCID: PMC6627271 DOI: 10.3390/cancers11060742] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/09/2019] [Accepted: 05/23/2019] [Indexed: 02/02/2023] Open
Abstract
Recent progress in understanding the molecular basis of cancer—including the discovery of cancer-associated genes such as oncogenes and tumor suppressor genes—has suggested that cancer can become a treatable disease. The identification of driver oncogenes such as EGFR, ALK, ROS1, BRAF and HER2 has already been successfully translated into clinical practice for individuals with solid tumor. Next-generation sequencing (NGS) technologies have led to the ability to test for multiple cancer-related genes at once with a small amount of cells and tissues. In Japan, several hospitals have started NGS-based mutational profiling screening in patients with solid tumor in order to guide patients to relevant clinical trials. The Ministry of Health, Labor, and Welfare of Japan has also approved several cancer gene panels for use in clinical practice. However, there is an urgent need to develop a medical curriculum of clinical variant interpretation and reporting. We review recent progress in the implementation of NGS in Japan.
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Affiliation(s)
- Masayuki Takeda
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
| | - Takayuki Takahama
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
| | - Kazuya Fukuoka
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
- Clinical Research Center, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka 589-8511, Japan.
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32
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Fielding D, Kurimoto N. Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for Diagnosis and Staging of Lung Cancer. Clin Chest Med 2019; 39:111-123. [PMID: 29433708 DOI: 10.1016/j.ccm.2017.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) is fundamental to the diagnosis of lung cancer, as many patients present with more advanced stages of lung cancer, with enlarged hilar and mediastinal lymph nodes. It also represents a way to sample pulmonary masses directly to make the diagnosis, whereby no other accessible tissue is present and the mass sits adjacent to a large central airway. Very importantly also, EBUS TBNA is the widely accepted first procedure in lung cancer staging. A combined procedure of EUS TBNA can be performed to improve diagnostic accuracy.
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Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, Royal Brisbane and Womens Hospital, Third Floor, James Mayne Building, Butterfield Street, Herston 4029, Australia.
| | - Noriaki Kurimoto
- Division of Medical Oncology and Respiratory Medicine, Shimane University Hospital, 89-1, Enyacho, Izumo, Shimane 693-8501, Japan
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33
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Bai Y, Wang G, Wei J, Dai C, Xu X, Cai X, Wu B, Sun W, Xu Q, Jiao S. Using clinical genomic sequencing to guide personalized cancer therapy in China. Per Med 2019; 16:287-299. [PMID: 30895868 DOI: 10.2217/pme-2018-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To evaluate whether clinical genomic sequencing may benefit Chinese patients with stage IV cancer. Patients & methods: Chinese patients with cancer and their oncologists were provided with genomic sequencing results and corresponding clinical treatment recommendations based on evidence-based medicine, defined as CWES (clinical whole-exome sequencing) analysis. Chinese patients with stage IV cancer who failed the previous treatment upon receiving the CWES reports were included for analyzing the impact of CWES on clinical outcomes in 1-year follow-ups. Results: A total of 88.6% of 953 Chinese patients with cancer had clinically actionable somatic genomic alterations. Eleven patients followed the CWES reports, and 11 patients did not follow the CWES suggestions. The median progression-free survival of two groups were 12 and 4 months, and 45 and 91% of patients failed this round of therapy, respectively. Conclusion: The current study suggested that CWES has the potential to increase clinical benefits for Chinese patients with stage IV cancer.
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Affiliation(s)
- Yuxian Bai
- Department of Digestive Internal Medicine & Photodynamic Therapy Center, Harbin Medical University Cancer Hospital
| | - Guan Wang
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Jinwang Wei
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Chun Dai
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Xiaoman Xu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Xin Cai
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Bing Wu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Wending Sun
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Qiang Xu
- GenomiCare Biotechnology Co. Ltd, Shanghai, China
| | - Shunchang Jiao
- Department of Medical Oncology, Chinese PLA General Hospital, Beijing
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34
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Horton RH, Lucassen AM. Recent developments in genetic/genomic medicine. Clin Sci (Lond) 2019; 133:697-708. [PMID: 30837331 PMCID: PMC6399103 DOI: 10.1042/cs20180436] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/21/2018] [Accepted: 02/27/2019] [Indexed: 12/23/2022]
Abstract
Advances in genetic technology are having a major impact in the clinic, and mean that many perceptions of the role and scope of genetic testing are having to change. Genomic testing brings with it a greater opportunity for diagnosis, or predictions of future diagnoses, but also an increased chance of uncertain or unexpected findings, many of which may have impacts for multiple members of a person's family. In the past, genetic testing was rarely able to provide rapid results, but the increasing speed and availability of genomic testing is changing this, meaning that genomic information is increasingly influencing decisions around patient care in the acute inpatient setting. The landscape of treatment options for genetic conditions is shifting, which has evolving implications for clinical discussions around previously untreatable disorders. Furthermore, the point of access to testing is changing with increasing provision direct to the consumer outside the formal healthcare setting. This review outlines the ways in which genetic medicine is developing in light of technological advances.
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Affiliation(s)
- Rachel H Horton
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Anneke M Lucassen
- Clinical Ethics and Law, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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35
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Kuang BH, Wang BC, Tong F, Yang JS, Zeng YL, Cao RB, Liu L. Application of dynamic monitoring of genomic profiles in non-small cell lung cancer: A case report. Medicine (Baltimore) 2018; 97:e13192. [PMID: 30572427 PMCID: PMC6319983 DOI: 10.1097/md.0000000000013192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
RATIONALE Although lung cancer is the leading cause of cancer-related death in the world, targeted therapy plays an essential role in improving the survival of lung cancer. Next-generation sequencing (NGS) technology can dynamically monitor the genomic profiles of tumors and assist cancer diagnosis and treatment. PATIENT CONCERNS We reported on a 55-year-old man who presented with chest tightness and wheezing for 1 month. DIAGNOSES The patient was diagnosed with stage cT4N2M1a non-small cell lung cancer (NSCLC) and was found to have wild-type EGFR by pleural effusion cytology. INTERVENTIONS The patient received systemic treatments, including chemotherapy, targeted therapy, and radiotherapy. During the cancer development, sequential DNA sequencing data that used circulating cell-free tumor DNA, and NGS revealed EGFR L858R and T790M mutations, MYC amplification, and other gene variations. OUTCOMES The patient died of brain and lung metastases, and had an overall survival as long as 37 months. LESSONS The dynamic monitoring of tumor genomic profiles has important implications for NSCLC diagnosis, treatment, and prognosis.
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Affiliation(s)
- Bo-Hua Kuang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Bi-Cheng Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Fan Tong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Jin-Song Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Yu-Lan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Ru-Bo Cao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan
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36
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Cho WCS, Tan KT, Ma VWS, Li JYC, Ngan RKC, Cheuk W, Yip TTC, Yang YT, Chen SJ. Targeted next-generation sequencing reveals recurrence-associated genomic alterations in early-stage non-small cell lung cancer. Oncotarget 2018; 9:36344-36357. [PMID: 30555633 PMCID: PMC6284742 DOI: 10.18632/oncotarget.26349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/01/2018] [Indexed: 12/14/2022] Open
Abstract
Purpose The identification of genomic alterations related to recurrence in early-stage non-small cell lung cancer (NSCLC) patients may help better stratify high-risk individuals and guide treatment strategies. This study aimed to identify the molecular biomarkers of recurrence in early-stage NSCLC. Results Of the 42 tumors evaluable for genomic alterations, TP53 and EGFR were the most frequent alterations with population frequency 52.4% and 50.0%, respectively. Fusion genes were detected in four patients, which had lower mutational burden and relatively better genomic stability. EGFR mutation and fusion gene were mutually exclusive in this study. CDKN2A, FAS, SUFU and SMARCA4 genomic alterations were only observed in the relapsed patients. Increased copy number alteration index was observed in early relapsed patients. Among these genomic alterations, early-stage NSCLCs harboring CDKN2A, FAS, SUFU and SMARCA4 genomic alterations were found to be significantly associated with recurrence. Some of these new findings were validated using The Cancer Genome Atlas (TCGA) dataset. Conclusions The genomic alterations of CDKN2A, FAS, SUFU and SMARCA4 in early-stage NSCLC are found to be associated with recurrence, but confirmation in a larger independent cohort is required to define the clinical impact. Materials and Methods Paired primary tumor and normal lung tissue samples were collected for targeted next-generation sequencing analysis. A panel targets exons for 440 genes was used to assess the mutational and copy number status of selected genes in three clinically relevant groups of stage I/II NSCLC patients: 1) Early relapse; 2) Late relapse; and 3) No relapse.
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Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Victor W S Ma
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Jacky Y C Li
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Roger K C Ngan
- Department of Clinical Oncology, The University of Hong Kong, Gleneagles Hong Kong Hospital, Wong Chuk Hang, Hong Kong
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
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37
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Hamard C, Mignard X, Pecuchet N, Mathiot N, Blons H, Laurent-Puig P, Leroy K, Lupo A, Chapron J, Giraud F, Arrondeau J, Goldwasser F, Alifano M, Damotte D, Wislez M. [IHC, FISH, CISH, NGS in non-small cell lung cancer: What changes in the biomarker era?]. REVUE DE PNEUMOLOGIE CLINIQUE 2018; 74:327-338. [PMID: 30343945 DOI: 10.1016/j.pneumo.2018.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lung cancer is the leading cause of cancer deaths in France, with about 30,000 deaths per year. The overwhelming majority (90 %) are tobacco-related. The prognosis is dark but great therapeutic advances have been made with the development of targeted therapies first and then immunotherapy afterwards. These medications are conditioned to the expression of biomarkers that require specific tools in routine to measure them. We will detail in this chapter several techniques of anatomopathology, cytogenetics and molecular biology necessary for the detection of biomarkers in lung cancers, and their applications in thoracic oncology in 2018.
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Affiliation(s)
- C Hamard
- Service de pneumologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 27, rue du Faubourg-St-Jacques, 75014 Paris, France; Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France
| | - X Mignard
- GRC n(o) 04, Theranoscan, Sorbonne université, hôpital Tenon, AP-HP, 75020 Paris, France
| | - N Pecuchet
- Inserm UMRS 1147, université Paris Descartes-Sorbonne Paris Cité, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris, 75015 Paris, France
| | - N Mathiot
- Service de pneumologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 27, rue du Faubourg-St-Jacques, 75014 Paris, France
| | - H Blons
- Inserm UMRS 1147, université Paris Descartes-Sorbonne Paris Cité, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris, 75015 Paris, France
| | - P Laurent-Puig
- Inserm UMRS 1147, université Paris Descartes-Sorbonne Paris Cité, hôpital européen Georges-Pompidou, Assistance publique-Hôpitaux de Paris, 75015 Paris, France
| | - K Leroy
- Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France
| | - A Lupo
- Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France; Service d'anatomie-pathologique, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - J Chapron
- Service de pneumologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 27, rue du Faubourg-St-Jacques, 75014 Paris, France
| | - F Giraud
- Service de pneumologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 27, rue du Faubourg-St-Jacques, 75014 Paris, France
| | - J Arrondeau
- Service d'oncologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - F Goldwasser
- Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France; Service d'oncologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - M Alifano
- Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France; Service de chirurgie thoracique, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - D Damotte
- Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France; Service d'anatomie-pathologique, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 75014 Paris, France
| | - M Wislez
- Service de pneumologie, hôpital Cochin, Assistance publique-Hôpitaux de Paris, 27, rue du Faubourg-St-Jacques, 75014 Paris, France; Inserm UMRS1138, équipe « cancer, immune control and escape », centre de recherche des Cordeliers, Paris Descartes université, 75006 Paris, France.
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38
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Kim S, Han Y, Kim SI, Kim HS, Kim SJ, Song YS. Tumor evolution and chemoresistance in ovarian cancer. NPJ Precis Oncol 2018; 2:20. [PMID: 30246154 PMCID: PMC6141595 DOI: 10.1038/s41698-018-0063-0] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 12/30/2022] Open
Abstract
Development of novel strategies to overcome chemoresistance is central goal in ovarian cancer research. Natural history of the cancer development and progression is being reconstructed by genomic datasets to understand the evolutionary pattern and direction. Recent studies suggest that intra-tumor heterogeneity (ITH) is the main cause of treatment failure by chemoresistance in many types of cancers including ovarian cancer. ITH increases the fitness of tumor to adapt to incompatible microenvironment. Understanding ITH in relation to the evolutionary pattern may result in the development of the innovative approach based on individual variability in the genetic, environment, and life style. Thus, we can reach the new big stage conquering the cancer. In this review, we will discuss the recent advances in understanding ovarian cancer biology through the use of next generation sequencing (NGS) and highlight areas of recent progress to improve precision medicine in ovarian cancer.
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Affiliation(s)
- Soochi Kim
- 1Seoul National University Hospital Biomedical Research Institute, Seoul, 03080 Republic of Korea.,2Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Youngjin Han
- 2Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea.,3WCU Biomodulation, Department of Agricultural Biotechnology, Seoul National University, Seoul, 03080 Republic of Korea
| | - Se Ik Kim
- 4Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Hee-Seung Kim
- 4Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
| | - Seong Jin Kim
- 5Precision Medicine Research Center, Advanced Institutes of Convergence Technology, Seoul National University, Suwon, Gyeonggi-do 16229 Republic of Korea.,6Department of transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Gyeonggi-do 16229 Republic of Korea
| | - Yong Sang Song
- 2Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea.,3WCU Biomodulation, Department of Agricultural Biotechnology, Seoul National University, Seoul, 03080 Republic of Korea.,4Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea.,7Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, 03080 Republic of Korea
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Clinical characteristics of non-small cell lung cancer harboring mutations in exon 20 of EGFR or HER2. Oncotarget 2018; 9:21132-21140. [PMID: 29765525 PMCID: PMC5940408 DOI: 10.18632/oncotarget.24958] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/15/2018] [Indexed: 12/26/2022] Open
Abstract
Unlike common epidermal growth factor receptor gene (EGFR) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), mutations in exon 20 of either EGFR or the human EGFR2 gene (HER2) are associated with insensitivity to EGFR-TKIs, with treatment options for patients with such mutations being limited. Clinical characteristics, outcome of EGFR-TKI or nivolumab treatment, and the presence of coexisting mutations were reviewed for NSCLC patients with exon-20 mutations of EGFR or HER2 as detected by routine application of an amplicon-based next-generation sequencing panel. Between July 2013 and June 2017, 206 patients with pathologically confirmed lung cancer were screened for genetic alterations including HER2 and EGFR mutations. Ten patients harbored HER2 exon-20 insertions (one of whom also carried an exon-19 deletion of EGFR), and 12 patients harbored EGFR exon-20 mutations. Five of the 13 patients with EGFR mutations were treated with EGFR-TKIs, two of whom manifested a partial response, two stable disease, and one progressive disease. Among the seven patients treated with nivolumab, one patient manifested a partial response, three stable disease, and three progressive disease, with most (86%) of these patients discontinuing treatment as a result of disease progression within 4 months. The H1047R mutation of PIK3CA detected in one patient was the only actionable mutation coexisting with the exon-20 mutations of EGFR or HER2. Potentially actionable mutations thus rarely coexist with exon-20 mutations of EGFR or HER2, and EGFR-TKIs and nivolumab show limited efficacy in patients with such exon-20 mutations.
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40
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Sato S, Nagahashi M, Koike T, Ichikawa H, Shimada Y, Watanabe S, Kikuchi T, Takada K, Nakanishi R, Oki E, Okamoto T, Akazawa K, Lyle S, Ling Y, Takabe K, Okuda S, Wakai T, Tsuchida M. Impact of Concurrent Genomic Alterations Detected by Comprehensive Genomic Sequencing on Clinical Outcomes in East-Asian Patients with EGFR-Mutated Lung Adenocarcinoma. Sci Rep 2018; 8:1005. [PMID: 29343775 PMCID: PMC5772517 DOI: 10.1038/s41598-017-18560-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/11/2017] [Indexed: 01/23/2023] Open
Abstract
Next-generation sequencing (NGS) has enabled comprehensive detection of genomic alterations in lung cancer. Ethnic differences may play a critical role in the efficacy of targeted therapies. The aim of this study was to identify and compare genomic alterations of lung adenocarcinoma between Japanese patients and the Cancer Genome Atlas (TCGA), which majority of patients are from the US. We also aimed to examine prognostic impact of additional genomic alterations in patients harboring EGFR mutations. Genomic alterations were determined in Japanese patients with lung adenocarcinoma (N = 100) using NGS-based sequencing of 415 known cancer genes, and correlated with clinical outcome. EGFR active mutations, i.e., those involving exon 19 deletion or an L858R point mutation, were seen in 43% of patients. Some differences in driver gene mutation prevalence were observed between the Japanese cohort described in the present study and the TCGA. Japanese cohort had significantly more genomic alterations in cell cycle pathway, i.e., CDKN2B and RB1 than TCGA. Concurrent mutations, in genes such as CDKN2B or RB1, were associated with worse clinical outcome in patients with EGFR active mutations. Our data support the utility of comprehensive sequencing to detect concurrent genomic variations that may affect clinical outcomes in this disease.
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Affiliation(s)
- Seijiro Sato
- Division of Thoracic and Cardiovascular Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masayuki Nagahashi
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Terumoto Koike
- Division of Thoracic and Cardiovascular Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroshi Ichikawa
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yoshifumi Shimada
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Satoshi Watanabe
- Department of Respiratory Medicine and Infectious Disease, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshiaki Kikuchi
- Department of Respiratory Medicine and Infectious Disease, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuki Takada
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryota Nakanishi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuro Okamoto
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kouhei Akazawa
- Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Stephen Lyle
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Yiwei Ling
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Takabe
- Breast Surgery, Department of Surgical Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA.,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biosciences, the State University of New York, Buffalo, New York, USA
| | - Shujiro Okuda
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshifumi Wakai
- Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Masanori Tsuchida
- Division of Thoracic and Cardiovascular Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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41
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Zugazagoitia J, Rueda D, Carrizo N, Enguita AB, Gómez-Sánchez D, Díaz-Serrano A, Jiménez E, Mérida A, Calero R, Lujan R, De Miguel E, Gámez P, Díaz-Hellín V, Nuñez JA, Iglesias L, Ferrer I, Paz-Ares L, Ponce-Aix S. Prospective Clinical Integration of an Amplicon-Based Next-Generation Sequencing Method to Select Advanced Non–Small-Cell Lung Cancer Patients for Genotype-Tailored Treatments. Clin Lung Cancer 2018; 19:65-73.e7. [DOI: 10.1016/j.cllc.2017.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/30/2017] [Accepted: 06/13/2017] [Indexed: 12/30/2022]
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42
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Liang J, Cai W, Feng D, Teng H, Mao F, Jiang Y, Hu S, Li X, Zhang Y, Liu B, Sun ZS. Genetic landscape of papillary thyroid carcinoma in the Chinese population. J Pathol 2017; 244:215-226. [PMID: 29144541 DOI: 10.1002/path.5005] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 11/11/2022]
Abstract
Improvement in the clinical outcome of human cancers requires characterization of the genetic alterations underlying their pathogenesis. Large-scale genomic and transcriptomic characterization of papillary thyroid carcinomas (PTCs) in Western populations has revealed multiple oncogenic drivers which are essential for understanding pathogenic mechanisms of this disease, while, so far, the genetic landscape in Chinese patients with PTC remains uncharacterized. Here, we conducted a large-scale genetic analysis of PTCs from patients in China to determine the mutational landscape of this cancer. By performing targeted DNA amplicon and targeted RNA deep-sequencing, we elucidated the landscape of somatic genetic alterations in 355 Chinese patients with PTC. A total of 88.7% of PTCs were found to harbor at least one candidate oncogenic driver genetic alteration. Among them, around 72.4% of the cases carried BRAF mutations; 2.8% of cases harbored RAS mutations; and 13.8% of cases were characterized with in-frame gene fusions, including seven newly identified kinase gene fusions. TERT promoter mutations were likely to occur in a sub-clonal manner in our PTC cohort. The prevalence of somatic genetic alterations in PTC was significantly different between our Chinese cohort and TCGA datasets for American patients. Additionally, combined analyses of genetic alterations and clinicopathologic features demonstrated that kinase gene fusion was associated with younger age at diagnosis, larger tumor size, and lymph node metastasis in PTC. With the analyses of DNA rearrangement sites of RET gene fusions in PTC, signatures of chromosome translocations related to RET fusion events were also depicted. Collectively, our results provide fundamental insight into the pathogenesis of PTC in the Chinese population. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jialong Liang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, PR China
| | - Dongdong Feng
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, PR China
| | - Fengbiao Mao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Shanshan Hu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
| | - Xianfeng Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, PR China
| | - Yujie Zhang
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Baoguo Liu
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, PR China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, PR China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, PR China
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43
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Mehrad M, Roy S, Bittar HT, Dacic S. Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations. Arch Pathol Lab Med 2017; 142:353-357. [DOI: 10.5858/arpa.2017-0046-oa] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context.—
Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance.
Objective.—
To determine the best testing algorithm for patients with lung cancer in our clinical practice.
Design.—
Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel.
Results.—
Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations.
Conclusions.—
The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.
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Affiliation(s)
| | | | | | - Sanja Dacic
- From the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee (Dr Mehrad); and the Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania (Drs Roy, Trejo Bittar, and Dacic)
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44
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Tsoulos N, Papadopoulou E, Metaxa-Mariatou V, Tsaousis G, Efstathiadou C, Tounta G, Scapeti A, Bourkoula E, Zarogoulidis P, Pentheroudakis G, Kakolyris S, Boukovinas I, Papakotoulas P, Athanasiadis E, Floros T, Koumarianou A, Barbounis V, Dinischiotu A, Nasioulas G. Tumor molecular profiling of NSCLC patients using next generation sequencing. Oncol Rep 2017; 38:3419-3429. [PMID: 29130105 PMCID: PMC5783588 DOI: 10.3892/or.2017.6051] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 10/05/2017] [Indexed: 01/10/2023] Open
Abstract
Non‑small cell lung cancer (NSCLC) is the most common type of lung cancer and a tumor with a broad spectrum of targeted therapies already available or in clinical trials. Thus, molecular characterization of the tumor using next generation sequencing (NGS) technology, has become a key tool for facilitating treatment decisions and the clinical management of NSCLC patients. The performance of a custom 23 gene multiplex amplification hot spot panel, based on Ion AmpliSeq™ technology, was evaluated for the analysis of tumor DNA extracted from formalin-fixed and paraffin-embedded (FFPE) tissues. Furthermore, the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel was used for fusion RNA transcript analysis. The mutation spectrum of the tumors was determined in a cohort of 502 patients with NSCLC using the aforementioned targeted gene panels. The panel used for tumor DNA analysis in this study exhibited high rates (100%) of sensitivity, specificity and reproducibility at a mutation allelic frequency of 3%. At least one DNA mutation was detected in 374 patients (74.5%) and an RNA fusion was identified in 16 patients, (3.2%). In total, alterations in a cancer-driver gene were identified (including point mutations, gene rearrangements and MET amplifications) in 77.6% of the tumors tested. Among the NSCLC patients, 23% presented a mutation in a gene associated with approved or emerging targeted therapy. More specifically, 13.5% (68/502) presented a mutation in a gene with approved targeted therapy (EGFR, ALK, ROS1) and 9.4% (47/502) had an alteration in a gene related to emerging targeted therapies (ERBB2, BRAF, MET and RET). Furthermore, 51.6% of the patients had a mutation in a gene that could be related to an off label therapy or indicative for access to a clinical trial. Thus, the targeted NGS panel used in this study is a reliable approach for tumor molecular profiling and can be applied in personalized treatment decision making for NSCLC patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pavlos Zarogoulidis
- Pulmonary Department, Oncology Unit, ‘G. Papanikolaou’ General Hospital, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - George Pentheroudakis
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina 45500, Greece
| | - Stylianos Kakolyris
- Department of Medical Oncology, University General Hospital of Alexandroupoli, Alexandroupoli 68100, Greece
| | - Ioannis Boukovinas
- Medical Oncology, ‘Bioclinic’ of Thessaloniki, Thessaloniki 54622, Greece
| | - Pavlos Papakotoulas
- Second Department of Medical Oncology, Theagenion Anticancer Hospital of Thessaloniki, Thessaloniki 54639, Greece
| | | | | | - Anna Koumarianou
- Hematology-Oncology Unit, Fourth Department of Internal Medicine, Attikon Hospital, National and Kapodistrian University of Athens, Athens 12462, Greece
| | - Vasileios Barbounis
- Third Medical Oncology Department, ‘Metropolitan’ Hospital, Pireas 18547, Greece
| | - Anca Dinischiotu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest 0050095, Romania
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45
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Ito M, Miyata Y, Hirano S, Kimura S, Irisuna F, Ikeda K, Kushitani K, Tsutani Y, Ueda D, Tsubokawa N, Takeshima Y, Okada M. Therapeutic strategies and genetic profile comparisons in small cell carcinoma and large cell neuroendocrine carcinoma of the lung using next-generation sequencing. Oncotarget 2017; 8:108936-108945. [PMID: 29312580 PMCID: PMC5752493 DOI: 10.18632/oncotarget.22426] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/07/2017] [Indexed: 01/07/2023] Open
Abstract
Small cell lung cancer (SCLC) and large cell neuroendocrine carcinoma (LCNEC) of the lung are classified as variants of endocrine carcinoma and subdivided into pure or combined type. Clinical benefit of target therapy has not been established in these tumors. This study aimed to compare genetic and clinicopathological features between SCLC and LCNEC or pure and combined types, and explore the possibility of target therapy using next-generation sequencing. In 13 SCLC and 22 LCNEC cases, 72 point mutations, 19 deletions, and 3 insertions were detected. As therapeutically targetable variants, mutations in EGFR (L858R), KRAS (G12D, G12A, G12V), and PIK3CA (E545K) were detected in 5 cases. The case harboring EGFR mutation showed response to EGFR-tyrosine kinase inhibitor. However, there are no clinicopathological features associated with therapeutically targetable cases. And there was no significant genetic feature between SCLC and LCNEC or pure and combined types. In conclusion, although patients with SCLC and LCNEC may benefit from target therapy, they were not identifiable by clinicopathologic background. And there was not significant genetic difference between SCLC and LCNEC, including between pure and combined types. Classifying SCLC and LCNEC in same category is reasonable. However, distinguishing the pure type from combined type was not validated. Comprehensive genetic analysis should be performed to detect targetable variants in any type of SCLC and LCNEC.
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Affiliation(s)
- Masaoki Ito
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yoshihiro Miyata
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Shoko Hirano
- Analysis Center of Life Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Shingo Kimura
- Analysis Center of Life Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Fumiko Irisuna
- Analysis Center of Life Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Kyoko Ikeda
- Analysis Center of Life Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Kei Kushitani
- Department of Pathology, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yasuhiro Tsutani
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Daisuke Ueda
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Norifumi Tsubokawa
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Yukio Takeshima
- Analysis Center of Life Science, Natural Science Center for Basic Research and Development, Hiroshima University, Hiroshima, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
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46
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Reeser JW, Martin D, Miya J, Kautto EA, Lyon E, Zhu E, Wing MR, Smith A, Reeder M, Samorodnitsky E, Parks H, Naik KR, Gozgit J, Nowacki N, Davies KD, Varella-Garcia M, Yu L, Freud AG, Coleman J, Aisner DL, Roychowdhury S. Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors. J Mol Diagn 2017; 19:682-696. [PMID: 28802831 DOI: 10.1016/j.jmoldx.2017.05.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/01/2017] [Accepted: 05/08/2017] [Indexed: 12/22/2022] Open
Abstract
Kinase gene fusions are important drivers of oncogenic transformation and can be inhibited with targeted therapies. Clinical grade diagnostics using RNA sequencing to detect gene rearrangements in solid tumors are limited, and the few that are available require prior knowledge of fusion break points. To address this, we have analytically validated a targeted RNA sequencing assay (OSU-SpARKFuse) for fusion detection that interrogates complete transcripts from 93 kinase and transcription factor genes. From a total of 74 positive and 36 negative control samples, OSU-SpARKFuse had 93.3% sensitivity and 100% specificity for fusion detection. Assessment of repeatability and reproducibility revealed 96.3% and 94.4% concordance between intrarun and interrun technical replicates, respectively. Application of this assay on prospective patient samples uncovered OLFM4 as a novel RET fusion partner in a small-bowel cancer and led to the discovery of a KLK2-FGFR2 fusion in a patient with prostate cancer who subsequently underwent treatment with a pan-fibroblast growth factor receptor inhibitor. Beyond fusion detection, OSU-SpARKFuse has built-in capabilities for discovery research, including gene expression analysis, detection of single-nucleotide variants, and identification of alternative splicing events.
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Affiliation(s)
- Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Dorrelyn Martin
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Jharna Miya
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Esko A Kautto
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Ezra Lyon
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Eliot Zhu
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Amy Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Matthew Reeder
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | | | - Hannah Parks
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Karan R Naik
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | | | - Nicholas Nowacki
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Kurtis D Davies
- Department of Pathology, University of Colorado, Anschutz Medical Campus, Denver, Colorado
| | | | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Aharon G Freud
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Joshua Coleman
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Dara L Aisner
- Department of Pathology, University of Colorado, Anschutz Medical Campus, Denver, Colorado
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio; Department of Internal Medicine, Division of Medical Oncology, The Ohio State University, Columbus, Ohio.
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47
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Pisapia P, Lozano MD, Vigliar E, Bellevicine C, Pepe F, Malapelle U, Troncone G. ALK and ROS1 testing on lung cancer cytologic samples: Perspectives. Cancer Cytopathol 2017; 125:817-830. [DOI: 10.1002/cncy.21899] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Maria D. Lozano
- Department of Pathology; University Clinic of Navarra; Pamplona Spain
| | - Elena Vigliar
- Department of Public Health; University of Naples Federico II; Naples Italy
| | | | - Francesco Pepe
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Umberto Malapelle
- Department of Public Health; University of Naples Federico II; Naples Italy
| | - Giancarlo Troncone
- Department of Public Health; University of Naples Federico II; Naples Italy
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48
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Sakai K, Ukita M, Schmidt J, Wu L, De Velasco MA, Roter A, Jevons L, Nishio K, Mandai M. Clonal composition of human ovarian cancer based on copy number analysis reveals a reciprocal relation with oncogenic mutation status. Cancer Lett 2017; 405:22-28. [PMID: 28734796 DOI: 10.1016/j.canlet.2017.07.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 12/17/2022]
Abstract
Intratumoral heterogeneity of cancer cells remains largely unexplored. Here we investigated the composition of ovarian cancer and its biological relevance. A whole-genome single nucleotide polymorphism array was applied to detect the clonal composition of 24 formalin-fixed, paraffin-embedded samples of human ovarian cancer. Genome-wide segmentation data consisting of the log2 ratio (log2R) and B allele frequency (BAF) were used to calculate an estimate of the clonal composition number (CC number) for each tumor. Somatic mutation profiles of cancer-related genes were also determined for the same 24 samples by next-generation sequencing. The CC number was estimated successfully for 23 of the 24 cancer samples. The mean ± SD value for the CC number was 1.7 ± 1.1 (range of 0-4). A somatic mutation in at least one gene was identified in 22 of the 24 ovarian cancer samples, with the mutations including those in the oncogenes KRAS (29.2%), PIK3CA (12.5%), BRAF (8.3%), FGFR2 (4.2%), and JAK2 (4.2%) as well as those in the tumor suppressor genes TP53 (54.2%), FBXW7 (8.3%), PTEN (4.2%), and RB1 (4.2%). Tumors with one or more oncogenic mutations had a significantly lower CC number than did those without such a mutation (1.0 ± 0.8 versus 2.3 ± 0.9, P = 0.0027), suggesting that cancers with driver oncogene mutations are less heterogeneous than those with other mutations. Our results thus reveal a reciprocal relation between oncogenic mutation status and clonal composition in ovarian cancer using the established method for the estimation of the CC number.
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Affiliation(s)
- Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Masayo Ukita
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | | | - Longyang Wu
- Thermo Fisher Scientific, 3420 Central Expy, Santa Clara, USA
| | - Marco A De Velasco
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Alan Roter
- Thermo Fisher Scientific, 3420 Central Expy, Santa Clara, USA
| | - Luis Jevons
- Thermo Fisher Scientific, 3420 Central Expy, Santa Clara, USA
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
| | - Masaki Mandai
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
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49
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Park J, Yoo HM, Jang W, Shin S, Kim M, Kim Y, Lee SW, Kim JG. Distribution of somatic mutations of cancer-related genes according to microsatellite instability status in Korean gastric cancer. Medicine (Baltimore) 2017; 96:e7224. [PMID: 28640116 PMCID: PMC5484224 DOI: 10.1097/md.0000000000007224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In studies of the molecular basis of gastric cancer (GC), microsatellite instability (MSI) is one of the key factors. Somatic mutations found in GC are expected to contribute to MSI-high (H) tumorigenesis. We estimated somatic mutation distribution according to MSI status in 52 matched pair GC samples using the Ion Torrent Ion S5 XL with the AmpliSeq Cancer Hotspot panel.Seventy-five (9.8%) somatic variants consisting of 34 hotspot mutations and 41 other likely pathogenic variants were identified in 34 GC samples. The TP53 mutations was most common (35%, 26/75), followed by EGFR (8%, 6/75), HNF1A (8%, 6/75), PIK3CA (8%, 6/75), and ERBB2 (5%, 4/75). To determine MSI status, 52 matched pair samples were estimated using 15 MSI markers. Thirty-nine MS stable (S), 5 MSI-low (L), and 8 MSI-H were classified. GCs with MSI-H tended to have more variants significantly compared with GCs with MS stable (MSS) and MSI-L (standardized J-T statistic = 3.161 for number of variants; P = .002). The mean number of all variants and hotspot mutations per tumor samples only in GCs with MSI-H were 3.9 (range, 1-6) and 1.1 (range, 0-3), respectively. Whereas, the mean number of all variants and hotspot mutations per tumor samples only in GCs with MSS/MSI-L were 1 (0-5)/0.8 (0-1) and 0.5 (0-3)/0.8 (0-1), respectively.In conclusion, GC with MSI-H harbored more mutations in genes that act as a tumor suppressor or oncogene compared to GC with MSS/MSI-L. This finding suggests that the accumulation of MSIs contributes to the genetic diversity and complexities of GC. In addition, targeted NGS approach allows for detection of common and also rare clinically actionable mutations and profiles of comutations in multiple patients simultaneously. Because GC shows distinctive patterns related to ethnics, further studies pertaining to different racial/ethnic groups or cancer types may reinforce our investigations.
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Affiliation(s)
| | - Han Mo Yoo
- Division of Gastrointestinal Surgery, Department of Surgery
| | | | | | | | | | - Seung-Woo Lee
- Division of Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jeong Goo Kim
- Division of Gastrointestinal Surgery, Department of Surgery
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50
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Lindquist KE, Karlsson A, Levéen P, Brunnström H, Reuterswärd C, Holm K, Jönsson M, Annersten K, Rosengren F, Jirström K, Kosieradzki J, Ek L, Borg Å, Planck M, Jönsson G, Staaf J. Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer. Oncotarget 2017; 8:34796-34810. [PMID: 28415793 PMCID: PMC5471012 DOI: 10.18632/oncotarget.16276] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.
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Affiliation(s)
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Per Levéen
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
| | - Hans Brunnström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karolina Holm
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Annersten
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Frida Rosengren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Karin Jirström
- Department of Pathology, Regional Laboratories Region Skåne, Lund SE 22185, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE 22185, Sweden
| | - Jaroslaw Kosieradzki
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Lars Ek
- Department of Respiratory Medicine and Allergology, Skane University Hospital, Lund SE22185, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- Department of Oncology, Skåne University Hospital, Lund SE 22381, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund SE 22381, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Medicon Village, Lund SE 22381, Sweden
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