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Ishikawa M, Nakamura K, Kawano R, Hayashi H, Ikeda T, Saito M, Niida Y, Sasaki J, Okuda H, Ishihara S, Yamaguchi M, Shimada H, Isobe T, Yuza Y, Yoshimura A, Kuroda H, Yukisawa S, Aoki T, Takeshita K, Ueno S, Nakazawa J, Sunakawa Y, Nohara S, Okada C, Nishimiya K, Tanishima S, Nishihara H. Clinical and Diagnostic Utility of Genomic Profiling for Digestive Cancers: Real-World Evidence from Japan. Cancers (Basel) 2024; 16:1504. [PMID: 38672586 PMCID: PMC11048180 DOI: 10.3390/cancers16081504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The usefulness of comprehensive genomic profiling (CGP) in the Japanese healthcare insurance system remains underexplored. Therefore, this large-scale study aimed to determine the usefulness of CGP in diagnosing digestive cancers. Patients with various cancer types recruited between March 2020 and October 2022 underwent the FoundationOne® CDx assay at the Keio PleSSision Group (19 hospitals in Japan). A scoring system was developed to identify potentially actionable genomic alterations of biological significance and actionable genomic alterations. The detection rates for potentially actionable genomic alterations, actionable genomic alterations, and alterations equivalent to companion diagnosis (CDx), as well as the signaling pathways associated with these alterations in each digestive cancer, were analyzed. Among the 1587 patients, 547 had digestive cancer. The detection rates of potentially actionable genomic alterations, actionable genomic alterations, and alterations equivalent to CDx were 99.5%, 62.5%, and 11.5%, respectively. APC, KRAS, and CDKN2A alterations were frequently observed in colorectal, pancreatic, and biliary cancers, respectively. Most digestive cancers, except esophageal cancer, were adenocarcinomas. Thus, the classification flowchart for digestive adenocarcinomas proposed in this study may facilitate precise diagnosis. CGP has clinical and diagnostic utility in digestive cancers.
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Affiliation(s)
- Marin Ishikawa
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
| | - Kohei Nakamura
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
| | - Ryutaro Kawano
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
| | - Hideyuki Hayashi
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
| | - Tatsuru Ikeda
- Department of Cancer Genome Medical Center, Hakodate Goryoukaku Hospital, 38-3, Goryoukakucho, Hakodate-shi 040-8611, Hokkaido, Japan;
| | - Makoto Saito
- Department of Genetic Medicine, Ibaraki Prefectural Center Hospital, 6528, Koibuchi, Kasama-shi 309-1793, Ibaraki, Japan;
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1, Daigaku, Uchinada 920-0293, Ishikawa, Japan;
| | - Jiichiro Sasaki
- Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara-shi 252-0329, Kanagawa, Japan;
| | - Hiroyuki Okuda
- Department of Medical Oncology, Keiyukai Sapporo Hospital, 1-1 Minami, Hondori 9, Chome, Shiroishi-ku, Sapporo 003-0026, Hokkaido, Japan;
| | - Satoshi Ishihara
- Cancer Genome Diagnosis and Treatment Center, Central Japan International Medical Center, 1-1 Kenkonomachi, Minokamo-shi 505-0010, Gifu, Japan;
| | - Masatoshi Yamaguchi
- Division of Clinical Genetics, Faculty of Medicine, University of Miyazaki Hospital, 5200 Kihara, Kiyotake-cho, Miyazaki-shi 889-1692, Miyazaki, Japan;
| | - Hideaki Shimada
- Department of Surgery and Clinical Oncology, Toho University Graduate School of Medicine, 6-11-1 Omori-nishi, Ota-ku, Tokyo 143-8541, Japan;
| | - Takeshi Isobe
- Cancer Genome Medical Center, Shimane University Hospital, 89-1, Enya-cho, Izumo-shi 693-8501, Shimane, Japan;
| | - Yuki Yuza
- Department of Hematology and Oncology, Tokyo Metropolitan Children’s Medical Center, 2-8-29 Musashidai, Fuchu-shi 183-8561, Tokyo, Japan;
| | - Akinobu Yoshimura
- Department of Clinical Oncology Director, Outpatient Chemotherapy Center, Tokyo Medical University Hospital, 6-7-1 Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan;
| | - Hajime Kuroda
- Department of Pathology, Tokyo Women’s Medical University, Adachi Medical Center, 4-33-1 Kohta, Adachi-ku, Tokyo 123-8558, Japan;
| | - Seigo Yukisawa
- Department of Medical Oncology, Saiseikai Utsunomiya Hospital, 911-1, Takebayashi, Utsunomiya-shi 321-0974, Tochigi, Japan;
| | - Takuya Aoki
- Department of Clinical Oncology, Tokyo Medical University Hachioji Medical Center, 1163, Tatemachi, Hachioji-shi 193-0998, Tokyo, Japan;
| | - Kei Takeshita
- Department of Clinical Genetics, Tokai University Hospital, 143, Shimokasuya, Isehara-shi 259-1193, Kanagawa, Japan;
| | - Shinichi Ueno
- Oncology Center, Kagoshima University Hospital, 8-35-1 Sakuragaoka, Kagoshima-shi 890-0075, Kagoshima, Japan;
| | - Junichi Nakazawa
- Department of Medical Oncology, Kagoshima City Hospital, 37-1, Uearatacho, Kagoshima-shi 890-8760, Kagoshima, Japan;
| | - Yu Sunakawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki 216-8511, Kanagawa, Japan;
| | - Sachio Nohara
- Biomedical Informatics Department, Communication Engineering Center, Mitsubishi Electric Software Corporation, Fuji Techno-Square, 5-4-36 Tsukaguchi-Honmachi, Amagasaki-shi 661-0001, Hyogo, Japan; (S.N.); (C.O.); (K.N.)
| | - Chihiro Okada
- Biomedical Informatics Department, Communication Engineering Center, Mitsubishi Electric Software Corporation, Fuji Techno-Square, 5-4-36 Tsukaguchi-Honmachi, Amagasaki-shi 661-0001, Hyogo, Japan; (S.N.); (C.O.); (K.N.)
| | - Ko Nishimiya
- Biomedical Informatics Department, Communication Engineering Center, Mitsubishi Electric Software Corporation, Fuji Techno-Square, 5-4-36 Tsukaguchi-Honmachi, Amagasaki-shi 661-0001, Hyogo, Japan; (S.N.); (C.O.); (K.N.)
| | - Shigeki Tanishima
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
- Biomedical Informatics Department, Communication Engineering Center, Mitsubishi Electric Software Corporation, Fuji Techno-Square, 5-4-36 Tsukaguchi-Honmachi, Amagasaki-shi 661-0001, Hyogo, Japan; (S.N.); (C.O.); (K.N.)
| | - Hiroshi Nishihara
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Integrated Medical Research Building 3-S5, 35, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; (K.N.); (R.K.); (H.H.); (S.T.); (H.N.)
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Ishigaki K, Nakai Y, Endo G, Kurihara K, Ishida K, Tange S, Fukuda R, Takaoka S, Tokito Y, Suzuki Y, Oyama H, Kanai S, Suzuki T, Sato T, Hakuta R, Saito T, Hamada T, Takahara N, Shinozaki‐Ushiku A, Fujishiro M. Feasibility of comprehensive genomic profiling using endoscopic ultrasound-guided tissue acquisition with a 22-gauge Franseen needle. DEN Open 2024; 4:e365. [PMID: 38628502 PMCID: PMC11019146 DOI: 10.1002/deo2.365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/25/2024] [Accepted: 03/31/2024] [Indexed: 04/19/2024]
Abstract
Aim Comprehensive genomic profiling (CGP) test for solid tumors is now increasingly utilized in clinical practice, especially in pancreatobiliary cancer, and specimens obtained by endoscopic ultrasound-guided tissue acquisition (EUS-TA) are often submitted for tissue-based CGP test. In this study, we evaluated the feasibility of EUS-TA using a 22-gauge Franseen needle for the CGP test. Methods Consecutive patients with solid tumors who underwent EUS-TA using a 22-gauge Franseen needle, and whose tissue samples were pre-checked for suitability for CGP test, were included in this single-center, retrospective analysis. The success rates of appropriate sample collection for CGP evaluated by pathologists (1st quality control) and CGP test (2nd quality control) were evaluated. In addition, The EUS-TA slides were evaluated for the tissue area and tumor area content, using the image software. Results A total of 50 cases, with 78% of pancreatic cancer, were included in the analysis. A median of 3 passes of EUS-TA were performed with an adverse event rate of 4%. The success rates for 1st and 2nd quality control for CGP tests were 86% and 76%, respectively. The image analyses suggested EUS-TA specimen did not always fulfill CGP test criteria, with 18% of tissue area ≥16 mm2 and 38% of tumor area content ≥20%, even in cases with successful CGP tests. The suction method yielded a significantly larger amount of DNA but without a significant difference in the multivariate analysis. Conclusions The present study demonstrated the feasibility of EUS-TA using a 22-gauge Franseen needle for CGP test.
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Affiliation(s)
- Kazunaga Ishigaki
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
- Department of ChemotherapyThe University of Tokyo HospitalTokyoJapan
| | - Yousuke Nakai
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
- Department of Endoscopy and Endoscopic SurgeryThe University of Tokyo HospitalTokyoJapan
| | - Go Endo
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Kohei Kurihara
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Kota Ishida
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Shuichi Tange
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Rintaro Fukuda
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Shinya Takaoka
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Yurie Tokito
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Yukari Suzuki
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroki Oyama
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Sachiko Kanai
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Tatsunori Suzuki
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Tatsuya Sato
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Ryunosuke Hakuta
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Tomotaka Saito
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Tsuyoshi Hamada
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Naminatsu Takahara
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | | | - Mitsuhiro Fujishiro
- Department of GastroenterologyGraduate School of MedicineThe University of TokyoTokyoJapan
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Choi SJ, Lee JB, Kim JH, Hong MH, Cho BC, Lim SM. Analysis of tumor mutational burden and mutational landscape comparing whole-exome sequencing and comprehensive genomic profiling in patients with resectable early-stage non-small-cell lung cancer. Ther Adv Med Oncol 2024; 16:17588359241240657. [PMID: 38523846 PMCID: PMC10958800 DOI: 10.1177/17588359241240657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Background Identifying actionable driver mutations via tissue-based comprehensive genomic profiling (CGP) is paramount in treatment decisions for metastatic non-squamous, non-small-cell lung cancer (NSCLC). However, the role of CGP remains elusive in resectable NSCLC. Here, we elucidate the feasibility of CGP in early-stage NSCLC Korean patients and compare the tumor mutational burden (TMB) and mutation landscape using three different platforms. Methods All surgically resected NSCLC samples (N = 96) were analyzed to assess the concordance in TMB calculation and targetable mutations using whole-exome sequencing (WES) and TruSight Oncology 500 (TSO500). In all, 26 samples were analyzed with Foundation One CDx Assay (F1CDx). Programmed death-ligand 1 (PD-L1) expression was evaluated using Vectra Polaris. Results Stage distribution post-surgery was 80% I (N = 77) and 20% II (N = 19). Ninety-nine percent (N = 95) were adenocarcinoma. The median TMB with WES and TSO500 was 1.6 and 4.7 mut/Mb, respectively (p < 0.05). Using all three platforms, the median TMB was 1.9, 5.5, and 4 mut/Mb for WES, TSO500, and F1CDx, respectively (p = 0.0048). Linear regression analysis of TMB values calculated between WES and TSO500 resulted in a concordance correlation coefficient of 0.83. For the PD-L1 tumor proportion score of <1% (negative, N = 18), 1-49% (low, N = 68), and ⩾50% (high, N = 10), the R2 values were 0.075, 0.79, and 0.95, respectively. The R2 values for TMB concordance were variable between the three platforms. Mutation landscape revealed EGFR mutation (51%, N = 49) as the most common actionable driver mutation, comprising L858R (N = 22), E19del (N = 20), and other non-common EGFR mutations (N = 7). Conclusion TSO500 and F1CDx showed robust analytical performance for TMB assessment with TSO500 showing stronger concordance of TMB with high PD-L1 expression. As the paradigm for the management of early-resected NSCLC continues to evolve, understanding TMB and the mutation landscape may help advance clinical outcomes for this subset of patients.
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Affiliation(s)
- Su-Jin Choi
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jii Bum Lee
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Jae Hwan Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Min Hee Hong
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Sun Min Lim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, 03722, South Korea
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Ishida M, Iwasaku M, Doi T, Ishikawa T, Tachibana Y, Sawada R, Ogura Y, Kawachi H, Katayama Y, Nishioka N, Morimoto K, Tokuda S, Yamada T, Takayama K. Nationwide data from comprehensive genomic profiling assays for detecting driver oncogenes in non-small cell lung cancer. Cancer Sci 2024. [PMID: 38450844 DOI: 10.1111/cas.16130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Driver oncogenes are investigated upfront at diagnosis using multi-CDx systems with next-generation sequencing techniques or multiplex reverse-transcriptase polymerase chain reaction assays. Additionally, from 2019, comprehensive genomic profiling (CGP) assays have been available in Japan for patients with advanced solid tumors who had completed or were expected to complete standard chemotherapy. These assays are expected to comprehensively detect the driver oncogenes, especially for patients with non-small cell lung cancer (NSCLC). However, there are no reports of nationwide research on the detection of driver oncogenes in patients with advanced NSCLC who undergo CGP assays, especially in those with undetected driver oncogenes at diagnosis. In this study, we investigated the proportion of driver oncogenes detected in patients with advanced NSCLC with undetectable driver oncogenes at initial diagnosis and in all patients with advanced NSCLC who underwent CGP assays. We retrospectively analyzed data from 986 patients with advanced NSCLC who underwent CGP assays between August 2019 and March 2022, using the Center for Cancer Genomics and Advanced Therapeutics database. The proportion of driver oncogenes newly detected in patients with NSCLC who tested negative for driver oncogenes at diagnosis and in all patients with NSCLC were investigated. Driver oncogenes were detected in 451 patients (45.7%). EGFR was the most common (16.5%), followed by KRAS (14.5%). Among the 330 patients with undetected EGFR, ALK, ROS1, and BRAF V600E mutations at diagnosis, 81 patients (24.5%) had newly identified driver oncogenes. CGP assays could be useful to identify driver oncogenes in patients with advanced NSCLC, including those initially undetected, facilitating personalized treatment.
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Affiliation(s)
- Masaki Ishida
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masahiro Iwasaku
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshifumi Doi
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takeshi Ishikawa
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yusuke Tachibana
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryo Sawada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuri Ogura
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hayato Kawachi
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuki Katayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naoya Nishioka
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenji Morimoto
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinsaku Tokuda
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koichi Takayama
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Kage H, Akiyama N, Chang H, Shinozaki‐Ushiku A, Ka M, Kawata J, Muto M, Okuma Y, Okita N, Tsuchihara K, Kikuchi J, Shirota H, Hayashi H, Kokuryo T, Yachida S, Hirasawa A, Kubo M, Kenmotsu H, Tanabe M, Ushiku T, Muto K, Seto Y, Oda K. Patient survey on cancer genomic medicine in Japan under the national health insurance system. Cancer Sci 2024; 115:954-962. [PMID: 38273803 PMCID: PMC10920978 DOI: 10.1111/cas.16065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/09/2023] [Accepted: 12/17/2023] [Indexed: 01/27/2024] Open
Abstract
In Japan, comprehensive genomic profiling (CGP) tests have been reimbursed under the national health care system for solid cancer patients who have finished standard treatment. More than 50,000 patients have taken the test since June 2019. We performed a nation-wide questionnaire survey between March 2021 and July 2022. Questionnaires were sent to 80 designated Cancer Genomic Medicine Hospitals. Of the 933 responses received, 370 (39.7%) were web based and 563 (60.3%) were paper based. Most patients (784, 84%) first learned about CGP tests from healthcare professionals, and 775 (83.1%) gave informed consent to their treating physician. At the time of informed consent, they were most worried about test results not leading to novel treatment (536, 57.4%). On a scale of 0-10, 702 respondents (75.2%) felt that the explanations of the test result were easy to understand (7 or higher). Ninety-one patients (9.8%) started their recommended treatment. Many patients could not receive recommended treatment because no approved drugs or clinical trials were available (102/177, 57.6%). Ninety-eight patients (10.5%) did not wish their findings to be disclosed. Overall satisfaction with the CGP test process was high, with 602 respondents (64.5%) giving a score of 7-10. The major reason for choosing 0-6 was that the CGP test result did not lead to new treatment (217/277, 78.3%). In conclusion, satisfaction with the CGP test process was high. Patients and family members need better access to information. More patients need to be treated with genomically matched therapy.
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Affiliation(s)
- Hidenori Kage
- Department of Clinical GenomicsThe University of Tokyo HospitalTokyoJapan
- Next‐Generation Precision Medicine Development Laboratory, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Nana Akiyama
- Department of Clinical GenomicsThe University of Tokyo HospitalTokyoJapan
| | - Hyangri Chang
- Department of Clinical GenomicsThe University of Tokyo HospitalTokyoJapan
| | - Aya Shinozaki‐Ushiku
- Department of Clinical GenomicsThe University of Tokyo HospitalTokyoJapan
- Division of Integrative Genomics, Graduate School of MedicineThe University of TokyoTokyoJapan
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Mirei Ka
- Division of Integrative Genomics, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Junichi Kawata
- Department of Public PolicyThe Institute of Medical Science, The University of TokyoTokyoJapan
| | - Manabu Muto
- Department of Therapeutic OncologyKyoto University Graduate School of MedicineKyotoJapan
| | - Yusuke Okuma
- Center for Cancer Genomics and Advanced TherapeuticsNational Cancer CenterTokyoJapan
| | - Natsuko Okita
- Center for Cancer Genomics and Advanced TherapeuticsNational Cancer CenterTokyoJapan
| | - Katsuya Tsuchihara
- Department of Genetic Medicine and ServicesNational Cancer Center Hospital EastChibaJapan
| | - Junko Kikuchi
- Division of Clinical Cancer GenomicsHokkaido University HospitalSapporoJapan
| | - Hidekazu Shirota
- Department of Clinical OncologyTohoku University HospitalSendaiJapan
| | - Hideyuki Hayashi
- Genomics Unit, Keio Cancer CenterKeio University School of MedicineTokyoJapan
| | - Toshio Kokuryo
- Division of Surgical Oncology, Department of SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of MedicineOsaka UniversityOsakaJapan
| | - Akira Hirasawa
- Department of Clinical Genomic MedicineOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical SciencesOkayamaJapan
| | - Makoto Kubo
- Department of Breast Surgical OncologyKyushu University HospitalFukuokaJapan
| | | | - Masahiko Tanabe
- Department of Breast and Endocrine Surgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Kaori Muto
- Department of Public PolicyThe Institute of Medical Science, The University of TokyoTokyoJapan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Katsutoshi Oda
- Department of Clinical GenomicsThe University of Tokyo HospitalTokyoJapan
- Division of Integrative Genomics, Graduate School of MedicineThe University of TokyoTokyoJapan
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Bando H, Yamaguchi K, Mitani S, Sawada K, Mishima S, Komine K, Okugawa Y, Hosoda W, Ebi H. Japanese Society of Medical Oncology clinical guidelines: Molecular testing for colorectal cancer treatment, 5th edition. Cancer Sci 2024; 115:1014-1021. [PMID: 38263580 PMCID: PMC10920993 DOI: 10.1111/cas.16039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024] Open
Abstract
Molecular testing to determine optimal therapies is essential for managing patients with colorectal cancer (CRC). In October 2022, the Japanese Society of Medical Oncology published the 5th edition of the Molecular Testing Guideline for Colorectal Cancer Treatment. In this guideline, in patients with unresectable CRC, RAS/BRAF V600E mutational and mismatch repair tests are strongly recommended prior to first-line chemotherapy to select optimal first- and second-line therapies. In addition, HER2 testing is strongly recommended because the pertuzumab plus trastuzumab combination is insured after fluoropyrimidine, oxaliplatin, and irinotecan in Japan. Circulating tumor DNA (ctDNA)-based RAS testing is also strongly recommended to assess the indications for the readministration of anti-EGFR antibodies. Both tissue- and ctDNA-based comprehensive genomic profiling tests are strongly recommended to assess the indications for targeted molecular drugs, although they are currently insured in patients with disease progression after receiving standard chemotherapy (or in whom disease progression is expected in the near future). Mutational and mismatch repair testing is strongly recommended for patients with resectable CRC, and RAS/BRAF V600E mutation testing is recommended to estimate the risk of recurrence. Mutational and mismatch repair and BRAF testing are also strongly recommended for screening for Lynch syndrome. Circulating tumor DNA-based minimal residual disease (MRD) testing is strongly recommended for estimating the risk of recurrence based on clinical evidence, although MRD testing was not approved in Japan at the time of the publication of this guideline.
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Affiliation(s)
- Hideaki Bando
- Department of Gastroenterology and Gastrointestinal OncologyNational Cancer Center Hospital EastChibaJapan
| | - Kyoko Yamaguchi
- Department of Hematology, Oncology, and Cardiovascular MedicineKyushu University HospitalFukuokaJapan
| | - Seiichiro Mitani
- Department of Medical OncologyKindai University Faculty of MedicineOsaka‐SayamaJapan
| | - Kentaro Sawada
- Department of Clinical OncologyKushiro Rosai HospitalKushiroJapan
| | - Saori Mishima
- Department of Gastroenterology and Gastrointestinal OncologyNational Cancer Center Hospital EastChibaJapan
| | - Keigo Komine
- Department of Medical OncologyTohoku University HospitalSendaiJapan
| | - Yoshinaga Okugawa
- Department of Genomic MedicineMie University Faculty of MedicineTsuJapan
| | - Waki Hosoda
- Department of Molecular DiagnosticsAichi Cancer CenterNagoyaJapan
| | - Hiromichi Ebi
- Division of Molecular TherapeuticsAichi Cancer Center Research InstituteNagoyaJapan
- Division of Advanced Cancer TherapeuticsNagoya University Graduate School of MedicineNagoyaJapan
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Nguyen Hoang TP, Nguyen TA, Tran NHB, Nguyen Hoang VA, Thi Dao HT, Tran VU, Nguyen YN, Nguyen AT, Nguyen Thi CT, Do Thi TT, Nguyen DS, Nguyen HN, Giang H, Tu LN. Analytical validation and clinical utilization of K-4CARE™: a comprehensive genomic profiling assay with personalized MRD detection. Front Mol Biosci 2024; 11:1334808. [PMID: 38404964 PMCID: PMC10886136 DOI: 10.3389/fmolb.2024.1334808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Background: Biomarker testing has gradually become standard of care in precision oncology to help physicians select optimal treatment for patients. Compared to single-gene or small gene panel testing, comprehensive genomic profiling (CGP) has emerged as a more time- and tissue-efficient method. This study demonstrated in-depth analytical validation of K-4CARE, a CGP assay that integrates circulating tumor DNA (ctDNA) tracking for residual cancer surveillance. Methods: The assay utilized a panel of 473 cancer-relevant genes with a total length of 1.7 Mb. Reference standards were used to evaluate limit of detection (LOD), concordance, sensitivity, specificity and precision of the assay to detect single nucleotide variants (SNVs), small insertion/deletions (Indels), gene amplification and fusion, microsatellite instability (MSI) and tumor mutational burden (TMB). The assay was then benchmarked against orthogonal methods using 155 clinical samples from 10 cancer types. In selected cancers, top tumor-derived somatic mutations, as ranked by our proprietary algorithm, were used to detect ctDNA in the plasma. Results: For detection of somatic SNVs and Indels, gene fusion and amplification, the assay had sensitivity of >99%, 94% and >99% respectively, and specificity of >99%. Detection of germline variants also achieved sensitivity and specificity of >99%. For TMB measurement, the correlation coefficient between whole-exome sequencing and our targeted panel was 97%. MSI analysis when benchmarked against polymerase chain reaction method showed sensitivity of 94% and specificity of >99%. The concordance between our assay and the TruSight Oncology 500 assay for detection of somatic variants, TMB and MSI measurement was 100%, 89%, and 98% respectively. When CGP-informed mutations were used to personalize ctDNA tracking, the detection rate of ctDNA in liquid biopsy was 79%, and clinical utility in cancer surveillance was demonstrated in 2 case studies. Conclusion: K-4CARE™ assay provides comprehensive and reliable genomic information that fulfills all guideline-based biomarker testing for both targeted therapy and immunotherapy. Integration of ctDNA tracking helps clinicians to further monitor treatment response and ultimately provide well-rounded care to cancer patients.
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Affiliation(s)
- Thien-Phuc Nguyen Hoang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Tien Anh Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Nam H. B. Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Van-Anh Nguyen Hoang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hong Thuy Thi Dao
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Vu-Uyen Tran
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Yen Nhi Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Anh Tuan Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Cam Tu Nguyen Thi
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | | | - Duy Sinh Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
| | - Lan N. Tu
- Medical Genetics Institute, Ho Chi Minh City, Vietnam
- Gene Solutions, Ho Chi Minh City, Vietnam
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8
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Heilmann AM, Riess JW, McLaughlin-Drubin M, Huang RSP, Hjulstrom M, Creeden J, Alexander BM, Erlich RL. Insights of Clinical Significance From 109 695 Solid Tumor Tissue-Based Comprehensive Genomic Profiles. Oncologist 2024; 29:e224-e236. [PMID: 37682776 PMCID: PMC10836312 DOI: 10.1093/oncolo/oyad251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 08/06/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND FoundationOneCDx is approved in the US and Japan as a companion diagnostic test to identify patients with cancer who may benefit from treatment with 30 drug therapies in the US and 23 in Japan. Tumor profiling with FoundationOneCDx also detects genomic findings with evidence of clinical significance that may inform clinical care decisions beyond companion diagnostic claims. This observational study reports the breadth and impact of clinical decision insights from FoundationOneCDx solid tumor profiles. MATERIALS AND METHODS Consecutive test result reports for patients with solid tumor diagnoses (n = 109 695) were retrospectively analyzed for clinically significant predictive, prognostic, and diagnostic genomic alterations and signatures, determined in accordance with professional guidelines. Interventional clinical trials with targeted therapies or immune checkpoint inhibitors were matched to tumor profiles based on evidence that the genomic finding may be an actionable, investigational, or hypothetical target in the patient's tumor type. RESULTS In 14 predefined cancer types (80.7% of analyzed solid tumors), predictive, prognostic, and diagnostic markers were reported in 47.6%, 13.2%, and 4.5% of samples, respectively, accounting for a total of 51.2% of tumor profiles. Pan-cancer predictive markers of tumor mutational burden (TMB) of 10 or more mutations per megabase, high microsatellite instability (MSI), or NTRK1/2/3 fusions were observed in 15.6%, 2.0%, and 0.1% of solid tumors, respectively. Most solid tumor profiles (89.2%) had genomic results that could theoretically inform decisions on the selection of immunotherapy and targeted therapy clinical trials. CONCLUSION For this real-world population of patients with FoundationOneCDx solid tumor profiles in the routine course of clinical care, clinically significant findings were reported for approximately half of patients with genomic results.
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Affiliation(s)
| | - Jonathan W Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
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9
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Mochizuki T, Ikegami M, Akiyama T. Factors predictive of second-line chemotherapy in soft tissue sarcoma: An analysis of the National Genomic Profiling Database. Cancer Sci 2024; 115:575-588. [PMID: 38115234 PMCID: PMC10859616 DOI: 10.1111/cas.16050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Of the drugs used in second-line chemotherapy for soft tissue sarcoma (STS), trabectedin is effective for liposarcoma and leiomyosarcoma (L-sarcoma), eribulin for liposarcoma, and pazopanib for non-liposarcoma. The indications for these drugs in STS other than L-sarcoma have not been established. Here we explored the prognosis, mutation profiles, and drug-response factors in STS using real-world big data. Clinicogenomic data on 1761 patients with sarcoma who underwent FoundationOne CDx were obtained from a national database in Japan. Patients with TP53 and KDM2D mutations had a significantly shorter survival period of 253 (95% CI, 99-404) and 330 (95% CI, 20-552) days, respectively, than those without mutations. Non-supervised clustering based on mutation profiles generated 13 tumor clusters. The response rate (RR) to trabectedin was highest in an MDM2-amplification cluster (odds ratio [OR]: 2.2; p = 0.2). The RR was lowest for eribulin in an MDM2-amplification cluster (OR: 0.4; p = 0.03) and highest in a TERT-mutation cluster (OR: 3.0; p = 0.03). The RR was highest for pazopanib in a PIK3CA/PTEN-wild type cluster (OR: 2.1; p = 0.03). In particular, patients harboring mutations in genes regulating the PI3K/Akt/mTOR pathway had a lower RR than patients without mutations (OR: 0.3; p = 0.04). In STS, mutation profiles were more useful in predicting the drug response than histology. The present study demonstrated the potential of tailored therapy guided by mutation profiles established by comprehensive genomic profiling testing in optimizing second-line chemotherapy for STS. The findings of this study will hopefully contribute some valuable insights into enhancing STS treatment strategies and outcomes.
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Affiliation(s)
- Takao Mochizuki
- Department of Orthopaedic Surgery, Saitama Medical CenterJichi Medical UniversitySaitamaJapan
- Department of Musculoskeletal OncologyTokyo Metropolitan Cancer and Infectious Diseases Center, Komagome HospitalTokyoJapan
| | - Masachika Ikegami
- Department of Musculoskeletal OncologyTokyo Metropolitan Cancer and Infectious Diseases Center, Komagome HospitalTokyoJapan
- Division of Cellular SignalingNational Cancer Center Research InstituteTokyoJapan
| | - Toru Akiyama
- Department of Orthopaedic Surgery, Saitama Medical CenterJichi Medical UniversitySaitamaJapan
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10
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Berrino E, Bellomo SE, Chesta A, Detillo P, Bragoni A, Gagliardi A, Naccarati A, Cereda M, Witel G, Sapino A, Bussolati B, Bussolati G, Marchiò C. Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling. J Transl Med 2024; 104:100280. [PMID: 38345263 DOI: 10.1016/j.labinv.2023.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 02/15/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
| | | | - Anita Chesta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | | | - Alberto Bragoni
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Amedeo Gagliardi
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Alessio Naccarati
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Matteo Cereda
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
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11
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Gamboa O, Bonilla CE, Quitian D, Torres GF, Buitrago G, Cardona AF. Cost-Effectiveness of Comprehensive Genomic Profiling in Patients With Non-Small Cell Lung Cancer for the Colombian Health System. Value Health Reg Issues 2024; 39:115-125. [PMID: 38101152 DOI: 10.1016/j.vhri.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/08/2023] [Accepted: 08/14/2023] [Indexed: 12/17/2023]
Abstract
INTRODUCTION The use of comprehensive genomic profiling (CGP) and target therapies is associated with substantial improvements in clinical outcomes among patients with non-small cell lung cancer (NSCLC). However, the costs of CGP may increase the financial pressures of NSCLC on health systems worldwide, especially in low- and middle-income countries. This study aimed to estimate the cost-effectiveness of CGP compared with current genomic tests in patients with NSCLC from the perspective of the Colombian Health System. METHODS To estimate the costs and benefits of CGP and its comparators, we developed a 2-stage cohort model with a lifetime horizon. In the first stage, we made up a decision tree that calculated the probability of receiving each therapy as result of identifying a specific, actionable target. In the second stage, we developed a partitioned survival model that estimated the time spent at each health state. Incremental cost-effectiveness ratios were calculated for life-years (LYs) and quality-adjusted LYs gained. All costs were expressed in 2019 international dollars (INT$). RESULTS CGP is associated with gains of 0.06 LYs and 0.04 quality-adjusted LYs compared with current genomic tests. Incremental cost-effectiveness ratios for CGP ranged from INT$861 to INT$7848, depending on the outcome and the comparator. Sensitivity analyses show that the cost-effectiveness decision was sensitive to prices of CGP above INT$7170 per test. These results are robust to most deterministic and probabilistic sensitivity analyses. CONCLUSIONS CGP may be cost-effective in patients with NSCLC from the perspective of the Colombian Health System (societal willingness-to-pay threshold of INT$15 630 to INT$46 890).
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Affiliation(s)
- Oscar Gamboa
- Instituto de Investigaciones Clínicas, Universidad Nacional de Colombia, Colombia, Bogotá DC, Bogotá.
| | | | | | - Gabriel Fernando Torres
- Instituto de Investigaciones Clínicas, Universidad Nacional de Colombia, Colombia, Bogotá DC, Bogotá
| | - Giancarlo Buitrago
- Faculty of Medicine, Universidad Nacional de Colombia, Colombia, Bogotá DC, Bogotá
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Colombia, Bogotá DC, Bogotá
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Xi Q, Kage H, Ogawa M, Matsunaga A, Nishijima A, Sone K, Kawana K, Oda K. Genomic Landscape of Endometrial, Ovarian, and Cervical Cancers in Japan from the Database in the Center for Cancer Genomics and Advanced Therapeutics. Cancers (Basel) 2023; 16:136. [PMID: 38201563 PMCID: PMC10778092 DOI: 10.3390/cancers16010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/17/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
This study aimed to comprehensively clarify the genomic landscape and its association with tumor mutational burden-high (TMB-H, ≥10 mut/Mb) and microsatellite instability-high (MSI-H) in endometrial, cervical, and ovarian cancers. We obtained genomic datasets of a comprehensive genomic profiling test, FoundationOne® CDx, with clinical information using the "Center for Cancer Genomics and Advanced Therapeutics" (C-CAT) database in Japan. Patients can undergo the tests only after standardized treatments under universal health insurance coverage. Endometrial cancers were characterized by a high frequency of TMB-H and MSI-H, especially in endometrioid carcinomas. The lower ratio of POLE exonuclease mutations and the higher ratio of TP53 mutations compared to previous reports suggested the prognostic effects of the molecular subtypes. Among the 839 cervical cancer samples, frequent mutations of KRAS, TP53, PIK3CA, STK11, CDKN2A, and ERBB2 were observed in adenocarcinomas, whereas the ratio of TMB-H was significantly higher in squamous cell carcinomas. Among the 1606 ovarian cancer samples, genomic profiling of serous, clear cell, endometrioid, and mucinous carcinomas was characterized. Pathogenic mutations in the POLE exonuclease domain were associated with high TMB, and the mutation ratio was low in both cervical and ovarian cancers. The C-CAT database is useful for determining the mutational landscape of each cancer type and histological subtype. As the dataset is exclusively collected from patients after the standardized treatments, the information on "druggable" alterations highlights the unmet needs for drug development in major gynecological cancers.
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Affiliation(s)
- Qian Xi
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan; (Q.X.)
| | - Hidenori Kage
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Miho Ogawa
- Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Asami Matsunaga
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan; (Q.X.)
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Nihon University, Tokyo 173-8610, Japan
| | - Akira Nishijima
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Nihon University, Tokyo 173-8610, Japan
| | - Katsutoshi Oda
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan; (Q.X.)
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13
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Pietrantonio F, Bergamo F, Rossini D, Ghelardi F, De Grandis MC, Germani MM, Barsotti G, Formica V, Frassineti GL, Boscolo G, Cinieri S, Di Donato S, Antonuzzo L, Antoniotti C, Ambrosini M, Piva VM, Nichetti F, Fassan M, Cremolini C, Lonardi S. Negative hyperselection of elderly patients with RAS and BRAF wild-type metastatic colorectal cancer receiving initial panitumumab plus FOLFOX or 5-FU/LV. Eur J Cancer 2023; 195:113396. [PMID: 37924647 DOI: 10.1016/j.ejca.2023.113396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Upfront anti-EGFR therapy represents the standard of care for patients with left-sided, MSS/pMMR, RAS and BRAF wild-type mCRC. Molecular 'hyperselection' may optimize EGFR inhibition by detecting additional resistance alterations. MATERIALS AND METHODS We used comprehensive genomic profiling on archival samples of elderly patients enrolled in the PANDA trial to detect: HER2 amplification/mutations; MET amplification; NTRK/ROS1/ALK/RET rearrangements; PIK3CA exon 20 mutations; PTEN alterations; AKT1 mutations; MAP2K1 mutations. We defined 'Gene Altered' (GA) patients whose tumour harboured at least one alteration, and 'Hyperselected' (HS) those without. Survival and tumour response outcomes were correlated to hyperselection status alone or combined with primary tumour sidedness or treatment arm. RESULTS Genomic alterations were detected in 41/147 patients (27.9%). PFS, OS and ORR were inferior in GA versus HS (median PFS: 7.6 versus 12.8 months, HR = 2.08, 95% CI: 1.43-3.03, p < 0.001; median OS: 20.0 versus 29.5 months, HR = 1.82, 95% CI:1.23-2.69, p = 0.002; ORR: 51% versus 71%; OR = 0.43, 95% CI: 0.21-0.91, p = 0.02). In the multivariable models, the impact of hyperselection on PFS and OS was confirmed. Lower ORR was observed with 5-FU/LV/panitumumab in GA (40% versus 62%), but not in HS (70% versus 72%). GA was associated with worse survival and response regardless of primary tumour sidedness, whereas in the HS subgroup, right-and left sided tumours had similar outcomes. CONCLUSIONS Molecular hyperselection and comprehensive genomic profiling have a potential usefulness in elderly patients with RAS/BRAF wild-type, pMMR/MSS mCRC, eligible for upfront EGFR inhibition.
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Affiliation(s)
- Filippo Pietrantonio
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori,, Milano, Italy
| | - Francesca Bergamo
- Department of Oncology, Veneto Institute of Oncology IOV - IRCCS, Padova, Italy
| | - Daniele Rossini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy; Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy
| | - Filippo Ghelardi
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori,, Milano, Italy
| | - Maria Caterina De Grandis
- Department of Oncology, Veneto Institute of Oncology IOV - IRCCS, Padova, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Marco Maria Germani
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy; Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy
| | - Giulia Barsotti
- Department of Oncology, Veneto Institute of Oncology IOV - IRCCS, Padova, Italy
| | | | - Giovanni Luca Frassineti
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" (IRST), Meldola, Italy
| | - Giorgia Boscolo
- Medical Specialties Department, Oncology and Oncological Haematology, ULSS 3 Serenissima, Venice, Italy
| | - Saverio Cinieri
- Medical Oncology Unit, Ospedale Antonio Perrino, Brindisi, Italy
| | - Samantha Di Donato
- Department of Medical Oncology, Nuovo Ospedale di Prato Santo Stefano, Prato, Italy
| | - Lorenzo Antonuzzo
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Clinical Oncology Unit, Careggi University Hospital, Florence, Italy
| | - Carlotta Antoniotti
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy; Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy
| | - Margherita Ambrosini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori,, Milano, Italy
| | | | - Federico Nichetti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori,, Milano, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, Padua, Italy; Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy; Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy
| | - Sara Lonardi
- Department of Oncology, Veneto Institute of Oncology IOV - IRCCS, Padova, Italy.
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14
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Kokkali S, Georgaki E, Mandrakis G, Valverde C, Theocharis S. Genomic Profiling and Clinical Outcomes of Targeted Therapies in Adult Patients with Soft Tissue Sarcomas. Cells 2023; 12:2632. [PMID: 37998367 PMCID: PMC10670373 DOI: 10.3390/cells12222632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Genomic profiling has improved our understanding of the pathogenesis of different cancers and led to the development of several targeted therapies, especially in epithelial tumors. In this review, we focus on the clinical utility of next-generation sequencing (NGS) to inform therapeutics in soft tissue sarcoma (STS). The role of NGS is still controversial in patients with sarcoma, given the low mutational burden and the lack of recurrent targetable alterations in most of the sarcoma histotypes. The clinical impact of genomic profiling in STS has not been investigated prospectively. A limited number of retrospective, mainly single-institution, studies have addressed this issue using various NGS technologies and platforms and a variety of criteria to define a genomic alteration as actionable. Despite the detailed reports on the different gene mutations, fusions, or amplifications that were detected, data on the use and efficacy of targeted treatment are very scarce at present. With the exception of gastrointestinal stromal tumors (GISTs), these targeted therapies are administered either through off-label prescription of an approved drug or enrollment in a matched clinical trial. Based mainly on anecdotal reports, the outcome of targeted therapies in the different STS histotypes is discussed. Prospective studies are warranted to assess whether genomic profiling improves the management of STS patients.
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Affiliation(s)
- Stefania Kokkali
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
- Oncology Unit, 2nd Department of Medicine, Medical School, Hippocratio General Hospital of Athens, National and Kapodistrian University of Athens, V. Sofias 114, 11527 Athens, Greece;
| | - Eleni Georgaki
- Oncology Unit, 2nd Department of Medicine, Medical School, Hippocratio General Hospital of Athens, National and Kapodistrian University of Athens, V. Sofias 114, 11527 Athens, Greece;
| | - Georgios Mandrakis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
| | - Claudia Valverde
- Medical Oncology Department, Vall d’Hebron University Hospital, Pg. Vall d’Hebron 119-12, 08035 Barcelona, Spain;
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece;
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15
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Tamada S, Ikarashi D, Yanagawa N, Toyoshima M, Takahashi K, Matsuura T, Maekawa S, Kato R, Kanehira M, Takata R, Obara W. Metastatic bladder cancer forming a sigmoidorectal fistula after enfortumab vedotin therapy: a case report. Front Oncol 2023; 13:1274494. [PMID: 38023224 PMCID: PMC10665906 DOI: 10.3389/fonc.2023.1274494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
We report the case of a 68-year-old man who developed a sigmoidorectal fistula after marked response to enfortumab vedotin for advanced bladder cancer. The patient had undergone radical cystectomy with ileal conduit after neoadjuvant chemotherapy. Six months after surgery, local recurrence in the pelvic cavity and multiple lung metastases were found, and the patient was administered pembrolizumab as second-line therapy. Due to worsening local recurrence and suspected invasion of the sigmoid colon and rectum, enfortumab vedotin was initiated as third-line therapy and comprehensive genomic profiling was simultaneously performed. Enfortumab vedotin was remarkably effective, the lung metastases disappeared, and the local recurrent lesion shrank in volume although a sigmoidorectal fistula was found to form through the tumor cavity. Immunohistochemical analysis of the tumor specimens exhibited increased nectin-4 expression. This rare case of metastatic bladder cancer with sigmoidorectal fistula associated with effective enfortumab vedotin therapy suggests that nectin-4 expression and comprehensive genomic profiling might be useful in predicting treatment response to enfortumab vedotin.
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Affiliation(s)
- Shinji Tamada
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Daiki Ikarashi
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Naoki Yanagawa
- Department of Pathology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Moe Toyoshima
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Kenta Takahashi
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Tomohiko Matsuura
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Shigekatsu Maekawa
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Renpei Kato
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Mitsugu Kanehira
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Ryo Takata
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
| | - Wataru Obara
- Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
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16
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Rock A, Uche A, Yoon J, Agulnik M, Chow W, Millis S. Bioinformatic Analysis of Recurrent Genomic Alterations and Corresponding Pathway Alterations in Ewing Sarcoma. J Pers Med 2023; 13:1499. [PMID: 37888109 PMCID: PMC10608227 DOI: 10.3390/jpm13101499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
Ewing Sarcoma (ES) is an aggressive, mesenchymal malignancy associated with a poor prognosis in the recurrent or metastatic setting with an estimated overall survival (OS) of <30% at 5 years. ES is characterized by a balanced, reciprocal chromosomal translocation involving the EWSR1 RNA-binding protein and ETS transcription factor gene (EWS-FLI being the most common). Interestingly, murine ES models have failed to produce tumors phenotypically representative of ES. Genomic alterations (GA) in ES are infrequent and may work synergistically with EWS-ETS translocations to promote oncogenesis. Aberrations in fibroblast growth factor receptor (FGFR4), a receptor tyrosine kinase (RTK) have been shown to contribute to carcinogenesis. Mouse embryonic fibroblasts (MEFs) derived from knock-in strain of homologous Fgfr4G385R mice display a transformed phenotype with enhanced TGF-induced mammary carcinogenesis. The association between the FGFRG388R SNV in high-grade soft tissue sarcomas has previously been demonstrated conferring a statistically significant association with poorer OS. How the FGFR4G388R SNV specifically relates to ES has not previously been delineated. To further define the genomic landscape and corresponding pathway alterations in ES, comprehensive genomic profiling (CGP) was performed on the tumors of 189 ES patients. The FGFR4G388R SNV was identified in a significant proportion of the evaluable cases (n = 97, 51%). In line with previous analyses, TP53 (n = 36, 19%), CDK2NA/B (n = 33, 17%), and STAG2 (n = 22, 11.6%) represented the most frequent alterations in our cohort. Co-occurrence of CDK2NA and STAG2 alterations was observed (n = 5, 3%). Notably, we identified a higher proportion of TP53 mutations than previously observed. The most frequent pathway alterations affected MAPK (n = 89, 24% of pathological samples), HRR (n = 75, 25%), Notch1 (n = 69, 23%), Histone/Chromatin remodeling (n = 57, 24%), and PI3K (n = 64, 20%). These findings help to further elucidate the genomic landscape of ES with a novel investigation of the FGFR4G388R SNV revealing frequent aberration.
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Affiliation(s)
- Adam Rock
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - An Uche
- Alameda Health System, 1411 E. 31st St., Oakland, CA 94602, USA;
| | - Janet Yoon
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Mark Agulnik
- City of Hope Comprehensive Cancer Center, 1500 E. Duarte Rd., Duarte, CA 91010, USA; (J.Y.); (M.A.)
| | - Warren Chow
- UCI Health, 101 The City Drive, South Orange, CA 92868, USA;
| | - Sherri Millis
- Foundation Medicine, Inc., 150 Second St., Cambridge, MA 02141, USA;
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17
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Saldivar JS, Harris J, Ayash E, Hong M, Tandon P, Sinha S, Hebron PM, Houghton EE, Thorne K, Goodman LJ, Li C, Marfatia TR, Anderson J, Morra M, Lyle J, Bartha G, Chen R. Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay. Oncotarget 2023; 14:789-806. [PMID: 37646774 PMCID: PMC10467627 DOI: 10.18632/oncotarget.28490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.
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Affiliation(s)
| | - Jason Harris
- Personalis, Inc., Fremont, CA 94555, USA
- These authors contributed equally to this work
| | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - John Lyle
- Personalis, Inc., Fremont, CA 94555, USA
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18
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Powles T, Young A, Nimeiri H, Madison RW, Fine A, Zollinger DR, Huang Y, Xu C, Gjoerup OV, Aushev VN, Wu HT, Aleshin A, Carter C, Davarpanah N, Degaonkar V, Gupta P, Mariathasan S, Schleifman E, Assaf ZJ, Oxnard G, Hegde PS. Molecular residual disease detection in resected, muscle-invasive urothelial cancer with a tissue-based comprehensive genomic profiling-informed personalized monitoring assay. Front Oncol 2023; 13:1221718. [PMID: 37601688 PMCID: PMC10433150 DOI: 10.3389/fonc.2023.1221718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Circulating tumor DNA (ctDNA) detection postoperatively may identify patients with urothelial cancer at a high risk of relapse. Pragmatic tools building off clinical tumor next-generation sequencing (NGS) platforms could have the potential to increase assay accessibility. Methods We evaluated the widely available Foundation Medicine comprehensive genomic profiling (CGP) platform as a source of variants for tracking of ctDNA when analyzing residual samples from IMvigor010 (ClinicalTrials.gov identifier NCT02450331), a randomized adjuvant study comparing atezolizumab with observation after bladder cancer surgery. Current methods often involve germline sampling, which is not always feasible or practical. Rather than performing white blood cell sequencing to filter germline and clonal hematopoiesis (CH) variants, we applied a bioinformatic approach to select tumor (non-germline/CH) variants for molecular residual disease detection. Tissue-informed personalized multiplex polymerase chain reaction-NGS assay was used to detect ctDNA postsurgically (Natera). Results Across 396 analyzed patients, prevalence of potentially actionable alterations was comparable with the expected prevalence in advanced disease (13% FGFR2/3, 20% PIK3CA, 13% ERBB2, and 37% with elevated tumor mutational burden ≥10 mutations/megabase). In the observation arm, 66 of the 184 (36%) ctDNA-positive patients had shorter disease-free survival [DFS; hazard ratio (HR) = 5.77; 95% confidence interval (CI), 3.84-8.67; P < 0.0001] and overall survival (OS; HR = 5.81; 95% CI, 3.41-9.91; P < 0.0001) compared with ctDNA-negative patients. ctDNA-positive patients had improved DFS and OS with atezolizumab compared with those in observation (DFS HR = 0.56; 95% CI, 0.38-0.83; P = 0.003; OS HR = 0.66; 95% CI, 0.42-1.05). Clinical sensitivity and specificity for detection of postsurgical recurrence were 58% (60/103) and 93% (75/81), respectively. Conclusion We present a personalized ctDNA monitoring assay utilizing tissue-based FoundationOne® CDx CGP, which is a pragmatic and potentially clinically scalable method that can detect low levels of residual ctDNA in patients with resected, muscle-invasive bladder cancer without germline sampling.
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Affiliation(s)
- Thomas Powles
- Barts Experimental Cancer Medicine Centre, Barts Cancer Institute, Queen Mary University of London ECMC, Barts Health, London, United Kingdom
| | - Amanda Young
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Yanmei Huang
- Foundation Medicine, Cambridge, MA, United States
| | - Chang Xu
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | - Corey Carter
- Roche/Genentech, South San Francisco, CA, United States
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19
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Ishido S, Tamaki N, Inada K, Itakura J, Takahashi Y, Uchihara N, Suzuki K, Tanaka Y, Miyamoto H, Yamada M, Matsumoto H, Nobusawa T, Keitoku T, Takaura K, Tanaka S, Maeyashiki C, Yasui Y, Tsuchiya K, Nakanishi H, Kurosaki M, Izumi N. Pemigatinib treatment for intrahepatic cholangiocarcinoma with FGFR2 fusion detected by a liquid comprehensive genomic profiling test. Clin Case Rep 2023; 11:e7664. [PMID: 37415592 PMCID: PMC10320371 DOI: 10.1002/ccr3.7664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
The liquid CGP was useful for detecting FGFR2 fusion and the patient experienced typical side effects (nail disorders, hyperphosphatemia, and taste disorders) of pemigatinib that required treatment.
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Affiliation(s)
- Shun Ishido
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Nobuharu Tamaki
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Kento Inada
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Jun Itakura
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Yuka Takahashi
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Naoki Uchihara
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Keito Suzuki
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Yuki Tanaka
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Haruka Miyamoto
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Michiko Yamada
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Hiroaki Matsumoto
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Tsubasa Nobusawa
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Taisei Keitoku
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Kenta Takaura
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Shohei Tanaka
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Chiaki Maeyashiki
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Yutaka Yasui
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Kaoru Tsuchiya
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Hiroyuki Nakanishi
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Masayuki Kurosaki
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
| | - Namiki Izumi
- Department of Gastroenterology and HepatologyMusashino Red Cross HospitalTokyoJapan
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20
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Čerina D, Krpina K, Jakopović M, Dedić Plavetić N, Seiwerth F, Tomić S, Radić J, Belac Lovasić I, Canjko I, Boban M, Samaržija M, Vrdoljak E. The Challenges and Opportunities of the Implementation of Comprehensive Genomic Profiling in Everyday Clinical Practice with Non-Small Cell Lung Cancer: National Results from Croatia. Cancers (Basel) 2023; 15:3395. [PMID: 37444505 DOI: 10.3390/cancers15133395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) has become the best example of precision oncology's impact on outcomes in everyday clinical practice, significantly changing the expectations of all stakeholders, including medical professionals, society, and most importantly, patients. Consequently, the implementation of the precision oncology concept in medical systems, in order to achieve optimal and proven curative effects in NSCLC, is imperative. In this study, we investigated the development, challenges, and results associated with the implementation of precision oncology in NSCLC on a national level in Croatia. We conducted a multicenter, retrospective, cross-sectional analysis on the total population of Croatian patients with metastatic lung cancer, on whose tumors specimen comprehensive genomic profiling (CGP) testing was performed during 2020 and 2021. A total of 48 patients were included in the study. CGP revealed clinically relevant genomic alterations (CRGA) in 37 patients (79%), with a median of 2 (IQR 1-3) CRGA per patient. From the panel of recommended tests, KRAS, MET, and EGFR were the most common alterations, detected in 16 (34%), 5 (11%), and 3 (6%) patients, respectively. CGP revealed additional targetable mutations in 29 (60%) patients who would not have been tested (and consequently, whose mutations would not have been detected) according to the existing everyday standard of practice in Croatia. The tumor mutational burden was reported as high (≥10 Muts/Mb) in 19 patients (40%). CGP analysis reported some kind of targeted therapy for 34 patients (72%). CGP revealed other potentially targetable mutations, and it also determined TMB to be high in a significant number of patients. In conclusion, when possible, CGP should be used as an upfront backbone diagnostic and treatment-oriented work-up in patients with NSCLC.
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Affiliation(s)
- Dora Čerina
- Department of Oncology, University Hospital Center Split, 21000 Split, Croatia
- School of Medicine, University of Split, 21000 Split, Croatia
| | - Kristina Krpina
- Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Marko Jakopović
- Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Natalija Dedić Plavetić
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Department of Oncology, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Fran Seiwerth
- Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Snježana Tomić
- School of Medicine, University of Split, 21000 Split, Croatia
- Department of Pathology, Citology and Forensic Medicine, University Hospital Center Split, 21000 Split, Croatia
| | - Jasna Radić
- Department of Oncology and Nuclear Medicine, Division of Medical Oncology, University Hospital for Tumors, Sestre Milosrdnice University Hospital Center, 10000 Zagreb, Croatia
| | | | - Ivana Canjko
- Department of Radiotherapy Oncology, University Hospital Center Osijek, 31000 Osijek, Croatia
| | - Marijo Boban
- Department of Oncology, University Hospital Center Split, 21000 Split, Croatia
- School of Medicine, University of Split, 21000 Split, Croatia
| | - Miroslav Samaržija
- Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Eduard Vrdoljak
- Department of Oncology, University Hospital Center Split, 21000 Split, Croatia
- School of Medicine, University of Split, 21000 Split, Croatia
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21
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Makino K, Otani Y, Fujii K, Ishida J, Hirano S, Suruga Y, Washio K, Nishida K, Yanai H, Tomida S, Ennishi D, Date I. Utility of Comprehensive Genomic Profiling for Precise Diagnosis of Pediatric-Type Diffuse High-Grade Glioma. Acta Med Okayama 2023; 77:323-330. [PMID: 37357634 DOI: 10.18926/amo/65502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
In the current World Health Organization classification of central nervous system tumors, comprehensive genetic and epigenetic analyses are considered essential for precise diagnosis. A 14-year-old male patient who presented with a cerebellar tumor was initially diagnosed with glioblastoma and treated with radiation and concomitant temozolomide chemotherapy after resection. During maintenance temozolomide therapy, a new contrast-enhanced lesion developed in the bottom of the cavity formed by the resection. A second surgery was performed, but the histological findings in specimens from the second surgery were different from those of the first surgery. Although genome-wide DNA methylation profiling was conducted using frozen tissue for a precise diagnosis, the proportion of tumor cells was insufficient and only normal cerebellum was observed. We then performed comprehensive genetic analysis using formalin-fixed paraffin-embedded sections, which revealed MYCN amplification without alteration of IDH1, IDH2, or Histone H3. Finally, the patient was diagnosed with pediatric-type diffuse high-grade glioma, H3-wildtype and IDH-wildtype. In conclusion, comprehensive genetic and epigenetic analysis should be considered in pediatric brain tumor cases.
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Affiliation(s)
- Keigo Makino
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Yoshihiro Otani
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Kentaro Fujii
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Joji Ishida
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Shuichiro Hirano
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Yasuki Suruga
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Kana Washio
- Departments of Pediatrics, Okayama University Hospital
| | - Kenji Nishida
- Departments of Pathology, Okayama University Hospital
| | | | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Isao Date
- Department of Neurological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
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22
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Kage H, Oda K, Muto M, Tsuchihara K, Okita N, Okuma Y, Kikuchi J, Shirota H, Hayashi H, Kokuryo T, Sakai D, Hirasawa A, Kubo M, Kenmotsu H, Akiyama N, Shinozaki-Ushiku A, Tanabe M, Ushiku T, Miyagawa K, Seto Y. Human resources for administrative work to carry out a comprehensive genomic profiling test in Japan. Cancer Sci 2023. [PMID: 37165760 DOI: 10.1111/cas.15833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/27/2023] [Accepted: 04/16/2023] [Indexed: 05/12/2023] Open
Abstract
Comprehensive genomic profiling (CGP) tests have been nationally reimbursed in Japan since June 2019 under strict restrictions, and over 46,000 patients have taken the test. Core Hospitals and Designated Hospitals host molecular tumor boards, which is more time-consuming than simply participating in them. We sent a questionnaire to government-designated Cancer Genomic Medicine Hospitals, including all 12 Core Hospitals, all 33 Designated Hospitals, and 117 of 188 Cooperative Hospitals. The questionnaire asked how much time physicians and nonphysicians spent on administrative work for cancer genomic medicine. For every CGP test, 7.6 h of administrative work was needed. Physicians spent 2.7 h/patient, while nonphysicians spent 4.9 h/patient. Time spent preparing for molecular tumor boards, called Expert Panels, was the longest, followed by time spent participating in Expert Panels. Assuming an hourly wage of ¥24,000/h for physicians and ¥2800/h for nonphysicians, mean labor cost was ¥78,071/patient. On a monthly basis, more time was spent on administrative work at Core Hospitals compared with Designated Hospitals and Cooperative Hospitals (385 vs. 166 vs. 51 h/month, respectively, p < 0.001). Consequently, labor cost per month was higher at Core Hospitals than at Designated Hospitals and Cooperative Hospitals (¥3,951,854 vs. ¥1,687,167 vs. ¥487,279/month, respectively, p < 0.001). Completing a CGP test for a cancer patient in Japan is associated with significant labor at each hospital, especially at Core Hospitals. Streamlining the exchange of information and simplifying Expert Panels will likely alleviate this burden.
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Affiliation(s)
- Hidenori Kage
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
- Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Oda
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Katsuya Tsuchihara
- Department of Genetic Medicine and Services, National Cancer Center Hospital East, Chiba, Japan
| | - Natsuko Okita
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Yusuke Okuma
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Junko Kikuchi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Hidekazu Shirota
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Hideyuki Hayashi
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Toshio Kokuryo
- Division of Surgical Oncology, Department of Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Sakai
- Center for Cancer Genomics and Personalized Medicine, Osaka University Hospital, Suita, Japan
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Makoto Kubo
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | | | - Nana Akiyama
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
| | - Aya Shinozaki-Ushiku
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiko Tanabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Department of Clinical Genomics, The University of Tokyo Hospital, Tokyo, Japan
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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23
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Ueda T, Tsubamoto H, Takimoto Y, Isono-Taniguchi R, Narita S, Nakagawa K, Wakimoto YU, Nishimura Y, Muroi Y, Nagahashi M, Hirota S, Sawai H, Shibahara H. Comprehensive Genomic Profiling Detects Hereditary Cancers and Confers Survival Advantage in Patients With Gynaecological Cancers. Anticancer Res 2023; 43:2091-2101. [PMID: 37097652 DOI: 10.21873/anticanres.16370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND/AIM The clinical benefits of comprehensive genomic profiling (CGP) of tumours in patients with gynaecological cancers remain unknown. We investigated the utility of CGP in assessing patient survival and its efficacy in detecting hereditary cancers in gynaecological patients. PATIENTS AND METHODS We retrospectively analysed the medical records of 104 gynaecological patients who underwent CGP between August 2018 and December 2022. The detection of actionable and accessible genomic alterations and administration of targeted therapy, as recommended by the molecular tumour board (MTB), were assessed. The overall survival (after second-line treatment in cervical and endometrial carcinomas and after platinum-resistant recurrence in ovarian carcinoma) was compared between patients with or without administration of MTB-recommended genotype-matched therapy. Germline findings were assessed using a variant allele frequency-tumour content graph. RESULTS Among 104 patients, actionable and accessible genomic alterations were observed in 53 patients. Matched therapy was applied in 21 patients, comprising administration of repurposing itraconazole (n=7), immune checkpoint inhibitors (n=7), poly (ADP-ribose) polymerase inhibitors (n=5), and others (n=2). The median overall survival of patients receiving and not receiving matched therapy were 19.3 months and 11.2 months, respectively (p=0.036, hazard ratio=0.48). Among 12 patients with hereditary cancers, 11 patients were previously undiagnosed. Seven patients had hereditary breast and ovarian cancer, and five had other cancer. CONCLUSION The implementation of CGP testing prolonged overall survival in gynaecological cancer as well as provided an opportunity for genetic counselling for newly-diagnosed patients with hereditary cancers and their families.
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Affiliation(s)
- Tomoko Ueda
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Hiroshi Tsubamoto
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan;
- Department of Clinical Genetics, Hyogo Medical University Hospital, Hyogo, Japan
| | - Yumi Takimoto
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Roze Isono-Taniguchi
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Sachiyo Narita
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Kohei Nakagawa
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Y U Wakimoto
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
| | | | - Yoshiko Muroi
- Cancer Center, Hyogo Medical University Hospital, Hyogo, Japan
| | - Masayuki Nagahashi
- Cancer Center, Hyogo Medical University Hospital, Hyogo, Japan
- Department of Breast and Endocrine Surgery, Hyogo Medical University Hospital, Hyogo, Japan
| | - Seiichi Hirota
- Department of Surgical Pathology, Hyogo Medical University Hospital, Hyogo, Japan
| | - Hideaki Sawai
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
- Department of Clinical Genetics, Hyogo Medical University Hospital, Hyogo, Japan
| | - Hiroaki Shibahara
- Department of Obstetrics and Gynecology, Hyogo Medical University Hospital, Hyogo, Japan
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Tang W, Hanada K, Motoo Y, Sakamaki H, Oda T, Furuta K, Abutani H, Ito S, Tsutani K. Budget impact analysis of comprehensive genomic profiling for untreated advanced or recurrent solid cancers in Japan. J Med Econ 2023; 26:614-626. [PMID: 37073487 DOI: 10.1080/13696998.2023.2202599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
AIMS In Japan, the use of comprehensive genomic profiling (CGP) is only available for cancer patients who have no standard of care (SoC), or those who have completed SoC. This may lead to missed treatment opportunities for patients with druggable alterations. In this study, we evaluated the potential impact of CGP testing before SoC on medical costs and clinical outcome in untreated patients with advanced or recurrent biliary tract cancer (BTC), non-squamous non-small cell lung cancer (NSQ-NSCLC), or colorectal cancer (CRC) in Japan between 2022 and 2026. MATERIALS AND METHODS We constructed a decision-tree model reflecting the healthcare environment of Japan, to estimate the clinical outcome and medical costs impact of CGP testing by comparing two groups (with vs without CGP testing before SoC). The epidemiological parameters, detection rates of druggable alterations, and overall survival were collected from literature and claims databases in Japan. Treatment options selected based on druggable alterations were set in the model based on clinical experts' opinions. RESULTS In 2026, the number of untreated patients with advanced or recurrent BTC, NSQ-NSCLC, and CRC was estimated to be 8,600, 32,103, and 24,896, respectively. Compared with the group without CGP testing before SoC, CGP testing before SoC increased druggable alteration detection and treatment rate with matched therapies in all three cancer types. The medical costs per patient per month were estimated to increase with CGP testing before SoC in the three cancer types by 19,600, 2,900, and 2,200 JPY (145, 21, and 16 USD), respectively. LIMITATIONS Only those druggable alterations with matched therapies were considered in the analysis model, while the potential impact of other genomic alterations provided by CGP testing was not considered. CONCLUSIONS The present study suggested that CGP testing before SoC may improve patient outcomes in various cancer types with a limited and controllable increase in medical costs.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kiichiro Tsutani
- Tokyo Ariake University of Medical and Health Sciences, Faculty of Health Sciences
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Danziger N, Sokol ES, Graf RP, Hiemenz MC, Maule J, Parimi V, Palmieri C, Pusztai L, Ross JS, Huang RSP. Variable Landscape of PD-L1 Expression in Breast Carcinoma as Detected by the DAKO 22C3 Immunohistochemistry Assay. Oncologist 2023; 28:319-326. [PMID: 36866462 PMCID: PMC10078903 DOI: 10.1093/oncolo/oyad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 01/09/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND In 2020, pembrolizumab was approved as a therapy for triple-negative breast cancer (TNBC) with the companion diagnostic DAKO 22C3 programmed death ligand-1 (PD-L1) immunohistochemistry assay. The study aimed to determine the landscape of PD-L1 expression as detected by the DAKO 22C3 PD-L1 assay in breast cancer subtypes and compare the clinicopathologic and genomic characteristics of PD-L1 positive and negative TNBC. METHODS PD-L1 expression using the DAKO 22C3 antibody was scored using a combined positive score (CPS) and positive status was defined as CPS ≥10. Comprehensive genomic profiling was performed using the FoundationOne CDx assay. RESULTS Of the 396 BC patients stained with DAKO 22C3, the majority were HR+/HER2- and TNBC (42% and 36%, respectively). Median PD-L1 expression and frequency of CPS ≥10 was highest in TNBC cases (median: 7.5, 50% CPS ≥10) and lowest in the HR+/HER2- group (median: 1.0, 15.5% CPS ≥10) (P < .0001). A comparison of PD-L1 positive and PD-L1 negative TNBC demonstrated no significant differences in clinicopathologic or genomic characteristics. TNBC tissue samples from the breast did have an observed enrichment for PD-L1 positivity compared to TNBC tissue samples from a metastatic site (57% vs. 44%), but this was not statistically significant (P = .1766). In the HR+/HER2- group, genomic alterations in TP53, CREBBP, and CCNE1 were more prevalent and genomic loss of heterozygosity was higher in the PD-L1(+) group compared to the PD-L1(-) group. CONCLUSIONS The subtypes of breast cancer have distinct patterns of PD-L1 expression, supporting that further research of immunotherapies may include specific evaluation of optimum cutoffs for non-TNBC patients. In TNBC, PD-L1 positivity is not associated with other clinicopathologic or genomic features and should be integrated into future studies of immunotherapy efficacy.
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Affiliation(s)
| | | | - Ryon P Graf
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Jake Maule
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Carlo Palmieri
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Lajos Pusztai
- The Clatterbridge Cancer Centre National Health Service (NHS) Foundation Trust, Liverpool, UK
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Departments of Pathology and Urology, State University of New York Upstate Medical University, Syracuse, NY, USA
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Boongird A, Lekcharoensombat N, Jinawath A, Theparee T, Jittapiromsak N, Shuangshoti S, Thorner PS, Teerapakpinyo C. Glioblastoma with novel EGFR mutations (T790M and exon 20 insertion) yet unresponsive to osimertinib: a case report. Genes Chromosomes Cancer 2023; 62:423-429. [PMID: 36994936 DOI: 10.1002/gcc.23143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 03/07/2023] [Accepted: 03/29/2023] [Indexed: 03/31/2023] Open
Abstract
Glioblastoma (GBM) is a high-grade adult-type IDH-wildtype diffuse glioma, commonly harboring EGFR amplification. Here we describe a case of a 49-year-old man with a GBM harboring a TERT promoter mutation. Despite surgical and chemoradiation therapy, the tumour recurred. At that time, comprehensive genomic profiling by next-generation sequencing identified two rare mutations in EGFR: T790M and an exon 20 insertion. Based on these findings, the patient elected to undergo off-label therapy with osimertinib, a third-generation EGFR tyrosine kinase inhibitor that has shown promising results in non-small cell lung carcinoma, including metastatic to brain, with exactly the same EGFR mutations. Moreover, the drug has excellent central nervous system penetration. Even so, no clinical response was observed, and the patient succumbed to the disease. The lack of response may be related to the specific nature of the EGFR mutations, and/or other unfavorable tumour biology overriding any benefit from osimertinib. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Atthaporn Boongird
- Neurosurgical Unit, Dept. of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Nopphon Lekcharoensombat
- Neurosurgical Unit, Dept. of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Artit Jinawath
- Dept. of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Talent Theparee
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Academic Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Shanop Shuangshoti
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Paul Scott Thorner
- Dept. of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Dept. of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada, M5S1A8
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
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Hacking SM, Pavlick D, Wang Y, Carneiro BA, Mullally M, Lu S, Canepa M, Bratslavsky G, Jacob J, Necchi A, Spiess PE, Wang L, Yakirevich E, Ross J. Comprehensive Genomic Profiling of NF2-Mutated Kidney Tumors Reveals Potential Targets for Therapy. Oncologist 2023:7077239. [PMID: 36917021 DOI: 10.1093/oncolo/oyad040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/27/2023] [Indexed: 03/15/2023] Open
Abstract
Genomic alterations (GA) in NF2 tumor-suppressor gene have been associated with aggressive behavior in kidney tumors. We used comprehensive genomic profiling (CGP) to evaluate the frequencies of NF2 GA in histologic subtypes of kidney tumors and co-occurring GA in other genes and biomarkers. Advanced kidney tumors included 1875 clear cell (ccRCC), 405 papillary (pRCC), 108 chromophobe (chRCC), 171 sarcomatoid (sRCC), 61 collecting duct (cdRCC), 49 medullary (mRCC), 134 unclassified (uRCC), 906 urothelial carcinoma of renal pelvis (UC), and 147 Wilms tumors underwent hybrid-capture based CGP to evaluate all classes of GA. 192 (4.9%) of kidney tumors featured NF2 GA which were predominantly structural variant mutations (89%), followed by copy number alterations (9%). Gender and age were similar between NF2-mutant (NF2mut) and NF2-wild type (NF2wt) cohorts with male preponderance. NF2 GA frequency was highest in cdRCC (30%), sRCC (21%), uRCC (15%), and pRCC (12%) while lowest in ccRCC (3%), UC (3%) Wilms tumor (1%), and chRCC (0%). NF2 mutational status was associated with loss of Ch 22 (P < .001). NF2mut RCC harbored co-occurring GA including CDKN2A, CDKN2B, SETD2, and BAP1. VHL, PBRM1, PTEN, and FGFR3 GA were significantly more frequent in NF2wt than in NF2mut tumors. MTOR pathway GAs were uncommon in NF2mut tumors. No NF2 mutated RCC featured MSI-high or high TMB. sRCC was associated with high PD-L1 expression. PD-L1 SP142 tumoral (P = .04) and immune cells (P = .013) were more frequent in NF2mut as compared to NF2wt group. Among histologic subtypes of RCC, cdRCC, sRCC, pRCC, and uRCC are enriched in NF2 GA. Co-occurrent GA in CDKN2A/B, SETD2, and BAP1 may represent potential therapeutic targets. Higher level of PD-L1 expression in NF2mut cohort suggests that these tumors might be sensitive to immune checkpoint inhibitor therapies.
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Affiliation(s)
- Sean M Hacking
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | | | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Benedito A Carneiro
- Lifespan Cancer Institute, Legorreta Cancer Center at Brown University, Providence, RI, USA
| | - Matthew Mullally
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Mariana Canepa
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Gennady Bratslavsky
- Department of Urology, State University of New York (SUNY), Upstate Medical University, Syracuse, NY, USA
| | - Joseph Jacob
- Department of Urology, State University of New York (SUNY), Upstate Medical University, Syracuse, NY, USA
| | - Andrea Necchi
- Department of GU Medical Oncology, San Raffaele University, Milan, Italy
| | - Philippe E Spiess
- Department of Genitourinary Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Li Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Evgeny Yakirevich
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
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Shirota H, Komine K, Takahashi M, Takahashi S, Miyauchi E, Niizuma H, Tada H, Shimada M, Niihori T, Aoki Y, Sugiyama I, Kawamura M, Yasuda J, Suzuki S, Iwaya T, Saito M, Saito T, Shibata H, Furukawa T, Ishioka C. Clinical decisions by the molecular tumor board on comprehensive genomic profiling tests in Japan: A retrospective observational study. Cancer Med 2023; 12:6170-6181. [PMID: 36251535 PMCID: PMC10028111 DOI: 10.1002/cam4.5349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND A paradigm shift has occurred in cancer chemotherapy from tumor-specific treatment with cytotoxic agents to personalized medicine with molecular-targeted drugs. Thus, it is essential to identify genomic alterations and molecular features to recommend effective targeted molecular medicines regardless of the tumor site. Nevertheless, it takes considerable expertise to identify treatment targets from primary-sequencing data in order to provide drug recommendations. The Molecular Tumor Board (MTB) denotes a platform that integrates clinical and molecular features for clinical decisions. METHODS This study retrospectively analyses all the cases of discussion and decision at the MTB in Tohoku University Hospital and summarizes genetic alterations and treatment recommendations. RESULTS The MTB discussed 1003 comprehensive genomic profiling (CGP) tests conducted in patients with solid cancer, and the resulting rate of assessing treatment recommendations was approximately 19%. Among hundreds of genes in the CGP test, only 30 genetic alterations or biomarkers were used to make treatment recommendations. The leading biomarkers that led to treatment recommendations were tumor mutational burden-high (TMB-H) (n = 32), ERBB2 amplification (n = 24), BRAF V600E (n = 16), and BRCA1/2 alterations (n = 32). Thyroid cancer accounted for most cancer cases for which treatment recommendation was provided (81.3%), followed by non-small cell lung cancer (42.4%) and urologic cancer (31.3%). The number of tests performed for gastrointestinal cancers was high (n = 359); however, the treatment recommendations for the same were below average (13%). CONCLUSION The results of this study may be used to simplify treatment recommendations from the CGP reports and help select patients for testing, thereby increasing the accuracy of personalized medicine.
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Affiliation(s)
- Hidekazu Shirota
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Keigo Komine
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Masanobu Takahashi
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Shin Takahashi
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
| | - Eisaku Miyauchi
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hidetaka Niizuma
- Department of Pediatrics, Tohoku University School of Medicine, Sendai, Japan
| | - Hiroshi Tada
- Department of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University School of Medicine, Sendai, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko Sugiyama
- Personalized Medicine Center, Tohoku University Hospital, Sendai, Japan
| | - Maako Kawamura
- Personalized Medicine Center, Tohoku University Hospital, Sendai, Japan
| | - Jun Yasuda
- Division of Molecular Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Shuhei Suzuki
- Department of Clinical Oncology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Takeshi Iwaya
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine, Morioka, Japan
| | - Motonobu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Tsuyoshi Saito
- Department of Breast Surgery, Japanese Red Cross Saitama Hospital, Saitama, Japan
| | - Hiroyuki Shibata
- Department of Clinical Oncology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Tohoku University Hospital, Sendai, Japan
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Tsai YL, Chang CJ. Budget Impact Analysis of Comprehensive Genomic Profiling in Advanced Non-Small Cell Lung Cancer in Taiwan. Value Health Reg Issues 2023; 35:48-56. [PMID: 36863067 DOI: 10.1016/j.vhri.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 03/04/2023]
Abstract
OBJECTIVES The concept of precision oncology using genetic testing has become popular for cancer treatment in recent years. This research aimed to evaluate the financial impact of comprehensive genomic profiling (CGP) in patients with advanced non-small cell lung cancer before receiving any systemic treatments, compared with current practice using single-gene testing, in the hope that the findings can inform the National Health Insurance Administration the decision regarding CGP reimbursement. METHODS A budget impact analysis model was developed comparing the sum of gene testing costs, the first-line and subsequent systemic treatment costs, and other medical costs between the current practice of traditional molecular testing and the new test strategy of CGP. The evaluation time horizon is 5 years from the perspective of the National Health Insurance Administration. Outcome endpoints were incremental budget impact and life-year gained. RESULTS This research indicated CGP reimbursement would benefit 1072 to 1318 more patients receiving target therapies than the current practice and consequently had incremental 232 to 1844 life-years gained from 2022 to 2026. The new test strategy also led to higher gene testing cost and systemic treatment cost. Nevertheless, less medical resource utilization and better patient outcome were demonstrated. The incremental budget impact ranged from US dollar 19 to US dollar 27 million in the 5-year period. CONCLUSION This research shows that CGP could pave the way for personalized healthcare with moderate increase of National Health Insurance budget.
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Affiliation(s)
- Yi-Ling Tsai
- Department of Biomedical Science, Chang Gung University, TaoYuan, Taiwan; Roche Product, Inc, Taipei, Taiwan
| | - Chee Jen Chang
- Department of Biomedical Science, Chang Gung University, TaoYuan, Taiwan; Graduate Institute of Clinical Medical Sciences, Chang Gung University, TaoYuan, Taiwan; Research Services Center for Health Information, Chang Gung University, TaoYuan, Taiwan; Clinical Informatics and Medical Statistics Research Center, Chang Gung University, TaoYuan, Taiwan; Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital. TaoYuan, Taiwan.
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Thapa B, Ahmed G, Szabo A, Kamgar M, Kilari D, Mehdi M, Menon S, Daniel S, Thompson J, Thomas J, George B. Comprehensive genomic profiling: Does timing matter? Front Oncol 2023; 13:1025367. [PMID: 36865796 PMCID: PMC9971445 DOI: 10.3389/fonc.2023.1025367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/03/2023] [Indexed: 02/16/2023] Open
Abstract
Purpose There is variability in utilization of Comprehensive Genomic Profiling (CGP) in most of the metastatic solid tumors (MST). We evaluated the CGP utilization patterns and its impact on outcomes at an academic tertiary center. Patients and Methods Institutional database was reviewed for CGP data in adult patients with MST between 01/2012 - 04/2020. Patients were categorized based on interval between CGP and metastatic diagnosis; 3 tertiles of distribution (T1-earliest to the diagnosis, T3-furthest), and pre-mets (CGP performed prior to diagnosis of metastasis). Overall survival (OS) was estimated from the time of metastatic diagnosis with left truncation at the time of CGP. Cox regression model was used to estimate the impact of timing of CGP on survival. Results Among 1,358 patients, 710 were female, 1,109 Caucasian, 186 Afro-Americans, and 36 Hispanic. The common histologies were lung cancer (254; 19%), colorectal cancer (203; 15%), gynecologic cancers (121; 8.9%), and pancreatic cancer (106; 7.8%). Time interval between diagnosis of metastatic disease and CGP was not statistically significantly different based on sex, race and ethnicity after adjusting for histologic diagnoses with 2 exceptions - Hispanics with lung cancer had delayed CGP compared to non-Hispanics (p =0.019) and females with pancreas cancer had delayed CGP compared to males (p =0.025). Lung cancer, gastro-esophageal cancer and gynecologic malignancies had better survival if they had CGP performed during the first tertile after metastatic diagnosis. Conclusion CGP utilization across cancer types was equitable irrespective of sex, race and ethnicity. Early CGP after metastatic diagnosis might have effect on treatment delivery and clinical outcomes in cancer type with more actionable targets.
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Affiliation(s)
- Bicky Thapa
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gulrayz Ahmed
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Aniko Szabo
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI,
United States
| | - Mandana Kamgar
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Deepak Kilari
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Maahum Mehdi
- Medical School, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Smitha Menon
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Sherin Daniel
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jonathan Thompson
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - James Thomas
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ben George
- Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Ben George,
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Bou Zerdan M, Kumar PA, Zaccarini D, Ross J, Huang R, Sivapiragasam A. Molecular Targets in Salivary Gland Cancers: A Comprehensive Genomic Analysis of 118 Mucoepidermoid Carcinoma Tumors. Biomedicines 2023; 11. [PMID: 36831055 DOI: 10.3390/biomedicines11020519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/24/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023] Open
Abstract
INTRODUCTION Salivary gland carcinomas (SGC) are histologically diverse cancers and next-generation sequencing (NGS) to identify key molecular targets is an important aspect in the management of advanced cases. METHODS DNA was extracted from paraffin embedded tissues of advanced SGC and comprehensive genomic profiling (CGP) was carried out to evaluate for base substitutions, short insertions, deletions, copy number changes, gene fusions and rearrangements. Tumor mutation burden (TMB) was calculated on approximately 1.25 Mb. Some 324 genes in the FoundationOne CDX panel were analyzed. RESULTS Mucoepidermoid carcinoma (MECa) mutations were assessed. CDKN2A and CDKN2B GA were common in mucoepidermoid carcinoma (MECa) (52.5 and 30.5%). PIK3CA was also common in MECa (16.9%). ERBB2 amplification/short variants (amp/SV) were found in MECa (5.9/0%). HRAS GA was common in MECa (14.4%) as well. Other targets, including BAP1, PTEN, and KRAS, were noted but had a low incidence. In terms of immunotherapy (IO)-predictive markers, TMB > 10 was more common in MECa (16.9%). PDL1 high was also seen in MECa (4.20%). CONCLUSION SGC are rare tumors with no FDA-approved treatment options. This large dataset reveals many opportunities for IO and targeted therapy contributing to the continuously increased precision in the selection of treatment for these patients.
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Takeshita K, Hijioka S, Nagashio Y, Maruki Y, Kawasaki Y, Maehara K, Murashima Y, Okada M, Ikeda G, Yamada N, Takasaki T, Agarie D, Hara H, Hagiwara Y, Okamoto K, Yamashige D, Ohba A, Kondo S, Morizane C, Ueno H, Saito Y, Ohe Y, Okusaka T. Diagnostic Ability of Endoscopic Ultrasound-Guided Tissue Acquisition Using 19-Gauge Fine-Needle Biopsy Needle for Abdominal Lesions. Diagnostics (Basel) 2023; 13:diagnostics13030450. [PMID: 36766558 PMCID: PMC9914510 DOI: 10.3390/diagnostics13030450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Attempts at performing endoscopic ultrasound-guided tissue acquisition (EUS-TA) with a 19G needle are increasing because histological diagnosis and comprehensive genomic profiling are a necessity. However, the diagnostic ability of the 19G fine-needle biopsy (FNB) needle, especially the third-generation FNB needle, is unclear and has been retrospectively reviewed. The 19G TopGain needle was used in 147 patients and 160 lesions between September 2020 and December 2021. The technical success rate of the biopsies was 99.4% (159/160). The early adverse event rate was 4.1% (6/147), and moderate or severe adverse event rate occurrence was 2.0% (3/147). The sensitivity, specificity, and accuracy of the 19G TopGain needle for 157 lesions with a confirmed diagnosis were 96.7%, 100%, and 96.8%, respectively. Rescue EUS-TA using the 19G TopGain needle was performed for nine lesions, and a successful diagnosis was made in six of these lesions (66.7%). The diagnostic ability of EUS-TA using the third-generation 19G TopGain needle was favorable. However, the use of 19G FNB needles may increase adverse events. Therefore, EUS-TA with a 19G FNB needle is mainly indicated in lesions where comprehensive genomic profiling may be necessary or the diagnosis could not be determined via EUS-TA using the 22G needle.
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Affiliation(s)
- Kotaro Takeshita
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
- Cancer Medicine, Jikei University Graduate School of Medicine, Tokyo 105-0003, Japan
| | - Susumu Hijioka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
- Correspondence: ; Tel.: +81-3-3542-2511
| | - Yoshikuni Nagashio
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuta Maruki
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Kawasaki
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Kosuke Maehara
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yumi Murashima
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Mao Okada
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Go Ikeda
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Natsumi Yamada
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Tetsuro Takasaki
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Daiki Agarie
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hidenobu Hara
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuya Hagiwara
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Kohei Okamoto
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Daiki Yamashige
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Akihiro Ohba
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Shunsuke Kondo
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Chigusa Morizane
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Hideki Ueno
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuichiro Ohe
- Cancer Medicine, Jikei University Graduate School of Medicine, Tokyo 105-0003, Japan
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
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Ishido S, Tsuchiya K, Kano Y, Yasui Y, Takaura K, Uchihara N, Suzuki K, Tanaka Y, Miyamoto H, Yamada M, Matsumoto H, Nobusawa T, Keitoku T, Tanaka S, Maeyashiki C, Tamaki N, Takahashi Y, Nakanishi H, Sakurai U, Asahina Y, Okamoto R, Kurosaki M, Izumi N. Clinical Utility of Comprehensive Genomic Profiling in Patients with Unresectable Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:cancers15030719. [PMID: 36765676 PMCID: PMC9913078 DOI: 10.3390/cancers15030719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/16/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023] Open
Abstract
The molecular mechanism of hepatocellular carcinoma (HCC) is partially demonstrated. Moreover, in the patients receiving multiple molecular-targeted therapies, the gene alternations are still unknown. Six molecular-targeted therapies of unresectable HCC (uHCC) and comprehensive genomic profiling (CGP) have been approved in clinical practice. Hence, the utility of CGP in patients with uHCC treated with multiple molecular-targeted agents is investigated. The data of the patients with uHCC who received CGP tests were collected, retrospectively, between February 2021 and May 2022. Gene alterations detected by foundation testing, excluding variants of unknown significance, were reported in all nine patients. The samples for CGP were derived from liver tumor biopsy (n = 2), surgical specimens of bone metastases (n = 2), and blood (n = 5). The median number of systemic therapies was four. Seven patients were candidates eligible for clinical trials. One patient with a high tumor mutation burden (TMB) could receive pembrolizumab after CGP. This study presented genomic alternations after receiving multiple molecular-targeted therapies. However, further investigation needs to be conducted to develop personalized therapies and invent newer agents for treating HCC.
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Affiliation(s)
- Shun Ishido
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Tsuchiya
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Yoshihito Kano
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
- Department of Clinical Oncology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Yutaka Yasui
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Kenta Takaura
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Naoki Uchihara
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Keito Suzuki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Yuki Tanaka
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Haruka Miyamoto
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Michiko Yamada
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroaki Matsumoto
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tsubasa Nobusawa
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Taisei Keitoku
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shohei Tanaka
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Chiaki Maeyashiki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Nobuharu Tamaki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Yuka Takahashi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Hiroyuki Nakanishi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Urara Sakurai
- Department of Pathology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
| | - Yasuhiro Asahina
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Ryuichi Okamoto
- Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Masayuki Kurosaki
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Correspondence: (M.K.); (N.I.); Tel.: +81-422-32-3111 (M.K. & N.I.); Fax: +81-422-32-9551 (M.K. & N.I.)
| | - Namiki Izumi
- Department of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo 180-8610, Japan
- Correspondence: (M.K.); (N.I.); Tel.: +81-422-32-3111 (M.K. & N.I.); Fax: +81-422-32-9551 (M.K. & N.I.)
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34
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Severson EA, Haberberger J, Hemmerich A, Huang RSP, Edgerly C, Schiavone K, Najafian A, Hiemenz M, Lechpammer M, Vergilio JA, Lesser G, Strowd R, Elvin J, Ross JS, Hegde P, Alexander B, Singer S, Ramkissoon S. Genomic Profiling Reveals Differences in Primary Central Nervous System Lymphoma and Large B-Cell Lymphoma, With Subtyping Suggesting Sensitivity to BTK Inhibition. Oncologist 2023; 28:e26-e35. [PMID: 36342081 PMCID: PMC9847534 DOI: 10.1093/oncolo/oyac190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND B-cell primary central nervous system (CNS) lymphoma (PCL) is diffuse large B-cell lymphoma (DLBCL) confined to the CNS. Less than 50% of patients with PCL achieve complete remission with current therapies. We describe the findings from comprehensive genomic profiling (CGP) of a cohort of 69 patients with PCL, 36 cases of secondary CNS lymphoma (SCL), and 969 cases of DLBCL to highlight their differences and characterize the PCL cohort. In addition, we highlight the differences in frequency of germinal center B-cell like (GCB) and non-GCB subtypes and molecular subtypes, particularly MCD and EZH subtypes, between PCL and DLBCL. MATERIALS AND METHODS Sixty-nine cases of B-cell PCL, 36 cases of secondary CNS lymphoma (SCL), and 969 cases of DLBCL were evaluated by CGP of 405 genes via DNAseq and 265 genes via RNAseq for fusions (FoundationOne Heme). Tumor mutational burden (TMB) was calculated from 1.23 Mb of sequenced DNA. RESULTS Genomic alterations with significant differences between PCL and DLBCL included MYD88, ETV6, PIM1, PRDM1, CXCR4, TP53, and CREBBP, while only MYD88 was significantly different between SCL and DLBCL. PCL cases were significantly enriched for the MCD molecular subtypes, which have an excellent response to BTKi. We report a patient with a durable complete response to BTKi consistent with their genomic profile. EBV status, CD274 amplification, and TMB status suggest that 38% of PCL patients may benefit from ICPI; however further study is warranted. CONCLUSION CGP of PCLs reveals biomarkers, genomic alterations, and molecular classifications predictive of BTKi efficacy and potential ICPI efficacy. Given the limitations of standard of care for PCL, CGP is critical to identify potential therapeutic approaches for patients in this rare form of lymphoma.
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Affiliation(s)
- Eric A Severson
- Corresponding author: Eric Severson, MD, PhD, 7010 Kit Creek Road, Morrisville, NC 27560, USA. Tel: +1 919 748 5886; E-mail:
| | | | | | | | | | | | | | | | | | | | - Glenn Lesser
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Roy Strowd
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | | | | | | | - Samuel Singer
- Hackensack University Medical Center, Hackensack, NJ, USA
| | - Shakti Ramkissoon
- Foundation Medicine, Morrisville, NC, USA,Wake Forest Baptist Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, USA
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35
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Kage H, Shinozaki-Ushiku A, Ishigaki K, Sato Y, Tanabe M, Tanaka S, Tanikawa M, Watanabe K, Kato S, Akagi K, Uchino K, Mitani K, Takahashi S, Miura Y, Ikeda S, Kojima Y, Watanabe K, Mochizuki H, Yamaguchi H, Kawazoe Y, Kashiwabara K, Kohsaka S, Tatsuno K, Ushiku T, Ohe K, Yatomi Y, Seto Y, Aburatani H, Mano H, Miyagawa K, Oda K. Clinical utility of Todai OncoPanel in the setting of approved comprehensive cancer genomic profiling tests in Japan. Cancer Sci 2023; 114:1710-1717. [PMID: 36601953 PMCID: PMC10067384 DOI: 10.1111/cas.15717] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 11/22/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Comprehensive cancer genome profiling (CGP) has been nationally reimbursed in Japan since June 2019. Less than 10% of the patients have been reported to undergo recommended treatment. Todai OncoPanel (TOP) is a dual DNA-RNA panel as well as a paired tumor-normal matched test. Two hundred patients underwent TOP as part of Advanced Medical Care B with approval from the Ministry of Health, Labour and Welfare between September 2018 and December 2019. Tests were carried out in patients with cancers without standard treatment or when patients had already undergone standard treatment. Data from DNA and RNA panels were analyzed in 198 and 191 patients, respectively. The percentage of patients who were given therapeutic or diagnostic recommendations was 61% (120/198). One hundred and four samples (53%) harbored gene alterations that were detected with the DNA panel and had potential treatment implications, and 14 samples (7%) had a high tumor mutational burden. Twenty-two samples (11.1%) harbored 30 fusion transcripts or MET exon 14 skipping that were detected by the RNA panel. Of those 30 transcripts, 6 had treatment implications and 4 had diagnostic implications. Thirteen patients (7%) were found to have pathogenic or likely pathogenic germline variants and genetic counseling was recommended. Overall, 12 patients (6%) received recommended treatment. In summary, patients benefited from both TOP DNA and RNA panels while following the same indication as the approved CGP tests. (UMIN000033647).
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Affiliation(s)
- Hidenori Kage
- Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aya Shinozaki-Ushiku
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazunaga Ishigaki
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Chemotherapy, The University of Tokyo Hospital, Tokyo, Japan
| | - Yusuke Sato
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiko Tanabe
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Gynecology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Kousuke Watanabe
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Clinical Laboratory, The University Tokyo Hospital, Tokyo, Japan
| | - Shingo Kato
- Department of Clinical Cancer Genomics, Yokohama City University Hospital, Kanagawa, Japan
| | - Kiwamu Akagi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Keita Uchino
- Department of Medical Oncology, NTT Medical Center Tokyo, Tokyo, Japan
| | - Kinuko Mitani
- Department of Hematology and Oncology, Dokkyo Medical University, Tochigi, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuji Miura
- Department of Medical Oncology and Clinical Genetics Center, Toranomon Hospital, Tokyo, Japan.,Clinical Genetics Center, Toranomon Hospital, Tokyo, Japan
| | - Sadakatsu Ikeda
- Department of Precision Cancer Medicine, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Yasushi Kojima
- Department of Gastroenterology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyotaka Watanabe
- Department of Medicine, School of Medicine, Teikyo University, Tokyo, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Yamanashi, Japan
| | - Hironori Yamaguchi
- Department of Clinical Oncology, Jichi Medical University Hospital, Tochigi, Japan
| | - Yoshimasa Kawazoe
- Department of Artificial Intelligence in Healthcare, The University of Tokyo, Tokyo, Japan.,Department of Healthcare Information Management, The University of Tokyo Hospital, Tokyo, Japan
| | - Kosuke Kashiwabara
- Clinical Research Promotion Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science and Medicine Laboratory, RCAST, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Ohe
- Department of Healthcare Information Management, The University of Tokyo Hospital, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory, The University Tokyo Hospital, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science and Medicine Laboratory, RCAST, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Oda
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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36
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Peleg Hasson S, Hershkovitz D, Adar L, Brezis M, Shachar E, Aks R, Galmor L, Raviv Y, Ben Neriah S, Merimsky O, Sabo E, Wolf I, Safra T. Implementation of Comprehensive Genomic Profiling in Ovarian Cancer Patients: A Retrospective Analysis. Cancers (Basel) 2022; 15. [PMID: 36612212 DOI: 10.3390/cancers15010218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022] Open
Abstract
Comprehensive genomic profiling (CGP) allows for the detection of driver alterations at high resolution, but the limited number of approved targeted therapies and their high costs have contributed to its limited clinical utilization. We retrospectively compared data of 946 women with ovarian cancer (11.4% were referred to CGP, and 88.6% served as control) to examine whether CGP provides a prognosis benefit. Patient baseline parameters were similar between the groups. Cox regression analysis adjusted for age, disease stage at diagnosis, and recurrence status showed statistically significantly longer median overall survival (mOS) in the CGP group versus the control (73.4 versus 54.5 months, p < 0.001). Fifty-four patients (52.9%) had actionable mutations with potential treatments; twenty-six (48.2%) were treated with matched targeted therapy, showing a trend for longer mOS than the eighty-six women in the CGP group who were not given a suggested treatment (105.5 versus 63.6 months, p = 0.066). None of the genomic alterations predicted metastasis location. CCNE1 amplification and KRAS mutations were associated with shorter mOS. Patients with tumor mutation burden ≥4 mutations/megabase had longer mOS. High loss of heterozygosity was associated with longer mOS (99.0 versus 48.2 months, p = 0.004). CGP testing may provide both prognostic and predictive insights for treatment of patients with ovarian cancer. Prospective studies of larger cohorts are warranted.
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Necchi A, Spiess PE, Bandini M, Basile G, Grivas P, Bratslavsky G, Jacob J, Danziger N, Lin D, Decker B, Sokol ES, Huang RSP, Kulkarni SB, Ross JS. Advanced Squamous Cell Carcinomas of the Pelvic and Perineal Region: A Comprehensive Genomic Profiling Study. Oncologist 2022; 27:1016-1024. [PMID: 35881043 DOI: 10.1093/oncolo/oyac144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/24/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Advanced pelvic squamous cell carcinoma (pSCC) is a broad category of cancers affecting different pelvic organs and usually featuring unfavorable clinical outcomes. Thus, we aimed to assess genomic differences among pSCC cases and learn whether pSCC could potentially benefit from targeted therapies and/or immunotherapy. MATERIALS AND METHODS A total of 1917 advanced pSCCs, including penile (penSCC), male urethral (murthSCC), male anal (manSCC), female urethral (furthSCC), vulvar (vulSCC), cervical (crvSCC), female anal (fanSCC), and vaginal (vagSCC), underwent comprehensive genomic profiling (CGP). We used hybrid capture-based CGP to evaluate recurrent genomic alterations (GAs). Tumor mutational burden (TMB) was determined on up to 1.1 Mb of sequenced DNA and microsatellite instability (MSI) was determined on up to 95 loci. Programmed cell-death-ligand-1 (PD-L1) expression was determined by immunohistochemistry (IHC; Dako 22C3). RESULTS PIK3CA was the most frequently identified potentially "actionable" GA (22%-43%), followed by mTOR pathway [PTEN (0%-18%), FBXW7 (7%-29%)], and cell-cycle GAs. DNA-damage response (DDR) GAs and receptor-tyrosine kinase (RTK) targeted options were uncommon. NOTCH1 GAs were present in >15% of penSCC and vulvSCC. TMB ≥10 mut/Mb was >15% in manSCC, fanSCC, crvSCC, and vagSCC. PD-L1 high expression was >18% in all pSCC except urthSCC, manSCC, and vagSCC. HPV-16/18 detection was highest in manSCC, fanSCC, and crvSCC. CONCLUSION Despite similar histology, pSCCs can differ in GAs and HPV status. Overall, PIK3CA is the most frequent potentially "targetable" GA followed by mTOR and cell cycle pathway. RTK and DDR GAs are rare in pSCC. Immunotherapy could be considered for pSCC management based on TMB and PD-L1 expression.
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Affiliation(s)
- Andrea Necchi
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | | | - Marco Bandini
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Giuseppe Basile
- IRCCS San Raffaele Hospital and Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Petros Grivas
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Joseph Jacob
- SUNY Upstate Medical University, Syracuse, NY, USA
| | | | - Douglas Lin
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | | | | | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA.,SUNY Upstate Medical University, Syracuse, NY, USA
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Okazawa-Sakai M, Yamamoto Y, Futagawa M, Okamura M, Miyawaki S, Nishina T, Takehara K, Kozuki T, Tomida S, Hyodo I, Ohsumi S, Hirasawa A. Handling of Germline Findings in Clinical Comprehensive Cancer Genomic Profiling. Acta Med Okayama 2022; 76:673-678. [PMID: 36549769 DOI: 10.18926/amo/64117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Patients found to have presumed germline pathogenic variants (PGPVs) during comprehensive genomic profiling (CGP) require genetic counseling (GC) referrals. We retrospectively investigated the outcomes of patients with PGPVs. Among 159 patients who underwent CGP, we recommended GC for the 16 patients with PGPVs (3 with [FG group] and 13 without [G Group] a family/personal history of hereditary cancer) as well as for the 8 patients with no PGPVs, but a history (F group); 2 (67%), 5 (38%), and 3 (38%) patients received GC in the FG, G, and F groups, respectively. Germline testing results were positive in 1 and 2 patients of the FG and G groups, respectively. Among the patients recommended for GC, 58% did not receive GC due to lack of interest, poor performance status, or death. CGP contributes to the identification of germline variants in patients without a history of hereditary cancer. However, the proportion of patients who undergo GC should be improved.
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Affiliation(s)
- Mika Okazawa-Sakai
- Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences.,Department of Gynecologic Oncology, National Hospital Organization Shikoku Cancer Center.,Department of Cancer Genomic Medicine, National Hospital Organization Shikoku Cancer Center
| | - Yasuko Yamamoto
- Department of Cancer Genomic Medicine, National Hospital Organization Shikoku Cancer Center.,Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Mashu Futagawa
- Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
| | - Miki Okamura
- Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Satoko Miyawaki
- Department of Cancer Genomic Medicine, National Hospital Organization Shikoku Cancer Center.,Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Tomohiro Nishina
- Department of Cancer Genomic Medicine, National Hospital Organization Shikoku Cancer Center.,Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Kazuhiro Takehara
- Department of Gynecologic Oncology, National Hospital Organization Shikoku Cancer Center.,Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Toshiyuki Kozuki
- Department of Clinical Research Center, National Hospital Organization Shikoku Cancer Center
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Ichinosuke Hyodo
- Department of Cancer Genomic Medicine, National Hospital Organization Shikoku Cancer Center
| | - Shozo Ohsumi
- Department of Hereditary Tumors, National Hospital Organization Shikoku Cancer Center
| | - Akira Hirasawa
- Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences
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40
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Ida H, Koyama T, Mizuno T, Sunami K, Kubo T, Sudo K, Tao K, Hirata M, Yonemori K, Kato K, Okusaka T, Ohe Y, Matsui Y, Yamazaki N, Ogawa C, Kawai A, Narita Y, Esaki M, Yamamoto N. Clinical utility of comprehensive genomic profiling tests for advanced or metastatic solid tumor in clinical practice. Cancer Sci 2022; 113:4300-4310. [PMID: 36106376 DOI: 10.1111/cas.15586] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/15/2022] Open
Abstract
Previous clinical trials indicate that 10%-25% of patients received genomically matched therapy after comprehensive genomic profiling (CGP) tests. However, the clinical utility of CGP tests has not been assessed in clinical practice. We assessed the clinical utility of CGP tests for advanced or metastatic solid tumor and determined the proportion of patients receiving genomically matched therapy among those with common and non-common cancers. From August 2019 to July 2020, a total of 418 patients had undergone CGP tests, and the results were discussed through the molecular tumor board at our site. The median age of patients was 57 (range: 3-86) years. Colorectal cancer was the most common, with 47 (11%) patients. Actionable genomic alterations (median 3, range: 1-17) were identified in 368 (88.0%) of 418 patients. Druggable genomic alterations were determined in 196 (46.9%) of 418 patients through the molecular tumor board. Genomically matched therapy was administered as the subsequent line of therapy in 51 (12.2%) patients, which is comparable to the proportion we previously reported in a clinical trial (13.4%) (p = 0.6919). The proportion of patients receiving genomically matched therapy was significantly higher among those with common cancers (16.2%) than non-common cancers (9.4%) (p = 0.0365). Genomically matched therapy after the CGP tests was administered to 12.2% of patients, which is similar to the proportion reported in the previous clinical trials. The clinical utility of CGP tests in patients with common cancers greatly exceeded that in patients with non-common cancers.
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Affiliation(s)
- Hanae Ida
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Takaaki Mizuno
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kubo
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuki Sudo
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan.,Department of Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kayoko Tao
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Kan Yonemori
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan.,Department of Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan.,Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiyuki Matsui
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Naoya Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Chitose Ogawa
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology and Rehabilitation, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshitaka Narita
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Minoru Esaki
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Noboru Yamamoto
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan.,Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
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41
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Lopes-Brás R, Lopez-Presa D, Esperança-Martins M, Melo-Alvim C, Gallego L, Costa L, Fernandes I. Genomic Profiling of Sarcomas: A Promising Weapon in the Therapeutic Arsenal. Int J Mol Sci 2022; 23. [PMID: 36430703 DOI: 10.3390/ijms232214227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Sarcomas are rare malignant mesenchymal neoplasms, and the knowledge of tumor biology and genomics is scarce. Chemotherapy is the standard of care in advanced disease, with poor outcomes. Identifying actionable genomic alterations may offer effective salvage therapeutic options when previous lines have failed. Here, we report a retrospective cohort study of sarcoma patients followed at our center and submitted to comprehensive genomic profiling between January 2020 and June 2021. Thirty patients were included, most (96.7%) with reportable genomic alterations. The most common alterations were linked to cell cycle regulation (TP53, CDKN2A/B, and RB1 deletions and CDK4, MDM2, and MYC amplifications). Most patients (96.7%) had microsatellite stability and low tumor mutational burden (≤10 muts/megabase (Mb); median 2 Muts/Mb). Two-thirds of patients had actionable mutations for targeted treatments, including five cases with alterations amenable to targeted therapies with clinical benefit within the patient's tumor type, ten cases with targetable alterations with clinical benefit in other tumor types, and five cases with alterations amenable to targeting with drugs under investigation in a clinical trial setting. A significant proportion of cases in this study had actionable genomic alterations with available targeted drugs. Next-generation sequencing is a feasible option for identifying molecular drivers that can provide therapeutic options for individual patients. Molecular Tumor Boards should be implemented in the clinical practice to discuss genomic findings and inform clinically relevant targeted therapies.
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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barbar J, Armach M, Hodroj MH, Assi S, El Nakib C, Chamseddine N, Assi HI. Emerging genetic biomarkers in lung adenocarcinoma. SAGE Open Med 2022; 10:20503121221132352. [PMID: 36277445 PMCID: PMC9583216 DOI: 10.1177/20503121221132352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Comprehensive genomic profiling is a next-generation sequencing approach used to
detect several known and emerging genomic alterations. Many genomic variants
detected by comprehensive genomic profiling have become recognized as
significant cancer biomarkers, leading to the development of major clinical
trials. Lung adenocarcinoma has become one of the most targeted cancers for
genomic profiling with a series of actionable mutations such as EGFR, KRAS,
HER2, BRAF, FGFR, MET, ALK, and many others. The importance of these mutations
lies in establishing targeted therapies that significantly change the outcome in
lung adenocarcinoma besides the prognostic value of some mutations. This review
sheds light on the development of the comprehensive genomic profiling field,
mainly lung adenocarcinoma, and discusses the role of a group of mutations in
this disease.
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Affiliation(s)
- Jawad Barbar
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon
| | - Maria Armach
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon
| | - Mohammad Hassan Hodroj
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon
| | - Sahar Assi
- Department of Internal Medicine,
American University of Beirut Medical Center, Beirut, Lebanon
| | - Clara El Nakib
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon
| | - Nathalie Chamseddine
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon
| | - Hazem I Assi
- Department of Internal Medicine,
Division of Hematology and Oncology, Naef K. Basile Cancer Institute, American
University of Beirut Medical Center, Beirut, Lebanon,Hazem I Assi, Department of Internal
Medicine, Division of Hematology and Oncology, Naef K. Basile Cancer Institute,
American University of Beirut Medical Center, P.O. Box: 11-0236, Riad El Solh,
Beirut 1107 2020, Lebanon.
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Zimmerman R, Bilen MA, Heath EI, Nandagopal L, Swami U, Kessel A, Jaeger E, Wesolowski S, Hernanadez EJ, Chipman J, Mack A, Ravindranathan D, Maughan BL, Nussenzveig R, Yandell M, Kohli M, Lilly MB, Sartor AO, Agarwal N, Barata PC. Comprehensive Genomic Profiling of Cell-Free DNA in Men With Advanced Prostate Cancer: Differences in Genomic Landscape Based on Race. Oncologist 2022; 27:e815-e818. [PMID: 36036607 PMCID: PMC9526493 DOI: 10.1093/oncolo/oyac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Advanced prostate cancer (aPC) in Black men was reported to present with aggressive features and to be associated with poor prognosis. Herein, we compared the cell-free DNA (cfDNA) genomic landscape of aPC in Black vs White men. Patients (pts) with aPC from 6 academic institutions and available cfDNA comprehensive genomic profiling (CGP) were included. Association between mutated genes and race was evaluated using Barnard’s test and a Probabilistic Graphical Model (PGM) machine learning approach. Analysis included 743 aPC pts (217 Black, 526 White) with available cfDNA CGP. The frequency of alterations in the androgen receptor gene was significantly higher in Black vs White men (55.3% vs 35% respectively, P < .001). Additionally, alterations in EGFR, MYC, FGFR1, and CTNNB1 were present at higher frequencies in Black men. PGM analysis and Barnard’s test were concordant. Findings from the largest cohort of Black men with aPC undergoing cfDNA CGP may guide further drug development in these men.
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Affiliation(s)
- Raquel Zimmerman
- University of Utah School of Medicine, Salt Lake City, UT, USA.,Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Mehmet A Bilen
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.,Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Elisabeth I Heath
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Umang Swami
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Adam Kessel
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Ellen Jaeger
- Deming Department of Medicine, Section of Hematology/Oncology, Tulane University Medical School, New Orleans, LA, USA
| | | | - Edgar J Hernanadez
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | | | - Alleda Mack
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Deepak Ravindranathan
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | | | | | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Manish Kohli
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael B Lilly
- Medical University of South Carolina Hollings Cancer Center, Charleston, SC, USA
| | - A Oliver Sartor
- Deming Department of Medicine, Section of Hematology/Oncology, Tulane University Medical School, New Orleans, LA, USA
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Pedro C Barata
- Deming Department of Medicine, Section of Hematology/Oncology, Tulane University Medical School, New Orleans, LA, USA
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Imai M, Nakamura Y, Sunami K, Kage H, Komine K, Koyama T, Amano T, Ennishi D, Kanai M, Kenmotsu H, Maeda T, Morita S, Sakai D, Bando H, Makiyama A, Suzuki T, Hirata M, Kohsaka S, Tsuchihara K, Naito Y, Yoshino T. Expert Panel Consensus Recommendations on the Use of Circulating Tumor DNA Assays for Patients with Advanced Solid Tumors. Cancer Sci 2022; 113:3646-3656. [PMID: 35876224 PMCID: PMC9633310 DOI: 10.1111/cas.15504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 12/01/2022] Open
Abstract
Comprehensive genomic profiling is increasingly used to facilitate precision oncology based on molecular stratification. In addition to conventional tissue comprehensive genomic profiling, comprehensive genomic profiling of circulating tumor DNA has become widely utilized in cancer care owing on its advantages, including less invasiveness, rapid turnaround time, and capturing heterogeneity. However, circulating tumor DNA comprehensive genomic profiling has some limitations, mainly false negatives due to low levels of plasma circulating tumor deoxyribonucleic acid and false positives caused by clonal hematopoiesis. Nevertheless, no guidelines and recommendations fully address these issues. Here, an expert panel committee involving representatives from 12 Designated Core Hospitals for Cancer Genomic Medicine in Japan was organized to develop expert consensus recommendations for the use of circulating tumor deoxyribonucleic acid‐based comprehensive genomic profiling. The aim was to generate guidelines for clinicians and allied healthcare professionals on the optimal use of the circulating tumor DNA assays in advanced solid tumors and to aid the design of future clinical trials that utilize and develop circulating tumor DNA assays to refine precision oncology. Fourteen clinical questions regarding circulating tumor deoxyribonucleic acid comprehensive genomic profiling including the timing of testing and considerations for interpreting results were established by searching and curating associated literatures, and corresponding recommendations were prepared based on the literature for each clinical question. Final consensus recommendations were developed by voting to determine the level of each recommendation by the Committee members.
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Affiliation(s)
- Mitsuho Imai
- Translational Research Support Section, National Cancer Center Hospital East.,Genomics Unit, Keio University School of Medicine
| | - Yoshiaki Nakamura
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital
| | - Hidenori Kage
- Department of Next-Generation Precision Medicine Development Laboratory, Graduate School of Medicine, The University of Tokyo
| | - Keigo Komine
- Department of Medical Oncology, Tohoku University Hospital
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital
| | - Toraji Amano
- Clinical Research and Medical Innovation Center, Hokkaido University Hospital
| | - Daisuke Ennishi
- Center for Comprehensive Genomic Medicine, Okayama University Hospital
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University
| | | | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences
| | - Sachi Morita
- Department of Clinical Oncology and Chemotherapy, Nagoya University Hospital
| | - Daisuke Sakai
- Center for Cancer Genomics and Personalized Medicine, Osaka University Hospital
| | - Hideaki Bando
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
| | | | - Tatsuya Suzuki
- Department of Hematology, National Cancer Center Hospital
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute
| | - Katsuya Tsuchihara
- Division of Translational Informatics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Japan
| | - Yoichi Naito
- Department of General Internal medicine/Experimental Therapeutics/Medical Oncology, National Cancer Center Hospital East
| | - Takayuki Yoshino
- Translational Research Support Section, National Cancer Center Hospital East.,Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East
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46
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Olsen S, Liao J, Hayashi H. 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; 29:4811-26. [PMID: 35877242 DOI: 10.3390/curroncol29070382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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47
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Ashok Kumar P, Graziano SL, Danziger N, Pavlick D, Severson EA, Ramkissoon SH, Huang RSP, Decker B, Ross JS. Genomic landscape of non-small-cell lung cancer with methylthioadenosine phosphorylase (MTAP) deficiency. Cancer Med 2022; 12:1157-1166. [PMID: 35747993 PMCID: PMC9883541 DOI: 10.1002/cam4.4971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/08/2022] [Accepted: 06/10/2022] [Indexed: 02/02/2023] Open
Abstract
INTRODUCTION New treatment strategies for advanced non-small-cell lung carcinoma (NSCLC) include synthetic lethality targets focused on protein arginine methyl transferases such as PRMT5 that exploit the impact of genomic loss of methylthioadenosine phosphorylase (MTAP). METHODS Twenty nine thousand three hundred seventy nine advanced NSCLC cases underwent hybrid-capture based comprehensive genomic profiling between June 1, 2018 and May 31, 2020. PD-L1 expression was determined by immunohistochemistry (Dako 22C3 PharmDx assay). RESULTS 13.4% (3928/29,379) NSCLC cases exhibited MTAP loss distributed in adenocarcinoma (59%), squamous cell carcinoma (22%), NSCLC not otherwise specified (16%), and 1% each for large-cell neuroendocrine, sarcomatoid, and adenosquamous carcinoma. Statistically significant differences in mitogenic driver alterations included more KRAS G12C mutations in MTAP-intact versus MTAP-lost (12% vs. 10%, p = 0.0003) and fewer EGFR short variant mutations in MTAP-intact versus MTAP-lost NSCLC (10% vs. 13%, p < 0.0001). Statistically significant differences in currently untargetable genomic alterations included higher frequencies of TP53 (70% vs. 63%, p < 0.0001) and RB1 inactivation (10% vs. 2%, p < 0.0001) in MTAP-intact compared to MTAP-lost NSCLC. SMARCA4 inactivation (7% vs. 10%, p < 0.0001) was less frequent in MTAP-intact versus MTAP-lost NSCLC. Alterations in ERBB2, MET, ALK, ROS1, and NTRK1 did not significantly differ between the two groups. Predictors of immunotherapy efficacy were higher in MTAP-intact versus MTAP-lost NSCLC including tumor mutational burden (9.4 vs. 8.6 mut/Mb, p = 0.001) and low (30% vs. 28%, p = 0.01) and high PD-L1 (32% vs. 30%, p = 0.01) expression. Alterations in biomarkers potentially predictive of immune checkpoint inhibitor resistance (STK11, KEAP1, and MDM2) were similar in the two groups. CONCLUSIONS MTAP loss occurs in 13% of NSCLC, supporting the development of targeted therapies to exploit PRMT5 hyper-dependence. MTAP loss is accompanied by small differences in targeted and immunotherapy options which may impact future combination strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jeffrey S. Ross
- Upstate Cancer CenterUpstate Medical UniversitySyracuseNew YorkUSA,Foundation MedicineCambridgeMassachusettsUSA
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48
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Williams EA, Montesion M, Lincoln V, Tse JY, Hiemenz MC, Mata DA, Shah BB, Shoroye A, Alexander BM, Werth AJ, Foley-Peres K, Milante RR, Ross JS, Ramkissoon SH, Williams KJ, Adhikari LJ, Zuna RE, LeBoit PE, Lin DI, Elvin JA. HPV51-associated Leiomyosarcoma: A Novel Class of TP53/RB1-Wildtype Tumor With Predilection for the Female Lower Reproductive Tract. Am J Surg Pathol 2022; 46:729-741. [PMID: 35034043 PMCID: PMC9093731 DOI: 10.1097/pas.0000000000001862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Inactivating mutations in tumor suppressor genes TP53 and RB1 are considered central drivers in leiomyosarcomas (LMSs). In high-risk human papillomavirus (HPV)-related tumors, a similar functional outcome is achieved through oncoproteins E6 and E7, which inactivate the p53 and RB1 proteins, respectively. Here, we hypothesized that HPV infection could provide an alternative mechanism for tumorigenesis in a subset of TP53/RB1-wildtype LMS. We evaluated tumor samples from 2585 consecutive unique patients carrying a diagnosis of gynecologic or soft tissue LMS. Tumor DNA and available RNA were analyzed by hybrid-capture-based next-generation sequencing/comprehensive genomic profiling of 406 genes and transcripts (FoundationOneHeme). Of the initial 2585 cases, we excluded 16 based on the presence of molecular alterations that are considered defining for sarcomas other than LMS. In the remaining 2569 cases, we searched for LMS that were TP53/RB1-wildtype (n=486 of 2569; 18.9%). We also searched LMS tumors for HPV sequences that we then classified into genotypes by de novo assembly of nonhuman sequencing reads followed by alignment to the RefSeq database. Among TP53/RB1-wildtype LMS, we identified 18 unique cases harboring HPV sequences. Surprisingly, most (n=11) were HPV51-positive, and these 11 represented all HPV51-positive tumors in our entire LMS database (n=11 of 2569; 0.4%). The absence of genomic alterations in TP53 or RB1 in HPV51-positive LMS represented a marked difference from HPV51-negative LMS (n=2558; 0% vs. 72% [P<0.00001], 0% vs. 53% [P=0.0002]). In addition, compared with HPV51-negative LMS, HPV51-positive LMS were significantly enriched for genomic alterations in ATRX (55% vs. 24%, P=0.027) and TSC1 (18% vs. 0.6%, P=0.0047). All HPV51-positive LMS were in women; median age was 54 years at surgery (range: 23 to 74 y). All known primary sites were from the gynecologic tract or adjacent anogenital area, including 5 cases of vaginal primary site. Histology was heterogeneous, with evaluable cases showing predominant epithelioid (n=5) and spindle (n=5) morphology. In situ hybridization confirmed the presence of high-risk HPV E6/E7 mRNA in tumor cells in three of three evaluable cases harboring HPV51 genomic sequences. Overall, in our pan-LMS analysis, HPV reads were identified in a subset of TP53/RB1-wildtype LMS. For all HPV51-associated LMS, the striking absence of any detectable TP53 or RB1 mutations and predilection for the female lower reproductive tract supports our hypothesis that high-risk HPV can be an alternative tumorigenic mechanism in this distinct class of LMS.
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Affiliation(s)
- Erik A. Williams
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
- Foundation Medicine Inc., Cambridge
| | | | - Vadim Lincoln
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
| | | | | | | | | | | | | | - Adrienne J. Werth
- Department of Women’s Health Services, Hartford Hospital, Hartford, CT
| | | | - Riza R. Milante
- Department of Dermatology, Jose R. Reyes Memorial Medical Center, Manila, Philippines
| | - Jeffrey S. Ross
- Foundation Medicine Inc., Cambridge
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, NY
| | - Shakti H. Ramkissoon
- Foundation Medicine Inc., Cambridge
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Laura J. Adhikari
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Rosemary E. Zuna
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Philip E. LeBoit
- Departments of Pathology and Dermatology, UCSF Dermatopathology Service, Helen Diller Family Cancer Center, University of California, San Francisco, CA
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49
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Fukuhara S, Oshikawa-Kumade Y, Kogure Y, Shingaki S, Kariyazono H, Kikukawa Y, Koya J, Saito Y, Tabata M, Yoshifuji K, Mizuno K, Maeshima AM, Matsushita H, Sugiyama M, Ogawa C, Inamoto Y, Fukuda T, Sugano M, Yamauchi N, Minami Y, Hirata M, Yoshida T, Kohno T, Kohsaka S, Mano H, Shiraishi Y, Ogawa S, Izutsu K, Kataoka K. Feasibility and clinical utility of comprehensive genomic profiling of hematological malignancies. Cancer Sci 2022; 113:2763-2777. [PMID: 35579198 PMCID: PMC9357666 DOI: 10.1111/cas.15427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/26/2022] [Accepted: 05/12/2022] [Indexed: 12/01/2022] Open
Abstract
Identification of genetic alterations through next‐generation sequencing (NGS) can guide treatment decision‐making by providing information on diagnosis, therapy selection, and prognostic stratification in patients with hematological malignancies. Although the utility of NGS‐based genomic profiling assays was investigated in hematological malignancies, no assays sufficiently cover driver mutations, including recently discovered ones, as well as fusions and/or pathogenic germline variants. To address these issues, here we have devised an integrated DNA/RNA profiling assay to detect various types of somatic alterations and germline variants at once. Particularly, our assay can successfully identify copy number alterations and structural variations, including immunoglobulin heavy chain translocations, IKZF1 intragenic deletions, and rare fusions. Using this assay, we conducted a prospective study to investigate the feasibility and clinical usefulness of comprehensive genomic profiling for 452 recurrently altered genes in hematological malignancies. In total, 176 patients (with 188 specimens) were analyzed, in which at least one alteration was detected in 171 (97%) patients, with a median number of total alterations of 7 (0–55). Among them, 145 (82%), 86 (49%), and 102 (58%) patients harbored at least one clinically relevant alteration for diagnosis, treatment, and prognosis, respectively. The proportion of patients with clinically relevant alterations was the highest in acute myeloid leukemia, whereas this assay was less informative in T/natural killer‐cell lymphoma. These results suggest the clinical utility of NGS‐based genomic profiling, particularly for their diagnosis and prognostic prediction, thereby highlighting the promise of precision medicine in hematological malignancies.
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Affiliation(s)
- Suguru Fukuhara
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Oshikawa-Kumade
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hirokazu Kariyazono
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Yoshiya Kikukawa
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Diagnostic Division, Otsuka Pharmaceutical Co., Ltd. Tokushima, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Hematology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kota Mizuno
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | - Hiromichi Matsushita
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Masanaka Sugiyama
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Chitose Ogawa
- Department of Pediatric Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshihiro Inamoto
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Takahiro Fukuda
- Department of Hematopoietic Stem Cell Transplantation, National Cancer Center Hospital, Tokyo, Japan
| | - Masato Sugano
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital East, Kashiwa, Japan
| | - Nobuhiko Yamauchi
- Department of Hematology and Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yosuke Minami
- Department of Hematology and Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Makoto Hirata
- Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Izutsu
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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50
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Higashigawa S, Matsubayashi H, Kiyozumi Y, Kado N, Nishimura S, Oishi T, Sugino T, Fushiki K, Shirasu H, Yasui H, Mamesaya N, Fukuzaki N, Kunitomo K, Horiuchi Y, Kenmotsu H, Serizawa M. Present status of germline findings in precision medicine for Japanese cancer patients: issues in the current system. Jpn J Clin Oncol 2022; 52:599-608. [PMID: 35411369 DOI: 10.1093/jjco/hyac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/11/2021] [Accepted: 03/07/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE Since 2019, precision cancer medicine has been covered by national insurance in Japan; however, to date, germline findings have not been fully reported. The aim of this study was to evaluate the current status and raise a problem of germline finding analysis and disclosure in Japanese precision cancer medicine. METHODS Germline findings of 52 genes were examined in 296 cases with advanced cancer by a case series study. RESULTS Six (2.0%) cases were examined by the Oncoguide™ NCC Oncopanel with germline testing, but no germline findings were reported. The remaining 290 (98.0%) cases were analyzed by FoundationOne® CDx (tumor-only testing), which recognized 404 pathogenic variants; those of BRCA1/2 were recognized in 16 (5.5%) tumors. Our institutional algorithm suggested 39 candidate germline findings in 34 cases, while the public algorithm listed at least 91 candidate germline findings. Four germline findings had been previously identified (BRCA1: 3 and ATM: 1). Nine of 30 cases with candidate germline findings excluding these known germline findings refused or deferred germline testing. Only 4 of 16 cases that received counseling underwent germline testing, and those 4 revealed 3 germline findings (BRCA2, CDK4 and RAD51C); in total, 8 (2.7%) germline findings were revealed. Reasons for refusing genetic counseling and/or germline testing included extra hospital visits, added expense for germline testing due to limited national insurance coverage, poor patient physical condition and no known family members associated with the possible germline finding. CONCLUSIONS In current Japanese precision cancer medicine, only a small fraction of the patients undergoes germline testing and demonstrated germline finding. The current results suggested a need for earlier indications for precision cancer medicine, broader insurance coverage and more efficient germline finding prediction algorithms, to increase the number of germline testings and to improve the following managements.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Yasue Horiuchi
- Division of Genetic Medicine Promotion.,Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | | | - Masakuni Serizawa
- Clinical Research Center, Shizuoka Cancer Center, Nagaizumi-cho, Sunto-gun, Shizuoka, Japan
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