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Aoyama R, Nishikubo H, Kawabata K, Kanei S, Yamamoto Y, Nishimura S, Yashiro M. Clinical Significance of Multi-Cancer Genome Profiling: Data from a Single Hospital in Japan. Cancer Genomics Proteomics 2024; 21:79-87. [PMID: 38151295 PMCID: PMC10756342 DOI: 10.21873/cgp.20431] [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: 10/13/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND/AIM Multi-cancer genome profiling (multi-CGP) testing intends to predict the therapeutic efficacy of anticancer medication treatments for eligible patients as part of "precision cancer care." The number of cases in which a new treatment was applied based on multi-CGP testing has been reported to be between 10% and 20% for all patients in Japan. This study aimed to determine the significance of multi-CGP testing in Japan by analyzing clinical data from multi-CGP testing in various solid cancers at our Hospital. PATIENTS AND METHODS A total of 230 patients examined by one of three tests for multi-CGP including NCC Oncopanel, FoundationOne CDx, and FoundationOne Liquid were retrospectively enrolled. Adequate treatment for each patient was discussed at the expert panel meeting according to the results from the genome profiling tests. RESULTS The most frequent cancer types enrolled in this study were pancreas cancer, bowel cancer, and biliary cancer. Of the 230 cases, 106 (46%) were druggable cases, and 21 (9.1%) were administered medication. Partial response (PR) effect was found in 7 (33.3%) of the 21 cases, of which 3 were biliary cancer and 3 had a BRCA2 mutation. Of all the 21 cases, 7 (33.3%) had the maximum treatment benefit of PR. Three cases of biliary tumors were found in the 7 PR cases within the 21 cases. CONCLUSION Of 230 patients, 21 were administered medication following multi-CGP testing data, especially frequent in biliary tumor patients. Multi-CGP testing might be particularly beneficial to patients with biliary tumors in Japan.
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Affiliation(s)
- Rika Aoyama
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Hinano Nishikubo
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Kyoka Kawabata
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Saki Kanei
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Yurie Yamamoto
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Sadaaki Nishimura
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
- Department of Gastroenterological Surgery, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
- Cancer Center for Translational Research, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan;
- Department of Gastroenterological Surgery, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
- Cancer Center for Translational Research, Osaka Metropolitan University, Graduate School of Medicine, Osaka, Japan
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Peña KB, Riu F, Hernandez A, Guilarte C, Elizalde-Horcada M, Parada D. Study of Liquid-Based Cytology Using Next-Generation Sequencing as a Liquid Biopsy Application in Patients with Advanced Oncological Disease. Biomedicines 2023; 11:1578. [PMID: 37371673 DOI: 10.3390/biomedicines11061578] [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: 04/04/2023] [Revised: 05/17/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
In patients with advanced cancer, it is necessary to detect driver mutations and genetic arrangements. If a mutation is found, targeted therapy may become an option. However, in most patients with advanced cancer, obtaining material can be challenging, and these determinations must be made based on small biopsies or cytologic samples. We analyzed the ability of liquid-based cytology to determine the mutational status in patients with advanced cancer by next-generation sequencing. We studied cytologic samples from 28 patients between 1 January 2018 and 31 December 2022. All samples were processed by next-generation sequencing using the Oncomine® Precision and Comprehensive Assay Panels for Solid Tumors. Eleven male and 17 female patients with a median age of 63.75 years were included. Clinical stage IV was predominant in 21 patients. Eleven patients died, and 17 survived. The DNA and RNA concentrations were 10.53 ng/µL and 13 ng/µL, respectively. Eleven patients showed actionable mutations, and 17 showed other genomic alterations. Liquid-based cytology can be used as a component of liquid biopsy, as it allows the identification of actionable mutations in patients with advanced oncological disease. Our findings expand the utility of liquid biopsy from different body fluids or cell aspirates.
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Affiliation(s)
- Karla Beatríz Peña
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
| | - Francesc Riu
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
| | - Anna Hernandez
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
| | - Carmen Guilarte
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
| | | | - David Parada
- Molecular Pathology Unit, Department of Pathology, Hospital Universitari de Sant Joan, 43202 Reus, Tarragona, Spain
- Institut d'Investigació Sanitària Pere Virgili, 43202 Reus, Tarragona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, 43002 Reus, Tarragona, Spain
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Ashktorab H, Azimi H, Varma S, Lee EL, Laiyemo AO, Nickerson ML, Brim H. Driver genes exome sequencing reveals distinct variants in African Americans with colorectal neoplasia. Oncotarget 2019; 10:2607-2624. [PMID: 31080553 PMCID: PMC6498998 DOI: 10.18632/oncotarget.26721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 08/28/2018] [Accepted: 01/31/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in the United States. African Americans are disproportionately affected by CRC. Our hypothesis is that driver genes with known and novel mutations have an impact on CRC outcome in this population. Therefore, we investigated the variants' profiles in a panel of 15 CRC genes. PATIENTS & METHODS Colorectal specimens (n=140) were analyzed by targeted exome sequencing using an Ion Torrent platform. Detected variants were validated in 36 samples by Illumina sequencing. The novel status of the validated variants was determined by comparison to publicly available databases. Annotated using ANNOVAR and in-silico functional analysis of these variants were performed to determine likely pathogenic variants. RESULTS Overall, 121 known and novel variants were validated: APC (27%), AMER1 (3%), ARID1 (7%), MSH3 (12%), MSH6 (10%), BRAF (4%), KRAS (6%), FBXW7 (4%), PIK3CA (6%), SMAD4 (5%), SOX9 (2%), TCF7L2 (2%), TGFBR2 (5%), TP53 (7%). From these validated variants, 12% were novel in 8 genes (AMER1, APC, ARID1A, BRAF, MSH6, PIK3CA, SMAD4, and TCF7L2). Of the validated variants, 23% were non-synonymous, 14% were stopgains, 24% were synonymous and 39% were intronic variants. CONCLUSION We here report the specifics of variants' profiles of African Americans with colorectal lesions. Validated variants showed that Tumor Suppressor Genes (TSGs) APC and ARID1 and DNA Mismatch repair (MMR) genes MSH3 and MSH6 are the genes with the highest numbers of validated variants. Oncogenes KRAS and PIK3CA are also altered and likely participate in the increased proliferative potential of the mutated colonic epithelial cells in this population.
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Affiliation(s)
- Hassan Ashktorab
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | - Hamed Azimi
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | | | - Edward L. Lee
- Department of Pathology, Howard University College of Medicine, Washington, DC, USA
| | - Adeyinka O. Laiyemo
- Department of Medicine, Cancer Center, Howard University, Washington, DC, USA
| | - Michael L. Nickerson
- Laboratory of Translational Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Hassan Brim
- Department of Pathology, Howard University College of Medicine, Washington, DC, USA
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Friedman K, Resnick MB, Safran H. Mutation Profiling of Clinically Advanced Cancers Using Next-Generation Sequencing for Targeted Therapy: A Lifespan Experience. R I Med J (2013) 2015; 98:16-20. [PMID: 26422540] [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] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The application of modern molecular tests such as next-generation sequencing (NGS) to human malignancies has led to better understanding of tumor biology and the design of targeted molecular therapies. In the research setting, important genomic alterations in tumors have been discovered with potential therapeutic implications but data regarding the impact of this technology in a real world oncology practice is limited. As a result, we decided to review the results of NGS in 144 advanced-stage cancer patients referred to the oncology practices of Lifespan-affiliated centers in Rhode Island. Most cancers revealed genomic alterations in genes commonly mutated in cancer. However, several unexpected genomic alterations were discovered in certain cancers with potential therapeutic intervention. Most cancers contained "actionable" genomic alterations despite being of advanced stage. Our experience demonstrates that application of NGS in the clinical setting contributes both to increasing the therapeutic armamentarium as well as our understanding of tumor biology.
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Affiliation(s)
- Kenneth Friedman
- Gastrointestinal Pathology Fellow in the Department of Pathology at Lifespan/Rhode Island Hospital
| | - Murray B Resnick
- Professor of Pathology at the Alpert Medical School of Brown University and Vice Chair of Pathology and Director of Gastrointestinal Pathology at Lifespan/Rhode Island Hospital
| | - Howard Safran
- Director of the Brown University Oncology Group and Professor of Medicine at the Alpert Medical School of Brown University
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Sweet K, Gordon ES, Sturm AC, Schmidlen TJ, Manickam K, Toland AE, Keller MA, Stack CB, García-España JF, Bellafante M, Tayal N, Embi P, Binkley P, Hershberger RE, Sadee W, Christman M, Marsh C. Design and implementation of a randomized controlled trial of genomic counseling for patients with chronic disease. J Pers Med 2014; 4:1-19. [PMID: 24926413 DOI: 10.3390/jpm4010001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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] [Indexed: 12/18/2022] Open
Abstract
We describe the development and implementation of a randomized controlled trial to investigate the impact of genomic counseling on a cohort of patients with heart failure (HF) or hypertension (HTN), managed at a large academic medical center, the Ohio State University Wexner Medical Center (OSUWMC). Our study is built upon the existing Coriell Personalized Medicine Collaborative (CPMC®). OSUWMC patient participants with chronic disease (CD) receive eight actionable complex disease and one pharmacogenomic test report through the CPMC® web portal. Participants are randomized to either the in-person post-test genomic counseling—active arm, versus web-based only return of results—control arm. Study-specific surveys measure: (1) change in risk perception; (2) knowledge retention; (3) perceived personal control; (4) health behavior change; and, for the active arm (5), overall satisfaction with genomic counseling. This ongoing partnership has spurred creation of both infrastructure and procedures necessary for the implementation of genomics and genomic counseling in clinical care and clinical research. This included creation of a comprehensive informed consent document and processes for prospective return of actionable results for multiple complex diseases and pharmacogenomics (PGx) through a web portal, and integration of genomic data files and clinical decision support into an EPIC-based electronic medical record. We present this partnership, the infrastructure, genomic counseling approach, and the challenges that arose in the design and conduct of this ongoing trial to inform subsequent collaborative efforts and best genomic counseling practices.
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