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Shikano K, Ikari J, Nakajima T, Ota M, Shiko Y, Naito A, Abe M, Kawasaki T, Ikeda JI, Ozawa Y, Suzuki T. Franseen needle in endobronchial ultrasound-guided transbronchial needle aspiration: a phase II prospective study. Jpn J Clin Oncol 2024; 54:1037-1044. [PMID: 38864253 DOI: 10.1093/jjco/hyae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has been used to diagnose and stage lung cancer. Acquire™ Pulmonary and Expect™ Pulmonary dedicated EBUS-TBNA needles were introduced as the Franseen and Lancet needles, respectively. It is still unclear whether the Franseen or Lancet needles yield a higher quality specimen especially focusing on next-generation sequencing-based molecular testing. METHODS A single-center, prospective study performed at the Chiba University Hospital randomly assigned patients to two groups: Group A, wherein the first and second EBUS-TBNA were performed using Lancet and Franseen needles, respectively, and Group B, wherein the first and second EBUS-TBNA were performed using Franseen and Lancet needles, respectively. Each specimen was compared and analyzed pathologically. The primary outcome was the histological tissue area except blood clot and the cellularity of each sample. We also examined the success rate of molecular testing. RESULTS Twelve patients who underwent EBUS-TBNA between November 2022 and February 2023 were enrolled in this study. The tissue area of the specimens obtained by the Franseen and Lancet needles was 13.3 ± 6.4 mm2 and 10.6 ± 6.3 mm2, respectively (P = .355). The tumor cellularity in the specimens obtained using the Franseen and Lancet needles was 54.0 ± 30.3 and 46.2 ± 36.3%, respectively (P = .608). The success rate of molecular testing using the single-pass sample by Franseen needle was 85.7 and 57.1% by Lancet needle. No serious complications were reported. CONCLUSIONS The Franseen needle tended to show a greater amount of specimen with higher tumor cellularity than the Lancet needle which may contribute higher success rate of molecular testing. Further studies must be conducted to validate the results of this study. KEY FINDINGS What is known and what is new? What is the implication, and what should change now?
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Affiliation(s)
- Kohei Shikano
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Jun Ikari
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Dokkyo Medical University, 880 Kitakobayashi, Mibu, Shimotsuga, Tochigi, Japan
| | - Masayuki Ota
- Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Yuki Shiko
- Biostatistics Section, Clinical Research Center, Chiba University Hospital, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Akira Naito
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Mitsuhiro Abe
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Takeshi Kawasaki
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Jun-Ichiro Ikeda
- Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Yoshihito Ozawa
- Biostatistics Section, Clinical Research Center, Chiba University Hospital, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
| | - Takuji Suzuki
- Department of Respirology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-Ku, Chiba, Japan
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Lu JJ, Tsai SH, Lin LC, Chiueh TS. Retrospective Analysis to Optimize the Detection of MET Exon 14 Skipping Mutations in Non-Small Cell Lung Cancer. Diagnostics (Basel) 2024; 14:1110. [PMID: 38893636 PMCID: PMC11171647 DOI: 10.3390/diagnostics14111110] [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: 04/15/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Our study optimized METex14 skipping mutation detection by analyzing 223 Oncomine™ Focus Assay-positive cases using Pan Lung Cancer PCR Panel and reverse transcription (RT)-PCR. Among the 11 METex14 skipping mutation-positive cases (average read counts: 1390), 2 with Oncomine™ Focus Assay read counts of 2540 and 10,177 were positive on all platforms. Those with Oncomine™ Focus Assay read counts ranging from 179 to 612 tested negative elsewhere. Specimens with low ratios (average ratio: 0.12% for nine cases) may yield false-positive results. Our results suggested that monitoring read counts and ratios and validating the results with RT-PCR are crucial to prevent false positives.
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Affiliation(s)
- Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Lin-Kou, 5 Fu-Shing St. Kweishan, Taoyuan 333, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, 259 Wen-Hwa 1st Rd. Kweishan, Taoyuan 333, Taiwan
| | - Shu-Hui Tsai
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Lin-Kou, 5 Fu-Shing St. Kweishan, Taoyuan 333, Taiwan
| | - Lee-Chung Lin
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Lin-Kou, 5 Fu-Shing St. Kweishan, Taoyuan 333, Taiwan
| | - Tzong-Shi Chiueh
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Lin-Kou, 5 Fu-Shing St. Kweishan, Taoyuan 333, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, 259 Wen-Hwa 1st Rd. Kweishan, Taoyuan 333, Taiwan
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Nakai T, Matsumoto Y, Ueda T, Kuwae Y, Tanaka S, Miyamoto A, Matsumoto Y, Sawa K, Sato K, Yamada K, Watanabe T, Asai K, Furuse H, Uchimura K, Imabayashi T, Uenishi R, Fukui M, Tanaka H, Ohsawa M, Kawaguchi T, Tsuchida T. Comparison of the specimen quality of endobronchial ultrasound-guided intranodal forceps biopsy using standard-sized forceps versus mini forceps for lung cancer: A prospective study. Respirology 2024; 29:396-404. [PMID: 38246887 DOI: 10.1111/resp.14659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND AND OBJECTIVE Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a diagnostic procedure with adequate performance; however, its ability to provide specimens of sufficient quality and quantity for treatment decision-making in advanced-stage lung cancer may be limited, primarily due to blood contamination. The use of a 0.96-mm miniforceps biopsy (MFB) permits true histological sampling, but the resulting small specimens are unsuitable for the intended applications. Therefore, we introduced a 1.9-mm standard-sized forceps biopsy (SFB) and compared its utility to that of MFB. METHODS We prospectively enrolled patients from three institutions who presented with hilar/mediastinal lymphadenopathy and suspected advanced-stage lung cancer, or those who were already diagnosed but required additional tissue specimens for biomarker analysis. Each patient underwent MFB followed by SFB three or four times through the tract created by TBNA using a 22-gauge needle on the same lymph node (LN). Two pathologists assessed the quality and size of each specimen using a virtual slide system, and diagnostic performance was compared between the MFB and SFB groups. RESULTS Among the 60 enrolled patients, 70.0% were diagnosed with adenocarcinoma. The most frequently targeted sites were the lower paratracheal LNs, followed by the interlobar LNs. The diagnostic yields of TBNA, MFB and SFB were 91.7%, 93.3% and 96.7%, respectively. The sampling rate of high-quality specimens was significantly higher in the SFB group. Moreover, the mean specimen size for SFB was three times larger than for MFB. CONCLUSION SFB is useful for obtaining sufficient qualitative and quantitative specimens.
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Affiliation(s)
- Toshiyuki Nakai
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuji Matsumoto
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takahiro Ueda
- Department of Respiratory Medicine, Izumi City General Hospital, Osaka, Japan
| | - Yuko Kuwae
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Sayaka Tanaka
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Atsushi Miyamoto
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshiya Matsumoto
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kenji Sawa
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kanako Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kazuhiro Yamada
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Tetsuya Watanabe
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kazuhisa Asai
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hideaki Furuse
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Keigo Uchimura
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsuya Imabayashi
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Riki Uenishi
- Department of Respiratory Medicine, Izumi City General Hospital, Osaka, Japan
| | - Mitsuru Fukui
- Laboratory of Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hidenori Tanaka
- Department of Respiratory Medicine, Izumi City General Hospital, Osaka, Japan
| | - Masahiko Ohsawa
- Department of Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Tomoya Kawaguchi
- Department of Respiratory Medicine, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Takaaki Tsuchida
- Department of Endoscopy, Respiratory Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
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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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Ohtaki Y, Nagashima T, Okano N, Kubo N, Ohtaka T, Sunaga N, Sakurai R, Miura Y, Nakazawa S, Kawatani N, Yazawa T, Yoshikawa R, Narusawa E, Shirabe K. Prognosis of non-small cell lung cancer with postoperative regional lymph node recurrence. Thorac Cancer 2024; 15:859-866. [PMID: 38414316 PMCID: PMC11016435 DOI: 10.1111/1759-7714.15265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Regional lymph node recurrence after radical surgery for non-small cell lung cancer (NSCLC) is an oligo-recurrent disease; however, no treatment strategy has been established. In the present study we aimed to determine the clinical outcomes of postoperative regional lymph node recurrence and identify prognostic predictors in the era of molecular-targeted therapy. METHODS We retrospectively analyzed data on clinical characteristics and outcomes of patients with regional lymph node recurrence after surgery who underwent treatment for NSCLC between 2002 and 2022. RESULTS A total of 53 patients were included in this study. The median time between surgery and detection of recurrence was 1.21 years. Radiotherapy (RT) alone and chemoradiotherapy (CRT) were performed in 38 and six patients, respectively. Driver gene alterations were detected in eight patients (EGFR: 6, ROS1:1, and BRAF: 1) and programmed death-ligand 1 (PD-L1) expression was examined in 22 patients after 2016. Median progression-free survival (PFS) and overall survival (OS) after lymph node recurrences were 1.32 and 4.34 years, respectively. Multiple lymph node recurrence was an independent prognostic factor for PFS, whereas driver gene alteration was the only prognostic factor for OS. There was no significant difference in the OS between patients stratified according to the initial treatment modality for lymph node recurrence. CONCLUSION Our results suggest that the number of tumor recurrences may correlate with PFS, while detection of driver gene alterations could guide decision-making for the appropriate molecular-targeted therapy to achieve longer OS.
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Affiliation(s)
- Yoichi Ohtaki
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Toshiteru Nagashima
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Naoko Okano
- Gunma University Heavy Ion Medical CenterMaebashiJapan
| | - Nobuteru Kubo
- Gunma University Heavy Ion Medical CenterMaebashiJapan
| | - Takeru Ohtaka
- Department of Radiation OncologyGunma University Graduate School of MedicineMaebashiJapan
| | - Noriaki Sunaga
- Division of Allergy and Respiratory MedicineIntegrative Center of Internal Medicine, Gunma University HospitalMaebashiJapan
| | - Reiko Sakurai
- Division of Allergy and Respiratory MedicineIntegrative Center of Internal Medicine, Gunma University HospitalMaebashiJapan
| | - Yosuke Miura
- Division of Allergy and Respiratory MedicineIntegrative Center of Internal Medicine, Gunma University HospitalMaebashiJapan
| | - Seshiru Nakazawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Natsuko Kawatani
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Tomohiro Yazawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Ryohei Yoshikawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Eiji Narusawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
| | - Ken Shirabe
- Department of General Surgical Science, Gunma University Graduate School of Medicine, Division of General Thoracic SurgeryIntegrative Center of General Surgery, Gunma University HospitalMaebashiJapan
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Murakami S, Shinada K, Otsutsumi Y, Komine F, Yuan Y, Nakamura J, Katakura S, Kondo T, Kato T, Yokose T, Saito H. Comparison between next-generation sequencing and multiplex polymerase chain reaction assays for nonsmall-cell lung cancer molecular diagnosis. Cancer Med 2024; 13:e7162. [PMID: 38572952 PMCID: PMC10993699 DOI: 10.1002/cam4.7162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
PURPOSE Genetic mutation detection has become an important step in nonsmall-cell lung cancer (NSCLC) treatment because of the increasing number of drugs that target genomic rearrangements. A multiplex test that can detect multiple gene mutations prior to treatment is thus necessary. Currently, either next-generation sequencing (NGS)-based or polymerase chain reaction (PCR)-based tests are used. We evaluated the performance of the Oncomine Dx Target Test (ODxTT), an NGS-based multiplex biomarker panel test, and the AmoyDx Pan Lung Cancer PCR Panel (AmoyDx PLC panel), a real-time PCR-based multiplex biomarker panel test. MATERIALS AND METHODS Patients with histologically diagnosed NSCLC and a sufficient sample volume to simultaneously perform the AmoyDx PLC panel and ODxTT-M were included in the study. The success and detection rates of both tests were evaluated. RESULTS Biopsies revealed 116 cases of malignancies, 100 of which were NSCLC. Of these, 59 met the inclusion criteria and were eligible for analysis. The success rates were 100% and 98% for AmoyDx PLC panel and ODxTT-M, respectively. Nine driver mutations were detected in 35.9% and 37.3% of AmoyDx PLC and ODxTT-M panels, respectively. EGFR mutations were detected in 14% and 12% of samples using the AmoyDx PLC panel and ODxTT-M, respectively. Of the 58 cases in which both NGS and AmoyDx PLC panels were successful, discordant results were observed in seven cases. These differences were mainly due to different sensitivities of the detection methods used and the gene variants targeted in each test. DISCUSSION The AmoyDx PLC panel, a PCR-based multiplex diagnostic test, exhibits a high success rate. The frequency of the nine genes targeted for treatment detected by the AmoyDx PLC panel was comparable to the frequency of mutations detected by ODxTT-M. Clinicians should understand and use the AmoyDx PLC panel and ODxTT-M with respect to their respective performances and limitations.
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Affiliation(s)
- Shuji Murakami
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Kanako Shinada
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Yuka Otsutsumi
- Department of PathologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | | | - Yuan Yuan
- Riken Genesis Co., Ltd.Shinagawa‐kuTokyoJapan
| | | | - Seigo Katakura
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Tetsuro Kondo
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Terufumi Kato
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Tomoyuki Yokose
- Department of PathologyKanagawa Cancer CenterYokohamaKanagawaJapan
| | - Haruhiro Saito
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaKanagawaJapan
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Hatanaka KC, Nakamura K, Katoh R, Ito K, Hirokawa M, Miyauchi A, Matsuno Y, Kano S, Okada Y, Mori J, Ito YM, Hatanaka Y. Impact of the quality of resected thyroid cancer tissue sample on next-generation sequencing testing. Pathol Int 2024; 74:77-86. [PMID: 38226479 DOI: 10.1111/pin.13399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Activating rearranged during transfection (RET) proto-oncogene alterations can be identified using next-generation sequencing (NGS) of tumor DNA/RNA. We assessed factors associated with NGS (Oncomine Dx Target Test [ODxTT]) success for resected thyroid cancer (TC) specimens, including sample age, processing conditions, and DNA/RNA quality. TC samples were from three Japanese hospitals, with sample age <1-<10 years, fixative 10%/15% neutralized buffered formalin (NBF), and fixation time ≤48 h/>48 h-≤72 h. NGS success rate was defined as the percentage of samples returning validated NGS results (RET fusion-positive/negative [RNA] or RET mutation-positive/negative [DNA], detected using ODxTT). DNA/RNA quality was assessed with indexes based on electrophoresis (DNA/RNA integrity number, DV200 ) and quantitative polymerase chain reaction (DNA/RNA integrity score [ddCq/ΔCq]). NGS success rate (N = 202) was 90%/93% (DNA/RNA) overall, 98%-100% (DNA and RNA) for samples <3 years old, and 91% (DNA and RNA) for samples ≥3-<5 years old fixed in 10% NBF for ≤48 h. Multivariate logistic regression analysis identified ddCq and ΔCq as significant predictors of DNA and RNA NGS success rates, respectively. Quality assessment of nucleic acid extracted from archival tissue samples is important for achieving high NGS success rates in clinical practice, especially for samples ≥3 years old.
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Affiliation(s)
- Kanako C Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Kenichi Nakamura
- Japan Drug Development & Medical Affairs, Eli Lilly Japan K.K., Kobe, Japan
| | - Ryohei Katoh
- Department of Pathology, Ito Hospital, Tokyo, Japan
| | - Koichi Ito
- Department of Surgery, Ito Hospital, Tokyo, Japan
| | | | | | - Yoshihiro Matsuno
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo, Japan
| | - Satoshi Kano
- Department of Otolaryngology-Head and Neck Surgery, Faculty and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yui Okada
- Japan Drug Development & Medical Affairs, Eli Lilly Japan K.K., Kobe, Japan
| | - Joji Mori
- Japan Drug Development & Medical Affairs, Eli Lilly Japan K.K., Kobe, Japan
| | - Yoichi M Ito
- Data Science Center, Promotion Unit, Institute of Health Science Innovation for Medical Care, Hokkaido University Hospital, Sapporo, Japan
| | - Yutaka Hatanaka
- Center for Development of Advanced Diagnostics, Hokkaido University Hospital, Sapporo, Japan
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8
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Kikuchi Y, Shimada H, Hatanaka Y, Kinoshita I, Ikarashi D, Nakatsura T, Kitano S, Naito Y, Tanaka T, Yamashita K, Oshima Y, Nanami T. Clinical practice guidelines for molecular tumor markers, 2nd edition review part 1. Int J Clin Oncol 2024; 29:1-19. [PMID: 38019341 DOI: 10.1007/s10147-023-02430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/14/2023] [Indexed: 11/30/2023]
Abstract
With advances in gene and protein analysis technologies, many target molecules that may be useful in cancer diagnosis have been reported. Therefore, the "Tumor Marker Study Group" was established in 1981 with the aim of "discovering clinically" useful molecules. Later, the name was changed to "Japanese Society for Molecular Tumor Marker Research" in 2000 in response to the remarkable progress in gene-related research. Currently, the world of cancer treatment is shifting from the era of representative tumor markers of each cancer type used for tumor diagnosis and treatment evaluation to the study of companion markers for molecular-targeted therapeutics that target cancer cells. Therefore, the first edition of the Molecular Tumor Marker Guidelines, which summarizes tumor markers and companion markers in each cancer type, was published in 2016. After publication of the first edition, the gene panel testing using next-generation sequencing became available in Japan in June 2019 for insured patients. In addition, immune checkpoint inhibitors have been indicated for a wide range of cancer types. Therefore, the 2nd edition of the Molecular Tumor Marker Guidelines was published in September 2021 to address the need to revise the guidelines. Here, we present an English version of the review (Part 1) of the Molecular Tumor Marker Guidelines, Second Edition.
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Affiliation(s)
| | - Hideaki Shimada
- Department of Clinical Oncology, Toho University, Tokyo, Japan.
- Division of General and Gastroenterological Surgery, Department of Surgery (Omori), Toho University, Tokyo, Japan.
| | - Yutaka Hatanaka
- Research Division of Genome Companion Diagnostics, Hokkaido University Hospital, Sapporo, Japan
| | - Ichiro Kinoshita
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Hokkaido, Japan
| | - Daiki Ikarashi
- Department of Urology, Iwate Medical University, Iwate, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Shigehisa Kitano
- Department of Advanced Medical Development, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoichi Naito
- Department of General Internal Medicine, National Cancer Center Hospital East, Chiba, Japan
| | - Toshimichi Tanaka
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Tokyo, Japan
| | - Keishi Yamashita
- Division of Advanced Surgical Oncology, Department of Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Tokyo, Japan
| | - Yoko Oshima
- Division of General and Gastroenterological Surgery, Department of Surgery (Omori), Toho University, Tokyo, Japan
| | - Tatsuki Nanami
- Division of General and Gastroenterological Surgery, Department of Surgery (Omori), Toho University, Tokyo, Japan
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9
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Uemura T, Kenmotsu H, Hazama D, Teraoka S, Kobe H, Azuma K, Yamaguchi T, Masuda T, Yokoyama T, Otsubo K, Haratani K, Hayakawa D, Oki M, Takemoto S, Ozaki T, Akashi Y, Hata A, Hashimoto H, Yamamoto N, Nakagawa K. Liquid biopsy detects genomic drivers in NSCLC without EGFR mutations by single-plex testing: WJOG13620L. Cancer Med 2023; 12:21097-21110. [PMID: 37948122 PMCID: PMC10726866 DOI: 10.1002/cam4.6668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/22/2023] [Accepted: 10/19/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Actionable tumor genomic alterations, primarily EGFR mutations, occur in nearly 70% of Japanese advanced nonsquamous non-small cell lung cancer (NSCLC) patients. Standard assessment of tumor tissue includes rapid testing for EGFR mutations, ALK fusions and ROS1 fusions. We conducted a prospective observational study (WJOG13620L) of follow-on next-generation sequencing of circulating tumor DNA (ctDNA) in patients without driver alterations after EGFR testing. METHODS Patients with untreated advanced (Stage IIIB-IV or relapsed) nonsquamous NSCLC without EGFR mutations according to single-plex testing of tumor tissue, were enrolled into this study. Patients with other known driver mutations or who underwent comprehensive genomic profiling were excluded. Plasma was analyzed by Guardant360, and the primary endpoint was the proportion of patients with pathogenic gene alterations in at least one of nine genes. RESULTS Among the 72 patients enrolled, ALK and ROS1 fusions were tested in 86.1% and 65.2%, respectively. Alterations in pre-defined genes were detected in 21 patients (29.2%; 95% confidence interval: 19.0-41.1, p < 0.001 [one-sided null hypothesis proportion of 10%]), including RET fusion (n = 1) and mutations in KRAS (n = 11), EGFR (n = 5), ERBB2 (n = 3), and BRAF (n = 1). Median time from sample submission to results was 8 days (range, 5-17 days). CONCLUSION Rapid follow-on comprehensive testing of ctDNA should be considered prior to first-line treatment for patients with advanced nonsquamous NSCLC when no alterations are detected after single-plex tissue testing.
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Affiliation(s)
- Takehiro Uemura
- Department of Respiratory Medicine, Allergy and Clinical Immunology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | | | - Daisuke Hazama
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shunsuke Teraoka
- Internal Medicine III, Wakayama Medical University, Wakayama, Wakayama, Japan
| | - Hiroshi Kobe
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Koichi Azuma
- Division of Respirology, Neurology, and Rheumatology, Department of Internal Medicine, Kurume University School of Medicine, Fukuoka, Japan
| | - Teppei Yamaguchi
- Department of Thoracic Oncology, Aichi Cancer Center, Nagoya, Aichi, Japan
| | - Takeshi Masuda
- Department of Respiratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Toshihide Yokoyama
- Department of Respiratory Medicine, Kurashiki Central Hospital, Okayama, Japan
| | - Kohei Otsubo
- Department of Respiratory Medicine, Kitakyushu Municipal Medical Center, Fukuoka, Japan
| | - Koji Haratani
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Daisuke Hayakawa
- Department of Respiratory Medicine, Juntendo University, Graduate School of Medicine, Tokyo, Japan
| | - Masahide Oki
- Department of Respiratory Medicine, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi, Japan
| | - Shinnosuke Takemoto
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomohiro Ozaki
- Department of Medical Oncology, Kishiwada City Hospital, Osaka, Japan
| | - Yusaku Akashi
- Department of Medical Oncology, Kindai University Nara Hospital, Nara, Japan
| | - Akito Hata
- Department of Thoracic Oncology, Kobe Minimally Invasive Cancer Center, Kobe, Hyogo, Japan
| | - Hiroya Hashimoto
- Clinical Research Management Center, Nagoya City University Hospital, Nagoya, Aichi, Japan
| | - Nobuyuki Yamamoto
- Internal Medicine III, Wakayama Medical University, Wakayama, Wakayama, Japan
| | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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10
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Hirakawa T, Doi M, Hamai K, Katsura R, Miyake S, Fujita S, Ueno S, Masuda K, Tanimoto T, Nishisaka T, Hinoi T, Hirasawa A, Ishikawa N. Comprehensive genomic profiling of Japanese patients with thoracic malignancies: A single-center retrospective study. Respir Investig 2023; 61:746-754. [PMID: 37714093 DOI: 10.1016/j.resinv.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Few studies have been conducted on comprehensive genomic profiling (CGP) panels in Japanese patients with thoracic malignancies after completing standard treatment. Consequently, its value in clinical practice remains unclear. METHODS We conducted a retrospective study of Japanese patients with thoracic malignancies who underwent CGP between June 2019 and November 2022 at our hospital. We evaluated the detection rate of actionable genetic alterations and percentage of patients who received genomically-matched therapy. Furthermore, we examined the value of the CGP panel in patients who underwent multiplex gene-panel testing prior to their initial treatment. This study was performed in accordance with the principles of the Declaration of Helsinki. RESULTS The study included 56 patients, of whom 47 (83.9%) had actionable genetic alterations and 8 (14.3%) received genomically-matched therapy. Of these, four patients were treated with approved drugs and three patients were treated with investigational agents. In addition, one patient was treated with approved drugs using the patient-directed care system. Of the 17 patients who had multiplex gene-panel testing performed at the start of their initial therapy, two (11.8%) were newly identified by the CGP panel and subsequently received genomically-matched therapy. EGFR L718Q and MET amplification were observed in two of the seven patients with epidermal growth factor receptor-tyrosine kinase inhibitor resistance. CONCLUSIONS The CGP panel could identify genetic alterations, thereby facilitating genomically-matched therapy, even in patients with thoracic malignancies who could not be identified using multiplex gene-panel testing.
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Affiliation(s)
- Tetsu Hirakawa
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Mihoko Doi
- Department of Genomic Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Kosuke Hamai
- Department of Respiratory Medicine, Onomichi General Hospital, 1-10-23 Hirahara, Onomichi, Hiroshima, 7220018, Japan
| | - Ryo Katsura
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Shinya Miyake
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Suguru Fujita
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Sayaka Ueno
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Ken Masuda
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Takuya Tanimoto
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Takashi Nishisaka
- Department of Pathology and Laboratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan
| | - Takao Hinoi
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-Ku, Hiroshima, Hiroshima, 7348551, Japan
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama, Okayama, 7008558, Japan
| | - Nobuhisa Ishikawa
- Department of Respiratory Medicine, Hiroshima Prefectural Hospital, 1-5-54 Ujina-kanda, Minami-ku, Hiroshima, Hiroshima, 7348530, Japan.
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11
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Kobayashi N, Miura K, Kaneko A, Matsumoto H, Somekawa K, Hirose T, Kajita Y, Tanaka A, Teranishi S, Sairenji Y, Kawashima H, Yumoto K, Tsukahara T, Fukuda N, Nishihira R, Kudo M, Miyazawa N, Kaneko T. Tailoring Therapeutic Strategies in Non-Small-Cell Lung Cancer: The Role of Genetic Mutations and Programmed Death Ligand-1 Expression in Survival Outcomes. Cancers (Basel) 2023; 15:5248. [PMID: 37958421 PMCID: PMC10648983 DOI: 10.3390/cancers15215248] [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: 09/24/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND This study aims to assess the real-world impact of advancements in first-line systemic therapies for non-small-cell lung cancer (NSCLC), focusing on the role of driver gene mutations and programmed death-ligand 1 (PD-L1) expression levels. METHODS Conducted across eight medical facilities in Japan, this multicenter, retrospective observational research included 863 patients diagnosed with NSCLC and treated between January 2015 and December 2022. The patients were categorized based on the type of systemic therapy received: cytotoxic agents, molecular targeting agents, immune checkpoint inhibitors, and combination therapies. Comprehensive molecular and immunohistochemical analyses were conducted, and statistical evaluations were performed. RESULTS The median overall survival (OS) shows significant variations among treatment groups, with targeted therapies demonstrating the longest OS. This study also revealed that high PD-L1 expression was common in the group treated with immune checkpoint inhibitors. Multivariate analysis was used to identify the type of anticancer drug and the expression of PD-L1 at diagnosis as the impactful variables affecting 5-year OS. CONCLUSIONS This study underscores the efficacy of targeted therapies and the critical role of comprehensive molecular diagnostics and PD-L1 expression in affecting OS in NSCLC patients, advocating for their integration into routine clinical practice.
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Affiliation(s)
- Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kenji Miura
- Department of Respiratory Medicine, Yokohama Sakae Kyosai Hospital, Yokohama 247-8581, Japan
| | - Ayami Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hiromi Matsumoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Kohei Somekawa
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tomofumi Hirose
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Yukihito Kajita
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Anna Tanaka
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Shuhei Teranishi
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Yu Sairenji
- Department of Respiratory Medicine, Yokohama Sakae Kyosai Hospital, Yokohama 247-8581, Japan
| | - Hidetoshi Kawashima
- Department of Respiratory Medicine, Kanto Rosai Hospital, Kawasaki 211-8510, Japan
| | - Kentaro Yumoto
- Department of Respiratory Medicine, Yokohama Minami Kyosai Hospital, Yokohama 236-0037, Japan
| | - Toshinori Tsukahara
- Department of Respiratory Medicine, Chigasaki Municipal Hospital, Chigasaki 253-0042, Japan
| | - Nobuhiko Fukuda
- Department of Respiratory Medicine, Fujisawa Municipal Hospital, Fujisawa 251-8550, Japan
| | - Ryuichi Nishihira
- Department of Respiratory Medicine, Kanto Rosai Hospital, Kawasaki 211-8510, Japan
| | - Makoto Kudo
- Department of Pulmonology, Yokohama City University Medical Center, Yokohama 232-0024, Japan
| | - Naoki Miyazawa
- Department of Respiratory Medicine, Yokohama Nanbu Hospital, Yokohama 234-0054, Japan
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
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12
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Goto T. Next-Generation Sequencing: The New Global Standard? J Thorac Oncol 2023; 18:e115-e116. [PMID: 37758350 DOI: 10.1016/j.jtho.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Taichiro Goto
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi, Japan.
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13
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Mori T, Ozawa E, Shimakura A, Takahashi K, Matsuo S, Tajima K, Nakao Y, Fukushima M, Sasaki R, Miuma S, Miyaaki H, Okano S, Nakao K. Comparison of the novel Franseen needle versus the fine-needle aspiration needle in endoscopic ultrasound-guided tissue acquisition for cancer gene panel testing: A propensity score-matching analysis. JGH Open 2023; 7:652-658. [PMID: 37744704 PMCID: PMC10517436 DOI: 10.1002/jgh3.12965] [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: 06/20/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/26/2023]
Abstract
Background and Aim Reports have indicated that a surface area of 4 mm2 or more of collected tissue sections could provide the recommended total DNA for the OncoGuide NCC Oncopanel system, which is a cancer gene panel test developed in Japan. We wished to compare the percentage of tissue sections collected by endoscopic ultrasound-assisted tissue acquisition (EUS-TA) with surface areas of ≥4 mm2 between a conventional needle, namely the EZ Shot 3 Plus (Olympus Medical Japan, Tokyo, Japan) (EZ3), and the recent SonoTip TopGain (MediGlobe, Rohrdorf, Germany) (TopGain). Method From April 2010 to December 2021, among 693 EUS-TA cases, EZ3 was used in 390 cases and TopGain in 45. The EZ3 and TopGain groups were matched in a 1:1 ratio with a tolerance of 0.2, with 35 patients each matched using propensity score analysis. Results The TopGain group had a significantly higher percentage of cases with a tissue area of ≥4 mm2 than the EZ3 group (42.9% vs 68.6%, P = 0.030). Multivariate analysis revealed an association between TopGain and tissue areas of ≥4 mm2 (odds ratio 2.996, 95% confidence interval 1.068-8.403, P = 0.037). Conclusions EUS-TA using TopGain significantly collected more ≥4 mm2 tissue area compared with EZ3, suggesting its usefulness for cancer gene panel testing.
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Affiliation(s)
- Tomotaka Mori
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Eisuke Ozawa
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Akane Shimakura
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kosuke Takahashi
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Satoshi Matsuo
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kazuaki Tajima
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Yasuhiko Nakao
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Masanori Fukushima
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Ryu Sasaki
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Satoshi Miuma
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Hisamitsu Miyaaki
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Shinji Okano
- Department of PathologyNagasaki University HospitalNagasakiJapan
| | - Kazuhiko Nakao
- Department of Gastroenterology and HepatologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
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14
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Enko D, Schaflinger E, Müller DJ. [Clinical Application Examples of a Next-Generation Sequencing based Multi-Genepanel Analysis]. Dtsch Med Wochenschr 2023; 148:695-702. [PMID: 37216946 DOI: 10.1055/a-2033-5329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review provides an overview of clinically useful applications of a next-generation sequencing (NGS)-based multi-gene panel testing strategy in the areas of oncology, hereditary tumor syndromes, and hematology. In the case of solid tumors (e.g. lung carcinoma, colon-rectal carcinoma), the detection of somatic mutations contributes not only to a better diagnostic but also therapeutic stratification of those affected. The increasing genetic complexity of hereditary tumor syndromes (e.g. breast and ovarian carcinoma, lynch syndrome/polyposis) requires a multi-gene panel analysis of germline mutations in affected families. Another useful indication for a multi-gene panel diagnostics and prognosis assessment are acute and chronic myeloid diseases. The criteria of the WHO-classification and the European LeukemiaNet-prognosis system for acute myeloid leukemia can only be met by a multi-gene panel test strategy.
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Affiliation(s)
- Dietmar Enko
- Medizinische Universität Graz Klinisches Institut für Medizinische und Chemische Labordiagnostik, Graz, Austria
| | - Erich Schaflinger
- Institut für Humangenetik, Medizinische Universität Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria
| | - Daniel J Müller
- Klinisches Institut für Pharmakogenetische Wissenschaft, Cambell Family Mental Health Research Institute, Zentrum für Suchtkrankheit und psychische Gesundheit, College Street 250, Toronto, ON M5T 1R8, Toronto, Kanada
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15
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Distribution and prognostic impact of EGFR and KRAS mutations according to histological subtype and tumor invasion status in pTis-3N0M0 lung adenocarcinoma. BMC Cancer 2023; 23:248. [PMID: 36918771 PMCID: PMC10015689 DOI: 10.1186/s12885-023-10716-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND The prognostic impact of EGFR mutation as major targetable somatic gene variant on lung adenocarcinoma is controversial. KRAS is another major somatic variant in lung adenocarcinoma, and a therapeutic agent for KRAS G12C became available in clinical settings. These mutations represent clinicopathological features of lung adenocarcinoma and can guide the treatment choice after recurrence. We evaluated the prognostic impact of EGFR and KRAS mutations by considering other clinicopathological recurrence risks in resected pTis-3N0M0 lung adenocarcinoma. METHODS Clinicopathological features related to recurrence and genetic status were estimated in consecutive 877 resected cases. Recurrence-free survival (RFS), cumulative recurrence rate (CRR), and overall survival (OS) were compared. Uni- and multivariate analyses for RFS were performed after excluding cases with little or no recurrence risks. RESULTS EGFR mutation was more likely to be harbored in female, never-smoker, or patients accompanied by > 5% lepidic component. KRAS mutation was more likely to be harbored in patients with current/ex-smoking history, International Association for the Study of Lung Cancer (IASLC) grade 3, or accompanied lymphatic or vascular invasion. In IASLC grade 2 and 3 patients, EGFR or KRAS mutation cases had significantly worse 5-year RFS than wild type patients (76.9% vs. 85.0%, hazard ratio [HR] = 1.55, 95% confidence interval [CI] = 1.62-6.41, P < 0.001). EGFR or KRAS mutation cases had significantly higher 5-year CRR than wild type patients (17.7% vs. 9.8%, HR = 1.69, 95% CI = 1.44-6.59, P = 0.0038). KRAS mutation cases had higher 5-year CRR than EGFR mutation cases (16.7% vs. 21.4%, HR = 1.62, 95% CI = 0.96-7.19, P = 0.061). There was no significant difference in OS between cohorts. Multivariate analysis revealed that a positive EGFR/KRAS mutation status was risk factor for worse RFS (HR = 2.007, 95% CI = 1.265-3.183, P = 0.003). CONCLUSION Positive EGFR and KRAS mutation statuses were risk factors for recurrence in resected IASLC grade 2 and 3 patients. KRAS mutations were more likely to be confirmed in cases with an increased risk of recurrence. EGFR and KRAS mutation statuses should be evaluated simultaneously when assessing the risk of recurrence.
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Next-Generation Sequencing Analysis of Pancreatic Cancer Using Residual Liquid Cytology Specimens from Endoscopic Ultrasound—Guided Fine-Needle Biopsy: A Prospective Comparative Study with Tissue Specimens. Diagnostics (Basel) 2023; 13:diagnostics13061078. [PMID: 36980386 PMCID: PMC10047095 DOI: 10.3390/diagnostics13061078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
This study evaluated the feasibility and clinical utility of liquid-based cytology (LBC) specimens via endoscopic ultrasound–guided fine-needle biopsy (EUS-FNB) for next-generation sequencing (NGS) of pancreatic cancer (PC). We prospectively evaluated the performance of DNA extraction and NGS using EUS-FNB samples obtained from PC. Thirty-three consecutive patients with PC who underwent EUS-FNB at our hospital were enrolled. DNA samples were obtained from 96.8% of the patients. When stratified with a variant allele frequency (VAF) > 10% tumor burden, the NGS success rate was 76.7% (n = 23) in formalin-fixed paraffin-embedded (FFPE), 83.3% (n = 25) in LBC, and 76.7% (n = 23) in frozen samples. The overall NGS success rate was 86.7% (n = 26) using FFPE, LBC, or frozen samples. The detection rates for the main mutated genes were as follows: 86.7% for KRAS, 73.3% for TP53, 66.7% for CDKN2A, 36.7% for SMAD4, and 16.7% for ARID1A. LBC had the highest median value of VAF (23.5%) for KRAS and TP53. PC mutation analysis using NGS was successfully performed using LBC compared with FFPE and frozen samples. This approach provides an alternative and affordable source of molecular testing materials.
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17
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Kunimasa K, Sugimoto N, Kawamura T, Yamasaki T, Honma K, Nagata S, Kukita Y, Fujisawa F, Inoue T, Yamaguchi Y, Kitasaka M, Wakamatsu T, Yamai T, Yamamoto S, Hayashi T, Inoue T, Tamiya M, Imamura F, Nishimura K, Nishino K. Clinical application of comprehensive genomic profiling panel to thoracic malignancies: A single-center retrospective study. Thorac Cancer 2022; 13:2970-2977. [PMID: 36100256 PMCID: PMC9626350 DOI: 10.1111/1759-7714.14643] [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: 08/19/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The usefulness of comprehensive genomic profiling (CGP) panels for thoracic malignancies after completion of the standard treatment is unclear. METHODS The results of CGP panels for malignant thoracic diseases performed at our hospital between December 2019 and June 2022 were collected. We examined whether CGP panel results led to new treatment, correlated with the effectiveness of immune checkpoint inhibitors (ICIs), or revealed secondary findings related to hereditary tumors. RESULTS A total of 60 patients were enrolled, of which 52 (86.6%) had lung cancer. In six (10%) patients, the panel results led to treatment with insurance-listed molecular-targeted agents; four patients had EGFR mutations not detected by the real-time polymerase chain reaction assay and two had MET ex.14 skipping mutations. In small-cell lung cancer, the tumor mutation burden was high in 4/6 (66.7%) patients and pembrolizumab was available. Another MET ex.14 skipping mutation was detected in two cases with EGFR-tyrosine kinase inhibitor resistance. ICI efficacy was ≤1 year in patients with STK-11, KEAP1, and NEF2L2 mutations. A BRCA2 mutation with a high probability of germline mutation was detected in one patient. A thymic carcinoma with no detectable oncogenic mutation responded to second-line treatment with Tegafur-Gimeracil-Oteracil Potassium (TS-1) for ≥9 years. CONCLUSIONS CGP panels are useful in thoracic malignancies, especially lung cancer, because they can detect overlooked driver mutations and genetic alterations. We believe that the significance of conducting a CGP panel prior to treatment may also exist, as it may lead to the prediction of ICI treatment efficacy.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Naotoshi Sugimoto
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Medical OncologyOsaka International Cancer InstituteOsakaJapan
| | - Takahisa Kawamura
- Department of Thoracic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Tomoyuki Yamasaki
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Endocrinology/Metabolism Internal Medicine, Clinical ExaminationOsaka International Cancer InstituteOsakaJapan
| | - Keiichiro Honma
- Department of Diagnostic Pathology and CytologyOsaka International Cancer InstituteOsakaJapan
| | - Shigenori Nagata
- Department of Diagnostic Pathology and CytologyOsaka International Cancer InstituteOsakaJapan
| | - Yoji Kukita
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Laboratory of Genomic PathologyOsaka International Cancer InstituteOsakaJapan
| | - Fumie Fujisawa
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Medical OncologyOsaka International Cancer InstituteOsakaJapan
| | - Tazuko Inoue
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Yuko Yamaguchi
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Mitsuko Kitasaka
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Toru Wakamatsu
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Musculoskeletal Oncology ServiceOsaka International Cancer InstituteOsakaJapan
| | - Takuo Yamai
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Hepatobiliary and Pancreatic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Sachiko Yamamoto
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of Gastrointestinal OncologyOsaka International Cancer InstituteOsakaJapan
| | - Takuji Hayashi
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of UrologyOsaka International Cancer InstituteOsakaJapan
| | - Takako Inoue
- Department of Thoracic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Motohiro Tamiya
- Department of Thoracic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Fumio Imamura
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan
| | - Kazuo Nishimura
- Department of Genetic OncologyOsaka International Cancer InstituteOsakaJapan,Department of UrologyOsaka International Cancer InstituteOsakaJapan
| | - Kazumi Nishino
- Department of Thoracic OncologyOsaka International Cancer InstituteOsakaJapan
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Murakami S, Yokose T, Shinada K, Isaka T, Katakura K, Ushio R, Kondo T, Kato T, Ito H, Saito H. Comparison of next-generation sequencing and cobas EGFR mutation test v2 in detecting EGFR mutations. Thorac Cancer 2022; 13:3217-3224. [PMID: 36203199 PMCID: PMC9663664 DOI: 10.1111/1759-7714.14685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND As the number of genetic mutations that must be tested increases, the Oncomine Dx Target test (ODxTT), which can simultaneously detect multiple cancer-related genes is becoming the main test used in preference to single-molecule testing. In this study, we evaluated the performance of ODxTT and cobas EGFR mutation test v2 (cobas EGFR), one of the single-molecule tests, in detecting EGFR mutations. METHODS Samples from 211 patients diagnosed with NS-NSCLC were tested simultaneously or sequentially with the cobas EGFR mutation test and ODxTT. We compared the success and detection rates of both tests and evaluated their equivalence by determining the concordance rate and k-coefficient of both tests. RESULTS The success rate in detecting EGFR mutations was 95.7% for ODxTT and 100% for cobas EGFR. EGFR mutations were detected in 26.5% of samples with ODxTT and in 28.0% with cobas EGFR. For the 200 samples successfully analyzed with both tests, the concordance rate and k-coefficient were 97.5% and 0.938, respectively. ODxTT failed to detect two exon 19 deletion mutations (p.E746_P753delinsVS and p.E746_P753delinsLS), and cobas EGFR failed to detect three instances of an exon 19 deletion (p.L747_P753delinsS), L861R, and an exon 20 insertion. DISCUSSION The success rate of ODxTT is slightly inferior to that of cobas EGFR. ODxTT shared a high concordance rate and k-coefficient with cobas EGFR in detecting EGFR mutations, but discordant results between the two tests were observed in a few cases, mainly due to the difference of detectable EGFR variants.
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Affiliation(s)
- Shuji Murakami
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | | | - Kanako Shinada
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Testuya Isaka
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Kengo Katakura
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Ryouta Ushio
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Tetsuro Kondo
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Terufumi Kato
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Hiroyuki Ito
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
| | - Haruhiro Saito
- Department of Thoracic OncologyKanagawa Cancer CenterYokohamaJapan
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Wu Q, Pennini ME, Bergmann JN, Kozak ML, Herring K, Sciarretta KL, Armstrong KL. Applying lessons learned from COVID-19 therapeutic trials to improve future ALI/ARDS trials. Open Forum Infect Dis 2022; 9:ofac381. [PMID: 35983268 PMCID: PMC9379817 DOI: 10.1093/ofid/ofac381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/28/2022] [Indexed: 12/15/2022] Open
Abstract
Host-directed therapeutics targeting immune dysregulation are considered the most promising approach to address the unmet clinical need for acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) related to coronavirus disease 2019 (COVID-19). To better understand the current clinical study landscape and gaps in treating hospitalized patients with severe or critical COVID-19, we identified COVID-19 trials developing host-directed therapies registered at ClinicalTrials.gov and discussed the factors contributing to the success vs failure of these studies. We have learned, instead of the one-size-fits-all approach, future clinical trials evaluating a targeted immunomodulatory agent in heterogeneous patients with ALI/ARDS due to COVID-19 or other infectious diseases can use immune-based biomarkers in addition to clinical and demographic characteristics to improve patient stratification and inform clinical decision-making. Identifying distinct patient subgroups based on immune profiles across the disease trajectory, regardless of the causative pathogen, may accelerate evaluating host-directed therapeutics in trials of ALI/ARDS and related conditions (eg, sepsis).
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Affiliation(s)
- Qun Wu
- Influenza and Emerging Infectious Diseases Division (IEIDD), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Meghan E Pennini
- Division of Research Innovation and Ventures (DRIVe), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Julie N Bergmann
- Division of Chemical Biological Radiological Nuclear (CBRN), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Marina L Kozak
- Division of Chemical Biological Radiological Nuclear (CBRN), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Kristen Herring
- Division of Chemical Biological Radiological Nuclear (CBRN), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Kimberly L Sciarretta
- Division of Research Innovation and Ventures (DRIVe), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
| | - Kimberly L Armstrong
- Influenza and Emerging Infectious Diseases Division (IEIDD), Biomedical Advanced Research and Development Authority (BARDA), Office of the Assistant Secretary for Preparedness and Response (ASPR), Department of Health and Human Services (HHS) , Washington, DC , United States of America
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21
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Mizote S, Matsumura M, Sekiya M, Sugiyama M, Sekine A, Kobayashi N, Kataoka T, Iwashita H, Okudela K. Pathological criteria for multiplex gene-panel testing using next-generation sequencing in non-small cell lung cancer. Cancer Treat Res Commun 2022; 32:100614. [PMID: 35878517 DOI: 10.1016/j.ctarc.2022.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Multiplex gene-panel tests have recently been developed, including the Oncomine Dx Target Test multi-CDx system (ODxTT), and are commonly used to determine the adaptation of molecular-targeting drugs in non-small cell lung cancer. However, in actual clinical settings, we obtain false results owing to the small biopsy samples. We aimed to optimize tissue preparation methods to improve the success rate. PATIENTS AND METHODS We investigated 88 biopsy samples. The area and nucleated cell count in the first cut section were quantified using a morphometric software. Pathological parameters, including "total tissue area" and "total nucleated cell count," were calculated by multiplying the total number of slides submitted to ODxTT. Optimal cutoff values to obtain the best success rate were also determined. Additionally, we morphometrically measured actual tumor cell proportions and attempted to determine the lower limit possible to detect mutations. RESULTS Optimal cutoff values for "total nucleated cell count" and "total tissue area" were 132,885 and 32.94 mm2, respectively. The actual tumor cell proportions ranged from 4.6 to 97.7%. Even in cases with actual tumor cell proportions of less than 20% (ranging from 4.6 to 19.7%), there was no false negative. CONCLUSION Thus, we proposed the pathological criteria for accurate ODxTT. Our result suggested that tumor cell proportions of less than 20% (around 5%) could be applicable for ODxTT. We hope that our results will help pathologists to choose between the multi-plex test (ODxTT) or single-plex test in routine diagnostics.
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Affiliation(s)
- Shihoko Mizote
- Department of Pathology, Graduate School of Medicine, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Mai Matsumura
- Division of Pathology, 16-1, Tomioka-higashi, Kanazawa-ku, Yokohama 230-0051, Japan
| | - Motoki Sekiya
- Division of Pathology, 16-1, Tomioka-higashi, Kanazawa-ku, Yokohama 230-0051, Japan
| | - Misaki Sugiyama
- Division of Pathology, 16-1, Tomioka-higashi, Kanazawa-ku, Yokohama 230-0051, Japan
| | - Akimasa Sekine
- Respiratory Medicine, Kanagawa Prefectural Cardiovascular and Respiratory Center Hospital, 6-16-1, Tomioka-higashi, Kanazawa-ku, Yokohama 230-0051, Japan
| | - Nobuaki Kobayashi
- Department of Pulmonology, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toshiaki Kataoka
- Department of Pathology, Graduate School of Medicine, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hiromichi Iwashita
- Department of Pathology, Graduate School of Medicine, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Koji Okudela
- Department of Pathology, Graduate School of Medicine, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan.
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22
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Role of Image-Guided Percutaneous Needle Biopsy in the Age of Precision Medicine. Curr Oncol Rep 2022; 24:1035-1044. [PMID: 35362826 DOI: 10.1007/s11912-022-01271-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW With the remarkable progress in cancer precision medicine, the demand for biopsy has been increasing, and the role of biopsy has been changing. In this review, we discuss the current state and recent advances in the role of image-guided percutaneous needle biopsy (PNB) in facilitating precision medicine. RECENT FINDINGS Biopsies are useful not only in the diagnosis of cancer and histological sub-type but also in the analysis of its molecular characteristics for targeted treatments. PNB specimens have been shown to provide high DNA yields for genomic analysis. Liquid biopsy is an emerging technology but is under development; therefore, PNB is the current standard of practice and is performed complimentarily with liquid biopsy. In the age of precision medicine, interventional oncologists play a key role in optimal tissue collection for adequate genomic analysis. Effective PNB may improve its diagnostic utility and help optimize precision medicine.
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Gómez-Flores-Ramos L, Barraza-Arellano AL, Mohar A, Trujillo-Martínez M, Grimaldo L, Ortiz-Lopez R, Treviño V. Germline Variants in Cancer Genes from Young Breast Cancer Mexican Patients. Cancers (Basel) 2022; 14:cancers14071647. [PMID: 35406420 PMCID: PMC8997148 DOI: 10.3390/cancers14071647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/03/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
Breast cancer (BC) is one of the most frequent cancer types in women worldwide. About 7% is diagnosed in young women (YBC) less than 40 years old. In Mexico, however, YBC reaches 15% suggesting a higher genetic susceptibility. There have been some reports of germline variants in YBC across the world. However, there is only one report from a Mexican population, which is not restricted by age and limited to a panel of 143 genes resulting in 15% of patients carrying putatively pathogenic variants. Nevertheless, expanding the analysis to whole exome involves using more complex tools to determine which genes and variants could be pathogenic. We used germline whole exome sequencing combined with the PeCanPie tool to analyze exome variants in 115 YBC patients. Our results showed that we were able to identify 49 high likely pathogenic variants involving 40 genes on 34% of patients. We noted many genes already reported in BC and YBC worldwide, such as BRCA1, BRCA2, ATM, CHEK2, PALB2, and POLQ, but also others not commonly reported in YBC in Latin America, such as CLTCL1, DDX3X, ERCC6, FANCE, and NFKBIE. We show further supporting and controversial evidence for some of these genes. We conclude that exome sequencing combined with robust annotation tools and further analysis, can identify more genes and more patients affected by germline mutations in cancer.
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Affiliation(s)
- Liliana Gómez-Flores-Ramos
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Angélica Leticia Barraza-Arellano
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
| | - Alejandro Mohar
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Dirección de Investigación, Instituto Nacional de Cancerología, Av. San Fernando #22, Col. Sección XVI, Delegación Tlalpan, Mexico City 14080, Mexico;
| | - Miguel Trujillo-Martínez
- Instituto Mexicano del Seguro Social, Hospital General de Zona con Medicina Familiar No. 7, Cuautla 62780, Morelos, Mexico;
| | - Lizbeth Grimaldo
- CONACYT/Center for Population Health Research, National Institute of Public Health, Universidad No. 655, Cuernavaca 62100, Morelos, Mexico; (L.G.-F.-R.); (L.G.)
| | - Rocío Ortiz-Lopez
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
| | - Víctor Treviño
- School of Medicine, Tecnologico de Monterrey, Morones Prieto Av 3000, Los Doctores, Monterrey 64710, Nuevo Leon, Mexico; (A.L.B.-A.); (R.O.-L.)
- The Institute for Obesity Research, Tecnologico de Monterrey, Eugenio Garza Sada Av 2501, Monterrey 64849, Nuevo Leon, Mexico
- Correspondence:
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24
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RIFS2D: A two-dimensional version of a randomly restarted incremental feature selection algorithm with an application for detecting low-ranked biomarkers. Comput Biol Med 2021; 133:104405. [PMID: 33930763 DOI: 10.1016/j.compbiomed.2021.104405] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022]
Abstract
The era of big data introduces both opportunities and challenges for biomedical researchers. One of the inherent difficulties in the biomedical research field is to recruit large cohorts of samples, while high-throughput biotechnologies may produce thousands or even millions of features for each sample. Researchers tend to evaluate the individual correlation of each feature with the class label and use the incremental feature selection (IFS) strategy to select the top-ranked features with the best prediction performance. Recent experimental data showed that a subset of continuously ranked features randomly restarted from a low-ranked feature (an RIFS block) may outperform the subset of top-ranked features. This study proposed a feature selection Algorithm RIFS2D by integrating multiple RIFS blocks. A comprehensive comparative experiment was conducted with the IFS, RIFS and existing feature selection algorithms and demonstrated that a subset of low-ranked features may also achieve promising prediction performance. This study suggested that a prediction model with promising performance may be trained by low-ranked features, even when top-ranked features did not achieve satisfying prediction performance. Further comparative experiments were conducted between RIFS2D and t-tests for the detection of early-stage breast cancer. The data showed that the RIFS2D-recommended features achieved better prediction accuracy and were targeted by more drugs than the t-test top-ranked features.
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