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Vanni I, Pastorino L, Andreotti V, Comandini D, Fornarini G, Grassi M, Puccini A, Tanda ET, Pastorino A, Martelli V, Mastracci L, Grillo F, Cabiddu F, Guadagno A, Coco S, Allavena E, Barbero F, Bruno W, Dalmasso B, Bellomo SE, Marchiò C, Spagnolo F, Sciallero S, Berrino E, Ghiorzo P. Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort. J Transl Med 2024; 22:462. [PMID: 38750555 PMCID: PMC11097509 DOI: 10.1186/s12967-024-05227-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.
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Affiliation(s)
- I Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - V Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - D Comandini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - G Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - M Grassi
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E T Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Pastorino
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - V Martelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Cabiddu
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Guadagno
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Allavena
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - F Barbero
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - W Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - B Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S E Bellomo
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
| | - C Marchiò
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - F Spagnolo
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Plastic Surgery, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
| | - S Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - P Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy.
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Laguna JC, Pastor B, Nalda I, Hijazo-Pechero S, Teixido C, Potrony M, Puig-Butillé JA, Mezquita L. Incidental pathogenic germline alterations detected through liquid biopsy in patients with solid tumors: prevalence, clinical utility and implications. Br J Cancer 2024; 130:1420-1431. [PMID: 38532104 PMCID: PMC11059286 DOI: 10.1038/s41416-024-02607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 03/28/2024] Open
Abstract
Liquid biopsy, a minimally invasive approach for detecting tumor biomarkers in blood, has emerged as a leading-edge technique in cancer precision medicine. New evidence has shown that liquid biopsies can incidentally detect pathogenic germline variants (PGVs) associated with cancer predisposition, including in patients with a cancer for which genetic testing is not recommended. The ability to detect these incidental PGV in cancer patients through liquid biopsy raises important questions regarding the management of this information and its clinical implications. This incidental identification of PGVs raises concerns about cancer predisposition and the potential impact on patient management, not only in terms of providing access to treatment based on the tumor molecular profiling, but also the management of revealing genetic predisposition in patients and families. Understanding how to interpret this information is essential to ensure proper decision-making and to optimize cancer treatment and prevention strategies. In this review we provide a comprehensive summary of current evidence of incidental PGVs in cancer predisposition genes identified by liquid biopsy in patients with cancer. We critically review the methodological considerations of liquid biopsy as a tool for germline diagnosis, clinical utility and potential implications for cancer prevention, treatment, and research.
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Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Belén Pastor
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Irene Nalda
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Sara Hijazo-Pechero
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), l'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Teixido
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Miriam Potrony
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
| | - Joan Antón Puig-Butillé
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
| | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain.
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain.
- Department of Medicine, University of Barcelona, Barcelona, Spain.
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De Bonis M, Nero C, Scambia G, Normanno N, Minucci A. Pitfalls in identifying intronic germline pathogenic variants by comprehensive cancer genomic profiling: technical limitations or biased clinical/diagnostic utility? Int J Gynecol Cancer 2024:ijgc-2024-005382. [PMID: 38460967 DOI: 10.1136/ijgc-2024-005382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2024] Open
Affiliation(s)
- Maria De Bonis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Genomics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Camilla Nero
- Department of Woman, Child, and Public Health, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
| | - Giovanni Scambia
- Dipartimento Scienze della Salute della Donna e del Bambino, Fondazione Policlinico Universitario A Gemelli IRCCS, Roma, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, National Cancer Institute IRCCS Pascale Foundation, Napoli, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
- Genomics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Roma, Italy
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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] [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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