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Kumbrink J, Demes MC, Jeroch J, Bräuninger A, Hartung K, Gerstenmaier U, Marienfeld R, Hillmer A, Bohn N, Lehning C, Ferch F, Wild P, Gattenlöhner S, Möller P, Klauschen F, Jung A. Development, testing and validation of a targeted NGS-panel for the detection of actionable mutations in lung cancer (NSCLC) using anchored multiplex PCR technology in a multicentric setting. Pathol Oncol Res 2024; 30:1611590. [PMID: 38605929 PMCID: PMC11006983 DOI: 10.3389/pore.2024.1611590] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
Lung cancer is a paradigm for a genetically driven tumor. A variety of drugs were developed targeting specific biomarkers requiring testing for tumor genetic alterations in relevant biomarkers. Different next-generation sequencing technologies are available for library generation: 1) anchored multiplex-, 2) amplicon based- and 3) hybrid capture-based-PCR. Anchored multiplex PCR-based sequencing was investigated for routine molecular testing within the national Network Genomic Medicine Lung Cancer (nNGM). Four centers applied the anchored multiplex ArcherDX-Variantplex nNGMv2 panel to re-analyze samples pre-tested during routine diagnostics. Data analyses were performed by each center and compiled centrally according to study design. Pre-defined standards were utilized, and panel sensitivity was determined by dilution experiments. nNGMv2 panel sequencing was successful in 98.9% of the samples (N = 90). With default filter settings, all but two potential MET exon 14 skipping variants were identified at similar allele frequencies. Both MET variants were found with an adapted calling filter. Three additional variants (KEAP1, STK11, TP53) were called that were not identified in pre-testing analyses. Only total DNA amount but not a qPCR-based DNA quality score correlated with average coverage. Analysis was successful with a DNA input as low as 6.25 ng. Anchored multiplex PCR-based sequencing (nNGMv2) and a sophisticated user-friendly Archer-Analysis pipeline is a robust and specific technology to detect tumor genetic mutations for precision medicine of lung cancer patients.
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Affiliation(s)
- Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Melanie-Christin Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan Jeroch
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Andreas Bräuninger
- Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Kristin Hartung
- Institute of Pathology, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Axel Hillmer
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | | | - Peter Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | | | - Peter Möller
- Institute of Pathology, University Ulm, Ulm, Germany
| | - Frederick Klauschen
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Andreas Jung
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
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2
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Canino F, Tornincasa A, Bettelli S, Manfredini S, Barbolini M, Moscetti L, Omarini C, Toss A, Tamburrano F, Antonelli G, Baglio F, Belluzzi L, Martinelli G, Natalizio S, Ponzoni O, Dominici M, Piacentini F. Real-World Data and Clinical Implications of Next-Generation Sequencing (NGS)-Based Analysis in Metastatic Breast Cancer Patients. Int J Mol Sci 2024; 25:2490. [PMID: 38473737 DOI: 10.3390/ijms25052490] [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: 01/16/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Over the last two decades, the use of Next-Generation Sequencing (NGS) in medical oncology has increased the likelihood of identifying druggable mutations that may be potentially susceptible to targeted treatments. The European Society for Medical Oncology (ESMO) currently does not recommend the use of the NGS test to determine the therapeutic course of patients with metastatic breast cancer (mBC) in daily clinical practice. However, the aim of this work is to evaluate the potential contribution of the NGS test in selecting targeted therapies for patients with mBC. Data were retrospectively collected from 101 patients diagnosed with metastatic breast cancer and treated at the Modena Cancer Center between January 2015 and April 2022. A NGS test was performed on the tumor tissue of each patient at the Laboratory of Molecular Pathology of the University Hospital of Modena. This study analyzed the clinical-pathological characteristics and mutational profile of the population using NGS tests, with a focus on actionable mutations that could be targeted in advanced stages of clinical development. The indicator of this study was to quantify the actionable mutations that resulted in a change of cancer treatment. In total, 101 patients with metastatic breast cancer were analyzed, including 86 with luminal phenotype, 10 who were HER2-positive and 5 who were triple-negative. Median age was 52 years. NGS analysis was conducted on 47 samples of primary breast cancer, 52 on metastatic sites of disease and 2 on liquid biopsies. A total of 85 gene mutations were found. The most common mutations were identified in the PIK3CA (47%), FGFR (19%) and ERBB2 genes (12%), and to a lesser extent in other genes. Of the 61 patients with pathogenic mutations, 46 (75%) had at least one actionable mutation. Of these, nine received treatment with a molecular target drug: eight patients with a mutation of the PIK3CA gene were treated with alpelisib and fulvestrant; one patient with FGFR1/2 amplifications received TAS120. Median PFS for these patients was 3.8 months. The study results show that using the NGS test on cancer tissue of metastatic breast cancer could influence the therapeutic choices, considering the small sample size and limited follow-up. About 9% of the study population had their therapy modified based on the results of NGS. The growing number of detectable mutations and increased accessibility of the test may lead to a greater number of potential therapeutic implications for the NGS assay. Perspectives suggest that NGS analysis can be implemented in daily clinical practice, particularly in contexts where a Molecular Tumor Board (MTB) is active.
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Affiliation(s)
- Fabio Canino
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Antonio Tornincasa
- Unità Operativa di Oncologia, ASL I dell'Umbria, 06012 Città di Castello, Italy
| | - Stefania Bettelli
- Molecular Pathology and Predictive Medicine, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Samantha Manfredini
- Molecular Pathology and Predictive Medicine, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Monica Barbolini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Luca Moscetti
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
- Division of Medical Oncology, Department of Oncology and Ematology, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Claudia Omarini
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
- Division of Medical Oncology, Department of Oncology and Ematology, Azienda Ospedaliero, Universitaria Policlinico di Modena, 41124 Modena, Italy
| | - Angela Toss
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Fabio Tamburrano
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Giuseppina Antonelli
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Federica Baglio
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Lorenzo Belluzzi
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Giulio Martinelli
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
| | - Salvatore Natalizio
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Ornella Ponzoni
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Massimo Dominici
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
| | - Federico Piacentini
- Division of Medical Oncology, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena, 41124 Modena, Italy
- Gruppo Oncologico Italiano di Ricerca Clinica (GOIRC), 43126 Parma, Italy
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3
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Radhakrishnan V, Kaifi JT, Suvilesh KN. Circulating Tumor Cells: How Far Have We Come with Mining These Seeds of Metastasis? Cancers (Basel) 2024; 16:816. [PMID: 38398206 PMCID: PMC10887304 DOI: 10.3390/cancers16040816] [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: 01/10/2024] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Circulating tumor cells (CTCs) are cancer cells that slough off from the tumor and circulate in the peripheral blood and lymphatic system as micro metastases that eventually results in macro metastases. Through a simple blood draw, sensitive CTC detection from clinical samples has proven to be a useful tool for determining the prognosis of cancer. Recent technological developments now make it possible to detect CTCs reliably and repeatedly from a simple and straightforward blood test. Multicenter trials to assess the clinical value of CTCs have demonstrated the prognostic value of these cancer cells. Studies on CTCs have filled huge knowledge gap in understanding the process of metastasis since their identification in the late 19th century. However, these rare cancer cells have not been regularly used to tailor precision medicine and or identify novel druggable targets. In this review, we have attempted to summarize the milestones of CTC-based research from the time of identification to molecular characterization. Additionally, the need for a paradigm shift in dissecting these seeds of metastasis and the possible future avenues to improve CTC-based discoveries are also discussed.
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Affiliation(s)
- Vijay Radhakrishnan
- Department of Surgery, Ellis Fischel Cancer Center, Roy Blunt NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA; (V.R.); (J.T.K.)
| | - Jussuf T. Kaifi
- Department of Surgery, Ellis Fischel Cancer Center, Roy Blunt NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA; (V.R.); (J.T.K.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
| | - Kanve N. Suvilesh
- Department of Surgery, Ellis Fischel Cancer Center, Roy Blunt NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA; (V.R.); (J.T.K.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
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4
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Riobello C, Sánchez-Fernández P, Córdoba MCC, González-Gutiérrez M, Vivanco B, Cabal VN, Fernández LS, García-Marín R, Codina-Martínez H, Lorenzo-Guerra SL, López F, Hermsen MA, Llorente JL. Next-generation sequencing reveals remarkable genetic stability in primary and corresponding recurrent intestinal-type sinonasal adenocarcinoma. Head Neck 2024. [PMID: 38362701 DOI: 10.1002/hed.27694] [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: 09/07/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Recurrent intestinal-type sinonasal adenocarcinoma (ITAC) can occur several years after primary treatment and with different histology. We aimed to clarify if such recurrences could be second primary tumors and to identify actionable mutations as targets for personalized treatment of recurrent ITAC. METHODS Twelve pairs of primary and recurrent ITAC were histologically examined and analyzed by next-generation sequencing. RESULTS Histological differences between primary and recurrent tumor pairs were observed in five cases. Frequent mutations included TP53, APC, TSC2, ATM, EPHA2, BRCA2, LRP1B, KRAS, and KMT2B. There was 86% concordance of somatic mutations between the tumor pairs, while four cases carried additional mutations in the recurrence. CONCLUSIONS We found all cases to be clonal recurrences and not second primary tumors. Moreover, tumor pairs showed a remarkable genomic stability, suggesting that personalized treatment of a recurrence may be based on actionable molecular genetic targets observed in the primary tumor.
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Affiliation(s)
- Cristina Riobello
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | | | | | | | - Blanca Vivanco
- Department of Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Virginia N Cabal
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - Laura Suárez Fernández
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - Rocío García-Marín
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - Helena Codina-Martínez
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - Sara Lucila Lorenzo-Guerra
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - Fernando López
- Department of Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Mario A Hermsen
- Department of Head and Neck Cancer, Health Research Institute of the Principality of Asturias, Oviedo, Spain
| | - José Luis Llorente
- Department of Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain
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Suthapot P, Chiangjong W, Chaiyawat P, Choochuen P, Pruksakorn D, Sangkhathat S, Hongeng S, Anurathapan U, Chutipongtanate S. Genomics-Driven Precision Medicine in Pediatric Solid Tumors. Cancers (Basel) 2023; 15:cancers15051418. [PMID: 36900212 PMCID: PMC10000495 DOI: 10.3390/cancers15051418] [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: 01/18/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/12/2023] Open
Abstract
Over the past decades, several study programs have conducted genetic testing in cancer patients to identify potential genetic targets for the development of precision therapeutic strategies. These biomarker-driven trials have demonstrated improved clinical outcomes and progression-free survival rates in various types of cancers, especially for adult malignancies. However, similar progress in pediatric cancers has been slow due to their distinguished mutation profiles compared to adults and the low frequency of recurrent genomic alterations. Recently, increased efforts to develop precision medicine for childhood malignancies have led to the identification of genomic alterations and transcriptomic profiles of pediatric patients which presents promising opportunities to study rare and difficult-to-access neoplasms. This review summarizes the current state of known and potential genetic markers for pediatric solid tumors and provides perspectives on precise therapeutic strategies that warrant further investigations.
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Affiliation(s)
- Praewa Suthapot
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Biomedical Science and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wararat Chiangjong
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Musculoskeletal Science and Translational Research Center, Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pongsakorn Choochuen
- Department of Biomedical Science and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Musculoskeletal Science and Translational Research Center, Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Surasak Sangkhathat
- Department of Biomedical Science and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Translational Medicine Research Center, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Usanarat Anurathapan
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (U.A.); or (S.C.)
| | - Somchai Chutipongtanate
- Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Correspondence: (U.A.); or (S.C.)
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Andrews LJ, Thornton ZA, Saleh R, Dawson S, Short SC, Daly R, Higgins JPT, Davies P, Kurian KM. Genomic landscape and actionable mutations of brain metastases derived from non-small cell lung cancer: A systematic review. Neurooncol Adv 2023; 5:vdad145. [PMID: 38130901 PMCID: PMC10734675 DOI: 10.1093/noajnl/vdad145] [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] [Indexed: 12/23/2023] Open
Abstract
Background Brain metastases derived from non-small cell lung cancer (NSCLC) represent a significant clinical problem. We aim to characterize the genomic landscape of brain metastases derived from NSCLC and assess clinical actionability. Methods We searched Embase, MEDLINE, Web of Science, and BIOSIS from inception to 18/19 May 2022. We extracted information on patient demographics, smoking status, genomic data, matched primary NSCLC, and programmed cell death ligand 1 expression. Results We found 72 included papers and data on 2346 patients. The most frequently mutated genes from our data were EGFR (n = 559), TP53 (n = 331), KRAS (n = 328), CDKN2A (n = 97), and STK11 (n = 72). Common missense mutations included EGFR L858R (n = 80) and KRAS G12C (n = 17). Brain metastases of ever versus never smokers had differing missense mutations in TP53 and EGFR, except for L858R and T790M in EGFR, which were seen in both subgroups. Of the top 10 frequently mutated genes that had primary NSCLC data, we found 37% of the specific mutations assessed to be discordant between the primary NSCLC and brain metastases. Conclusions To our knowledge, this is the first systematic review to describe the genomic landscape of brain metastases derived from NSCLC. These results provide a comprehensive outline of frequently mutated genes and missense mutations that could be clinically actionable. These data also provide evidence of differing genomic landscapes between ever versus never smokers and primary NSCLC compared to the BM. This information could have important consequences for the selection and development of targeted drugs for these patients.
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Affiliation(s)
- Lily J Andrews
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Zak A Thornton
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Ruqiya Saleh
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan C Short
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Richard Daly
- Cellular Pathology Department, North Bristol NHS Trust, Bristol, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philippa Davies
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
- Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, UK
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7
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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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8
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Rivas S, Marín A, Samtani S, González-Feliú E, Armisén R. MET Signaling Pathways, Resistance Mechanisms, and Opportunities for Target Therapies. Int J Mol Sci 2022; 23:ijms232213898. [PMID: 36430388 PMCID: PMC9697723 DOI: 10.3390/ijms232213898] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The MET gene, known as MET proto-oncogene receptor tyrosine kinase, was first identified to induce tumor cell migration, invasion, and proliferation/survival through canonical RAS-CDC42-PAK-Rho kinase, RAS-MAPK, PI3K-AKT-mTOR, and β-catenin signaling pathways, and its driver mutations, such as MET gene amplification (METamp) and the exon 14 skipping alterations (METex14), activate cell transformation, cancer progression, and worse patient prognosis, principally in lung cancer through the overactivation of their own oncogenic and MET parallel signaling pathways. Because of this, MET driver alterations have become of interest in lung adenocarcinomas since the FDA approval of target therapies for METamp and METex14 in 2020. However, after using MET target therapies, tumor cells develop adaptative changes, favoring tumor resistance to drugs, the main current challenge to precision medicine. Here, we review a link between the resistance mechanism and MET signaling pathways, which is not only limited to MET. The resistance impacts MET parallel tyrosine kinase receptors and signals shared hubs. Therefore, this information could be relevant in the patient's mutational profile evaluation before the first target therapy prescription and follow-up to reduce the risk of drug resistance. However, to develop a resistance mechanism to a MET inhibitor, patients must have access to the drugs. For instance, none of the FDA approved MET inhibitors are registered as such in Chile and other developing countries. Constant cross-feeding between basic and clinical research will thus be required to meet future challenges imposed by the acquired resistance to targeted therapies.
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Affiliation(s)
- Solange Rivas
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
| | - Arnaldo Marín
- Departamento de Oncología Básico Clínica, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Suraj Samtani
- Departamento de Oncología Médica, Clínica Las Condes, Santiago 7550000, Chile
- Hospital Félix Bulnes, Santiago 9080000, Chile
| | - Evelin González-Feliú
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7550000, Chile
- Correspondence:
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9
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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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10
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Shao J, Ma J, Zhang S, Li J, Dai H, Liang S, Yu Y, Li W, Wang C. Radiogenomic System for Non-Invasive Identification of Multiple Actionable Mutations and PD-L1 Expression in Non-Small Cell Lung Cancer Based on CT Images. Cancers (Basel) 2022; 14:4823. [PMID: 36230746 DOI: 10.3390/cancers14194823] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/07/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
PURPOSE Personalized treatments such as targeted therapy and immunotherapy have revolutionized the predominantly therapeutic paradigm for non-small cell lung cancer (NSCLC). However, these treatment decisions require the determination of targetable genomic and molecular alterations through invasive genetic or immunohistochemistry (IHC) tests. Numerous previous studies have demonstrated that artificial intelligence can accurately predict the single-gene status of tumors based on radiologic imaging, but few studies have achieved the simultaneous evaluation of multiple genes to reflect more realistic clinical scenarios. METHODS We proposed a multi-label multi-task deep learning (MMDL) system for non-invasively predicting actionable NSCLC mutations and PD-L1 expression utilizing routinely acquired computed tomography (CT) images. This radiogenomic system integrated transformer-based deep learning features and radiomic features of CT volumes from 1096 NSCLC patients based on next-generation sequencing (NGS) and IHC tests. RESULTS For each task cohort, we randomly split the corresponding dataset into training (80%), validation (10%), and testing (10%) subsets. The area under the receiver operating characteristic curves (AUCs) of the MMDL system achieved 0.862 (95% confidence interval (CI), 0.758-0.969) for discrimination of a panel of 8 mutated genes, including EGFR, ALK, ERBB2, BRAF, MET, ROS1, RET and KRAS, 0.856 (95% CI, 0.663-0.948) for identification of a 10-molecular status panel (previous 8 genes plus TP53 and PD-L1); and 0.868 (95% CI, 0.641-0.972) for classifying EGFR / PD-L1 subtype, respectively. CONCLUSIONS To the best of our knowledge, this study is the first deep learning system to simultaneously analyze 10 molecular expressions, which might be utilized as an assistive tool in conjunction with or in lieu of ancillary testing to support precision treatment options.
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11
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Ai X, Yu Y, Zhao J, Sheng W, Bai J, Fan Z, Liu X, Ji W, Chen R, Lu S. Comprehensive analysis of MET mutations in NSCLC patients in a real-world setting. Ther Adv Med Oncol 2022; 14:17588359221112474. [PMID: 35860830 PMCID: PMC9290171 DOI: 10.1177/17588359221112474] [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: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Aberrant mesenchymal–epithelial transition/hepatocyte growth factor (MET/HGF) regulation presented in a wide variety of human cancers. MET exon 14 skipping, copy number gain (CNG), and kinase domain mutations/arrangements were associated with increased MET activity, and considered to be oncogenic drivers of non-small cell lung cancers (NSCLCs). Methods: We retrospectively analyzed 564 patients with MET alterations. MET alterations were classified into structural mutations or small mutations. MET CNG, exon 14 skipping, gain of function (GOF) mutations, and kinase domain rearrangement were defined as actionable mutations. Results: Six hundred thirty-two MET mutations were identified including 199 CNG, 117 exon 14 skipping, 12 GOF mutations, and 2 actionable fusions. Higher percentage of MET structural alterations (CNG + fusion) were detected in advanced NSCLC patients. Moreover, MET CNG was enriched while exon 14 skipping was rare in epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI)-treated advanced NSCLC patients. Ten of the 12 MET GOF mutations were also in EGFR-TKI-treated patients. Fifteen (68.1%) of the 22 patients treated with crizotinib or savolitinib had a partial response. Interestingly, one patient had a great response to savolitinib with a novel MET exon 14 skipping mutation identified after failure of immune-checkpoint inhibitor. Conclusions: Half of the MET alterations were actionable mutations. MET CNG, exon 14 skipping and GOF mutations had different distribution in different clinical scenario but all defined a molecular subgroup of NSCLCs for which MET inhibition was active.
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Affiliation(s)
- Xinghao Ai
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yongfeng Yu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wang Sheng
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Bai
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zaiwen Fan
- Department of Medical Oncology, Air Force Medical Center, PLA, Beijing, China
| | - Xuemei Liu
- Department of Radiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Rongrong Chen
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, No.241, Huaihai West Road, Shanghai 200032, China
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12
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Ramarao-Milne P, Kondrashova O, Patch AM, Nones K, Koufariotis LT, Newell F, Addala V, Lakis V, Holmes O, Leonard C, Wood S, Xu Q, Mukhopadhyay P, Naeini MM, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Basirzadeh F, Fielding D, Dalley AJ, Chittoory H, Simpson PT, Aoude LG, Bonazzi VF, Patel K, Barbour AP, Fennell DA, Robinson BW, Creaney J, Hollway G, Pearson JV, Waddell N. Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open 2022; 7:100540. [PMID: 35849877 PMCID: PMC9463385 DOI: 10.1016/j.esmoop.2022.100540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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] [Received: 10/21/2021] [Revised: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 12/14/2022] Open
Abstract
Background Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. Patients and methods We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. Results We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. Conclusions There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy. Genome analysis revealed that treatment biomarkers are shared across solid tumours, highlighting repurposing opportunities. Comprehensive panels detect most known biomarkers; however, WGS detects more biomarkers for treatments in clinical trials. TMB is well correlated between sequencing methods, but absolute values vary and are dependent on mutation types considered.
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Affiliation(s)
- P Ramarao-Milne
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia; Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - O Kondrashova
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - A-M Patch
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - K Nones
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - L T Koufariotis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - F Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - V Lakis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - O Holmes
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - C Leonard
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - S Wood
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Q Xu
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P Mukhopadhyay
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - M M Naeini
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - D Steinfort
- Department of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia
| | - J P Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, Australia
| | - M Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia
| | - C Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Australia
| | - P T Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia
| | - S Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - D Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - C Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia
| | - F Basirzadeh
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - D Fielding
- Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - A J Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - H Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - P T Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - L G Aoude
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - V F Bonazzi
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - K Patel
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - A P Barbour
- The University of Queensland Diamantina Institute, Faculty of Medicine, University of Queensland, Brisbane, Australia; Upper Gastro-intestinal Surgical Unit, Department of Surgery, Princess Alexandra Hospital, Brisbane, Australia
| | - D A Fennell
- Cancer Research UK Centre Leicester, University of Leicester & University Hospitals of Leicester NHS Trust, Leicester, UK
| | - B W Robinson
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - J Creaney
- National Centre for Asbestos Related Disease, Institute of Respiratory Health, University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - G Hollway
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - J V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - N Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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13
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Araujo JM, Rosas G, Belmar-López C, Raez LE, Rolfo CD, Schwarz LJ, Infante-Huaytalla U, Paez KJ, García LR, Alvarado H, Ramos FP, Delgado-Espinoza SS, Cardenas-Farfan JB, Cornejo M, Zanabria D, Colonio-Cossio C, Rojas-Jefferson M, Pinto JA. Influence of Sex in the Molecular Characteristics and Outcomes of Malignant Tumors. Front Oncol 2021; 11:752918. [PMID: 34737960 PMCID: PMC8562721 DOI: 10.3389/fonc.2021.752918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/03/2021] [Accepted: 09/29/2021] [Indexed: 01/22/2023] Open
Abstract
Background Sex is frequently underestimated as a prognostic biomarker in cancer. In this study, we evaluated a large cohort of patients and public datasets to determine the influence of sex on clinical outcomes, mutational status, and activation of immune pathways in different types of cancer. Methods A cohort of 13,619 Oncosalud-affiliated patients bearing sex-unrelated cancers was followed over a 20-year period. Hazard ratios (HRs) for death were estimated for female vs. male patients for each cancer type and then pooled in a meta-analysis to obtain an overall HR. In addition, the mutational status of the main actionable genes in melanoma (MEL), colorectal cancer (CRC), and lung cancer was compared between sexes. Finally, a gene set enrichment analysis (GSEA) of publicly available data was conducted, to assess differences in immune processes between sexes in MEL, gastric adenocarcinoma (GC), head and neck cancer (HNC), colon cancer (CC), liver cancer (LC), pancreatic cancer (PC), thyroid cancer (TC), and clear renal cell carcinoma (CCRCC). Results Overall, women had a decreased risk of death (HR = 0.73, CI95: 8%-42%), with improved overall survival (OS) in HNC, leukemia, lung cancer, lymphoma, MEL, multiple myeloma (MM), and non-melanoma skin cancer. Regarding the analysis of actionable mutations, only differences in EGFR alterations were observed (27.7% for men vs. 34.4% for women, p = 0.035). The number of differentially activated immune processes was higher in women with HNC, LC, CC, GC, MEL, PC, and TC and included cellular processes, responses to different stimuli, immune system development, immune response activation, multiorganism processes, and localization of immune cells. Only in CCRCC was a higher activation of immune pathways observed in men. Conclusions The study shows an improved survival rate, increased activation of immune system pathways, and an enrichment of EGFR alterations in female patients of our cohort. Enhancement of the immune response in female cancer patients is a phenomenon that should be further explored to improve the efficacy of immunotherapy.
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Affiliation(s)
- Jhajaira M Araujo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru.,Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - Gina Rosas
- Departamento de Patología, Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Carolina Belmar-López
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru.,Departamento de Genómica, Oncogenomics, Lima, Peru
| | - Luis E Raez
- Memorial Cancer Institute/Memorial Health Care System, Florida International University (FIU), Pembroke Pines, FL, United States
| | - Christian D Rolfo
- Center for Thoracic Oncology/Tisch Cancer Institute, Mount Sinai, New York, NY, United States
| | - Luis J Schwarz
- Escuela Profesional de Medicina Humana-Filial Ica, Universidad Privada San Juan Bautista, Ica, Peru
| | | | - Kevin J Paez
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Luis R García
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Hober Alvarado
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Fany P Ramos
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | | | - Jhon B Cardenas-Farfan
- Facultad de Ciencias Biológicas, Universidad Nacional San Luis Gonzaga de Ica, Ica, Peru
| | - Melanie Cornejo
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru
| | | | | | | | - Joseph A Pinto
- Centro de Investigación Básica y Traslacional, AUNA Ideas, Lima, Peru
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14
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El Achi H, Kanagal-Shamanna R. Biomarkers in Acute Myeloid Leukemia: Leveraging Next Generation Sequencing Data for Optimal Therapeutic Strategies. Front Oncol 2021; 11:748250. [PMID: 34660311 PMCID: PMC8514876 DOI: 10.3389/fonc.2021.748250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 12/19/2022] Open
Abstract
Next generation sequencing (NGS) is routinely used for mutation profiling of acute myeloid leukemia. The extensive application of NGS in hematologic malignancies, and its significant association with the outcomes in multiple large cohorts constituted a proof of concept that AML phenotype is driven by underlying mutational signature and is amenable for targeted therapies. These findings urged incorporation of molecular results into the latest World Health Organization (WHO) sub-classification and integration into risk-stratification and treatment guidelines by the European Leukemia Net. NGS mutation profiling provides a large amount of information that guides diagnosis and management, dependent on the type and number of gene mutations, variant allele frequency and amenability to targeted therapeutics. Hence, molecular mutational profiling is an integral component for work-up of AML and multiple leukemic entities. In addition, there is a vast amount of informative data that can be obtained from routine clinical NGS sequencing beyond diagnosis, prognostication and therapeutic targeting. These include identification of evidence regarding the ontogeny of the disease, underlying germline predisposition and clonal hematopoiesis, serial monitoring to assess the effectiveness of therapy and resistance mutations, which have broader implications for management. In this review, using a few prototypic genes in AML, we will summarize the clinical applications of NGS generated data for optimal AML management, with emphasis on the recently described entities and Food and Drug Administration approved target therapies.
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Affiliation(s)
- Hanadi El Achi
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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15
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Macías M, Cañada-Higueras E, Alegre E, Bielsa A, Gracia J, Patiño-García A, Ferrer-Costa R, Sendino T, Andueza MP, Mateos B, Rodríguez J, Corral J, Gúrpide A, Lopez-Picazo JM, Perez-Gracia JL, Gil-Bazo I, Alkorta-Aranburu G, González Á. Performance comparison of two next-generation sequencing panels to detect actionable mutations in cell-free DNA in cancer patients. Clin Chem Lab Med 2021; 58:1341-1348. [PMID: 32623849 DOI: 10.1515/cclm-2019-1267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/09/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023]
Abstract
Background Genomic alterations studies in cell-free DNA (cfDNA) have increasing clinical use in oncology. Next-generation sequencing (NGS) technology provides the most complete mutational analysis, but nowadays limited data are available related to the comparison of results reported by different platforms. Here we compare two NGS panels for cfDNA: Oncomine™ Pan-Cancer Cell-Free Assay (Thermo Fisher Scientific), suitable for clinical laboratories, and Guardant360® (GuardantHealth), with more genes targeted but only available in an outsourcing laboratory. Methods Peripheral blood was obtained from 16 advanced cancer patients in which Guardant360® (G360) was requested as part of their clinical assistance. Blood samples were sent to be analyzed with G360 panel, and an additional blood sample was drawn to obtain and analyze cfDNA with Oncomine™ Pan-Cancer (OM) panel in an Ion GeneStudio S5™ System. Results cfDNA analysis globally rendered 101 mutations. Regarding the 55/101 mutations claimed to be included by manufacturers in both panels, 17 mutations were reported only by G360, 10 only by OM and 28 by both. In those coincident cases, there was a high correlation between the variant allele fractions (VAFs) calculated with each panel (r = 0.979, p < 0.01). Regarding the six actionable mutations with an FDA-approved therapy reported by G360, one was missed with OM. Also, 12 mutations with clinical trials available were reported by G360 but not by OM. Conclusions In summary, G360 and OM can produce different mutational profile in the same sample, even in genes included in both panels, which is especially important if these mutations are potentially druggable.
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Affiliation(s)
- Mónica Macías
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Estibaliz Alegre
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Arancha Bielsa
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Javier Gracia
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Ana Patiño-García
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Roser Ferrer-Costa
- Department of Biochemistry, Hospital Universitari Vall D'Hebron, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Teresa Sendino
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - María P Andueza
- Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Beatriz Mateos
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain
| | - Javier Rodríguez
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jesús Corral
- CIMA LAB Diagnostics Universidad de Navarra, Pamplona, Spain
| | - Alfonso Gúrpide
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - José M Lopez-Picazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Jose L Perez-Gracia
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain
| | - Ignacio Gil-Bazo
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain.,Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Program of Solid Tumors, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Álvaro González
- Service of Biochemistry, Clínica Universidad de Navarra, Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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16
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Li D, Song Z, Dong B, Song W, Cheng C, Zhang Y, Zhang W. Advances in targeted therapy in non-small cell lung cancer with actionable mutations and leptomeningeal metastasis. J Clin Pharm Ther 2021; 47:24-32. [PMID: 34309914 DOI: 10.1111/jcpt.13489] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/19/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE?: Leptomeningeal metastasis (LM) is a serious complication of advanced non-small cell lung cancer (NSCLC) that is diagnosed in approximately 3%-5% of patients. LM occurs more frequently in patients with NSCLC harbouring epidermal growth factor receptor (EGFR) mutations or anaplastic lymphoma kinase (ALK) rearrangements and is usually accompanied by a poor prognosis, with a median overall survival (OS) of several months if patients receive conventional treatments. However, tyrosine kinase inhibitor (TKI) therapy after LM diagnosis is an independent predictive factor for extended survival. Here, we aim to summarize the latest advances in targeted therapy for LM and provide patients with better treatment options. METHODS: By reviewing the recent progress of targeted therapy in NSCLC with LM, especially the efficacy of newer generation TKIs, we aim to provide clinicians with a reference to further optimize patient treatment plans. RESULTS AND DISCUSSION: Osimertinib was confirmed to have a several-fold higher CNS permeability than other EGFR-TKIs and was recommended as the preferred choice for patients with EGFR-positive LM whether or not they harboured the T790M mutation. Second-generation ALK-TKIs have a higher rate of intracranial response and can be positioned as front-line drugs in NSCLC with LM. However, the sequence in which ALK-TKIs are administered for effective disease control requires further evaluation. In addition, targeted therapy revealed a potential choice in patients with LM and rare mutations, such as ROS1 and BRAF. WHAT IS NEW AND CONCLUSIONS?: The development of therapeutic agents with greater CNS penetration is vital for the management of CNS metastasis from NSCLC, particularly in the EGFR-mutant and ALK-rearranged subtypes. Systemic therapy with newer generation TKIs is preferred as the initial intervention. This is because newer generation TKIs are designed to penetrate the blood-brain barrier and possess significantly higher intracranial activities. However, their further effectiveness is limited by inadequate blood-brain barrier penetration and acquired drug resistance. Further studies are needed to further understand the mechanisms underlying resistance to treatment.
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Affiliation(s)
- Ding Li
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Zhengzhou, China
| | - Zhenguo Song
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Zhengzhou, China
| | - Bingqi Dong
- Department of Urology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Wenping Song
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Zhengzhou, China
| | - Cheng Cheng
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yongna Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Zhengzhou, China
| | - Wenzhou Zhang
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.,Henan Engineering Research Center for Tumor Precision Medicine and Comprehensive Evaluation, Zhengzhou, China
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17
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Huang CS, Liu CY, Lu TP, Huang CJ, Chiu JH, Tseng LM, Huang CC. Targeted Sequencing of Taiwanese Breast Cancer with Risk Stratification by the Concurrent Genes Signature: A Feasibility Study. J Pers Med 2021; 11:jpm11070613. [PMID: 34203389 PMCID: PMC8306786 DOI: 10.3390/jpm11070613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/04/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common female malignancy in Taiwan, while conventional clinical and pathological factors fail to provide full explanation for prognostic heterogeneity. The aim of the study was to evaluate the feasibility of targeted sequencing combined with concurrent genes signature to identify somatic mutations with clinical significance. The extended concurrent genes signature was based on the coherent patterns between genomic and transcriptional alterations. Targeted sequencing of 61 Taiwanese breast cancers revealed 1036 variants, including 76 pathogenic and 545 likely pathogenic variants based on the ACMG classification. The most frequently mutated genes were NOTCH, BRCA1, AR, ERBB2, FANCA, ATM, and BRCA2 and the most common pathogenic deletions were FGFR1, ATM, and WT1, while BRCA1 (rs1799965), FGFR2 (missense), and BRCA1 (rs1799949) were recurrent pathogenic SNPs. In addition, 38 breast cancers were predicted into 12 high-risk and 26 low-risk cases based on the extended concurrent genes signature, while the pathogenic PIK3CA variant (rs121913279) was significantly mutated between groups. Two deleterious SH3GLB2 mutations were further revealed by multivariate Cox’s regression (hazard ratios: 29.4 and 16.1). In addition, we identified several significantly mutated or pathogenic variants associated with differentially expressed signature genes. The feasibility of targeted sequencing in combination with concurrent genes risk stratification was ascertained. Future study to validate clinical applicability and evaluate potential actionability for Taiwanese breast cancers should be initiated.
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Affiliation(s)
- Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan;
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Chih-Yi Liu
- Department of Pathology, Cathay General Hospital Sijhih, New Taipei 221, Taiwan;
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 110, Taiwan;
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106, Taiwan;
- National Defense Medical Center, Department of Biochemistry, Taipei 114, Taiwan
| | - Jen-Hwey Chiu
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11121, Taiwan;
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Ling-Ming Tseng
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 1121, Taiwan
- School of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Correspondence:
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18
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Rodrigues JM, Porwit A, Hassan M, Ek S, Jerkeman M. Targeted genomic investigations in a population-based cohort of mantle cell lymphoma reveal novel clinically relevant targets. Leuk Lymphoma 2021; 62:2637-2647. [PMID: 34080947 DOI: 10.1080/10428194.2021.1933480] [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: 10/21/2022]
Abstract
Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm that follows a heterogeneous clinical course. Recurrent mutations have been described, but their applicability in the clinical setting is currently limited. The main reasons are challenges in the sequencing of DNA retrieved from formalin-fixed tissue commonly used for tissue collection in clinical biobanks. In this study, we sequenced 77 samples from a population-based de novo MCL cohort to investigate the utility of targeted sequencing in guiding personalized treatment approaches. Tumors were genetically variable, and a similar genetic landscape as previous studies using non-formalin fixed samples was identified, with recurrent mutations including ATM, KMT2D, and TP53. Novel alterations that can be considered actionable and/or indicative of treatment response were also identified. Our approach shows the potential benefits of using target sequencing of formalin fixed samples to facilitate treatment selection and individualized clinical decisions in MCL.
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Affiliation(s)
| | - Anna Porwit
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - May Hassan
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Sara Ek
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Mats Jerkeman
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
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Waterhouse DM, Tseng WY, Espirito JL, Robert NJ. Understanding Contemporary Molecular Biomarker Testing Rates and Trends for Metastatic NSCLC Among Community Oncologists. Clin Lung Cancer 2021; 22:e901-e910. [PMID: 34187757 DOI: 10.1016/j.cllc.2021.05.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Although guidelines recommend testing for actionable biomarkers for patients with advanced or metastatic non-small cell lung cancer (NSCLC), testing rates have varied. This study aimed to assess molecular testing patterns in a large network of US community-based oncology practices. METHODS This retrospective observational study examined adult patients with newly diagnosed stage IV NSCLC with ≥ 2 visits in The US Oncology Network from July 1, 2016 to September 30, 2019. Testing patterns were examined using electronic health record structured fields and chart review. Structured data were analyzed for the overall study population (cohort A), and structured and unstructured data were analyzed for a select cohort of 300 patients (cohort B). RESULTS In cohort A (n = 3337), programmed death ligand 1 (37%) was the most frequently tested biomarker documented in structured data, followed by epidermal growth factor receptor (36%), anaplastic lymphoma kinase (35%), ROS1 (20%), and BRAF (16%). According to unstructured data in cohort B (n = 300), epidermal growth factor receptor (80%) was the most frequently tested biomarker, followed by anaplastic lymphoma kinase (79%), programmed death ligand 1 (72%), ROS1 (71%), and BRAF (56%). The proportion of tests ordered prior to first-line (1L) treatment increased from 2016 to 2018 for all biomarkers, as did the proportion of test results available prior to 1L treatment. However, some of the test results became available after 1L or later lines of treatment were in progress. CONCLUSION Our study found increased testing rates over time and decreases in testing turnaround times. However, rates of testing for all biomarkers still need to improve, as does completion of testing prior to initiation of therapy.
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20
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Martínez-Fernández P, Pose P, Dolz-Gaitón R, García A, Trigo-Sánchez I, Rodríguez-Zarco E, Garcia-Ruiz MJ, Barba I, Izquierdo-García M, Valero-Garcia J, Ruiz C, Lázaro M, Carbonell P, Gargallo P, Méndez C, Ríos-Martín JJ, Palmeiro-Uriach A, Camarasa-Lillo N, Forteza-Vila J, Calabria I. Comprehensive NGS Panel Validation for the Identification of Actionable Alterations in Adult Solid Tumors. J Pers Med 2021; 11:jpm11050360. [PMID: 33947144 PMCID: PMC8145002 DOI: 10.3390/jpm11050360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/24/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023] Open
Abstract
The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx's utility in adult solid tumors.
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Affiliation(s)
- Paula Martínez-Fernández
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Patricia Pose
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Raquel Dolz-Gaitón
- Servicio de Anatomía Patológica, Hospital Universitario de la Ribera, 46600 Alcira, Spain; (P.P.); (R.D.-G.)
| | - Arantxa García
- Servicio de Genética Molecular y Radiobiología, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Inmaculada Trigo-Sánchez
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Enrique Rodríguez-Zarco
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - MJose Garcia-Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Ibon Barba
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marta Izquierdo-García
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Jennifer Valero-Garcia
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Ruiz
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Marián Lázaro
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Paula Carbonell
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Pablo Gargallo
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
| | - Carlos Méndez
- Servicio de Oncología Médica, Centro Oncológico de Galicia, 15009 A Coruña, Spain;
| | - Juan José Ríos-Martín
- Servicio de Anatomía Patológica, Hospital Universitario Virgen Macarena, 41009 Sevilla, Spain; (I.T.-S.); (E.R.-Z.); (J.J.R.-M.)
| | - Alberto Palmeiro-Uriach
- Laboratorio de Anatomía Patológica, Hospital General Universitario de Castellón, 12004 Castellón, Spain;
| | | | - Jerónimo Forteza-Vila
- Anatomía Patológica, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain;
| | - Inés Calabria
- Imegen-Health in Code Group, 46980 Paterna, Spain; (P.M.-F.); (M.G.-R.); (I.B.); (M.I.-G.); (J.V.-G.); (C.R.); (M.L.); (P.C.); (P.G.)
- Correspondence:
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Wang D, Ma K, Deng W, Li J, Xiang S, Zhang Y, Fu Y, Dai H, Huang B. Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy. Onco Targets Ther 2021; 14:2423-2431. [PMID: 33854338 PMCID: PMC8039190 DOI: 10.2147/ott.s299381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background The ability to rapidly, inexpensively, and accurately identify cancer patients based on actionable genomic mutations in tumour specimens is becoming critically important in routine clinical diagnostics. Targeted panel sequencing is becoming popular because it enables comprehensive and cost-effective diagnosis. However, the implementation of a next-generation sequencing (NGS) assay in clinical settings requires careful analytical validation to demonstrate its ability to detect multiple genomic variants. Materials and Methods Here, we developed a custom-targeted NGS panel to identify actionable variants, including single nucleotide variants, insertions, and deletions; copy number variants; and gene fusions, across 73 genes for targeted cancer therapy. We implemented a practical validation strategy with diluted samples and reference standard samples that modelled key determinants of accuracy, including mutant allele frequency, insertion/deletion length, amplitude of copy number, and hotspot gene fusions. Results The analytical validation results demonstrated that our panel can identify different types of genomic alterations in these test samples with high levels of accuracy, sensitivity, and reproducibility. Conclusion Our panel could be deployed as a routine clinical test to comprehensively detect actionable variants in cancer patients to guide targeted therapy decisions.
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Affiliation(s)
- Dandan Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China.,Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Kai Ma
- Department of Thoracic Surgery, National Cancer Center, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, People's Republic of China
| | - Wei Deng
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University & National Clinical Research Center for Digestive Disease, Beijing, 100050, People's Republic of China
| | - Jingyu Li
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China
| | - Shaohua Xiang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China
| | - Yang Zhang
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Ying Fu
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Heng Dai
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China.,Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
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Wang H, Xu X, Luo L, Wang C, Jiang Z, Lin Y. Mutational landscape of thymic epithelial tumors in a Chinese population: insights into potential clinical implications. Gland Surg 2021; 10:1410-1417. [PMID: 33968692 PMCID: PMC8102230 DOI: 10.21037/gs-21-157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/05/2023]
Abstract
BACKGROUND Thymic epithelial tumors (TETs) are a heterogeneous group of rare malignancies which may be devastating, difficult to treat, and for which treatment options are limited. Herein, we investigated the comprehensive genomic alterations of TETs in a Chinese population for providing clinical management, especially targeted therapy. METHODS Comprehensive genomic profiling (CGP) was performed with DNA targeted sequencing of cancer-associated genes (CSYS) from a cohort of 40 Chinese TET patients. TMB was measured by an in-house algorithm. MSI status was inferred based on the MANTIS (Microsatellite Analysis for Normal-Tumor InStability) score. The expression status of PD-L1 was estimated by immunohistochemistry. RESULTS The mutational profiling of thymomas (Ts) and thymic neuroendocrine tumors (TNETs) showed scattered mutation distributions with no recurrently mutated genes. In contrast, thymic carcinomas (TCs) did show highly recurrent mutations including CDKN2A, CYLD, CDKN2B, and TP53. Among them, CDKN2A and CDKN2B mutations were the top potentially actionable alterations in TCs. PD-L1 expression was mainly present in Ts and TCs, and was predominant in males and smokers. CONCLUSIONS Our study provided a comprehensive genetic alteration view on the largest Chinese cohort of TETs to date. The results identified different genomic mutational profiles of Ts, TCs, and TNETs, and analyzed potential druggable biomarkers with clinical implications in Chinese TET patients, which provided the evidence for precision medicine of rare TET patients.
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Affiliation(s)
- Hongbiao Wang
- Medical Oncology Session No.1, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xiaohua Xu
- Cardiothoracic surgery department, The Second Affiliated Hospital of Shantou University Medical College, Guangzhou, China
| | - Lan Luo
- Department of Oncology, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Chunbing Wang
- Medical Oncology Department, Cancer Hospital Chinese Academy of Medical Science, Shenzhen, China
| | - Zeyong Jiang
- Department of Thoracic Surgery, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Yingcheng Lin
- Medical Oncology Session No.1, Cancer Hospital of Shantou University Medical College, Shantou, China
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Balasubramanian SK, Sharma M, Venur VA, Schmitt P, Kotecha R, Chao ST, Suh JH, Angelov L, Mohammadi AM, Vogelbaum MA, Barnett GH, Jia X, Pennell NA, Ahluwalia MS. Impact of EGFR mutation and ALK rearrangement on the outcomes of non-small cell lung cancer patients with brain metastasis. Neuro Oncol 2021; 22:267-277. [PMID: 31648302 DOI: 10.1093/neuonc/noz155] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 12/24/2022] Open
Abstract
BACKGROUND The impact of activating alterations in non-small cell lung cancer (NSCLC) (epidermal growth factor receptor [EGFR] mutation/anaplastic lymphoma kinase [ALK] translocation) in prognosticating patients with brain metastasis (BM) is not well defined. This study was sought to identify this impact in NSCLC patients with BM accounting for the known validated variables. METHODS Among 1078 NSCLC-BM patients diagnosed/treated between January 1, 2000 and December 31, 2015, three hundred and forty-eight with known EGFR/ALK status were analyzed. Overall survival (OS) and intracranial progression-free survival (PFS) were measured from the time of BM. RESULTS Ninety-one patients had either ALK (n = 23) alterations or EGFR (n = 68) mutation and 257 were wild type (WT; negative actionable mutations/alterations). Median age of EGFR/ALK+ NSCLC BM patients was 60 years (range 29.8-82.6 y) and ~50% (n = 44) had Karnofsky performance status (KPS) score >80. Median number of BM was 2 (1 to ≥99). The median OS for the ALK/EGFR+ NSCLC BM was 19.9 versus 10.1 months for the WT (P = 0.028). The number of BM in the EGFR/ALK+ group did not impact OS (BM = 1 with 21.1 months vs 2-3 with 19.1 months and >3 with 23.7 months, P = 0.74), whereas fewer BM in the WT cohort had significantly better OS (BM = 1 with 13.8 mo, 2-3 with 11.0 mo and >3 with 8.1 mo; P = 0.006) with the adjustment of age, KPS, symptoms from BM and synchronicity. CONCLUSIONS Number of BM does not impact outcomes in the EGFR/ALK+ NSCLC patients, implying that targeted therapy along with surgery and/or radiation may improve OS irrespective of the number of BM. Number of BM, extracranial metastasis (ECM), and KPS independently affected OS/PFS in WT NSCLC BM, which was consistent with the known literature.
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Affiliation(s)
| | - Mayur Sharma
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio
| | | | - Philipp Schmitt
- Research Volunteer, Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio
| | - Rupesh Kotecha
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Samuel T Chao
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio
| | - John H Suh
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, Ohio
| | - Lilyana Angelov
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Neurosurgery, Neurological Institute, Cleveland Clinic, Cleveland, Ohio
| | - Alireza M Mohammadi
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Neurosurgery, Neurological Institute, Cleveland Clinic, Cleveland, Ohio
| | - Michael A Vogelbaum
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Neurosurgery, Neurological Institute, Cleveland Clinic, Cleveland, Ohio
| | - Gene H Barnett
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Neurosurgery, Neurological Institute, Cleveland Clinic, Cleveland, Ohio
| | - Xuefei Jia
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio
| | - Nathan A Pennell
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Hematology/Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
| | - Manmeet S Ahluwalia
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio.,Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio.,Department of Hematology/Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
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24
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Walter C, Hartkopf A, Koch A, Klaumünzer M, Schulze M, Grischke EM, Taran FA, Brucker S, Battke F, Biskup S. Sequencing for an interdisciplinary molecular tumor board in patients with advanced breast cancer: experiences from a case series. Oncotarget 2020; 11:3279-3285. [PMID: 32934773 PMCID: PMC7476733 DOI: 10.18632/oncotarget.27704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/30/2020] [Accepted: 07/27/2020] [Indexed: 11/25/2022] Open
Abstract
Purpose: High throughput panel sequencing to tailor therapy in precision oncology promises to improve outcome in patients with metastatic breast cancer. However, data that clearly show any benefit from such an approach is still pending. Materials and Methods: We performed a retrospective analysis of advanced breast cancer patients that underwent panel sequencing for suggestion of target related drugs. We aimed to (i) determine the frequency of actionable mutations per patient and to (ii) assess the clinical impact of results on treatment options. Results: A total of 52 patients underwent panel sequencing of archived tumor tissue. Every sample showed at least one affected gene, accounting for actionable mutations in 45 of 52 patients (87%). New treatment options that would not have been used as indicated by standard predictive markers (such as hormonal receptor status or HER2-status) were found in 22 of 52 patients (42%). We detected therapeutic relevant pathogenic germline variants in 9,6% (5/52) of the patients. Conclusions: Using a high throughput-panel sequencing approach to identify actionable mutations in patients with metastatic breast cancer, we identified potential target-related treatment options in a large proportion of our patients, some of which would not have been considered without this data. Prospective clinical trials with compounds targeting the identified actionable mutations are needed to determine which treatments can indeed improve survival or quality of life by limiting exposure to ineffective drugs in advanced breast cancer.
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Affiliation(s)
- Christina Walter
- Department of Women's Health, University of Tuebingen, Tuebingen, Germany
| | - Andreas Hartkopf
- Department of Women's Health, University of Tuebingen, Tuebingen, Germany
| | - Andre Koch
- Department of Women's Health, University of Tuebingen, Tuebingen, Germany
| | | | - Martin Schulze
- Praxis fuer Humangenetik and CeGaT GmbH, Tuebingen, Germany
| | - Eva-Maria Grischke
- Department of Women's Health, University of Tuebingen, Tuebingen, Germany
| | | | - Sara Brucker
- Department of Women's Health, University of Tuebingen, Tuebingen, Germany
| | - Florian Battke
- Praxis fuer Humangenetik and CeGaT GmbH, Tuebingen, Germany
| | - Saskia Biskup
- Praxis fuer Humangenetik and CeGaT GmbH, Tuebingen, Germany
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25
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Tran LS, Nguyen QTT, Nguyen CV, Tran VU, Nguyen THT, Le HT, Nguyen MLT, Le VT, Pham LS, Vo BT, Dang ATH, Nguyen LT, Nguyen TCV, Pham HAT, Tran TT, Nguyen LH, Nguyen TTT, Nguyen KHT, Vu YV, Nguyen NH, Bui VQ, Bui HH, Do TTT, Lam NV, Truong Dinh K, Phan MD, Nguyen HN, Giang H. Ultra-Deep Massive Parallel Sequencing of Plasma Cell-Free DNA Enables Large-Scale Profiling of Driver Mutations in Vietnamese Patients With Advanced Non-Small Cell Lung Cancer. Front Oncol 2020; 10:1351. [PMID: 32850431 PMCID: PMC7418519 DOI: 10.3389/fonc.2020.01351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/28/2020] [Accepted: 06/26/2020] [Indexed: 01/15/2023] Open
Abstract
Population-specific profiling of mutations in cancer genes is of critical importance for the understanding of cancer biology in general as well as the establishment of optimal diagnostics and treatment guidelines for that particular population. Although genetic analysis of tumor tissue is often used to detect mutations in cancer genes, the invasiveness and limited accessibility hinders its application in large-scale population studies. Here, we used ultra-deep massive parallel sequencing of plasma cell free DNA (cfDNA) to identify the mutation profiles of 265 Vietnamese patients with advanced non-small cell lung cancer (NSCLC). Compared to a cohort of advanced NSCLC patients characterized by sequencing of tissue samples, cfDNA genomic testing, despite lower mutation detection rates, was able to detect major mutations in tested driver genes that reflected similar mutation composition and distribution pattern, as well as major associations between mutation prevalence and clinical features. In conclusion, ultra-deep sequencing of plasma cfDNA represents an alternative approach for population-wide genetic profiling of cancer genes where recruitment of patients is limited to the accessibility of tumor tissue site.
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Affiliation(s)
| | | | | | | | | | - Ha Thu Le
- Ha Noi Oncology Hospital, Hanoi, Vietnam
| | | | | | - Lam-Son Pham
- Vietnam National Cancer Hospital, Hanoi, Vietnam
| | | | - Anh-Thu Huynh Dang
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | | | | | | | | | | | - Yen-Vi Vu
- Gene Solutions, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Nien Vinh Lam
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | | | - Hoai-Nghia Nguyen
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoa Giang
- Gene Solutions, Ho Chi Minh City, Vietnam
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26
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Salgia R, Mambetsariev I, Tan T, Schwer A, Pearlstein DP, Chehabi H, Baroz A, Fricke J, Pharaon R, Romo H, Waddington T, Babikian R, Buck L, Kulkarni P, Cianfrocca M, Djulbegovic B, Pal SK. Complex Oncological Decision-Making Utilizing Fast-and-Frugal Trees in a Community Setting-Role of Academic and Hybrid Modeling. J Clin Med 2020; 9:E1884. [PMID: 32560187 PMCID: PMC7356888 DOI: 10.3390/jcm9061884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/15/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/24/2022] Open
Abstract
Non-small cell lung cancer is a devastating disease and with the advent of targeted therapies and molecular testing, the decision-making process has become complex. While established guidelines and pathways offer some guidance, they are difficult to utilize in a busy community practice and are not always implemented in the community. The rationale of the study was to identify a cohort of patients with lung adenocarcinoma at a City of Hope community site (n = 11) and utilize their case studies to develop a decision-making framework utilizing fast-and-frugal tree (FFT) heuristics. Most patients had stage IV (N = 9, 81.8%) disease at the time of the first consultation. The most common symptoms at initial presentation were cough (N = 5, 45.5%), shortness of breath (N = 3, 27.2%), and weight loss (N = 3, 27.2%). The Eastern Cooperative Oncology Group (ECOG) performance status ranged from 0-1 in all patients in this study. Distribution of molecular drivers among the patients were as follows: EGFR (N = 5, 45.5%), KRAS (N = 2, 18.2%), ALK (N = 2, 18.2%), MET (N = 2, 18.2%), and RET (N = 1, 9.1%). Seven initial FFTs were developed for the various case scenarios, but ultimately the decisions were condensed into one FFT, a molecular stage IV FFT, that arrived at accurate decisions without sacrificing initial information. While these FFT decision trees may seem arbitrary to an experienced oncologist at an academic site, the simplicity of their utility is essential for community practice where patients often do not get molecular testing and are not assigned proper therapy.
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Affiliation(s)
- Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Tingting Tan
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Amanda Schwer
- Newport Diagnostic Center, Newport Beach, CA 92660, USA; (A.S.); (H.C.)
| | | | - Hazem Chehabi
- Newport Diagnostic Center, Newport Beach, CA 92660, USA; (A.S.); (H.C.)
| | - Angel Baroz
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Jeremy Fricke
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Rebecca Pharaon
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Hannah Romo
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Thomas Waddington
- Department of Medicine, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Razmig Babikian
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Linda Buck
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Mary Cianfrocca
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
| | - Benjamin Djulbegovic
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, CA 91010, USA;
| | - Sumanta K. Pal
- Department of Medical Oncology and Therapeutics Research, 1500 E Duarte Road, City of Hope National Medical Center, Duarte, CA 91010, USA; (I.M.); (T.T.); (A.B.); (J.F.); (R.P.); (H.R.); (R.B.); (L.B.); (P.K.); (M.C.); (S.K.P.)
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27
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Mohd Yunos RI, Ab Mutalib NS, Tieng FYF, Abu N, Jamal R. Actionable Potentials of Less Frequently Mutated Genes in Colorectal Cancer and Their Roles in Precision Medicine. Biomolecules 2020; 10:biom10030476. [PMID: 32245111 PMCID: PMC7175115 DOI: 10.3390/biom10030476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Global statistics have placed colorectal cancer (CRC) as the third most frequently diagnosed cancer and the fourth principal cause of cancer-related deaths worldwide. Improving survival for CRC is as important as early detection. Personalized medicine is important in maximizing an individual's treatment success and minimizing the risk of adverse reactions. Approaches in achieving personalized therapy in CRC have included analyses of specific genes with its clinical implications. Tumour genotyping via next-generation sequencing has become a standard practice to guide clinicians into predicting tumor behaviour, disease prognosis, and treatment response. Nevertheless, better prognostic markers are necessary to further stratify patients for personalized treatment plans. The discovery of new markers remains indispensable in providing the most effective chemotherapy in order to improve the outcomes of treatment and survival in CRC patients. This review aims to compile and discuss newly discovered, less frequently mutated genes in CRC. We also discuss how these mutations are being used to assist therapeutic decisions and their potential prospective clinical utilities. In addition, we will summarize the importance of profiling the large genomic rearrangements, gene amplification, and large deletions and how these alterations may assist in determining the best treatment option for CRC patients.
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Affiliation(s)
| | | | | | | | - Rahman Jamal
- Correspondence: (N.S.A.M.); (R.J.); Tel.: +60-3-91459073 (N.S.A.M.); +60-3-91459000 (R.J.)
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28
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Kulasinghe A, Kapeleris J, Cooper C, Warkiani ME, O'Byrne K, Punyadeera C. Phenotypic Characterization of Circulating Lung Cancer Cells for Clinically Actionable Targets. Cancers (Basel) 2019; 11:cancers11030380. [PMID: 30889898 PMCID: PMC6468795 DOI: 10.3390/cancers11030380] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 02/28/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022] Open
Abstract
Objectives: In non-small cell lung cancers (NSCLC), tumour biopsy can often be an invasive procedure. The development of a non-invasive methodology to study genetic changes via circulating tumour cells (CTCs) is an appealing concept. Whilst CTCs typically remain as rare cells, improvements in epitope-independent CTC isolation techniques has given rise to a greater capture of CTCs. In this cross sectional study, we demonstrate the capture and characterization of NSCLC CTCs for the clinically actionable markers epidermal growth factor receptor (EGFR) alterations, anaplastic lymphoma kinase (ALK) rearrangements and programmed death ligand-1 (PD-L1) expression. The study identified CTCs/CTC clusters in 26/35 Stage IV NSCLC patients, and subsequently characterized the CTCs for EGFR mutation, ALK status and PD-L1 status. This pilot study demonstrates the potential of a non-invasive fluid biopsy to determine clinically relevant biomarkers in NSCLC.
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Affiliation(s)
- Arutha Kulasinghe
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Joanna Kapeleris
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
| | - Carolina Cooper
- Department of Anatomical Pathology, Pathology Queensland, QLD 4006, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia.
| | - Majid Ebrahimi Warkiani
- The School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia.
- Department of Biomedical Engineering, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russia.
| | - Kenneth O'Byrne
- Translational Research Institute, Brisbane, QLD 4102, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia.
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Room 603D, Institute of Health and Biomedical Innovation, Queensland University of Technology, 60 Musk Avenue, Kelvin Grove, QLD 4059, Australia.
- Translational Research Institute, Brisbane, QLD 4102, Australia.
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Ahmed AA, Vundamati DS, Farooqi MS, Guest E. Precision Medicine in Pediatric Cancer: Current Applications and Future Prospects. High Throughput 2018; 7:E39. [PMID: 30551569 DOI: 10.3390/ht7040039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022] Open
Abstract
Precision oncologic medicine is an emerging approach for cancer treatment that has recently taken giant steps in solid clinical practice. Recent advances in molecular diagnostics that can analyze the individual tumor’s variability in genes have provided greater understanding and additional strategies to treat cancers. Although tumors can be tested by several molecular methods, the use of next-generation sequencing (NGS) has greatly facilitated our understanding of pediatric cancer and identified additional therapeutic opportunities. Pediatric tumors have a different genetic make-up, with a fewer number of actionable targets than adult tumors. Nevertheless, precision oncology in the pediatric population has greatly improved the survival of patients with leukemia and solid tumors. This review discusses the current status of pediatric precision oncology and the different clinical scenarios in which it can be effectively applied.
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AlDubayan SH, Giannakis M, Moore ND, Han GC, Reardon B, Hamada T, Mu XJ, Nishihara R, Qian Z, Liu L, Yurgelun MB, Syngal S, Garraway LA, Ogino S, Fuchs CS, Van Allen EM. Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet 2018; 102:401-14. [PMID: 29478780 DOI: 10.1016/j.ajhg.2018.01.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/24/2018] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) heritability has been estimated to be around 30%. However, mutations in the known CRC-susceptibility genes explain CRC risk in fewer than 10% of affected individuals. Germline mutations in DNA-repair genes (DRGs) have recently been reported in CRC, but their contribution to CRC risk is largely unknown. We evaluated the gene-level germline mutation enrichment of 40 DRGs in 680 unselected CRC individuals and 27,728 ancestry-matched cancer-free adults. Significant findings were then examined in independent cohorts of 1,661 unselected CRC individuals and 1,456 individuals with early-onset CRC. Of the 680 individuals in the discovery set, 31 (4.56%) individuals harbored germline pathogenic mutations in known CRC-susceptibility genes, and another 33 (4.85%) individuals had DRG mutations that have not been previously associated with CRC risk. Germline pathogenic mutations in ATM and PALB2 were enriched in both the discovery (OR = 2.81 and p = 0.035 for ATM and OR = 4.91 and p = 0.024 for PALB2) and validation (OR = 2.97 and adjusted p = 0.0013 for ATM and OR = 3.42 and adjusted p = 0.034 for PALB2) sets. Biallelic loss of ATM was evident in all individuals with matched tumor profiling. CRC individuals also had higher rates of actionable mutations in the HR pathway, which can substantially increase the risk of developing cancers other than CRC. Our analysis provides evidence for ATM and PALB2 as CRC-risk genes, underscoring the importance of the homologous recombination pathway in CRC. In addition, we identified frequent complete homologous recombination deficiency in CRC tumors, representing a unique opportunity to explore targeted therapeutic interventions such as poly-ADP ribose polymerase inhibitor (PARPi).
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31
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Gray PN, Vuong H, Tsai P, Lu HM, Mu W, Hsuan V, Hoo J, Shah S, Uyeda L, Fox S, Patel H, Janicek M, Brown S, Dobrea L, Wagman L, Plimack E, Mehra R, Golemis EA, Bilusic M, Zibelman M, Elliott A. TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy. Oncotarget 2018; 7:68206-68228. [PMID: 27626691 PMCID: PMC5356550 DOI: 10.18632/oncotarget.11910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 06/16/2016] [Accepted: 08/26/2016] [Indexed: 01/08/2023] Open
Abstract
The development of targeted therapies for both germline and somatic DNA mutations has increased the need for molecular profiling assays to determine the mutational status of specific genes. Moreover, the potential of off-label prescription of targeted therapies favors classifying tumors based on DNA alterations rather than traditional tissue pathology. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext, which can detect single nucleotide variants, small insertions and deletions in 142 genes that are frequently mutated in somatic and/or germline cancers. TumorNext also detects gene fusions and structural variants, such as tandem duplications and inversions, in 15 frequently disrupted oncogenes and tumor suppressors. The assay uses a matched control and custom bioinformatics pipeline to differentiate between somatic and germline mutations, allowing precise variant classification. We tested 170 previously characterized samples, of which > 95% were formalin-fixed paraffin embedded tissue from 8 different cancer types, and highlight examples where lack of germline status may have led to the inappropriate prescription of therapy. We also describe the validation of the Affymetrix OncoScan platform, an array technology for high resolution copy number variant detection for use in parallel with the NGS panel that can detect single copy amplifications and hemizygous deletions. We analyzed 80 previously characterized formalin-fixed paraffin-embedded specimens and provide examples of hemizygous deletion detection in samples with known pathogenic germline mutations. Thus, the TumorNext combined approach of NGS and OncoScan potentially allows for the identification of the “second hit” in hereditary cancer patients.
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Affiliation(s)
| | - Huy Vuong
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Pei Tsai
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Wenbo Mu
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | - Jayne Hoo
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Swati Shah
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Lisa Uyeda
- Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | | | | | | | | | | | | | | | - Ranee Mehra
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
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Chandrani P, Prabhash K, Prasad R, Sethunath V, Ranjan M, Iyer P, Aich J, Dhamne H, Iyer DN, Upadhyay P, Mohanty B, Chandna P, Kumar R, Joshi A, Noronha V, Patil V, Ramaswamy A, Karpe A, Thorat R, Chaudhari P, Ingle A, Choughule A, Dutt A. Drug-sensitive FGFR3 mutations in lung adenocarcinoma. Ann Oncol 2017; 28:597-603. [PMID: 27998968 PMCID: PMC5391708 DOI: 10.1093/annonc/mdw636] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related deaths across the world. In this study, we present therapeutically relevant genetic alterations in lung adenocarcinoma of Indian origin. MATERIALS AND METHODS Forty-five primary lung adenocarcinoma tumors were sequenced for 676 amplicons using RainDance cancer panel at an average coverage of 1500 × (reads per million mapped reads). To validate the findings, 49 mutations across 23 genes were genotyped in an additional set of 363 primary lung adenocarcinoma tumors using mass spectrometry. NIH/3T3 cells over expressing mutant and wild-type FGFR3 constructs were characterized for anchorage independent growth, constitutive activation, tumor formation and sensitivity to FGFR inhibitors using in vitro and xenograft mouse models. RESULTS We present the first spectrum of actionable alterations in lung adenocarcinoma tumors of Indian origin, and shows that mutations of FGFR3 are present in 20 of 363 (5.5%) patients. These FGFR3 mutations are constitutively active and oncogenic when ectopically expressed in NIH/3T3 cells and using a xenograft model in NOD/SCID mice. Inhibition of FGFR3 kinase activity inhibits transformation of NIH/3T3 overexpressing FGFR3 constructs and growth of tumors driven by FGFR3 in the xenograft models. The reduction in tumor size in the mouse is paralleled by a reduction in the amounts of phospho-ERK, validating the in vitro findings. Interestingly, the FGFR3 mutations are significantly higher in a proportion of younger patients and show a trend toward better overall survival, compared with patients lacking actionable alterations or those harboring KRAS mutations. CONCLUSION We present the first actionable mutation spectrum in Indian lung cancer genome. These findings implicate FGFR3 as a novel therapeutic in lung adenocarcinoma.
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Affiliation(s)
- P. Chandrani
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - K. Prabhash
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Prasad
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - V. Sethunath
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - M. Ranjan
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - J. Aich
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - H. Dhamne
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - D. N. Iyer
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Upadhyay
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
| | - B. Mohanty
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - P. Chandna
- AceProbe Technologies Pvt. Ltd, New Delhi, India
| | - R. Kumar
- Department of Pathology, Tata Memorial Hospital
| | - A. Joshi
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Noronha
- Department of Medical Oncology, Tata Memorial Hospital
| | - V. Patil
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Ramaswamy
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Karpe
- Department of Medical Oncology, Tata Memorial Hospital
| | - R. Thorat
- Department of Pathology, Tata Memorial Hospital
| | - P. Chaudhari
- Small Animal Imaging Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Ingle
- Laboratory Animal Facility, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
| | - A. Choughule
- Department of Medical Oncology, Tata Memorial Hospital
| | - A. Dutt
- Integrated Genomics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai
- Correspondence to: Dr Amit Dutt, Wellcome Trust/DBT India Alliance Intermediate Fellow, Tata Memorial Centre, ACTREC, Navi Mumbai 410 210, India. Tel: +91-22-27405056; E-mail:
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Dumur CI. Available resources and challenges for the clinical annotation of somatic variations. Cancer Cytopathol 2014; 122:730-6. [PMID: 25111663 PMCID: PMC4231254 DOI: 10.1002/cncy.21471] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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] [Received: 06/11/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a number of such resources that have been designed to catalog and mine a plethora of germline variants or mutations. However, when analyzing tumor specimens in clinical settings, one may need to use different or ancillary resources that are specific for somatic variants or actionable mutations that may have clinical or treatment implications. The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology. In addition, the current need for collating various annotation sources into one-stop solutions to facilitate faster query execution and better integration into existing laboratory information systems are discussed.
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Affiliation(s)
- Catherine I Dumur
- Department of Pathology, Virginia Commonwealth UniversityRichmond, Virginia
- Corresponding author: Catherine I. Dumur, PhD, Department of Pathology, Virginia Commonwealth University, Clinical Support Center, Room 247, 403 North 13th Street, Richmond, VA 23298; Fax: (804) 827-4738;
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Lee J, Kim KM, Kang WK, Ou SHI. Innovative personalized medicine in gastric cancer: time to move forward. Clin Genet 2014; 86:37-43. [PMID: 24749947 DOI: 10.1111/cge.12408] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 01/15/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/13/2022]
Abstract
Globally, gastric cancer (GC) is the second leading cancer cause of death. To date, only one targeted therapy trial generated positive survival outcomes in a selected population among many targeted therapy trials. This trial showed the addition of trastuzumab to fluoropyrimidine/platinum chemotherapy as first-line chemotherapy for human epidermal growth factor receptor 2 (HER2)-positive GC that resulted in an overall survival (OS) benefit. The increasing use of next generation sequencing approach to genomically profile GC patients allows the identification of many more GC patients who could benefit from specific targeted agents. Here we provide a comprehensive review of targeted therapy trials in GC and discuss future potential actionable driver mutations in GC.
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Affiliation(s)
- J Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center,Sungkyunkwan University School of Medicine, Seoul, South Korea
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