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Dutta R, Vallurupalli M, McVeigh Q, Huang FW, Rebbeck TR. Understanding inequities in precision oncology diagnostics. NATURE CANCER 2023; 4:787-794. [PMID: 37248397 DOI: 10.1038/s43018-023-00568-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/13/2023] [Indexed: 05/31/2023]
Abstract
Advances in molecular diagnostics have enabled the identification of targetable driver pathogenic variants, forming the basis of precision oncology care. However, the adoption of new technologies, such as next-generation sequencing (NGS) panels, can exacerbate healthcare disparities. Here, we summarize data on use patterns of advanced biomarker testing, highlight the disparities in both accessing NGS testing and using this data to match patients to appropriate personalized therapies and propose multidisciplinary strategies to address inequities looking forward.
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Affiliation(s)
- Ritika Dutta
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Mounica Vallurupalli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Quinn McVeigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute, Cambridge, MA, USA
| | - Franklin W Huang
- Cancer Program, Broad Institute, Cambridge, MA, USA.
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- San Francisco Veterans Health Care System, San Francisco, CA, USA.
| | - Timothy R Rebbeck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard TH Chan School of Public Health, Boston, MA, USA.
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2
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Wilmott JS, Tawbi H, Engh JA, Amankulor N, Shivalingam B, Banerjee H, Vergara IA, Lee H, Johansson PA, Ferguson PM, Saiag P, Robert C, Grob JJ, Butterfield LH, Scolyer RA, Kirkwood JM, Long GV, Davies MA. Clinical Features Associated with Outcomes and Biomarker Analysis of Dabrafenib plus Trametinib Treatment in Patients with BRAF-Mutant Melanoma Brain Metastases. Clin Cancer Res 2023; 29:521-531. [PMID: 36477181 PMCID: PMC9898142 DOI: 10.1158/1078-0432.ccr-22-2581] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE This study aimed to identify baseline clinical features associated with the outcomes of patients enrolled in the COMBI-MB phase II study of dabrafenib and trametinib treatment in patients with V600 BRAF-mutant metastatic melanoma with melanoma brain metastases (MBM). Exploratory biomarker analysis was also conducted as part of the synergistic COMBI-BRV trial (BRV116521), to identify molecular and immunologic changes associated with dabrafenib in MBMs and extracranial metastases (ECM). PATIENTS AND METHODS Post hoc analysis was performed for baseline features of patients (n = 125) enrolled in COMBI-MB. Analyses were performed to identify baseline clinical features associated with intracranial response rate (ICRR), progression-free survival (PFS), and overall survival (OS). Exploratory biomarker analysis was performed on biospecimen collected in the COMBI-BRV trial in which patients with BRAF-mutant, resectable MBM were treated with dabrafenib for 10 to 14 days prior to craniotomy. Accessible ECM were resected or biopsied at the time of craniotomy. Biospecimens underwent molecular and immunologic profiling for comparative analyses. RESULTS In COMBI-MB baseline treatment with corticosteroids was independently associated with lower ICRR [39% vs. 63%; OR, 0.323; 95 % confidence interval (CI), 0.105-0.996; P = 0.049] and shorter PFS (HR, 1.93; 95% CI, 1.06-3.51; P = 0.031). Additional significant associations identified in the multivariate analysis were improved PFS in patients with a BRAFV600E genotype (HR, 0.565; 95% CI, 0.321-0.996; P = 0.048) and improved OS in patients with Eastern Cooperative Oncology Group 0 (HR, 0.44; 95% CI, 0.25-0.78; P = 0.005). CONCLUSIONS Corticosteroid treatment was associated with reduced ICRR and PFS in COMBI-MB, similar to results with immunotherapy for MBMs. Baseline corticosteroid treatment is a key factor to consider in MBM patient management and clinical trial design/interpretation.
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Affiliation(s)
- James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Hussein Tawbi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Johnathan A Engh
- The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Nduka Amankulor
- The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Brindha Shivalingam
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Department of Neurosurgery, Royal Prince Alfred Hospital, NSW, Australia
| | - Hiya Banerjee
- Novartis Pharmaceuticals Corporation, Basel, Switzerland
| | - Ismael A. Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Hansol Lee
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Peter A. Johansson
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Philippe Saiag
- Dermatology Department, Ambroise Paré Hospital, APHP, Versailles University – Paris-Saclay, Boulogne-Billancourt, France
| | - Caroline Robert
- Gustave Roussy and Paris Saclay University, Villejuif, France
| | | | - Lisa H. Butterfield
- The Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - John M Kirkwood
- The University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia,Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
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3
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Meggendorfer M, Jobanputra V, Wrzeszczynski KO, Roepman P, de Bruijn E, Cuppen E, Buttner R, Caldas C, Grimmond S, Mullighan CG, Elemento O, Rosenquist R, Schuh A, Haferlach T. Analytical demands to use whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:16-22. [PMID: 34119643 DOI: 10.1016/j.semcancer.2021.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/24/2022]
Abstract
Interrogating the tumor genome in its entirety by whole-genome sequencing (WGS) offers an unprecedented insight into the biology and pathogenesis of cancer, with potential impact on diagnostics, prognostication and therapy selection. WGS is able to detect sequence as well as structural variants and thereby combines central domains of cytogenetics and molecular genetics. Given the potential of WGS in directing targeted therapeutics and clinical decision-making, we envision a gradual transition of the method from research to clinical routine. This review is one out of three within this issue aimed at facilitating this effort, by discussing in-depth analytical validation, clinical interpretation and clinical utility of WGS. The review highlights the requirements for implementing, validating and maintaining a clinical WGS pipeline to obtain high-quality patient-specific data in accordance with the local regulatory landscape. Every step of the WGS pipeline, which includes DNA extraction, library preparation, sequencing, bioinformatics analysis, and data storage, is considered with respect to its logistics, necessities, potential pitfalls, and the required quality management. WGS is likely to drive clinical diagnostics and patient care forward, if requirements and challenges of the technique are recognized and met.
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Affiliation(s)
| | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, USA; Columbia University Medical Center, 650 W 168th St, New York, USA
| | | | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, USA
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
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4
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Furukawa K, Hatakeyama K, Terashima M, Nagashima T, Urakami K, Ohshima K, Notsu A, Sugino T, Yagi T, Fujiya K, Kamiya S, Hikage M, Tanizawa Y, Bando E, Kanai Y, Akiyama Y, Yamaguchi K. Molecular classification of gastric cancer predicts survival in patients undergoing radical gastrectomy based on project HOPE. Gastric Cancer 2022; 25:138-148. [PMID: 34476642 DOI: 10.1007/s10120-021-01242-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer (GC) has been classified based on molecular profiling like The Cancer Genome Atlas (TCGA) and Asian Cancer Research Group (ACRG), and attempts have been made to establish therapeutic strategies based on these classifications. However, it is difficult to predict the survival according to these classifications especially in radically resected patients. We aimed to establish a new molecular classification of GC which predicts the survival in patients undergoing radical gastrectomy. METHODS The present study included 499 Japanese patients with advanced GC undergoing radical (R0/R1) gastrectomy. Whole-exome sequencing, panel sequencing, and gene expression profiling were conducted (High-tech Omics-based Patient Evaluation [Project HOPE]). We classified patients according to TCGA and ACRG subtypes, and evaluated the clinicopathologic features and survival. Then, we attempted to classify patients according to their molecular profiles associated with biological features and survival (HOPE classification). RESULTS TCGA and ACRG classifications failed to predict the survival. In HOPE classification, hypermutated (HMT) tumors were selected first as a distinctive feature, and T-cell-inflamed expression signature-high (TCI) tumors were then extracted. Finally, the remaining tumors were divided by the epithelial-mesenchymal transition (EMT) expression signature. HOPE classification significantly predicted the disease-specific and overall survival (p < 0.001 and 0.020, respectively). HMT + TCI showed the best survival, while EMT-high showed the worst survival. The HOPE classification was successfully validated in the TCGA cohort. CONCLUSIONS We established a new molecular classification of gastric cancer that predicts the survival in patients undergoing radical surgery.
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Affiliation(s)
- Kenichiro Furukawa
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.,Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.,SRL Inc., Shinjuku Mitsui Building, 2-1-1 Nishishinjuku, Shinjuku, Tokyo, 163-0403, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Akifumi Notsu
- Clinical Research Center, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo,Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Taisuke Yagi
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Keiichi Fujiya
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Satoshi Kamiya
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Makoto Hikage
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yutaka Tanizawa
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Etsuro Bando
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
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5
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Calvanese F, Jacquesson T, Manet R, Vasiljevic A, Lasolle H, Ducray F, Raverot G, Jouanneau E. Neoadjuvant B-RAF and MEK Inhibitor Targeted Therapy for Adult Papillary Craniopharyngiomas: A New Treatment Paradigm. Front Endocrinol (Lausanne) 2022; 13:882381. [PMID: 35757402 PMCID: PMC9228029 DOI: 10.3389/fendo.2022.882381] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/04/2022] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Surgical and clinical management of craniopharyngiomas is associated with high long-term morbidity especially in the case of hypothalamic involvement. Improvements in knowledge of craniopharyngioma molecular biology may offer the possibility of safe and effective medical neoadjuvant treatments in a subset of patients harboring papillary subtype tumors with a BRAFV600E mutation. METHOD We report herein two cases of tubero-infundibular and ventricular Papillary Craniopharyngiomas in which BRAF/MEK inhibitor combined therapy was used as adjuvant (Case 1) or neoadjuvant (Case 2) treatment, with a 90% reduction in tumor volume observed after only 5 months. In Case 2 the only surgical procedure used was a minimal invasive biopsy by the trans-ventricular neuroendoscopic approach. As a consequence, targeted therapy was administered in purely neoadjuvant fashion. After shrinkage of the tumor, both patients underwent fractionated radiotherapy on the small tumor remnant to achieve long-term tumor control. A review of a previously reported case has also been performed. RESULT This approach led to tumor control with minimal long-term morbidity in both cases. No side effects or complications were reported after medical treatment and adjuvant radiotherapy. CONCLUSION Our experience and a review of the literature argue for a change in the current treatment paradigm for Craniopharyngiomas (CPs). In giant and invasive tumors, confirmation of BRAFV600E mutated PCPs by biopsy and BRAF/MEK inhibitor therapy before proposing other treatments may be useful to improve long term outcomes for patients.
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Affiliation(s)
- Francesco Calvanese
- Pituitary and Skull Base Neurosurgical Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Pierre Wertheimer, Lyon, France
- Department of Neurosurgery, I.R.C.C.S. San Raffaele Scientific Institute, Vita-Salute University, Milan, Italy
- *Correspondence: Francesco Calvanese, ; orcid.org/0000-0002-0966-2487
| | - Timothée Jacquesson
- Pituitary and Skull Base Neurosurgical Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Pierre Wertheimer, Lyon, France
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- CREATIS Laboratory CNRS UMR5220, Inserm U1206, INSA-Lyon, University of Lyon 1, Lyon, France
| | - Romain Manet
- Pituitary and Skull Base Neurosurgical Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Pierre Wertheimer, Lyon, France
| | - Alexandre Vasiljevic
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- Department of Pathology, Groupement Hospitalier, Lyon, France
- INSERM U1052, CNRS UMR5286, Cancer Research Center of Lyon, Lyon, France
- INSERM U1028, CNRS UMR5292, Lyon Neuroscience Research Center, Neuro-Oncology & Neuro–Inflammation Team, Lyon, France
| | - Hélène Lasolle
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- INSERM U1052, CNRS UMR5286, Cancer Research Center of Lyon, Lyon, France
- Endocrinology Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Louis Pradel, Lyon, France
| | - Francois Ducray
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- Cancerology Research Center of Lyon, INSERM U1052, CNRS UMR 5286, Cancer Cell Plasticity Department, Transcriptome Diversity in Stem Cells Laboratory, Lyon, France
- Service of Neuro-Oncology, Hospices Civils de Lyon, Groupement Hospitalier Est, Neurology Hospital, Lyon, France
| | - Gerald Raverot
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- INSERM U1052, CNRS UMR5286, Cancer Research Center of Lyon, Lyon, France
- Endocrinology Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Louis Pradel, Lyon, France
| | - Emmanuel Jouanneau
- Pituitary and Skull Base Neurosurgical Department, Reference Center for Rare Pituitary Diseases HYPO, “Groupement Hospitalier Est” Hospices Civils de Lyon, “Claude Bernard” Lyon 1 University, Hôpital Pierre Wertheimer, Lyon, France
- Lyon University, Université Claude Bernard Lyon 1, Lyon, France
- CREATIS Laboratory CNRS UMR5220, Inserm U1206, INSA-Lyon, University of Lyon 1, Lyon, France
- INSERM U1052, CNRS UMR5286, Cancer Research Center of Lyon, Lyon, France
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6
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Yam C, Ma BBY, Yap TA. Global Implementation of Precision Oncology. JCO Precis Oncol 2021; 5:PO.21.00001. [PMID: 34250385 PMCID: PMC8232074 DOI: 10.1200/po.21.00001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/17/2021] [Indexed: 01/12/2023] Open
Affiliation(s)
- Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brigette B Y Ma
- Department of Clinical Oncology, Phase I Clinical Trial Center, Kingboard Precision Oncology Program, The Chinese University of Hong Kong, Hong Kong, China
| | - Timothy A Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX.,Khalifa Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.,The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Qu M, Lian B, Wang Y, Zhang W, Zhu F, Wang T, Yue X, Jia Z, Chen H, Li H, Li J, Gao X. Transperineal Parallel Biopsy of the Prostate: A New Approach of Tissue Sampling for Precision Medicine. Int J Gen Med 2021; 14:1631-1640. [PMID: 33976563 PMCID: PMC8104976 DOI: 10.2147/ijgm.s302105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/30/2021] [Indexed: 12/26/2022] Open
Abstract
Purpose Through an observational study to present a new approach for obtaining high-quality samples for the targeted therapy of prostate cancer. Patients and Methods Parallel biopsy, which was defined as collecting the tissue from the same site by two biopsies, was performed on patients with elevated PSA. Each tissue was stained by ink to identify the pathological characteristics, including Gleason score and tumor tissue ratio. Kendall tau-b test and intraclass correlation coefficient test were used to compare the consistency between each paired sample. Then, based on the pathology of the biopsies, high-quality tissues would be selected for sequencing, and PyClone model was used to track the clonal evolution. Results In total, 252 pairs of biopsies were collected. The consistency of Gleason score between each paired biopsy is 0.777 (p<0.01), and the consistency of tumor tissue ratio is 0.853 (p<0.01). With the application of parallel biopsy, on average five nonsynonymous mutations could be identified in patients with castration-resistant prostate cancer. Six out of eight had at least one biology-relevant alteration in patients, guiding further treatment. Meanwhile, clonal evolution was constructed to investigate the progress of tumor. Conclusion Parallel biopsy is a reliable approach to collect high-quality tissue and shows potential application in precision medicine.
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Affiliation(s)
- Min Qu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Bijun Lian
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Department of Urology, The 903th PLA Hospital, Hangzhou, People's Republic of China
| | - Yan Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Wenhui Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Feng Zhu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Department of Urology, Tianyou Hospital, Tongji University, Shanghai, People's Republic of China
| | - Tao Wang
- Department of Urology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, People's Republic of China
| | - Xiaodong Yue
- Shanghai Institute for Advanced Communication and Data Science, Shanghai University, Shanghai, People's Republic of China
| | - Zepeng Jia
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Huan Chen
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Husheng Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
| | - Jing Li
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China.,Center for Translational Medicine, Second Military Medical University, Shanghai, People's Republic of China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, People's Republic of China
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8
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Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro JB, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D'Andrea AD. Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res 2021; 81:2774-2787. [PMID: 33514515 DOI: 10.1158/0008-5472.can-20-2912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/17/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR)-deficient cancers are sensitive to poly-ADP ribose polymerase inhibitors (PARPi), which have shown clinical efficacy in the treatment of high-grade serous cancers (HGSC). However, the majority of patients will relapse, and acquired PARPi resistance is emerging as a pressing clinical problem. Here we generated seven single-cell clones with acquired PARPi resistance derived from a PARPi-sensitive TP53 -/- and BRCA1 -/- epithelial cell line generated using CRISPR/Cas9. These clones showed diverse resistance mechanisms, and some clones presented with multiple mechanisms of resistance at the same time. Genomic analysis of the clones revealed unique transcriptional and mutational profiles and increased genomic instability in comparison with a PARPi-sensitive cell line. Clonal evolutionary analyses suggested that acquired PARPi resistance arose via clonal selection from an intrinsically unstable and heterogenous cell population in the sensitive cell line, which contained preexisting drug-tolerant cells. Similarly, clonal and spatial heterogeneity in tumor biopsies from a clinical patient with BRCA1-mutant HGSC with acquired PARPi resistance was observed. In an imaging-based drug screening, the clones showed heterogenous responses to targeted therapeutic agents, indicating that not all PARPi-resistant clones can be targeted with just one therapy. Furthermore, PARPi-resistant clones showed mechanism-dependent vulnerabilities to the selected agents, demonstrating that a deeper understanding on the mechanisms of resistance could lead to improved targeting and biomarkers for HGSC with acquired PARPi resistance. SIGNIFICANCE: This study shows that BRCA1-deficient cells can give rise to multiple genomically and functionally heterogenous PARPi-resistant clones, which are associated with various vulnerabilities that can be targeted in a mechanism-specific manner.
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Affiliation(s)
- Anniina Färkkilä
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Alfredo Rodríguez
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jaana Oikkonen
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Julieta Domínguez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sandra Ramos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Caitlin E Mills
- Laboratory of Systems Pharmacology, Harvard Medical School, Massachusetts
| | - Fernando Pérez-Villatoro
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lisa A Moreau
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Massachusetts
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Sara Frias
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México.,Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, México
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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9
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Chong IY, Starling N, Rust A, Alexander J, Aronson L, Llorca-Cardenosa M, Chauhan R, Chaudry A, Kumar S, Fenwick K, Assiotis I, Matthews N, Begum R, Wotherspoon A, Terlizzo M, Watkins D, Chau I, Lord CJ, Haider S, Rao S, Cunningham D. The Mutational Concordance of Fixed Formalin Paraffin Embedded and Fresh Frozen Gastro-Oesophageal Tumours Using Whole Exome Sequencing. J Clin Med 2021; 10:E215. [PMID: 33435284 PMCID: PMC7826535 DOI: 10.3390/jcm10020215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/01/2021] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
1. BACKGROUND The application of massively parallel sequencing has led to the identification of aberrant druggable pathways and somatic mutations within therapeutically relevant genes in gastro-oesophageal cancer. Given the widespread use of formalin-fixed paraffin-embedded (FFPE) samples in the study of this disease, it would be beneficial, especially for the purposes of biomarker evaluation, to assess the concordance between comprehensive exome-wide sequencing data from archival FFPE samples originating from a prospective clinical study and those derived from fresh-frozen material. 2. METHODS We analysed whole-exome sequencing data to define the mutational concordance of 16 matched fresh-frozen and FFPE gastro-oesophageal tumours (N = 32) from a prospective clinical study. We assessed DNA integrity prior to sequencing and then identified coding mutations in genes that have previously been implicated in other cancers. In addition, we calculated the mutant-allele heterogeneity (MATH) for these samples. 3. RESULTS Although there was increased degradation of DNA in FFPE samples compared with frozen samples, sequencing data from only two FFPE samples failed to reach an adequate mapping quality threshold. Using a filtering threshold of mutant read counts of at least ten and a minimum of 5% variant allele frequency (VAF) we found that there was a high median mutational concordance of 97% (range 80.1-98.68%) between fresh-frozen and FFPE gastro-oesophageal tumour-derived exomes. However, the majority of FFPE tumours had higher mutant-allele heterogeneity (MATH) scores when compared with corresponding frozen tumours (p < 0.001), suggesting that FFPE-based exome sequencing is likely to over-represent tumour heterogeneity in FFPE samples compared to fresh-frozen samples. Furthermore, we identified coding mutations in 120 cancer-related genes, including those associated with chromatin remodelling and Wnt/β-catenin and Receptor Tyrosine Kinase signalling. 4. CONCLUSIONS These data suggest that comprehensive genomic data can be generated from exome sequencing of selected DNA samples extracted from archival FFPE gastro-oesophageal tumour tissues within the context of prospective clinical trials.
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Affiliation(s)
- Irene Y. Chong
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Naureen Starling
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Alistair Rust
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - John Alexander
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Lauren Aronson
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
| | - Marta Llorca-Cardenosa
- The Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (L.A.); (M.L.-C.)
| | - Ritika Chauhan
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Asif Chaudry
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Sacheen Kumar
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Kerry Fenwick
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Ioannis Assiotis
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Nik Matthews
- The Tissue Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (A.R.); (R.C.); (K.F.); (I.A.); (N.M.)
| | - Ruwaida Begum
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Andrew Wotherspoon
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Monica Terlizzo
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - David Watkins
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Ian Chau
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - Christopher J. Lord
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; (J.A.); (C.J.L.); (S.H.)
| | - Sheela Rao
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
| | - David Cunningham
- The Royal Marsden Hospital NHS Foundation Trust, 203 Fulham Road, London SW3 6JJ, UK; (N.S.); (A.C.); (S.K.); (R.B.); (A.W.); (M.T.); (D.W.); (I.C.); (S.R.); (D.C.)
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10
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Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn 2020; 23:375-388. [PMID: 33387698 DOI: 10.1016/j.jmoldx.2020.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/20/2020] [Accepted: 12/14/2020] [Indexed: 11/22/2022] Open
Abstract
DNA junctions (DNAJs) frequently impact clinically relevant genes in tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. Through optimized whole-genome sequencing and specialized bioinformatics algorithms, complete structural variance analysis is reported, including DNAJs, from formalin-fixed DNA. Selective library assembly from larger fragments (>500 bp) and economical sequencing depths (300 to 400 million reads) provide representative genomic coverage profiles and increased allelic coverage to levels compatible with DNAJ calling (40× to 60×). Although consistently fragmented, more recently formalin-fixed, specimens (<2 years' storage) revealed consistent populations of larger DNA fragments. Optimized bioinformatics efficiently detected >90% of DNAJs in two prostate tumors (approximately 60% tumor) previously analyzed by mate-pair sequencing on fresh frozen tissue, with evidence of at least one spanning-read in 99% of DNAJs. Rigorous masking with data from unrelated formalin-fixed tissue progressively eliminated many false-positive DNAJs, without loss of true positives, resulting in low numbers of false-positive passing current filters. This methodology enables more comprehensive clinical genomics testing on formalin-fixed clinical specimens.
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11
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Rabbie R, Ansari-Pour N, Cast O, Lau D, Scott F, Welsh SJ, Parkinson C, Khoja L, Moore L, Tullett M, Wong K, Ferreira I, Gómez JMM, Levesque M, Gallagher FA, Jiménez-Sánchez A, Riva L, Miller ML, Allinson K, Campbell PJ, Corrie P, Wedge DC, Adams DJ. Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases. Nat Commun 2020; 11:4306. [PMID: 32855398 PMCID: PMC7453196 DOI: 10.1038/s41467-020-18060-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/27/2020] [Indexed: 01/06/2023] Open
Abstract
Metastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.
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Affiliation(s)
- Roy Rabbie
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oliver Cast
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Doreen Lau
- Department of Radiology, School of Clinical Medicine, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, UK
| | - Francis Scott
- Department of Radiology, School of Clinical Medicine, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, UK
| | - Sarah J Welsh
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Christine Parkinson
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Leila Khoja
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, Vincent Drive, University of Birmingham, Birmingham, UK
| | - Luiza Moore
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mark Tullett
- St Richard's Hospital, Spitalfield Lane, Chichester, UK
| | - Kim Wong
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Ingrid Ferreira
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Julia M Martínez Gómez
- Department of Dermatology, University of Zurich, University of Zurich Hospital, Gloriastrasse 31, CH-8091, Zurich, Switzerland
| | - Mitchell Levesque
- Department of Dermatology, University of Zurich, University of Zurich Hospital, Gloriastrasse 31, CH-8091, Zurich, Switzerland
| | - Ferdia A Gallagher
- Department of Radiology, School of Clinical Medicine, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, UK
| | - Alejandro Jiménez-Sánchez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Laura Riva
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Kieren Allinson
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Peter J Campbell
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Pippa Corrie
- Cambridge Cancer Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK.
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.
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12
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Mathieson W, Thomas GA. Why Formalin-fixed, Paraffin-embedded Biospecimens Must Be Used in Genomic Medicine: An Evidence-based Review and Conclusion. J Histochem Cytochem 2020; 68:543-552. [PMID: 32697619 PMCID: PMC7400666 DOI: 10.1369/0022155420945050] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fresh-frozen tissue is the “gold standard” biospecimen type for next-generation sequencing (NGS). However, collecting frozen tissue is usually not feasible because clinical workflows deliver formalin-fixed, paraffin-embedded (FFPE) tissue blocks. Some clinicians and researchers are reticent to embrace the use of FFPE tissue for NGS because FFPE tissue can yield low quantities of degraded DNA, containing formalin-induced mutations. We describe the process by which formalin-induced deamination can lead to artifactual cytosine (C) to thymine (T) and guanine (G) to adenine (A) (C:G > T:A) mutation calls and perform a literature review of 17 publications that compare NGS data from patient-matched fresh-frozen and FFPE tissue blocks. We conclude that although it is indeed true that sequencing data from FFPE tissue can be poorer than those from frozen tissue, any differences occur at an inconsequential magnitude, and FFPE biospecimens can be used in genomic medicine with confidence:
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13
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de Schaetzen van Brienen L, Larmuseau M, Van der Eecken K, De Ryck F, Robbe P, Schuh A, Fostier J, Ost P, Marchal K. Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples. BMC Med Genomics 2020; 13:94. [PMID: 32631411 PMCID: PMC7336445 DOI: 10.1186/s12920-020-00746-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/22/2020] [Indexed: 02/04/2023] Open
Abstract
Background Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor. Methods Four variant callers (i.e. Strelka2, Mutect2, VarScan2 and Shimmer) were used to call somatic variants on matching FF and FFPE WGS samples from a metastatic prostate tumor. Using the variants identified by these callers, we developed a heuristic to maximize the overlap between the FF and its FFPE counterpart in terms of sensitivity and precision. The proposed variant calling approach was then validated on nine matched primary samples. Finally, we assessed what fraction of the discrepancy could be attributed to intra-tumor heterogeneity (ITH), by comparing the overlap in clonal and subclonal somatic variants. Results We first compared variants between an FF and an FFPE sample from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between callers. Combining the variants of the different callers using a simple heuristic, increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to ITH. Conclusion This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.
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Affiliation(s)
- Louise de Schaetzen van Brienen
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, Ghent, Belgium
| | - Maarten Larmuseau
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, Ghent, Belgium
| | - Kim Van der Eecken
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
| | - Frederic De Ryck
- Department of Vascular Surgery, Ghent University Hospital, Ghent, Belgium
| | - Pauline Robbe
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, University of Oxford, Oxford, United Kingdom.,Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Anna Schuh
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Jan Fostier
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, Ghent, Belgium
| | - Piet Ost
- Department of Radiotherapy, Ghent University Hospital, Ghent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Department of Information Technology, IDLab, imec, iGent Toren, Ghent, Belgium. .,Department of Genetics, University of Pretoria, Pretoria, SA, South Africa.
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14
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Wei S, Levy B, Hoffman N, Cujar C, Rodney-Sandy R, Wapner R, D'Alton M, Williams Z. A rapid and simple bead-bashing-based method for genomic DNA extraction from mammalian tissue. Biotechniques 2020; 68:240-244. [PMID: 32054310 PMCID: PMC7252492 DOI: 10.2144/btn-2019-0172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Conventional genomic DNA (gDNA) extraction methods can take hours to complete, may require fume hoods and represent the most time-consuming step in many gDNA-based molecular assays. We systematically optimized a bead bashing-based (BBB) approach for rapid gDNA extraction without the need for a fume hood. Human tissue specimens (n = 34) subjected to the 12-min BBB method yielded 0.40 ± 0.17 (mean ± SD) μg of gDNA per milligram of tissue, sufficient for many downstream applications, and 3- and 6-min extensions resulted in an additional 0.43 ± 0.23 μg and 0.48 ± 0.43 μg per milligram of tissue, respectively. The BBB method provides a simple and rapid method for gDNA extraction from mammalian tissue that is applicable to time-sensitive clinical applications.
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Affiliation(s)
- Shan Wei
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Nataly Hoffman
- Clinical Cytogenetics Laboratory, Columbia University Medical Center & the New York Presbyterian Hospital, New York, NY 10032, USA
| | - Claudia Cujar
- Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Reunet Rodney-Sandy
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ronald Wapner
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mary D'Alton
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zev Williams
- Department of Obstetrics & Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
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15
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Gao XH, Li J, Gong HF, Yu GY, Liu P, Hao LQ, Liu LJ, Bai CG, Zhang W. Comparison of Fresh Frozen Tissue With Formalin-Fixed Paraffin-Embedded Tissue for Mutation Analysis Using a Multi-Gene Panel in Patients With Colorectal Cancer. Front Oncol 2020; 10:310. [PMID: 32232001 PMCID: PMC7083147 DOI: 10.3389/fonc.2020.00310] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 02/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Next generation sequencing (NGS)-based multi-gene panel tests have been performed to predict the treatment response and prognosis in patients with colorectal cancer (CRC). Whether the multi-gene mutation results of formalin-fixed paraffin-embedded (FFPE) tissues are identical to those of fresh frozen tissues remains unknown. Methods: A 22-gene panel with 103 hotspots was used to detect mutations in paired fresh frozen tissue and FFPE tissue from 118 patients with CRC. Results: In our study, 117 patients (99.2%) had one or more variants, with 226 variants in FFPE tissue and 221 in fresh frozen tissue. Of the 129 variants identified in this study, 96 variants were present in both FFPE and fresh frozen tissues; 27 variants were found in FFPE tissues only; 6 variants were found only in fresh frozen tissues. The mutation results demonstrated >94.0% concordance in all variants, with Kappa coefficient >0.500 in 64.3% (83/129) of variants. At the gene level, concordance ranged from 73.8 to 100.0%, with Kappa coefficient >0.500 in 81.3% (13/16) of genes. Conclusions: The results of mutation analysis performed with a multi-gene panel and FFPE and fresh frozen tissue were highly concordant in patients with CRC, at both the variant and gene levels. There were, however, some important differences in mutation results between the two tissue types. Therefore, fresh frozen tissue should not routinely be replaced with FFPE tissue for mutation analysis with a multi-gene panel. Rather, FFPE tissue is a reasonable alternative for fresh frozen tissue when the latter is unavailable.
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Affiliation(s)
- Xian Hua Gao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Juan Li
- Department of Nephrology, Changhai Hospital, Shanghai, China
| | - Hai Feng Gong
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Guan Yu Yu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Peng Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Li Qiang Hao
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Lian Jie Liu
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
| | - Chen Guang Bai
- Department of Pathology, Changhai Hospital, Shanghai, China
| | - Wei Zhang
- Department of Colorectal Surgery, Changhai Hospital, Shanghai, China
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16
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Nechifor-Boilă A, Banescu C, Zahan AE, Moldovan V, Szasz E, Borda A. DNA isolation from achieved formalin-fixed paraffin-embedded tissues in a series of 212 thyroid carcinoma cases: the influence of preanalytical factors on DNA quantity and purity. J Investig Med 2019; 68:792-798. [PMID: 31801793 DOI: 10.1136/jim-2019-001134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2019] [Indexed: 11/03/2022]
Abstract
OBJECTIVE The present study aimed to investigate the influence of several important preanalytical factors (storage period of the tumor block, maximal diameter of the tumor circled area, tumor volume and tumor fraction) on the isolated DNA from formalin-fixed paraffin-embedded (FFPE) tissues in a series of thyroid carcinomas. DESIGN Our study included 212 FFPE blocks, archived in the Department of Pathology, Târgu-Mureș Emergency County Hospital for up to 10 years. DNA isolation was performed using a commercially available kit (MasterPure DNA purification kit, Epicentre). The DNA parameters (concentration and purity) were determined using a spectrophotometer and the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) for an accurate and sensitive DNA quantification. RESULTS The mean DNA concentration and purity for the study cases were 489.3±372.6 ng/µl and 1.667±0.1912, respectively. The DNA concentration was correlated with the maximal diameter of the tumor circled area (p<0.0001), the tumor volume (p<0.0001) and tumor fraction (p=0.0462). No statistically significant differences both in terms of DNA concentration (p=0.374) and purity (p=0.125) in relation with the storage period of the tumor blocks were observed. When using a fluorometric quantification method, the DNA concentration was lower (mean DNA concentration: 47.15±32.85 ng/µl), but similar correlations with the morphological factors were observed. Apart for three cases, the real-time PCR amplification of the BRAF gene was successfully assessed in all cases. CONCLUSION The maximal diameter of the tumor circled area, tumor volume and tumor fraction are important morphological factors that correlate with the DNA concentration and should be carefully assessed in routine practice prior to performing DNA isolation from FFPE tissues.
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Affiliation(s)
- Adela Nechifor-Boilă
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Claudia Banescu
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Ancuta Elena Zahan
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Valeriu Moldovan
- Department of Genetics, Center for Advanced Medical and Pharmaceutical Research, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Emoke Szasz
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
| | - Angela Borda
- Department of Histology, George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Targu Mures, Targu Mures, Romania
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Lightbody G, Haberland V, Browne F, Taggart L, Zheng H, Parkes E, Blayney JK. Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application. Brief Bioinform 2019; 20:1795-1811. [PMID: 30084865 PMCID: PMC6917217 DOI: 10.1093/bib/bby051] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/01/2018] [Indexed: 12/28/2022] Open
Abstract
There has been an exponential growth in the performance and output of sequencing technologies (omics data) with full genome sequencing now producing gigabases of reads on a daily basis. These data may hold the promise of personalized medicine, leading to routinely available sequencing tests that can guide patient treatment decisions. In the era of high-throughput sequencing (HTS), computational considerations, data governance and clinical translation are the greatest rate-limiting steps. To ensure that the analysis, management and interpretation of such extensive omics data is exploited to its full potential, key factors, including sample sourcing, technology selection and computational expertise and resources, need to be considered, leading to an integrated set of high-performance tools and systems. This article provides an up-to-date overview of the evolution of HTS and the accompanying tools, infrastructure and data management approaches that are emerging in this space, which, if used within in a multidisciplinary context, may ultimately facilitate the development of personalized medicine.
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Affiliation(s)
- Gaye Lightbody
- School of Computing, Ulster University, Newtownabbey, UK
| | - Valeriia Haberland
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Fiona Browne
- School of Computing, Ulster University, Newtownabbey, UK
| | | | - Huiru Zheng
- School of Computing, Ulster University, Newtownabbey, UK
| | - Eileen Parkes
- Centre for Cancer Research & Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Jaine K Blayney
- Centre for Cancer Research & Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
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18
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Evaluation of a DNA Extraction and Purification Protocol Using Archived Formalin-fixed Paraffin-embedded Tissues for BRAF Mutations Analysis in Papillary Thyroid Microcarcinomas. Appl Immunohistochem Mol Morphol 2019; 27:70-76. [DOI: 10.1097/pai.0000000000000535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Appenzeller S, Gesierich A, Thiem A, Hufnagel A, Jessen C, Kneitz H, Regensburger M, Schmidt C, Zirkenbach V, Bischler T, Schilling B, Siedel C, Goebeler ME, Houben R, Schrama D, Gehrig A, Rost S, Maurus K, Bargou R, Rosenwald A, Schartl M, Goebeler M, Meierjohann S. The identification of patient-specific mutations reveals dual pathway activation in most patients with melanoma and activated receptor tyrosine kinases in BRAF/NRAS wild-type melanomas. Cancer 2018; 125:586-600. [PMID: 30561760 DOI: 10.1002/cncr.31843] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/23/2018] [Accepted: 10/02/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND Increasing knowledge of cancer genomes has triggered the development of specific targeted inhibitors, thus providing a valuable therapeutic pool. METHODS In this report, the authors analyze the presence of targetable alterations in 136 tumor samples from 92 patients with melanoma using a comprehensive approach based on targeted DNA sequencing and supported by RNA and protein analysis. Three topics of high clinical relevance are addressed: the identification of rare, activating alterations; the detection of patient-specific, co-occurring single nucleotide variants (SNVs) and copy number variations (CNVs) in parallel pathways; and the presence of cancer-relevant germline mutations. RESULTS The analysis of patient-matched blood and tumor samples was done with a custom-designed gene panel that was enriched for genes from clinically targetable pathways. To detect alterations with high therapeutic relevance for patients with unknown driver mutations, genes that are untypical for melanoma also were included. Among all patients, CNVs were identified in one-third of samples and contained amplifications of druggable kinases, such as CDK4, ERBB2, and KIT. Considering SNVs and CNVs, 60% of patients with metastases exhibited co-occurring activations of at least 2 pathways, thus providing a rationale for individualized combination therapies. Unexpectedly, 9% of patients carry potentially protumorigenic germline mutations frequently affecting receptor tyrosine kinases. Remarkably two-thirds of BRAF/NRAS wild-type melanomas harbor activating mutations or CNVs in receptor tyrosine kinases. CONCLUSIONS The results indicate that the integrated analysis of SNVs, CNVs, and germline mutations reveals new druggable targets for combination tumor therapy.
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Affiliation(s)
- Silke Appenzeller
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Anja Gesierich
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Alexander Thiem
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Anita Hufnagel
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Christina Jessen
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Hermann Kneitz
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Martina Regensburger
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Cornelia Schmidt
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Vanessa Zirkenbach
- Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
| | - Thorsten Bischler
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Bastian Schilling
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Claudia Siedel
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | | | - Roland Houben
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - David Schrama
- Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Katja Maurus
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | | | - Manfred Schartl
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Matthias Goebeler
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Dermatology, Venereology, and Allergology and Skin Cancer Center, University Hospital Würzburg, Würzburg, Germany
| | - Svenja Meierjohann
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany.,Department of Physiological Chemistry, University of Würzburg, Würzburg, Germany
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20
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Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A. Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project. Genet Med 2018; 20:1196-1205. [PMID: 29388947 PMCID: PMC6520241 DOI: 10.1038/gim.2017.241] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
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Affiliation(s)
- Pauline Robbe
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Niko Popitsch
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Samantha J L Knight
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Pavlos Antoniou
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Becq
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Miao He
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | | | | | - Dimitrios V Vavoulis
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Mark T Ross
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Zoya Kingsbury
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Maite Cabes
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sara D C Ramos
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Suzanne Page
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Helene Dreau
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate Ridout
- Oxford Molecular Diagnostics Centre, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Louise J Jones
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Alice Tuff-Lacey
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shirley Henderson
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Joanne Mason
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Francesca M Buffa
- Computational Biology and Integrative Genomics, Department of Oncology, University of Oxford, Oxford, UK
| | - Clare Verrill
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David Maldonado-Perez
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Ioannis Roxanis
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Elena Collantes
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Sunanda Dhar
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Stephen Damato
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Susan Davies
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- NIHR Biomedical Research Centre at Barts Health NHS Trust, London, UK
| | - David R Bentley
- Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK
| | - Jenny C Taylor
- Wellcome Trust Centre of Human Genetics, University of Oxford, Old Road Campus Research Building, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
| | - Clare Turnbull
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
- Department of Cellular Pathology, Oxford University Hospital Foundation Trust, Oxford, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Anna Schuh
- Oxford Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford Molecular Diagnostics Centre, Department of Oncology, University of Oxford, Oxford, UK
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21
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Gaffney EF, Riegman PH, Grizzle WE, Watson PH. Factors that drive the increasing use of FFPE tissue in basic and translational cancer research. Biotech Histochem 2018; 93:373-386. [PMID: 30113239 DOI: 10.1080/10520295.2018.1446101] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.
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Affiliation(s)
- E F Gaffney
- a Biobank Ireland Trust , Malahide , Co Dublin , Ireland
| | - P H Riegman
- b Erasmus Medical Centre , Department of Pathology , Rotterdam , The Netherlands
| | - W E Grizzle
- c Department of Pathology , University of Alabama at Birmingham (UAB) , Birmingham , Alabama , USA
| | - P H Watson
- d BC Cancer Agency , Vancouver Island Center , Victoria , BC , Canada
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Abstract
BACKGROUND The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome. Using an in-silico approach, we designed probes targeting the rat exome and compared captured mutations in cancer-related genes from four chemically induced rat tumor cell lines (C6, FAT7, DSL-6A/C1, NBTII) to validated cancer genes in the human database, Catalogue of Somatic Mutations in Cancer (COSMIC) as well as normal rat DNA. Paired, fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) liver tissue from naive rats were sequenced to confirm known dbSNP variants and identify any additional variants. RESULTS Informatics analysis of available gene annotation from rat RGSC6.0/rn6 RefSeq and Ensembl transcripts provided 223,636 unique exons representing a total of 26,365 unique genes and untranslated regions. Using this annotation and the Rn6 reference genome, an in-silico probe design generated 826,878 probe sequences of which 94.2% were uniquely aligned to the rat genome without mismatches. Further informatics analysis revealed 25,249 genes (95.8%) covered by at least one probe and 23,603 genes (93.5%) had every exon covered by one or more probes. We report high performance metrics from exome sequencing of our probe set and Sanger validation of annotated, highly relevant, cancer gene mutations as cataloged in the human COSMIC database, in addition to several exonic variants in cancer-related genes. CONCLUSIONS An in-silico probe set was designed to enrich the rat exome from isolated DNA. The platform was tested on rat tumor cell lines and normal FF and FFPE liver tissue. The method effectively captured target exome regions in the test DNA samples with exceptional sensitivity and specificity to obtain reliable sequencing data representing variants that are likely chemically induced somatic mutations. Genomic discovery conducted by means of high throughput WES queries should benefit investigators in discovering rat genomic variants in disease etiology and in furthering human translational research.
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23
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Chin SF, Santonja A, Grzelak M, Ahn S, Sammut SJ, Clifford H, Rueda OM, Pugh M, Goldgraben MA, Bardwell HA, Cho EY, Provenzano E, Rojo F, Alba E, Caldas C. Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers. Exp Mol Pathol 2018; 104:161-169. [PMID: 29608913 PMCID: PMC5993858 DOI: 10.1016/j.yexmp.2018.03.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.
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Affiliation(s)
- Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
| | - Angela Santonja
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Marta Grzelak
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Soomin Ahn
- Department of Pathology, Seoul National University Bundang Hospital, 82, Gumi-ro 173 Beon-gil, Bundang-gu, Seongnam, Gyeonggi 13620, Republic of Korea; Inivata, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen-John Sammut
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Harry Clifford
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Michelle Pugh
- Inivata UK, The Portway Building, Granta Park, Cambridge CB21 6GS, UK
| | - Mae A Goldgraben
- Department of Medical Genetics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Helen A Bardwell
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Eun Yoon Cho
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul 135-710, Republic of Korea
| | - Elena Provenzano
- Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK
| | - Federico Rojo
- Pathology Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain
| | - Emilio Alba
- Medical Oncology Service, Hospital Universitario Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain; GEICAM-Spanish Breast Cancer Research Group, Madrid, Spain; Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK; Department of Oncology, University of Cambridge, Cambridge CB2 2QQ, UK; Cambridge Breast Unit, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre, Cambridge CB2 2QQ, UK; Cancer Research UK Cambridge Cancer Centre, Cambridge CB2 0QQ, UK.
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Dissecting the Mutational Landscape of Cutaneous Melanoma: An Omic Analysis Based on Patients from Greece. Cancers (Basel) 2018; 10:cancers10040096. [PMID: 29596374 PMCID: PMC5923351 DOI: 10.3390/cancers10040096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022] Open
Abstract
Melanoma is a lethal type of skin cancer, unless it is diagnosed early. Formalin-fixed, paraffin-embedded (FFPE) tissue is a valuable source for molecular assays after diagnostic examination, but isolated nucleic acids often suffer from degradation. Here, for the first time, we examine primary melanomas from Greek patients, using whole exome sequencing, so as to derive their mutational profile. Application of a bioinformatic framework revealed a total of 10,030 somatic mutations. Regarding the genes containing putative protein-altering mutations, 73 were common in at least three patients. Sixty-five of these 73 top common genes have been previously identified in melanoma cases. Biological processes related to melanoma were affected by varied genes in each patient, suggesting differences in the components of a pathway possibly contributing to pathogenesis. We performed a multi-level analysis highlighting a short list of candidate genes with a probable causative role in melanoma.
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25
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Hussan H, Clinton SK, Roberts K, Bailey MT. Fusobacterium's link to colorectal neoplasia sequenced: A systematic review and future insights. World J Gastroenterol 2017; 23:8626-8650. [PMID: 29358871 PMCID: PMC5752723 DOI: 10.3748/wjg.v23.i48.8626] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/09/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development. METHODS Two independent investigators systematically reviewed all original scientific articles published between January, 2000, and July, 2017, using PubMed, EMBASE, and MEDLINE. A total of 355 articles were screened at the abstract level. Of these, only original scientific human, animal, and in vitro studies investigating Fusobacterium and its relationship with colorectal cancer (CRC) were included in the analysis. Abstracts, review articles, studies investigating other colonic diseases, and studies written in other languages than English were excluded from our analysis. Ninety articles were included after removing duplicates, resolving disagreements between the two reviewers, and applying the above criteria. RESULTS Studies have consistently identified positive associations between Fusobacterium, especially Fusobacterium nucleatum (F. nucleatum), and CRC. Stronger associations were seen in CRCs proximal to the splenic flexure and CpG island methylator phenotype (CIMP)-high CRCs. There was evidence of temporality and a biological gradient, with increased F. nucleatum DNA detection and quantity along the traditional adenoma-carcinoma sequence and in CIMP-high CRC precursors. Diet may have a differential impact on colonic F. nucleatum enrichment; evidence suggests that high fiber diet may reduce the risk of a subset of CRCs that are F. nucleatum DNA-positive. Data also suggest shorter CRC and disease-specific survival with increased amount of F. nucleatum DNA in CRC tissue. The pathophysiology of enrichment of F. nucleatum and other Fusobacterium species in colonic tissue is unclear; however, the virulence factors and changes to the local colonic environment with disruption of the protective mucus layer may contribute. The presence of a host lectin (Gal-GalNAc) in the colonic epithelium may also mediate F. nucleatum attachment to CRC and precursors through interaction with an F. nucleatum protein, fibroblast activation protein 2 (FAP2). The clinical significance of detection or enrichment of Fusobacterium in colorectal neoplasia is ambiguous, but data suggest a procarcinogenic effect of F. nucleatum, likely due to activation of oncogenic and inflammatory pathways and modulation of the tumor immune environment. This is hypothesized to be mediated by certain F. nucleatum strains carrying invasive properties and virulence factors such as FadA and FAP. CONCLUSION Evidence suggests a potential active role of Fusobacterium, specifically F. nucleatum, in CRC. Future prospective and experimental human studies would fill an important gap in this literature.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Steven K Clinton
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, United States
| | - Kristen Roberts
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Michael T Bailey
- Department of Pediatrics, OSU College of Medicine And Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, United States
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Horak P, Fröhling S, Glimm H. Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open 2016; 1:e000094. [PMID: 27933214 PMCID: PMC5133384 DOI: 10.1136/esmoopen-2016-000094] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach. The basic assumption of precision oncology is that molecular markers detected by NGS will predict response to targeted therapies independently from tumour histology. However, along with a ubiquitous availability of NGS, the complexity and heterogeneity at the individual patient level had to be acknowledged. Not only does the latter present challenges to clinical decision-making based on sequencing data, it is also an obstacle to the rational design of clinical trials. Novel tissue-agnostic trial designs were quickly developed to overcome these challenges. Results from some of these trials have recently demonstrated the feasibility and efficacy of this approach. On the other hand, there is an increasing amount of whole-exome and whole-genome NGS data which allows us to assess ever smaller differences between individual patients with cancer. In this review, we highlight different tumour sequencing strategies currently used for precision oncology, describe their individual strengths and weaknesses, and emphasise their feasibility in different clinical settings. Further, we evaluate the possibility of NGS implementation in current and future clinical trials, and point to the significance of NGS for translational research.
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Affiliation(s)
- Peter Horak
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan Fröhling
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Hanno Glimm
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
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Bonfiglio S, Vanni I, Rossella V, Truini A, Lazarevic D, Dal Bello MG, Alama A, Mora M, Rijavec E, Genova C, Cittaro D, Grossi F, Coco S. Performance comparison of two commercial human whole-exome capture systems on formalin-fixed paraffin-embedded lung adenocarcinoma samples. BMC Cancer 2016; 16:692. [PMID: 27578032 PMCID: PMC5004269 DOI: 10.1186/s12885-016-2720-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 03/01/2023] Open
Abstract
Background Next Generation Sequencing (NGS) has become a valuable tool for molecular landscape characterization of cancer genomes, leading to a better understanding of tumor onset and progression, and opening new avenues in translational oncology. Formalin-fixed paraffin-embedded (FFPE) tissue is the method of choice for storage of clinical samples, however low quality of FFPE genomic DNA (gDNA) can limit its use for downstream applications. Methods To investigate the FFPE specimen suitability for NGS analysis and to establish the performance of two solution-based exome capture technologies, we compared the whole-exome sequencing (WES) data of gDNA extracted from 5 fresh frozen (FF) and 5 matched FFPE lung adenocarcinoma tissues using: SeqCap EZ Human Exome v.3.0 (Roche NimbleGen) and SureSelect XT Human All Exon v.5 (Agilent Technologies). Results Sequencing metrics on Illumina HiSeq were optimal for both exome systems and comparable among FFPE and FF samples, with a slight increase of PCR duplicates in FFPE, mainly in Roche NimbleGen libraries. Comparison of single nucleotide variants (SNVs) between FFPE-FF pairs reached overlapping values >90 % in both systems. Both WES showed high concordance with target re-sequencing data by Ion PGM™ in 22 lung-cancer genes, regardless the source of samples. Exon coverage of 623 cancer-related genes revealed high coverage efficiency of both kits, proposing WES as a valid alternative to target re-sequencing. Conclusions High-quality and reliable data can be successfully obtained from WES of FFPE samples starting from a relatively low amount of input gDNA, suggesting the inclusion of NGS-based tests into clinical contest. In conclusion, our analysis suggests that the WES approach could be extended to a translational research context as well as to the clinic (e.g. to study rare malignancies), where the simultaneous analysis of the whole coding region of the genome may help in the detection of cancer-linked variants. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2720-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Bonfiglio
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy.
| | - Irene Vanni
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Valeria Rossella
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Anna Truini
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy.,Department of Internal Medicine and Medical Specialties (DIMI), University of Genoa, Italy, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Dejan Lazarevic
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Maria Giovanna Dal Bello
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Angela Alama
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Marco Mora
- Department of Pathology, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Erika Rijavec
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Carlo Genova
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina 58, Milan, 20132, Italy
| | - Francesco Grossi
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy
| | - Simona Coco
- Lung Cancer Unit, IRCCS AOU San Martino - IST National Cancer Research Institute, L.go R. Benzi 10, Genoa, 16132, Italy.
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Wargo JA, Reddy SM, Reuben A, Sharma P. Monitoring immune responses in the tumor microenvironment. Curr Opin Immunol 2016; 41:23-31. [PMID: 27240055 DOI: 10.1016/j.coi.2016.05.006] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/12/2016] [Indexed: 12/15/2022]
Abstract
Immune monitoring in the tumor microenvironment allows for important insights into immune mechanisms of response and resistance to various cancer treatments; however clinical challenges exist using current strategies. Significant questions remain regarding monitoring of archival versus fresh tissue, assessment of static versus dynamic markers, evaluation of limited tissue samples, and the translation of insights gained from immunologically 'hot' tumors such as melanoma to other 'cold' tumor microenvironments prevalent in other cancer types. Current and emerging immune monitoring strategies will be examined herein, and genomic-based assays complementing these techniques will also be discussed. Finally, host genomic and external environmental factors influencing anti-tumor immune responses will be considered, including the role of the gut microbiome. Though optimal immune monitoring techniques are in evolution, great promise exists in recent advances that will help guide patient selection as far as type, sequence, and combination of therapeutic regimens to enhance anti-tumor immunity and clinical responses.
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Affiliation(s)
- Jennifer A Wargo
- Department of Surgical Oncology, Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Unit 463, Houston, TX 77030, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Unit 1374, Houston, TX 77030, USA.
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