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Imoto K, Yamamoto H, Ohkawa C, Shimada N, Ikuzawa R, Takeda H, Ohhara T, Kojima Y, Furuya N, Motoyoshi A, Migita O, Kuga A, Keira T, Wakamatsu H, Sato T, Oike N, Koike J, Yamano Y, Sunakawa Y. An approach for improvement of the accuracy of cancer gene panel testing. Int J Clin Oncol 2024; 29:571-581. [PMID: 38472663 DOI: 10.1007/s10147-024-02483-6] [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: 08/18/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Tissue-based comprehensive genomic profiling (CGP) is increasingly being employed for genotype-directed therapies in patients with advanced cancer. However, tissue availability may limit their potential applications. In Japan, the cost of cancer gene panel tests is covered by public insurance for patients diagnosed with advanced solid tumors once in their lifetime. Therefore, it is essential to improve the success rate (reportability) and accuracy of CGP tests. The purpose of this study was to identify the factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data. METHODS This study included 159 samples analyzed using tumor-only panel FoundationOne® CDx cancer genome profiling (F1CDx) and 85 samples analyzed using matched-pair panel OncoGuide™ NCC Oncopanel system (NCCOP) at St. Marianna University Hospital. Sample characteristics (fixation conditions, storage period, histology, tumor cell ratio, and genomic tumor cell content), CGP performance, and quality control status were evaluated across all 244 tested samples. RESULTS In 237/244 samples (97.1%), CGP testing results were successfully obtained [F1CDx, 99.4% (158/159) and NCCOP, 92.9% (79/85)]. An increased number of fibroblasts, inflammatory cells, and necrotic tumor cells, long-term storage, and/or prolonged fixation of tissue sections were involved in the unreported results and/or qualified CGP results. In addition, a negative correlation between median insert size values and ΔΔCq was observed in the NCCOP system. CONCLUSION We identified various factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data, suggesting that thorough selection and preparation of tissue sections could optimize CGP and maximize useful information.
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Affiliation(s)
- Kiyomi Imoto
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Yamamoto
- Department of Bioinformatics, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa, 216-8511, Japan.
- Department of Gastroenterology, St. Marianna University School of Medicine, Kawasaki, Japan.
| | - Chie Ohkawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Naoki Shimada
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Ryo Ikuzawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tatsuru Ohhara
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yasuyuki Kojima
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Furuya
- Department of Respiratory Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ai Motoyoshi
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Asami Kuga
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Takayuki Keira
- Department of Pharmacy, St. Marianna University Hospital, Kawasaki, Japan
| | | | - Tomoo Sato
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Nobuyuki Oike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junki Koike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshihisa Yamano
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yu Sunakawa
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
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Nibid L, Sabarese G, Righi D, Rossi SM, Merlini G, Crucitti P, Vincenzi B, Tonini G, Perrone G. Feasibility of Comprehensive Genomic Profiling (CGP) in Real-Life Clinical Practice. Diagnostics (Basel) 2023; 13:diagnostics13040782. [PMID: 36832270 PMCID: PMC9955416 DOI: 10.3390/diagnostics13040782] [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: 01/03/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
In advanced or metastatic settings, Comprehensive Genomic Profiling (CGP) allows the evaluation of thousands of gene alterations with the goal of offering new opportunities for personalized treatment in solid tumors. This study evaluated the CGP Success Rate in a real-life cohort of 184 patients enrolled in a prospective clinical trial. CGP data were compared with the routine molecular testing strategy adopted in-house. Sample age, tumor area, and the percentage of tumor nuclei were recorded for CGP analysis. We found that 150/184 (81.5%) samples resulted in satisfying CGP reports. The CGP Success Rate was higher in samples from surgical specimens (96.7%) and in specimens that had been stored (sample age) for less than six months (89.4%). Among the inconclusive CGP reports, 7/34 (20.6%) were optimal samples, according to CGP sample requirements. Moreover, with the in-house molecular testing approach, we could obtain clinically relevant molecular data in 25/34 (73.5%) samples that had inconclusive CGP reports. In conclusion, despite the fact that CGP offers specific therapeutical options in selected patients, our data suggest that the standard molecular testing strategy should not be replaced in routine molecular profiling.
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Affiliation(s)
- Lorenzo Nibid
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Correspondence: (L.N.); (G.P.)
| | - Giovanna Sabarese
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
| | - Daniela Righi
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
| | - Silvia Maria Rossi
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
| | - Giorgia Merlini
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
| | - Pierfilippo Crucitti
- Research Unit of General Surgery, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Thoracic Surgery Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
| | - Bruno Vincenzi
- Research Unit of Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Medical Oncology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
| | - Giuseppe Tonini
- Research Unit of Oncology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Medical Oncology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
| | - Giuseppe Perrone
- Research Unit of Anatomical Pathology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21-00128 Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200-00128 Roma, Italy
- Correspondence: (L.N.); (G.P.)
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Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, Haberberger J, Alexander BM, Cloughesy T, Yong WH, Liau LM, Nghiemphu PL, Ji M, Lai A, Ramkissoon SH, Albacker LA. FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neurooncol Adv 2021; 3:vdab017. [PMID: 33778493 PMCID: PMC7986056 DOI: 10.1093/noajnl/vdab017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Molecular profiling of gliomas is vital to ensure diagnostic accuracy, inform prognosis, and identify clinical trial options for primary and recurrent tumors. This study aimed to determine the accuracy of reporting the whole arm 1p19q codeletion status from the FoundationOne platform. METHODS Testing was performed on glioma samples as part of clinical care and analyzed up to 395 cancer-associated genes (including IDH1/2). The whole arm 1p19q codeletion status was predicted from the same assay using a custom research-use only algorithm, which was validated using 463 glioma samples with available fluorescence in-situ hybridization (FISH) data. For 519 patients with available outcomes data, progression-free and overall survival were assessed based on whole arm 1p19q codeletion status derived from sequencing data. RESULTS Concordance between 1p19q status based on FISH and our algorithm was 96.7% (449/463) with a positive predictive value (PPV) of 100% and a positive percent agreement (PPA) of 91.0%. All discordant samples were positive for codeletion by FISH and harbored genomic alterations inconsistent with oligodendrogliomas. Median overall survival was 168 months for the IDH1/2 mutant, codeleted group, and 122 months for IDH1/2 mutant-only (hazard ratio (HR): 0.42; P < .05). CONCLUSIONS 1p19q codeletion status derived from FoundationOne testing is highly concordant with FISH results. Genomic profiling may be a reliable substitute for traditional FISH testing while also providing IDH1/2 status.
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Affiliation(s)
- Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Garrett M Frampton
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Maureen Cooper
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Jacqueline Jenkins
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Natalie Danziger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - James Haberberger
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Brian M Alexander
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - William H Yong
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Phioanh L Nghiemphu
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Matthew Ji
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Albert Lai
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Shakti H Ramkissoon
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
- Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Lee A Albacker
- Foundation Medicine, Inc., Cambridge, Massachusetts and Morrisville, North Carolina
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