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Duan Z, Feng J, Guan Y, Li S, Wu B, Shao Y, Ma Z, Hu Z, Xiang L, Zhu M, Fan X, Qi X. Enrichment of oligodendrocyte precursor phenotypes in subsets of low-grade glioneuronal tumours. Brain Commun 2024; 6:fcae156. [PMID: 38764775 PMCID: PMC11099663 DOI: 10.1093/braincomms/fcae156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/06/2024] [Accepted: 05/06/2024] [Indexed: 05/21/2024] Open
Abstract
Current histological classification of low-grade glioneuronal tumours does not adequately represent their underlying biology. The neural lineage(s) and differentiation stage(s) involved and the cell state(s) affected by the recurrent genomic alterations are unclear. Here, we describe dysregulated oligodendrocyte lineage developmental programmes in three low-grade glioneuronal tumour subtypes. Ten dysembryoplastic neuroepithelial tumours, four myxoid glioneuronal tumours and five rosette-forming glioneuronal tumours were collected. Besides a comprehensive characterization of clinical features, known diagnostic markers and genomic alterations, we used comprehensive immunohistochemical stainings to characterize activation of rat sarcoma/mitogen-activated protein kinase pathway, involvement of neuronal component, resemblance to glial lineages and differentiation blockage along the stages of oligodendrocyte lineage. The findings were further complemented by gene set enrichment analysis with transcriptome data of dysembryoplastic neuroepithelial tumours from the literature. Dysembryoplastic neuroepithelial tumours, myxoid glioneuronal tumours and rosette-forming glioneuronal tumours occur at different ages, with symptoms closely related to tumour location. Dysembryoplastic neuroepithelial tumours and myxoid glioneuronal tumours contain oligodendrocyte-like cells and neuronal component. Rosette-forming glioneuronal tumours contained regions of rosette-forming neurocytic and astrocytic features. Scattered neurons, identified by neuronal nuclei antigen and microtubule-associated protein-2 staining, were consistently observed in all dysembryoplastic neuroepithelial tumours and myxoid glioneuronal tumours examined, but only in one rosette-forming glioneuronal tumour. Pervasive neurofilament-positive axons were observed only in dysembryoplastic neuroepithelial tumour and myxoid glioneuronal tumour samples. Alterations in B-Raf proto-oncogene, serine/threonine kinase, fibroblast growth factor receptor 1, fibroblast growth factor receptor 3 and platelet-derived growth factor receptor alpha occurred in a mutually exclusive manner, coinciding with strong staining of phospho-p44/42 mitogen-activated protein kinase and low apoptotic signal. All dysembryoplastic neuroepithelial tumours, myxoid glioneuronal tumours and the neurocytic regions of rosette-forming glioneuronal tumours showed strong expression of neuron-glia antigen 2, platelet-derived growth factor receptor alpha (markers of oligodendrocyte precursor cells) and neurite outgrowth inhibitor-A (a marker of developing oligodendrocytes), but lacked the expression of oligodendrocyte markers ectonucleotide pyrophosphatase/phosphodiesterase family member 6 and myelin basic protein. Notably, transcriptomes of dysembryoplastic neuroepithelial tumours were enriched in oligodendrocyte precursor cell signature, but not in signatures of neural stem cells, myelinating oligodendrocytes and astrocytes. Dysembryoplastic neuroepithelial tumour, myxoid glioneuronal tumour and rosette-forming glioneuronal tumour resemble oligodendrocyte precursor cells, and their enrichment of oligodendrocyte precursor cell phenotypes is closely associated with the recurrent mutations in rat sarcoma/mitogen-activated protein kinase pathway.
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Affiliation(s)
- Zejun Duan
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Jing Feng
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Yuguang Guan
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Shouwei Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Bin Wu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Yang Shao
- Nanjing Geneseq Technology Inc., Nanjing 211899, China
- School of Public Health, Nanjing Medical University, Nanjing 211198, China
| | - Zhong Ma
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Zejuan Hu
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Lei Xiang
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Mingwang Zhu
- Department of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
| | - Xiaolong Fan
- Department of Biology, Beijing Key Laboratory of Gene Resource and Molecular Development, School of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, School of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xueling Qi
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing 100093, China
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Kakumoto A, Jamiyan T, Kuroda H, Harada O, Yamaguchi-Isochi T, Baba S, Kato Y, Nishihara H, Kawami H. Prognostic impact of tumor-associated neutrophils in breast cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2024; 17:51-62. [PMID: 38577697 PMCID: PMC10988089 DOI: 10.62347/jqdq1527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES Neutrophils are the most common type of leukocyte in mammals and play an essential role in the innate immune system and anti-cancer responses. However, recent studies identified the presence of tumor-associated neutrophils (TANs) as a poor prognostic factor. The present study investigated whether relationships exist between TANs and the clinicopathological factors and genetic status of breast cancer. METHODS A total of 196 breast cancer patients with sufficient biopsy, breast-conserving surgery, or mastectomy specimens between 2014 and 2021 in Hokuto Hospital were included. RESULTS TANs were individually counted in the tumor stroma (TS) and tumor nest (TN). A higher density of TANs in both TS and TN correlated with tumor size (TS P = 0.010; TN P = 0.001), a high histological grade (TS P < 0.001; TN P < 0.001), the histological type (TS P = 0.009; TN P = 0.034), a high ratio of lymph node metastasis (TS P < 0.001; TN P < 0.001), an advanced stage of cancer (TS P < 0.001; TN P = 0.002), intrinsic subtypes (TS P < 0.001; TN P < 0.001), ERBB2 (TS P < 0.001; TN P < 0.001), MAP3K1 (TS P = 0.002; TN P = 0.023), and TP53 (TS P < 0.001; TN P < 0.001). A higher density of TANs in TS and TN also correlated with shorter disease-free survival and overall survival (P < 0.001). CONCLUSION The present results suggest that a higher density of TANs correlates with unfavorable prognostic factors in breast cancer. Further research on clinicopathological and genetic factors associated with TANs in breast cancer is needed.
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Affiliation(s)
- Akinari Kakumoto
- Department of Diagnostic Pathology, Tokyo Women’s Medical University Adachi Medical Center 4-33-1 KohokuAdachi-Ku, Tokyo 123-0872, Japan
| | - Tsengelmaa Jamiyan
- Department of Pathology and Forensic Medicine, Mongolian National University of Medical SciencesUlan Bator 14210, Mongolia
| | - Hajime Kuroda
- Department of Diagnostic Pathology, Tokyo Women’s Medical University Adachi Medical Center 4-33-1 KohokuAdachi-Ku, Tokyo 123-0872, Japan
- Department of Clinical Pathology, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
| | - Oi Harada
- Department of Clinical Pathology, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
- Breast Center, Showa UniversityTokyo 142-8666, Japan
| | | | - Shogo Baba
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
| | - Yasutaka Kato
- Department of Clinical Pathology, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
- Genomics Unit, Keio Cancer Center, Clinical and Translational Research Center, Keio University School of MedicineTokyo 160-8582, Japan
| | - Hiroshi Nishihara
- Department of Clinical Pathology, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
- Genomics Unit, Keio Cancer Center, Clinical and Translational Research Center, Keio University School of MedicineTokyo 160-8582, Japan
| | - Hiroyuki Kawami
- Department of Clinical Pathology, Hokuto HospitalObihiro, Hokkaido 080-0833, Japan
- Center for Breast Diseases and Breast Cancer, Hokuto Hospital and ClinicObihiro, Hokkaido 080-0833, Japan
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Cimadamore A, Rescigno P, Conteduca V, Caliò A, Allegritti M, Calò V, Montagnani I, Lucianò R, Patruno M, Bracarda S. SIUrO best practice recommendations to optimize BRCA 1/2 gene testing from DNA extracted from bone biopsy in mCRPC patients (BRCA Optimal Bone Biopsy Procedure: BOP). Virchows Arch 2023; 483:579-589. [PMID: 37794204 DOI: 10.1007/s00428-023-03660-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/11/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023]
Abstract
The main guidelines and recommendations for the implementation of the BRCA1/2 somatic test do not focus on the clinical application of predictive testing on bone metastases, a frequent condition in metastatic prostate cancer, by analyzing the critical issues encountered by laboratory practice. Our goal is to produce a document (protocol) deriving from a multidisciplinary team approach to obtain high quality nucleic acids from biopsy of bone metastases. This document aims to compose an operational check-list of three phases: the pre-analytical phase concerns tumor cellularity, tissue processing, sample preservation (blood/FFPE), fixation and staining, but above all the decalcification process, the most critical phase because of its key role in allowing the extraction of somatic DNA with a good yield and high quality. The analytical phase involves the preparation of the libraries that can be analyzed in various NGS genetic sequencing platforms and with various bioinformatics software for the interpretation of sequence variants. Finally, the post-analytical phase that allows to report the variants of the BRCA1/2 genes in a clear and usable way to the clinician who will use these data to manage cancer therapy with PARP Inhibitors.
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Affiliation(s)
- Alessia Cimadamore
- Institute of Pathological Anatomy, Department of Medicine (DAME), University of Udine, Via Palladio 8, 33100, Udine, Italy.
| | - Pasquale Rescigno
- Translational and Clinical Research Institute, Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Italy
| | - Vincenza Conteduca
- Unit of Medical Oncology and Biomolecular Therapy, Department of Medical and Surgical Sciences - Policlinico Riuniti, University of Foggia, 71122, Foggia, Italy
| | - Anna Caliò
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Largo L. Scuro 10, 37134, Verona, Italy
| | - Massimiliano Allegritti
- Interventional radiology Unit, Azienda ospedaliera Santa Maria Terni, Viale Tristano di Joannuccio, 05100, Terni, Italy
| | - Valentina Calò
- Central Laboratory of Advanced Diagnosis and Biomedical Research, (CLADIBIOR) Policlinico Paolo Giaccone Hospital, University of Palermo, 90127, Palermo, Italy
| | - Ilaria Montagnani
- Pathology Unit, USL Toscana Centro - Ospedale San Giuseppe, Empoli, Italy
| | - Roberta Lucianò
- Department of Pathology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Margherita Patruno
- Center for Study of Heredo-Familial Tumors - IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Sergio Bracarda
- Medical and Translational Oncology, Department of Oncology, Azienda Ospedaliera Santa Maria, Viale Tristano di Joannuccio, 05100, Terni, Italy
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Morgan RD, Burghel GJ, Flaum N, Bulman M, Smith P, Clamp AR, Hasan J, Mitchell C, Salih Z, Woodward ER, Lalloo F, Shaw J, Desai S, Crosbie EJ, Edmondson RJ, Schlecht H, Wallace AJ, Jayson GC, Evans DGR. Predicting the likelihood of a BRCA1/2 pathogenic variant being somatic by testing only tumour DNA in non-mucinous high-grade epithelial ovarian cancer. J Clin Pathol 2023; 76:684-689. [PMID: 35738887 DOI: 10.1136/jcp-2022-208369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/04/2022]
Abstract
AIMS Clinical guidelines recommend testing both germline and tumour DNA for BRCA1/2 pathogenic variants (PVs) in non-mucinous high-grade epithelial ovarian cancer (NMEOC). In this study, we show that some tumour BRCA1/2 PVs are highly likely to be somatic based on certain clinical and variant characteristics, meaning it may not be necessary to test all NMEOC cases for germline BRCA1/2 PVs. METHODS An observational study that included all tumour BRCA1/2 PVs detected in cases of NMEOC in the Northwest of England between July 2017 and February 2022. All tumour BRCA1/2 PVs were compared with PVs recorded in a prospectively gathered pan-cancer germline BRCA1/2 (gBRCA) testing database for the same geographical region (gBRCA1 PVs=910 and gBRCA2 PVs=922). Tumour BRCA1/2 PVs were categorised as common (≥1%), uncommon (<1%) or absent from the germline database. RESULTS One hundred and thirteen tumour BRCA1/2 PVs were detected in 111 NMEOC cases. There were 69 germline and 44 somatic variants. The mean age at diagnosis for gBRCA and somatic BRCA1/2 (sBRCA) PVs was 56.9 and 68.5 years, respectively (Student's t-test p<0.0001). All sBRCA PVs were detected in non-familial cases. All tumour BRCA1/2 PVs with a variant allele frequency (VAF) <35% in non-familial cases were somatic variants. Eighty-one per cent of germline-tumour BRCA1/2 PVs were present (common=31, uncommon=25) in the gBRCA testing database, while 89% of somatic-tumour BRCA1/2 PVs were absent (n=39). CONCLUSIONS We predict the likelihood of a tumour BRCA1/2 PV being somatic is 99.8% in non-familial cases of NMEOC diagnosed aged ≥75, where the VAF is ≤30% and there is no regional germline commonality.
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Affiliation(s)
- Robert D Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - George J Burghel
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Nicola Flaum
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
| | - Michael Bulman
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Philip Smith
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Claire Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Emma R Woodward
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Joseph Shaw
- Department of Histopathology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Sudha Desai
- Department of Histopathology, The Christie NHS Foundation Trust, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, University of Manchester, Manchester, UK
- Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew J Wallace
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gordon C Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - D Gareth R Evans
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, University of Manchester, Manchester, UK
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
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5
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Morgan RD, Clamp AR, Barnes BM, Timms K, Schlecht H, Yarram-Smith L, Wallis Y, Valganon-Petrizan M, MacMahon S, White R, Morgan S, McKenna S, Hudson E, Tookman L, George A, Manchanda R, Sundar SS, Nicum S, Brenton JD, Kristeleit RS, Banerjee S, McNeish IA, Ledermann JA, Taylor SS, Evans DGR, Jayson GC. Homologous recombination deficiency in newly diagnosed FIGO stage III/IV high-grade epithelial ovarian cancer: a multi-national observational study. Int J Gynecol Cancer 2023; 33:1253-1259. [PMID: 37072323 DOI: 10.1136/ijgc-2022-004211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
OBJECTIVE Olaparib plus bevacizumab maintenance therapy improves survival outcomes in women with newly diagnosed, advanced, high-grade ovarian cancer with a deficiency in homologous recombination. We report data from the first year of routine homologous recombination deficiency testing in the National Health Service (NHS) in England, Wales, and Northern Ireland between April 2021 and April 2022. METHODS The Myriad myChoice companion diagnostic was used to test DNA extracted from formalin-fixed, paraffin-embedded tumor tissue in women with newly diagnosed International Federation of Gynecology and Obstetrics (FIGO) stage III/IV high-grade epithelial ovarian, fallopian tube, or primary peritoneal cancer. Tumors with homologous recombination deficiency were those with a BRCA1/2 mutation and/or a Genomic Instability Score (GIS) ≥42. Testing was coordinated by the NHS Genomic Laboratory Hub network. RESULTS The myChoice assay was performed on 2829 tumors. Of these, 2474 (87%) and 2178 (77%) successfully underwent BRCA1/2 and GIS testing, respectively. All complete and partial assay failures occurred due to low tumor cellularity and/or low tumor DNA yield. 385 tumors (16%) contained a BRCA1/2 mutation and 814 (37%) had a GIS ≥42. Tumors with a GIS ≥42 were more likely to be BRCA1/2 wild-type (n=510) than BRCA1/2 mutant (n=304). The distribution of GIS was bimodal, with BRCA1/2 mutant tumors having a higher mean score than BRCA1/2 wild-type tumors (61 vs 33, respectively, χ2 test p<0.0001). CONCLUSION This is the largest real-world evaluation of homologous recombination deficiency testing in newly diagnosed FIGO stage III/IV high-grade epithelial ovarian, fallopian tube, or primary peritoneal cancer. It is important to select tumor tissue with adequate tumor content and quality to reduce the risk of assay failure. The rapid uptake of testing across England, Wales, and Northern Ireland demonstrates the power of centralized NHS funding, center specialization, and the NHS Genomic Laboratory Hub network.
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Affiliation(s)
- Robert D Morgan
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Andrew R Clamp
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Bethany M Barnes
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Yvonne Wallis
- Central and South Genomic Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mikel Valganon-Petrizan
- North Thames Genomic Laboratory Hub, The Royal Marsden Hospital NHS Foundation Trust, Surrey, UK
| | - Suzanne MacMahon
- North Thames Genomic Laboratory Hub, The Royal Marsden Hospital NHS Foundation Trust, Surrey, UK
| | - Rhian White
- All Wales Genomics Laboratory, Institute of Medical Genetics, University Hospital Wales, Cardiff, UK
| | - Sian Morgan
- All Wales Genomics Laboratory, Institute of Medical Genetics, University Hospital Wales, Cardiff, UK
| | | | | | | | - Angela George
- The Royal Marsden NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Ranjit Manchanda
- Barts Health NHS Trust, London, UK
- Department of Health Services Research, The Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, London, UK
- Wolfson Institute of Population Health, Queen Mary's University of London, London, UK
| | - Sudha S Sundar
- Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Shibani Nicum
- University College London Hospitals NHS Foundation Trust, London, UK
- UCL Cancer Institute, London, UK
| | - James D Brenton
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Susana Banerjee
- The Royal Marsden NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Iain A McNeish
- Imperial College Healthcare NHS Trust, London, UK
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jonathan A Ledermann
- University College London Hospitals NHS Foundation Trust, London, UK
- UCL Cancer Institute, London, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - D Gareth R Evans
- Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gordon C Jayson
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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Nomoto K, Hata Y, Ichimata S, Mizuno S, Nishida N. An autopsy case of infective aortic aneurysm with Pasteurella multocida infection: clinicopathological appearance and a review of literatures. Ann Clin Microbiol Antimicrob 2023; 22:58. [PMID: 37434170 DOI: 10.1186/s12941-023-00611-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023] Open
Abstract
Here, we showed our clinicopathological findings of infected aortic aneurysm (IAA) with Pasteurella multocida, which is a Gram-negative coccobacillus and is part of the normal oral flora of many animals. The patient was a 76-year-old male animal owner with a history of diabetes mellitus, alcoholic liver damage, and laryngeal cancer. He died 16 days after admission without undergoing operation because of poor general condition. Autopsy showed saccular outpouching with loss of the existing aortic wall and marked neutrophilic infiltration in the suprarenal abdominal aorta. Rupture was not evident. A polymerase chain reaction assay using DNA extracted from formalin-fixed paraffin-embedded specimen of the aneurysmal wall detected the Pasteurella multocida gene, therefore we conclude that the present case was IAA of native aorta with Pasteurella multocida infection. A review of the literature showed that IAA of native aorta with Pasteurella multocida infection is opportunistic and that liver disorder, alcohol addiction, diabetes mellitus, and animal bite may increase its risk. On the other hand, aortic endograft infection with Pasteurella multocida frequently occurred without an immunocompromised state. Pasteurella multocida may be a distinct causative microorganism in IAA, and/or sepsis when the participant is an animal owner.
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Affiliation(s)
- Kazuhiro Nomoto
- Department of Pathology, Koseiren Takaoka Hospital, 5-10 Eiraku-cho, Takaoka, Toyama, 933-8555, Japan
| | - Yukiko Hata
- Department of Legal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Shojiro Ichimata
- Department of Legal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan
| | - Syu Mizuno
- Division of General Medicine and Infectious Diseases, Koseiren Takaoka Hospital, 5-10 Eiraku-cho, Takaoka, Toyama, 933-8555, Japan
| | - Naoki Nishida
- Department of Pathology, Koseiren Takaoka Hospital, 5-10 Eiraku-cho, Takaoka, Toyama, 933-8555, Japan.
- Department of Legal Medicine, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama, Toyama, 930-0194, Japan.
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Lau-Min KS, McCarthy AM, Nathanson KL, Domchek SM. Nationwide Trends and Determinants of Germline BRCA1/2 Testing in Patients With Breast and Ovarian Cancer. J Natl Compr Canc Netw 2023; 21:351-358.e4. [PMID: 37015340 PMCID: PMC10256435 DOI: 10.6004/jnccn.2022.7257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/21/2022] [Indexed: 04/06/2023]
Abstract
BACKGROUND Germline genetic testing (GT) for BRCA1/2 is instrumental in identifying patients with breast and ovarian cancers who are eligible for PARP inhibitors (PARPi). Little is known about recent trends and determinants of GT since PARPi were approved for these patients. PATIENTS AND METHODS We performed a retrospective cohort study of patients in a nationwide electronic health record (EHR)-derived oncology-specific database with the following GT eligibility criteria: breast cancer diagnosed at age ≤45 years, triple-negative breast cancer diagnosed at age ≤60 years, male breast cancer, or ovarian cancer. GT within 1 year of diagnosis was assessed and stratified by tumor type. Multivariable log-binomial regressions estimated adjusted relative risks (RRs) of GT by patient and tumor characteristics. RESULTS Among 2,982 eligible patients with breast cancer, 56.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.08; 95% CI, 1.05-1.11, for each year), independent of when PARPi were approved for BRCA1/2-mutated metastatic breast cancer in January 2018. In multivariable analyses, older age (RR, 0.93; 95% CI, 0.90-0.96, for every 5 years) and Medicare coverage (RR, 0.69; 95% CI, 0.49-0.96 vs commercial insurance) were associated with less GT. Among 5,563 eligible patients with ovarian cancer, 35.4% underwent GT between January 2011 and March 2020, with a significant increase in GT over time (RR, 1.11; 95% CI, 1.07-1.14, for each year) that accelerated after approval of PARPi for BRCA1/2-mutated, chemotherapy-refractory ovarian cancer in December 2014 (RR, 1.42; 95% CI, 1.19-1.70). Older age (RR, 0.95; 95% CI, 0.93-0.97, for every 5 years) and Black or African American race (RR, 0.80; 95% CI, 0.65-0.98 vs White race) were associated with less GT. CONCLUSIONS GT remains underutilized nationwide among patients with breast and ovarian cancers. Although GT has increased over time, significant disparities by age, race, and insurance status persist. Additional work is needed to design, implement, and evaluate strategies to ensure that all eligible patients receive GT.
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Affiliation(s)
- Kelsey S. Lau-Min
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School
| | - Anne Marie McCarthy
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Katherine L. Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania
| | - Susan M. Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
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Zannini G, Facchini G, De Sio M, De Vita F, Ronchi A, Orditura M, Vietri MT, Ciardiello F, Franco R, Accardo M, Zito Marino F. Implementation of BRCA mutations testing in formalin-fixed paraffin-embedded (FFPE) samples of different cancer types. Pathol Res Pract 2023; 243:154336. [PMID: 36736144 DOI: 10.1016/j.prp.2023.154336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023]
Abstract
BRCA1 and BRCA2 are onco-suppressor genes involved in the DNA repair mechanism. The presence of BRCA1/2 mutations confers a higher risk of developing several cancer types. To date, the FDA approved various PARP inhibitors to treat selected BRCA1/2 mutated oncologic patients. At first, PARP inhibitors were approved for patients with ovarian and breast cancers, and subsequently for metastatic pancreatic adenocarcinoma and metastatic castration-resistant prostate cancer after the treatment with chemotherapy. The current guidelines for BRCA testing are very heterogeneous between the different types of tumors regarding the diagnostic algorithm and the type of sample to analyze, such as the blood for the germline mutations and the tumoral tissue for the somatic mutations. Few data have currently been described regarding the detection of BRCA1/2 somatic mutations in formalin-fixed paraffin-embedded (FFPE) samples. In this review, we propose an overview of the BRCA mutations in FFPE samples of several cancers, including breast, ovarian, fallopian tube, primary peritoneal, prostate, and pancreatic cancer. We summarize the types and the frequency of BRCA mutations, the guidelines approved for the test, the molecular assays used for the detection and the PARP inhibitors approved for each tumor type.
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Affiliation(s)
- Giuseppa Zannini
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, Naples 80138, Italy.
| | - Gaetano Facchini
- Medical Oncology Unit, SM delle Grazie Hospital, Via Domitiana, Pozzuoli 80078, Italy.
| | - Marco De Sio
- Urology Unit, Department of Woman, Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via S. Pansini 5, Naples 80131, Italy.
| | - Ferdinando De Vita
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via S. Pansini 5, Naples 80131, Italy.
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, Naples 80138, Italy.
| | - Michele Orditura
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via S. Pansini 5, Naples 80131, Italy.
| | - Maria Teresa Vietri
- U.O.C. Clinical and Molecular Pathology, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio 7, Naples 80138, Italy.
| | - Fortunato Ciardiello
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, University of Campania "Luigi Vanvitelli", Via S. Pansini 5, Naples 80131, Italy.
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, Naples 80138, Italy.
| | - Marina Accardo
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, Naples 80138, Italy.
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "Luigi Vanvitelli", Via L. Armanni 5, Naples 80138, Italy.
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9
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Morgan RD, Burghel GJ, Flaum N, Bulman M, Smith P, Clamp AR, Hasan J, Mitchell CL, Salih Z, Woodward ER, Lalloo F, Crosbie EJ, Edmondson RJ, Schlecht H, Jayson GC, Evans DGR. Is Reflex Germline BRCA1/2 Testing Necessary in Women Diagnosed with Non-Mucinous High-Grade Epithelial Ovarian Cancer Aged 80 Years or Older? Cancers (Basel) 2023; 15:730. [PMID: 36765687 PMCID: PMC9913244 DOI: 10.3390/cancers15030730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Women diagnosed with non-mucinous high-grade epithelial ovarian cancer (EOC) in England are often reflex-tested for germline and tumour BRCA1/2 variants. The value of germline BRCA1/2 testing in women diagnosed aged ≥80 is questionable. We performed an observational study of all women diagnosed with non-mucinous high-grade EOC who underwent germline and tumour BRCA1/2 testing by the North West of England Genomic Laboratory Hub. A subgroup of women also underwent germline testing using a panel of homologous recombination repair (HRR) genes and/or tumour testing for homologous recombination deficiency (HRD) using Myriad's myChoice® companion diagnostic. Seven-hundred-two patients successfully underwent both germline and tumour BRCA1/2 testing. Of these, 48 were diagnosed with non-mucinous high-grade EOC aged ≥80. In this age group, somatic BRCA1/2 pathogenic/likely pathogenic variants (PV/LPVs) were detected nine times more often than germline BRCA1/2 PV/LPVs. The only germline PV reported in a patient aged ≥80 was detected in germline and tumour DNA (BRCA2 c.4478_4481del). No patient aged ≥80 had a germline PV/LPVs in a non-BRCA1/2 HRR gene. Thirty-eight percent of patients aged ≥80 had a tumour positive for HRD. Our data suggest that tumour BRCA1/2 and HRD testing is adequate for patients diagnosed with non-mucinous high-grade EOC aged ≥80, with germline BRCA1/2 testing reserved for women with a tumour BRCA1/2 PV/LPVs.
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Affiliation(s)
- Robert D. Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Nicola Flaum
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Philip Smith
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Andrew R. Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Claire L. Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - Emma R. Woodward
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Fiona Lalloo
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Emma J. Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Gynaecological Oncology, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Richard J. Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Gynaecological Oncology, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Gordon C. Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, North West Genomic Laboratory Hub, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Department of Clinical Genetics, Saint Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK
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10
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Chu DT, Vu Ngoc Suong M, Vu Thi H, Vu TD, Nguyen MH, Singh V. The expression and mutation of BRCA1/2 genes in ovarian cancer: a global systematic study. Expert Rev Mol Diagn 2023; 23:53-61. [PMID: 36634123 DOI: 10.1080/14737159.2023.2168190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION This systematic review was designed to summarize the findings on expression and mutation of BRCA1/2 genes in ovarian cancer (OC) patients, focusing on mutation detection technology and taking clinical decisions for better treatment. AREAS COVERED We conducted a systematic review by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses document selection guidelines for the document selection process and the PICOT standard for developing the keywords to search for. A total of 5729 publications were included, and 50 articles were put into the final screening. The results showed that Next-Generation Sequencing was a breakthrough technology in detecting Breast Cancer 1/2 (BRCA1/2) gene mutations because of its efficacy and affordability. Other technologies are also being applied now for mutation detection. The most prominent associations of BRCA1/2 gene mutations were age, heredity, and family history. Furthermore, mutations of BRCA1/2 could improve survival rate and overall survival. There is no sufficient study available to conclude a systematic analysis for the expression of BRCA1/2 gene in OC. EXPERT OPINION Research will continue to develop more diagnostic techniques based on the expression and mutation of BCRA1/2 genes for OC in the near future.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Mai Vu Ngoc Suong
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Manh-Hung Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, India
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11
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Morgan RD, Burghel GJ, Flaum N, Bulman M, Smith P, Clamp AR, Hasan J, Mitchell CL, Salih Z, Woodward ER, Lalloo F, Crosbie EJ, Edmondson RJ, Wallace AJ, Jayson GC, Evans DGR. BRCA1/2 in non-mucinous epithelial ovarian cancer: tumour with or without germline testing? Br J Cancer 2022; 127:163-167. [PMID: 35260807 PMCID: PMC9276796 DOI: 10.1038/s41416-022-01773-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/04/2022] [Accepted: 02/22/2022] [Indexed: 11/09/2022] Open
Abstract
National guidelines recommend testing all cases of non-mucinous epithelial ovarian cancer (NMEOC) for germline (blood) and somatic (tumour) BRCA1/2 pathogenic variants (PVs). We performed paired germline and somatic BRCA1/2 testing in consecutive cases of NMEOC (n = 388) to validate guidelines. Thirty-four somatic BRCA1/2 (sBRCA) PVs (9.7%) were detected in 350 cases with germline BRCA1/2 (gBRCA) wild-type. All sBRCA PVs were detected in non-familial cases. By analysing our regional germline BRCA1/2 database there were 92/1114 (8.3%) gBRCA PVs detected in non-familial cases (only 3% ≥70 years old) and 245/641 (38.2%) in familial cases. Germline non-familial cases were dominated by BRCA2 in older women (8/271 ≥ 70 years old, all BRCA2). The ratio of sBRCA-to-gBRCA was ≤1.0 in women aged <70 years old, compared to 5.2 in women aged ≥70 years old (P = 0.005). The likelihood of missed germline BRCA1/2 PVs (copy-number variants missed on most somatic assays) by testing only tumour DNA was 0.4% in women aged ≥70 years old. We recommend reflex tumour BRCA1/2 testing in all NMEOC cases, and that gBRCA testing is not required for women aged ≥70 years old with no identifiable tumour BRCA1/2 PV and/or family history of breast, ovarian, prostate and/or pancreatic cancer.
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Affiliation(s)
- Robert D Morgan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK. .,Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Nicola Flaum
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK.,Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Clamp
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK.,Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jurjees Hasan
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Claire L Mitchell
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Zena Salih
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK
| | - Emma R Woodward
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Fiona Lalloo
- Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Department of Gynaecological Surgery, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gordon C Jayson
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK.,Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - D Gareth R Evans
- Division of Evolution & Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Department of Clinical Genetics, Manchester University NHS Foundation Trust, Manchester, UK
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12
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Graphene-Oxide and Ionic Liquid Modified Electrodes for Electrochemical Sensing of Breast Cancer 1 Gene. BIOSENSORS 2022; 12:bios12020095. [PMID: 35200355 PMCID: PMC8870019 DOI: 10.3390/bios12020095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/29/2022] [Accepted: 01/30/2022] [Indexed: 12/23/2022]
Abstract
Graphene-oxide and ionic liquid composite-modified pencil graphite electrodes (GO-IL-PGEs) were developed and used as a sensing platform for breast cancer 1 (BRCA1) gene detection. The characterization of GO-IL modified electrodes was executed by scanning electron microscopy (SEM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). The nucleic-acid hybridization was monitored by a differential pulse voltammetry (DPV) technique by directly measuring the guanine oxidation signal without using any indicator. The effects of the IL concentration, the probe concentration, and the hybridization time were optimized to the biosensor response. The limit of detection (LOD) was calculated in the concentration range of 2–10 μg/mL for the BRCA1 gene and found to be 1.48 µg/mL. The sensitivity of the sensor was calculated as 1.49 µA mL/µg cm2. The developed biosensor can effectively discriminate the complementary target sequence in comparison to a three-base-mismatched sequence or the non-complementary one.
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13
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Duan Z, Yao K, Yang S, Qu Y, Ren M, Zhang Y, Fan T, Zhao H, Gao J, Feng J, Fan X, Qi X. Primary adult sellar SMARCB1/INI1-deficient tumor represents a subtype of atypical teratoid/rhabdoid tumor. Mod Pathol 2022; 35:1910-1920. [PMID: 35804041 PMCID: PMC9708584 DOI: 10.1038/s41379-022-01127-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 12/24/2022]
Abstract
Loss of function in SMARCB1/INI1 has been observed in a group of malignancies collectively defined as SMARCB1/INI1-deficient neoplasms. Primary intracranial SMARCB1/INI1-deficient tumors in adults are extremely rare. We collected eight primary adult sellar SMARCB1/INI1-deficient tumors to study their clinicopathological and (epi)genetic characteristics. We performed a comprehensive assessment of the clinical, radiological, morphological and immunohistochemical features. FISH analysis for the SMARCB1 locus and target exome sequencing for 425 cancer relevant genes were performed. Furthermore, six bona fide proximal epithelioid sarcoma (PES), fourteen atypical teratoid/rhabdoid tumors (ATRT) in brain and five pediatric poorly differentiated chordomas (PDC) in the clivus were collected for comparative analysis of differential diagnostic maker expression and DNA methylation profile. The median age was 47.1 years, ranging from 26 to 73 years. On morphology, tumors were characterized by sheets of monomorphic larger epithelioid-like cells, in two cases with rhabdoid cells. "Stag-horn" vasculatures were observed in five cases. The loss of INI1 protein expression, co-expression of epithelial makers and mesenchymal markers were observed in all cases. CD34 expression was observed in six cases. Heterozygous deletion of SMARCB1/INI1 was confirmed using FISH in six cases. The results of target exome sequencing showed three patients harbored heterozygous point mutations in SMARCB1. The epigenetic features of the primary adult sellar SMARCB1/INI1-deficient tumors resembled the ATRT-MYC subgroup, but clustered apart from PES and PDC. Based on epigenetic characteristics, primary adult sellar SMARCB1/INI1-deficient tumors represent a subtype of ATRT with similar epigenetic characteristics of ATRT-MYC subgroup. Our findings suggest that DNA methylation profiling should be utilized for differential diagnosis for the majority of epithelioid sarcoma and (sellar) rhabdoid tumor.
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Affiliation(s)
- Zejun Duan
- grid.24696.3f0000 0004 0369 153XDepartment of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Kun Yao
- grid.24696.3f0000 0004 0369 153XDepartment of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Shaomin Yang
- grid.11135.370000 0001 2256 9319Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, 100191 China
| | - Yanming Qu
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Ming Ren
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Yongli Zhang
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Tao Fan
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Heqian Zhao
- grid.24696.3f0000 0004 0369 153XDepartment of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Jie Gao
- grid.24696.3f0000 0004 0369 153XDepartment of Radiology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093 China
| | - Jing Feng
- grid.20513.350000 0004 1789 9964Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, School of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Xiaolong Fan
- grid.20513.350000 0004 1789 9964Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, School of Life Sciences, Beijing Normal University, Beijing, 100875 China
| | - Xueling Qi
- Department of Pathology, Sanbo Brain Hospital, Capital Medical University, Beijing, 100093, China.
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14
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Chandrasekaran D, Sobocan M, Blyuss O, Miller RE, Evans O, Crusz SM, Mills-Baldock T, Sun L, Hammond RFL, Gaba F, Jenkins LA, Ahmed M, Kumar A, Jeyarajah A, Lawrence AC, Brockbank E, Phadnis S, Quigley M, El Khouly F, Wuntakal R, Faruqi A, Trevisan G, Casey L, Burghel GJ, Schlecht H, Bulman M, Smith P, Bowers NL, Legood R, Lockley M, Wallace A, Singh N, Evans DG, Manchanda R. Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study. Cancers (Basel) 2021; 13:cancers13174344. [PMID: 34503154 PMCID: PMC8431198 DOI: 10.3390/cancers13174344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline BRCA1/BRCA2/RAD51C/RAD51D/BRIP1 and parallel somatic BRCA1/BRCA2 testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97.7%. Counselling by clinical-nurse-specialist more frequently needed >1 consultation (53.6% (30/56)) compared to a medical (15.0% (21/137)) or surgical oncologist (15.3% (17/110)) (p < 0.001). The median age was 54 (IQR = 51-62) years in germline pathogenic-variant (PV) versus 61 (IQR = 51-71) in BRCA wild-type (p = 0.001). There was no significant difference in distribution of PVs by ethnicity, stage, surgery timing or resection status. A total of 15.5% germline and 7.8% somatic BRCA1/BRCA2 PVs were identified. A total of 2.3% patients had RAD51C/RAD51D/BRIP1 PVs. A total of 11% germline PVs were large-genomic-rearrangements and missed by somatic testing. A total of 20% germline PVs are missed by somatic first BRCA-testing approach and 55.6% germline PVs missed by family history ascertainment. The somatic testing failure rate is higher (23%) for patients undergoing diagnostic biopsies. Our findings favour a prospective parallel somatic and germline panel testing approach as a clinically efficient strategy to maximise variant identification. UK Genomics test-directory criteria should be expanded to include a panel of OC genes.
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Affiliation(s)
- Dhivya Chandrasekaran
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Monika Sobocan
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Divison for Gynaecology and Perinatology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Oleg Blyuss
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Rowan E. Miller
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Olivia Evans
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Shanthini M. Crusz
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Tina Mills-Baldock
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Li Sun
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Rory F. L. Hammond
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Faiza Gaba
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Lucy A. Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Arjun Jeyarajah
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Alexandra C. Lawrence
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Elly Brockbank
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Saurabh Phadnis
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Mary Quigley
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Fatima El Khouly
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Rekha Wuntakal
- Department of Gynaecology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK;
| | - Asma Faruqi
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Giorgia Trevisan
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Laura Casey
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Rosa Legood
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naveena Singh
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
- Correspondence:
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15
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Bennett S, Alexander E, Fraser H, Bowers N, Wallace A, Woodward ER, Lalloo F, Quinn AM, Huang S, Schlecht H, Evans DG. Germline FFPE inherited cancer panel testing in deceased family members: implications for clinical management of unaffected relatives. Eur J Hum Genet 2021; 29:861-871. [PMID: 33654310 PMCID: PMC8110779 DOI: 10.1038/s41431-021-00817-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/29/2023] Open
Abstract
Where previously, germline genetic testing in deceased affected relatives was not possible due to the absence of lymphocytic DNA, the North-West-Genomic-Laboratory Hub (NWGLH) has developed and validated next-generation sequencing based gene panels utilising formalin-fixed-paraffin-embedded (FFPE) tissue DNA from deceased individuals. This technology has been utilised in the clinical setting for the management of unaffected relatives seen in the Clinical Genetics Service (CGS). Here we assess the clinical impact. At the time of data collection, the NWGLH had analysed 180 FFPE tissue samples from deceased affected individuals: 134 from breast and/or ovarian cancer cases for germline variants in the BRCA1/BRCA2 genes and 46 from colorectal, gastric, ovarian and endometrial cancer cases for germline variants in a panel of 13 genes implicated in inherited colorectal cancer and gastric cancer conditions. Successful analysis was achieved in 140/180 cases (78%). In total, 29 germline pathogenic/likely pathogenic variants were identified in autosomal dominant cancer predisposition genes where the gene was pertinent to the cancer family history (including BRCA1/BRCA2, the mismatch-repair genes and APC). Of the 180 cases, the impact of the result on clinical management of unaffected relatives was known in 143 cases. Of these, the results in 54 cases (38%) directly impacted the clinical management of relatives seen by the CGS. This included changes to risk assessments, screening recommendations and the availability of predictive genetic testing to unaffected relatives. Our data demonstrate how FFPE testing in deceased relatives is an accurate and informative tool in the clinical management of patients referred to the CGS.
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Affiliation(s)
- Sarah Bennett
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Elizabeth Alexander
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Harry Fraser
- Northern Regional Genetic Service, Genetics Health Service New Zealand, Auckland City Hospital, Auckland, New Zealand
| | - Naomi Bowers
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Andrew Wallace
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emma R. Woodward
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anne Marie Quinn
- Department of Anatomic Pathology, University Hospital Galway, Galway, Ireland
| | - Shuwen Huang
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - D. Gareth Evans
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
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16
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BRCA1/2 Mutation Detection in the Tumor Tissue from Selected Polish Patients with Breast Cancer Using Next Generation Sequencing. Genes (Basel) 2021; 12:genes12040519. [PMID: 33918338 PMCID: PMC8065856 DOI: 10.3390/genes12040519] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although, in the mutated BRCA detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare BRCA1/2 variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the BRCA1/2 genes. (3) Results: We detected nine pathogenic variants in 8 out of 75 selected patients (10.7%). We identified one somatic and eight germline variants. We also used different bioinformatic NGS software programs to analyze NGS FASTQ files and established that tertiary analysis performed with different tools was more likely to give the same outcome if we analyzed files received from secondary analysis using the same method. (4) Conclusions: Our study emphasizes (i) the importance of an NGS validation process with a bioinformatic procedure included; (ii) the importance of screening both somatic and germline pathogenic variants; (iii) the urgent need to identify additional susceptible genes in order to explain the high percentage of non-BRCA-related hereditary cases of breast cancer.
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17
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Yao K, Duan Z, Du Z, Fan X, Qu Y, Zhang M, Wang Y, Liu H, Sun L, Qi X. PRKCA D463H Mutation in Chordoid Glioma of the Third Ventricle: A Cohort of 16 Cases, Including Two Cases Harboring BRAFV600E Mutation. J Neuropathol Exp Neurol 2021; 79:1183-1192. [PMID: 33085976 DOI: 10.1093/jnen/nlaa107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chordoid gliomas (CG) of the third ventricle are characterized by chordoid and glial features, but the extent of histological variations across CG is not fully understood. Herein, we report 16 consecutive cases of CG. All 16 patients had histories of headache and vision loss; their median age was 41.7 years at the surgery. Histological examination revealed typical features of CG, including cords of epithelioid cells within the mucinous stroma and lymphoplasmacytic infiltration. Two cases exhibited atypical histological features including histiocyte-like cells. PRKCA mutation was found in 14 cases, including the 2 with histiocytic features. BRAFV600E mutation was found only in the 2 cases with histiocytic features. The patients underwent gross total tumor resection without radiotherapy or chemotherapy. Three patients died between 1 and 4 months postsurgery. Only one had a recurrence. Eleven were alive at the most recent follow-up (range: 2-58 months). These data indicate that PRKCA mutation was a good diagnostic marker for CG and additionally suggest that histiocyte-like features can be present in CG in association with BRAF mutations.
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Affiliation(s)
- Kun Yao
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China
| | - Zejun Duan
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China.,The Department of Pathology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zunguo Du
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China
| | - Xiaolong Fan
- Beijing Key Laboratory of Gene Resource and Molecular Development, Laboratory of Neuroscience and Brain Development, School of Life Sciences Beijing Normal University
| | - Yanming Qu
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China
| | - Mingshan Zhang
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China
| | - Yin Wang
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China.,The Department of Pathology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hailong Liu
- The Department of Neurosurgery, Chinese PLA General Hospital (301 Hospital)
| | - Lingyan Sun
- The Department of Molecular Pathology Laboratory, Shanghai Ackermann Medical Laboratory, Shanghai, China
| | - Xueling Qi
- Departments of Pathology and Neurosurgery, San Bo Brain Hospital, Capital Medical University, Haidian District, Beijing, China
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18
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De Paolis E, De Bonis M, Concolino P, Piermattei A, Fagotti A, Urbani A, Scambia G, Minucci A, Capoluongo E. Droplet digital PCR for large genomic rearrangements detection: A promising strategy in tissue BRCA1 testing. Clin Chim Acta 2020; 513:17-24. [PMID: 33301768 DOI: 10.1016/j.cca.2020.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS With the introduction of Olaparib as target therapy for High Grade Serous Ovarian Cancer (HGSOC) patients with germline and somatic BRCA1/2 mutations, the genetic test performed on tumor tissue has become important like the germline test. In somatic testing the evaluation of Large Genomic Rearrangements (LGRs) represents the main challenge. We describe a droplet digital PCR (ddPCR) assay for the evaluation of target BRCA1 LGRs on blood and formalin-fixed paraffin-embedded (FFPE)/Fresh Frozen Tissue (FFT) samples. MATERIALS AND METHODS We analyzed blood, FFPE and FFT samples in a validation setting of n = 78 HGSOC patients. We applied the ddPCR to BRCA1 exons 2, 20 and 21 as some of the most common BRCA1 exons involved in LGRs in our cohort of patients. RESULTS The ddPCR custom assays allowed the identification of LGRs in all sample types, including FFPE specimens. Moreover, we were able to clearly detect LGRs accounted as somatic event. CONCLUSION The introduction of ddPCR in a comprehensive workflow, encompassing both germline and somatic tests, represents an improvement in BRCA1/2 testing. ddPCR can overcome challenges related to BRCA testing, especially on FFPE analysis. Finally, ddPCR represents a promising alternative strategy to the established standard methods currently used in clinical setting.
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Affiliation(s)
- Elisa De Paolis
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Maria De Bonis
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Paola Concolino
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Alessia Piermattei
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Anna Fagotti
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Andrea Urbani
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Giovanni Scambia
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Angelo Minucci
- Molecular Diagnostic and Genomic Laboratory, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy.
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, 80131 Naples, Italy; Federico II University, CEINGE, Advanced Biotechnology, 80131 Naples, Italy.
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19
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Kitson SJ, Bafligil C, Ryan NAJ, Lalloo F, Woodward ER, Clayton RD, Edmondson RJ, Bolton J, Crosbie EJ, Evans DG. BRCA1 and BRCA2 pathogenic variant carriers and endometrial cancer risk: A cohort study. Eur J Cancer 2020; 136:169-175. [PMID: 32698099 PMCID: PMC7441309 DOI: 10.1016/j.ejca.2020.05.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 12/15/2022]
Abstract
Background An association between BRCA pathogenic variants and an increased endometrial cancer risk, specifically serous-like endometrial cancer, has been postulated but remains unproven, particularly for BRCA2 carriers. Mechanistic evidence is lacking, and any link may be related to tamoxifen exposure or testing bias. Hysterectomy during risk-reducing bilateral salpingo-oophorectomy is, therefore, of uncertain benefit. Data from a large, prospective cohort will be informative. Methods Data on UK BRCA pathogenic variant carriers were interrogated for endometrial cancer diagnoses. Standardised incidence ratios (SIRs) were calculated in four distinct cohorts using national endometrial cancer rates; either from 1/1/1980 or age 20, prospectively from date of personal pathogenic variant report, date of family pathogenic variant report or date of risk-reducing salpingo-oophorectomy. Somatic BRCA sequencing of 15 serous endometrial cancers was performed to detect pathogenic variants. Results Fourteen cases of endometrial cancer were identified in 2609 women (1350 BRCA1 and 1259 BRCA2), of which two were prospectively diagnosed. No significant increase in either overall or serous-like endometrial cancer risk was identified in any of the cohorts examined (SIR = 1.70, 95% confidence interval = 0.74–3.33; no cases of serous endometrial cancer diagnosed). Results were unaffected by the BRCA gene affected, previous breast cancer or tamoxifen use. No BRCA pathogenic variants were detected in any of the serous endometrial cancers tested. Conclusions Women with a BRCA pathogenic variant do not appear to have a significant increased risk of all-type or serous-like endometrial cancer compared with the general population. These data provide some reassurance that hysterectomy is unlikely to be of significant benefit if performed solely as a preventive measure. Endometrial cancer risk was not increased in BRCA1/2 pathogenic variant carriers. Results were unaffected by BRCA gene, previous breast cancer or tamoxifen use. No specific increase in serous-like endometrial cancer risk was identified. Sequencing of 15 serous endometrial tumours revealed no pathogenic BRCA1/2 variants.
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Affiliation(s)
- Sarah J Kitson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Cemsel Bafligil
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Neil A J Ryan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK; Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Richard D Clayton
- Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Richard J Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK; Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - James Bolton
- Department of Histopathology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK; Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK; Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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20
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Kim Y, Cho CH, Ha JS, Kim DH, Kwon SY, Oh SC, Lee KA. An optimized BRCA1/2 next-generation sequencing for different clinical sample types. J Gynecol Oncol 2019; 31:e9. [PMID: 31788999 PMCID: PMC6918881 DOI: 10.3802/jgo.2020.31.e9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 02/04/2023] Open
Abstract
Objective A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. Methods We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. Results The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. Conclusions On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation.
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Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Do Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Seoung Chul Oh
- Department of Laboratory Medicine, Gangnam Severance Hospital, Seoul, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
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21
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Ivanov M, Ivanov M, Kasianov A, Rozhavskaya E, Musienko S, Baranova A, Mileyko V. Novel bioinformatics quality control metric for next-generation sequencing experiments in the clinical context. Nucleic Acids Res 2019; 47:e135. [PMID: 31511888 PMCID: PMC6868350 DOI: 10.1093/nar/gkz775] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 07/22/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
As the use of next-generation sequencing (NGS) for the Mendelian diseases diagnosis is expanding, the performance of this method has to be improved in order to achieve higher quality. Typically, performance measures are considered to be designed in the context of each application and, therefore, account for a spectrum of clinically relevant variants. We present EphaGen, a new computational methodology for bioinformatics quality control (QC). Given a single NGS dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associates this dataset with a single arbiter parameter. Intrinsically, EphaGen estimates the probability to miss any variant from the defined spectrum within a particular NGS dataset. Such performance measure virtually resembles the diagnostic sensitivity of given NGS dataset. Here we present case studies of the use of EphaGen in context of BRCA1/2 and CFTR sequencing in a series of 14 runs across 43 blood samples and 504 publically available NGS datasets. EphaGen is superior to conventional bioinformatics metrics such as coverage depth and coverage uniformity. We recommend using this software as a QC step in NGS studies in the clinical context. Availability: https://github.com/m4merg/EphaGen or https://hub.docker.com/r/m4merg/ephagen.
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Affiliation(s)
- Maxim Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Mikhail Ivanov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation
| | - Artem Kasianov
- Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Ekaterina Rozhavskaya
- Vavilov Institute of General Genetics, Moscow, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
| | | | - Ancha Baranova
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation.,Research Centre for Medical Genetics, Moscow, Russian Federation.,School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
| | - Vladislav Mileyko
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russian Federation.,Atlas Oncology Diagnostics, Ltd, Moscow, Russian Federation
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22
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Teixeira LA, Candido Dos Reis FJ. Immunohistochemistry for the detection of BRCA1 and BRCA2 proteins in patients with ovarian cancer: a systematic review. J Clin Pathol 2019; 73:191-196. [PMID: 31719105 DOI: 10.1136/jclinpath-2019-206276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/28/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Loss of function in either breast cancer type 1 susceptibility protein (BRCA1) or breast cancer type 2 susceptibility protein (BRCA2) is a major risk factor for epithelial ovarian cancer (EOC) development. BRCA1 or BRCA2 deficiencies are associated with short-term prognosis and might have importance for the treatment of women with the disease. However, the screening of all possible mechanisms of dysfunction is expensive, time-consuming and difficult to apply in clinical practice. On the other hand, immunohistochemistry (IHC) is a simple and reliable method to access the expression of several proteins in tumour tissues. MATERIALS AND METHODS This systematic review aims to evaluate the current usage of IHC to detect BRCA1 and BRCA2 deficiencies in EOC. We searched and evaluated all primary literature on the use of IHC for evaluating BRCA1 and BRCA2 proteins expression in EOC. The main concepts for the search were: ovarian neoplasms, IHC, BRCA1 and BRCA2. RESULTS Forty-four studies from 925 unique titles were included. A total of 4206 tumour samples were evaluated for BRCA1 and 1041 for BRCA2 expression. Twelve BRCA1 primary antibodies were used in 41 studies, and the most common was the MS110 clone (75.6%). Seven BRCA2 primary antibodies were used in ten studies. Using the cut-off of 10%, 47.0% of EOCs are associated with loss of BRCA1 and 34.5% with the loss of BRCA2 expression. CONCLUSION IHC was effective to detect loss of BRCA1 protein expression in EOC; however, data on BRCA2 expression were heterogeneous and difficult to interpret.
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Affiliation(s)
- Lorena Alves Teixeira
- Postgraduate Program in Gynecology and Obstetrics, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Francisco Jose Candido Dos Reis
- Postgraduate Program in Gynecology and Obstetrics, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
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23
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Nicolussi A, Belardinilli F, Mahdavian Y, Colicchia V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Valentini V, Ottini L, Giannini G, Capalbo C, Coppa A. Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer. PeerJ 2019; 7:e6661. [PMID: 31065452 PMCID: PMC6482939 DOI: 10.7717/peerj.6661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Valeria Colicchia
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy.,U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
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24
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Bandoh N, Akahane T, Goto T, Kono M, Ichikawa H, Sawada T, Yamaguchi T, Nakano H, Kawase Y, Kato Y, Kamada H, Harabuchi Y, Shimizu K, Nishihara H. Targeted next-generation sequencing of cancer-related genes in thyroid carcinoma: A single institution's experience. Oncol Lett 2018; 16:7278-7286. [PMID: 30546467 DOI: 10.3892/ol.2018.9538] [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: 06/12/2018] [Accepted: 09/25/2018] [Indexed: 01/05/2023] Open
Abstract
Thyroid carcinoma (TC) has characteristic genetic alterations, including point mutations in proto-oncogenes and chromosomal rearrangements that vary by histologic subtype. Recent developments in next-generation sequencing (NGS) technology enable simultaneous analysis of cancer-associated genes of interest, thus improving diagnostic accuracy and allowing precise personalized treatment for human cancer. A total of 50 patients who underwent thyroidectomy between 2014 and 2016 at Hokuto Hospital were enrolled. Total DNA was extracted from formalin-fixed, paraffin-embedded tissue sections and quantified. Targeted regions of 24 cancer-associated genes were amplified by PCR, barcoded and sequenced using an Illumina MiSeq platform. Subjects included 30 patients with papillary carcinoma (PC), two with PC tall cell variant (TVPC), two with PC follicular variant (FVPC), eight with follicular carcinoma, seven with poorly differentiated carcinoma (PDC), and one with anaplastic carcinoma (AC). The BRAF V600E mutation was present in 25 of 30 (83%) patients with PC, 2 of 2 (100%) patients with TVPC, 6 of 7 (86%) patients of PDC, and one patient with AC. PIK3CA mutations were present in 3 of 30 (delPV104P, A1046T and C420R; 10%) patients with PC and 1 of 7 (H1047R; 14%) patients with PDC. The TP53 mutation was present in 1 of 30 (R306*; 3.3%) patients with PC and 1 of 7 (Q152*; 14%) patients with PDC. The NRAS mutation was present in 1 of 2 (Q61K, 50%) patients with FVPC. Statistical analysis showed that patients without the BRAF V600E mutation had advanced pathologic T and N stages compared with those with the mutation (P=0.047 and P=0.019, respectively). The BRAF V600E mutation was not correlated with overall and disease-free survival in patients with PC. A patient with PC with a mutation in EGFR (K852Q) and the PIK3CA mutation had an aggressive course with multiple bone and lung metastases. Detection of mutations in cancer-associated genes using NGS could enhance the understanding of the clinical behavior of TC.
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Affiliation(s)
- Nobuyuki Bandoh
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Toshiaki Akahane
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Takashi Goto
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Michihisa Kono
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Haruyuki Ichikawa
- Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Takahiro Sawada
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Tomomi Yamaguchi
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Hiroshi Nakano
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Yumiko Kawase
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Yasutaka Kato
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Hajime Kamada
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan
| | - Yasuaki Harabuchi
- Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan
| | - Kazuo Shimizu
- Department of Endocrine Surgery, Kanaji Hospital, Tokyo 114-0015, Japan
| | - Hiroshi Nishihara
- Department of Biology and Genetics, Laboratory of Cancer Medical Science, Hokuto Hospital, Obihiro, Hokkaido 080-0833, Japan.,Keio Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
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25
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Kono M, Bandoh N, Matsuoka R, Goto T, Akahane T, Kato Y, Nakano H, Yamaguchi T, Harabuchi Y, Nishihara H. Glomangiopericytoma of the Nasal Cavity with CTNNB1 p.S37C Mutation: A Case Report and Literature Review. Head Neck Pathol 2018; 13:298-303. [PMID: 30206803 PMCID: PMC6684555 DOI: 10.1007/s12105-018-0961-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/18/2018] [Indexed: 12/25/2022]
Abstract
Glomangiopericytoma (GPC) is a rare mesenchymal tumor arising from the nasal cavity or paranasal sinuses. GPC was categorized as a borderline and low-malignant-potential tumor by the World Health Organization in 2005 and accounts for less than 0.5% of all sinonasal tumors. We report a case of GPC in a 74-year-old woman with a history of recurrent epistaxis and nasal obstruction. A reddish tumor was seen in the right nasal cavity. Enhanced computed tomography showed a mass lesion occupying the right nasal cavity. The tumor, which originated from the nasal septum in the olfactory fissure area, was resected with 5-mm mucosal margins by endoscopic sinus surgery. Histologic examination revealed a uniform proliferation of oval-to-short spindle-shaped cells beneath the epithelium. Immunohistologic analysis demonstrated the tumor cells were positive for α-smooth muscle actin, β-catenin and Vimentin, and negative for AE1/AE3, Bcl-2, CD34, CD117, Factor VIIIR Ag, S-100 protein, or STAT6. The percentage of Ki-67-positive cells was approximately 5%. Genetic analysis using next-generation sequencing revealed a missense mutation in the CTNNB1 gene (c.110C > G, p.S37C). While other CTNNB1 mutations have been described in GPC; this is the first report of this specific mutation. The mutation was confirmed using Sanger sequencing.
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Affiliation(s)
- Michihisa Kono
- 0000 0004 0595 9093grid.452447.4Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan ,0000 0000 8638 2724grid.252427.4Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, 078-8510 Japan
| | - Nobuyuki Bandoh
- 0000 0004 0595 9093grid.452447.4Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Ryosuke Matsuoka
- 0000 0004 0531 3030grid.411731.1Center for Diagnostic Pathology, Mita Hospital, International University of Health and Welfare, Tokyo, 108-8329 Japan
| | - Takashi Goto
- 0000 0004 0595 9093grid.452447.4Department of Otolaryngology-Head and Neck Surgery, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Toshiaki Akahane
- 0000 0004 0595 9093grid.452447.4Laboratory of Cancer Medical Science, Department of Biology and Genetics, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Yasutaka Kato
- 0000 0004 0595 9093grid.452447.4Laboratory of Cancer Medical Science, Department of Biology and Genetics, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Hiroshi Nakano
- 0000 0004 0595 9093grid.452447.4Laboratory of Cancer Medical Science, Department of Biology and Genetics, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Tomomi Yamaguchi
- 0000 0004 0595 9093grid.452447.4Laboratory of Cancer Medical Science, Department of Biology and Genetics, Hokuto Hospital, Inadacho Kisen 7-5, Obihiro, 080-0833 Japan
| | - Yasuaki Harabuchi
- 0000 0000 8638 2724grid.252427.4Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa, 078-8510 Japan
| | - Hiroshi Nishihara
- 0000 0004 1936 9959grid.26091.3cKeio Cancer Center, Keio University School of Medicine, 35 Shinanomachi, Shinjukuku, Tokyo, 160-8582 Japan
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26
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Inadequate Rates of BRCA Testing with its Negative Consequences for Women with Epithelial Ovarian Cancer and their Families: an Overview of the Literature. Clin Oncol (R Coll Radiol) 2018; 30:472-483. [DOI: 10.1016/j.clon.2018.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/18/2018] [Indexed: 12/19/2022]
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27
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Vendrell JA, Vilquin P, Larrieux M, Van Goethem C, Solassol J. Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection. J Mol Diagn 2018; 20:754-764. [PMID: 30055349 DOI: 10.1016/j.jmoldx.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022] Open
Abstract
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs). Four assays (BRCA Tumor, BRCA HC, Ion AmpliSeq BRCA, and Access Array BRCA) and two commercial bioinformatics solutions (SeqNext software version 4.3.1 and Sophia DDM version 5.0.13) were tested on a set of 28 previously genotyped samples. All solutions exhibited accurate detection of single-nucleotide variants and insertion/deletion variants, except for Ion AmpliSeq BRCA, which exhibited a decrease in coverage. Of interest, for CNV analysis, the best accuracy was observed with the Sophia DDM platform regardless of the BRCA kit used. Finally, the performance of the most relevant combination (BRCA Tumor and Sophia DDM) was blindly validated on an independent set of 152 samples. Altogether, our results emphasize the need to accurately compare and control both molecular next-generation sequencing approaches and bioinformatics pipelines to limit the number of discrepant alterations and to provide a powerful tool for reliable detection of genetic alterations in BRCA1 and BRCA2, notably CNVs.
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Affiliation(s)
- Julie A Vendrell
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Paul Vilquin
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Marion Larrieux
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Charles Van Goethem
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Jérôme Solassol
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France; The Institute of Cancer Research of Montpellier, INSERM U1194, University of Montpellier, Montpellier, France.
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28
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de Jonge MM, Ruano D, van Eijk R, van der Stoep N, Nielsen M, Wijnen JT, Ter Haar NT, Baalbergen A, Bos MEMM, Kagie MJ, Vreeswijk MPG, Gaarenstroom KN, Kroep JR, Smit VTHBM, Bosse T, van Wezel T, van Asperen CJ. Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue. J Mol Diagn 2018; 20:600-611. [PMID: 29936257 DOI: 10.1016/j.jmoldx.2018.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/01/2018] [Indexed: 12/19/2022] Open
Abstract
BRCA1/2 variant analysis in tumor tissue could streamline the referral of patients with epithelial ovarian, fallopian tube, or primary peritoneal cancer to genetic counselors and select patients who benefit most from targeted treatment. We investigated the sensitivity of BRCA1/2 variant analysis in formalin-fixed, paraffin-embedded tumor tissue using a combination of next-generation sequencing and copy number variant multiplex ligation-dependent probe amplification. After optimization using a training cohort of known BRCA1/2 mutation carriers, validation was performed in a prospective cohort in which screening of BRCA1/2 tumor DNA and leukocyte germline DNA was performed in parallel. BRCA1 promoter hypermethylation and pedigree analysis were also performed. In the training cohort, 45 of 46 germline BRCA1/2 variants were detected (sensitivity, 98%). In the prospective cohort (n = 62), all six germline variants were identified (sensitivity, 100%), together with five somatic BRCA1/2 variants and eight cases with BRCA1 promoter hypermethylation. In four BRCA1/2 variant-negative patients, surveillance or prophylactic management options were offered on the basis of positive family histories. We conclude that BRCA1/2 formalin-fixed, paraffin-embedded tumor tissue analysis reliably detects BRCA1/2 variants. When taking family history of BRCA1/2 variant-negative patients into account, tumor BRCA1/2 variant screening allows more efficient selection of epithelial ovarian cancer patients for genetic counseling and simultaneously selects patients who benefit most from targeted treatment.
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Affiliation(s)
- Marthe M de Jonge
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Natalja T Ter Haar
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Astrid Baalbergen
- Department of Gynaecology, Reinier de Graaf Hospital, Delft, the Netherlands
| | - Monique E M M Bos
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marjolein J Kagie
- Department of Gynecology, Haaglanden Medisch Centrum, The Hague, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Katja N Gaarenstroom
- Department of Gynecology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith R Kroep
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent T H B M Smit
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
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29
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Pike KG, Barlaam B, Cadogan E, Campbell A, Chen Y, Colclough N, Davies NL, de-Almeida C, Degorce SL, Didelot M, Dishington A, Ducray R, Durant ST, Hassall LA, Holmes J, Hughes GD, MacFaul PA, Mulholland KR, McGuire TM, Ouvry G, Pass M, Robb G, Stratton N, Wang Z, Wilson J, Zhai B, Zhao K, Al-Huniti N. The Identification of Potent, Selective, and Orally Available Inhibitors of Ataxia Telangiectasia Mutated (ATM) Kinase: The Discovery of AZD0156 (8-{6-[3-(Dimethylamino)propoxy]pyridin-3-yl}-3-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,3-dihydro-2H-imidazo[4,5-c]quinolin-2-one). J Med Chem 2018; 61:3823-3841. [DOI: 10.1021/acs.jmedchem.7b01896] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Kurt G. Pike
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Bernard Barlaam
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Elaine Cadogan
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Andrew Campbell
- Pharmaceutical Sciences, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Yingxue Chen
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicola Colclough
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Nichola L. Davies
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Camila de-Almeida
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Sebastien L. Degorce
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Myriam Didelot
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Allan Dishington
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Richard Ducray
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Stephen T. Durant
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Lorraine A. Hassall
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Jane Holmes
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Gareth D. Hughes
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Philip A. MacFaul
- Oncology, IMED Biotech Unit, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Keith R. Mulholland
- Chemical Development, AstraZeneca, Silk Road Business Park, Macclesfield SK10 2NA, U.K
| | - Thomas M. McGuire
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Gilles Ouvry
- Oncology, IMED Biotech Unit, AstraZeneca, Centre de Recherches, Z. I. la Pompelle, BP 1050, 51689 Reims Cedex 2, France
| | - Martin Pass
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Graeme Robb
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Natalie Stratton
- Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | - Zhenhua Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Joanne Wilson
- Oncology, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, 319 Milton Road, Cambridge CB4 0WG, U.K
| | - Baochang Zhai
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Kang Zhao
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, P.R. China
| | - Nidal Al-Huniti
- Oncology, IMED Biotech Unit, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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30
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Enyedi MZ, Jaksa G, Pintér L, Sükösd F, Gyuris Z, Hajdu A, Határvölgyi E, Priskin K, Haracska L. Simultaneous detection of BRCA mutations and large genomic rearrangements in germline DNA and FFPE tumor samples. Oncotarget 2018; 7:61845-61859. [PMID: 27533253 PMCID: PMC5308695 DOI: 10.18632/oncotarget.11259] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 11/25/2022] Open
Abstract
The development of breast and ovarian cancer is strongly connected to the inactivation of the BRCA1 and BRCA2 genes by different germline and somatic alterations, and their diagnosis has great significance in targeted tumor therapy, since recently approved PARP inhibitors show high efficiency in the treatment of BRCA-deficient tumors. This raises the need for new diagnostic methods that are capable of performing an integrative mutation analysis of the BRCA genes not only from germline DNA but also from formalin-fixed and paraffin-embedded (FFPE) tumor samples. Here we describe the development of such a methodology based on next-generation sequencing and a new bioinformatics software for data analysis. The diagnostic method was initially developed on an Illumina MiSeq NGS platform using germline-mutated stem cell lines and then adapted for the Ion Torrent PGM NGS platform as well. We also investigated the usability of NGS coverage data for the detection of copy number variations and exon deletions as a replacement of the conventional MLPA technique. Finally, we tested the developed workflow on FFPE samples from breast and ovarian cancer patients. Our method meets the sensitivity and specificity requirements for the genetic diagnosis of breast and ovarian cancers both from germline and FFPE samples.
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Affiliation(s)
- Márton Zsolt Enyedi
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | | | | | - Farkas Sükösd
- Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | - Adrienn Hajdu
- Delta Bio 2000 Ltd., Szeged 6726, Hungary.,Department of Pathology, Faculty of Medicine, University of Szeged, Szeged 6720, Hungary
| | | | | | - Lajos Haracska
- Institute of Genetics, Biological Research Centre of the Hungarian Academy of Sciences, Szeged 6726, Hungary
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31
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Hirotsu Y, Ooka Y, Sakamoto I, Nakagomi H, Omata M. Simultaneous detection of genetic and copy number alterations in BRCA1/2 genes. Oncotarget 2017; 8:114463-114473. [PMID: 29383094 PMCID: PMC5777706 DOI: 10.18632/oncotarget.22962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/11/2017] [Indexed: 12/13/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 genes (BRCA1/2) predispose to hereditary breast and ovarian cancer syndrome (HBOC), and their dysregulation increases the risk of cancers. The detection of pathogenic BRCA1/2 variants is essential for the diagnosis and prevention of HBOC, and for offering treatment decisions for patients. Therefore, there is a growing demand for the development of accurate, rapid assay systems that simultaneously detect pathogenic variants and copy number alterations. Here, we tested Thermo Fisher Scientific's newly developed Oncomine®BRCA1/2 Panel. We showed that all mutations in standard reference DNA were detected with high accuracy, and that values of allelic fractions were detected with high concordance (R2 = 0.9986). The Oncomine®BRCA1/2 Panel detected 21 pathogenic germline variants in 147 patients with breast and/or ovarian cancer, of which 20 were detected by the previously-launched Ion AmpliSeq™ BRCA1/2 Panel, except for one frameshift mutation. The Oncomine®BRCA1/2 Panel precisely captured one additional frameshift mutation, which is difficult to detect because of the homopolymer site. Large genomic deletion was identified in one sample, which was previously detected by multiplex ligation-dependent probe amplification. Oncomine®BRCA1/2 Panel could accurately detect pathogenic variant and copy number alteration, and be an alternative assay to investigate BRCA1/2 germline and somatic mutations.
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Affiliation(s)
- Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi 400-8506, Japan
| | - Yoshihiko Ooka
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi 400-8506, Japan
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Ikuko Sakamoto
- Department of Obstetrics and Gynecology, Yamanashi Central Hospital, Fujimi Kofu-City, Yamanashi 400-8506, Japan
| | - Hiroshi Nakagomi
- Department of Breast Surgery, Yamanashi Central Hospital, Yamanashi 400-8506, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi 400-8506, Japan
- University of Tokyo, Hongo, Bunkyo-Ku, Tokyo 113-8655, Japan
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32
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Ellison G, Ahdesmäki M, Luke S, Waring PM, Wallace A, Wright R, Röthlisberger B, Ludin K, Merkelbach-Bruse S, Heydt C, Ligtenberg MJL, Mensenkamp AR, de Castro DG, Jones T, Vivancos A, Kondrashova O, Pauwels P, Weyn C, Hahnen E, Hauke J, Soong R, Lai Z, Dougherty B, Carr TH, Johnson J, Mills J, Barrett JC. An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice. Hum Mutat 2017; 39:394-405. [PMID: 29215764 PMCID: PMC5838520 DOI: 10.1002/humu.23375] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/06/2017] [Accepted: 11/26/2017] [Indexed: 01/19/2023]
Abstract
Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with poly ADP ribose polymerase (PARP) inhibitors. Tumor BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin-fixed paraffin embedded (FFPE), the tumor genome is complex, and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumors to compare different approaches to identify clinically important variants within FFPE tumor DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues. Each laboratory received the same tumor DNA samples ranging in genotype, quantity, quality, and variant allele frequency (VAF). Each laboratory performed their preferred next-generation sequencing method to report on the variants. No false positive results were reported in this small study and the majority of methods detected the low VAF variants. A number of variants were not detected due to the bioinformatics analysis, variant classification, or insufficient DNA. The use of hybridization capture or short amplicon methods are recommended based on a bioinformatic assessment of the data. The study highlights the importance of establishing standards and standardization for tBRCA testing particularly when the test results dictate clinical decisions regarding life extending therapies.
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Affiliation(s)
- Gillian Ellison
- Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - Miika Ahdesmäki
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Sally Luke
- R&D Information, AstraZeneca, Cambridge, UK
| | - Paul M Waring
- Department of Pathology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Andrew Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Ronnie Wright
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
| | - Benno Röthlisberger
- Kantonsspital Aarau, Institut für Labormedizin, Abteilung für Medizinische Genetik, Aarau, Switzerland
| | - Katja Ludin
- Kantonsspital Aarau, Institut für Labormedizin, Abteilung für Medizinische Genetik, Aarau, Switzerland
| | | | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - David Gonzalez de Castro
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.,The Centre for Molecular Pathology, The Royal Marsden NHS FT, Sutton, UK
| | - Thomas Jones
- The Centre for Molecular Pathology, The Royal Marsden NHS FT, Sutton, UK
| | - Ana Vivancos
- Laboratory 2.01, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Olga Kondrashova
- Department of Pathology, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Pathology Department, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Christine Weyn
- Center for Oncological Research (CORE), Pathology Department, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer and Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Richie Soong
- Cancer Science Institute of Singapore, and Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Zhongwu Lai
- Bioscience, Oncology, IMED Biotech Unit, AstraZeneca, IMED Oncology, Waltham, Massachusetts
| | - Brian Dougherty
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
| | - T Hedley Carr
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Justin Johnson
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
| | - John Mills
- Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Macclesfield, UK
| | - J Carl Barrett
- Translational Science, Oncology, IMED Biotech Unit, AstraZeneca, Waltham, Massachusetts
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Bartosch C, Clarke B, Bosse T. Gynaecological neoplasms in common familial syndromes (Lynch and HBOC). Pathology 2017; 50:222-237. [PMID: 29287922 DOI: 10.1016/j.pathol.2017.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
Recognising hereditary predisposition in a cancer patient has implications both for the patient and the patient's kindred. For the latter, cascade germline testing can reassure those not-at-risk family members while carriers can be enrolled in cancer screening and prevention programs that are medically effective and economically sustainable for health care systems. Furthermore, in many of these syndromes, ramifications of molecular phenotypes are increasing, and it is now emerging that, in addition, they convey prognostic and predictive information. Although cancer predisposition syndromes are rare, these molecular phenotypes also occur as somatic events in sporadic cancer settings. The information obtained from these molecular phenotypes, regardless of germline or somatic origin, is being incorporated into clinical management in view of their manifold significance. Thus, increasingly, bespoke management of cancer patients involves testing for both germline and somatic mutations in tumours. Lynch syndrome and BRCA-1 and BRCA-2-associated hereditary breast and ovarian cancer are hereditary cancer syndromes frequently involving the gynaecological tract but tumours associated with similar molecular alterations may also occur sporadically. Thus, the molecular phenotype of mismatch repair deficiency, microsatellite instability or hypermutator phenotype may be attributable to germline or somatic events. Similarly, homologous recombination deficiency or 'BRCAness' in ovarian cancers may be syndromic or sporadic. While hereditary syndromes are well recognised, the prognostic and predictive implications of these molecular phenotypes have only recently been elucidated and these aspects will finally ensure that molecular screening may become standard of care. Thus, nowadays pathologists are asked to designate the molecular phenotype of these cancers and then determine whether it is due to hereditary or sporadic causes.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Blaise Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, University Health Network, Toronto, Ontario, Canada
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, The Netherlands.
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Borghei YS, Hosseini M, Ganjali MR. Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters. Methods Appl Fluoresc 2017; 6:015001. [PMID: 28858858 DOI: 10.1088/2050-6120/aa8988] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here we describe a label-free detection strategy for large deletion mutation in breast cancer (BC) related gene BRCA1 based on a DNA-silver nanocluster (NC) fluorescence upon recognition-induced hybridization. The specific hybridization of DNA templated silver NCs fluorescent probe to target DNAs can act as effective templates for enhancement of AgNCs fluorescence, which can be used to distinguish the deletion of BRCA1 due to different fluorescence intensities. Under the optimal conditions, the fluorescence intensity of the DNA-AgNCs at emission peaks around 440 nm (upon excitation at 350 nm) increased with the increasing deletion type within a dynamic range from 1.0 × 10-10 to 2.4 × 10-6 M with a detection limit (LOD) of 6.4 × 10-11 M. In this sensing system, the normal type shows no significant fluorescence; on the other hand, the deletion type emits higher fluorescence than normal type. Using this nanobiosensor, we successfully determined mutation using the non-amplified genomic DNAs that were isolated from the BC cell line.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
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35
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Hoskins PJ, Gotlieb WH. Missed therapeutic and prevention opportunities in women with BRCA-mutated epithelial ovarian cancer and their families due to low referral rates for genetic counseling and BRCA testing: A review of the literature. CA Cancer J Clin 2017; 67:493-506. [PMID: 28881380 DOI: 10.3322/caac.21408] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 12/24/2022] Open
Abstract
Answer questions and earn CME/CNE Fifteen percent of women with epithelial ovarian cancer have inherited mutations in the BRCA breast cancer susceptibility genes. Knowledge of her BRCA status has value both for the woman and for her family. A therapeutic benefit exists for the woman with cancer, because a new family of oral drugs, the poly ADP-ribose polymerase (PARP) inhibitors, has recently been approved, and these drugs have the greatest efficacy in women who carry the mutation. For her family, there is the potential to prevent ovarian cancer in those carrying the mutation by using risk-reducing surgery. Such surgery significantly reduces the chance of developing this, for the most part, incurable cancer. Despite these potential benefits, referral rates for genetic counseling and subsequent BRCA testing are low, ranging from 10% to 30%, indicating that these therapeutic and prevention opportunities are being missed. The authors have reviewed the relevant available literature. Topics discussed are BRCA and its relation to ovarian cancer, the rates of referral for genetic counseling/BRCA testing, reasons for these low rates, potential strategies to improve on those rates, lack of effectiveness of current screening strategies, the pros and cons of risk-reducing surgery, other prevention options, and the role and value of PARP inhibitors. CA Cancer J Clin 2017;67:493-506. © 2017 American Cancer Society.
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Affiliation(s)
- Paul J Hoskins
- Medical Oncologist and Past President, Society of Gynecologic Oncology Canada, British Columbia Cancer Agency, Vancouver Center, BC, Canada
| | - Walter H Gotlieb
- Gynecologic Oncologist and President, Society of Gynecologic Oncology Canada, McGill University, Jewish General Hospital, Montreal, QC, Canada
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Capoluongo E, Ellison G, López-Guerrero JA, Penault-Llorca F, Ligtenberg MJL, Banerjee S, Singer C, Friedman E, Markiefka B, Schirmacher P, Büttner R, van Asperen CJ, Ray-Coquard I, Endris V, Kamel-Reid S, Percival N, Bryce J, Röthlisberger B, Soong R, de Castro DG. Guidance Statement On BRCA1/2 Tumor Testing in Ovarian Cancer Patients. Semin Oncol 2017; 44:187-197. [PMID: 29248130 DOI: 10.1053/j.seminoncol.2017.08.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/28/2017] [Accepted: 08/28/2017] [Indexed: 01/25/2023]
Abstract
The approval, in 2015, of the first poly (adenosine diphosphate-ribose) polymerase inhibitor (PARPi; olaparib, Lynparza) for platinum-sensitive relapsed high-grade ovarian cancer with either germline or somatic BRCA1/2 deleterious mutations is changing the way that BRCA1/2 testing services are offered to patients with ovarian cancer. Ovarian cancer patients are now being referred for BRCA1/2 genetic testing for treatment decisions, in addition to familial risk estimation, and irrespective of a family history of breast or ovarian cancer. Furthermore, testing of tumor samples to identify the estimated 3%-9% of patients with somatic BRCA1/2 mutations who, in addition to germline carriers, could benefit from PARPi therapy is also now being considered. This new testing paradigm poses some challenges, in particular the technical and analytical difficulties of analyzing chemically challenged DNA derived from formalin-fixed, paraffin-embedded specimens. The current manuscript reviews some of these challenges and technical recommendations to consider when undertaking BRCA1/2 testing in tumor tissue samples to detect both germline and somatic BRCA1/2 mutations. Also provided are considerations for incorporating genetic analysis of ovarian tumor samples into the patient pathway and ethical requirements.
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Affiliation(s)
- Ettore Capoluongo
- Catholic University of the Sacred Heart and A. Gemelli Teaching Hospital Foundation, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | | | - Jane Bryce
- Nazionale Tumori IRCCS Pascale, Naples, Italy
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37
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Wu H, Wu X, Liang Z. Impact of germline and somatic BRCA1/2 mutations: tumor spectrum and detection platforms. Gene Ther 2017; 24:601-609. [PMID: 28771233 DOI: 10.1038/gt.2017.73] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/10/2017] [Accepted: 07/27/2017] [Indexed: 12/13/2022]
Abstract
The BRCA1/2 genes are long and complex and mutation carriers are at risk of developing malignancies, mainly of gynecological origin. Various mutations arise in these genes and their characterization is a time-consuming, cost intensive, complicated process. Tumors of BRCA1/2 origin have distinct molecular and histological features that can impact responses to therapy. Therefore, detection of these mutations constitutes an important step in the risk assessment, prevention strategy and treatment of subjects. Although Sanger sequencing is the gold standard for the detection of genetic mutations, several next generation sequencing-based high throughput platforms have been developed and adapted for the detection of BRCA1/2 mutations. This review provides a comprehensive overview of the sequencing platforms available for the screening and identification of these mutations. We also summarize what is known about the different types of mutations that arise in these genes and the tumor spectra they result in. Finally, we present a short discussion on existing clinical guidelines which assist physicians in the decision-making process. These parameters have important consequences for the management of patients and an urgent need exists for the development of detection platforms that are cost effective and can provide clinicians with conclusive results within a significantly shorter time.
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Affiliation(s)
- H Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - X Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Z Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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38
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Deans ZC, Costa JL, Cree I, Dequeker E, Edsjö A, Henderson S, Hummel M, Ligtenberg MJ, Loddo M, Machado JC, Marchetti A, Marquis K, Mason J, Normanno N, Rouleau E, Schuuring E, Snelson KM, Thunnissen E, Tops B, Williams G, van Krieken H, Hall JA. Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL. Virchows Arch 2017; 470:5-20. [PMID: 27678269 PMCID: PMC5243883 DOI: 10.1007/s00428-016-2025-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/27/2016] [Accepted: 09/16/2016] [Indexed: 10/31/2022]
Abstract
The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK.
| | - Jose Luis Costa
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ian Cree
- Department of Pathology, University Hospital Coventry and Warwickshire, Coventry, CV2 2DX, UK
| | - Els Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven-University of Leuven, Leuven, Belgium
| | - Anders Edsjö
- Clinical Pathology, Laboratory Medicine, Medical Services, Region Skåne, Lund, Sweden
| | - Shirley Henderson
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Michael Hummel
- Institute of Pathology, Berlin, Germany and the DGP, German Society of Pathology, Charite, University Medicine Berlin, Berlin, Germany
| | - Marjolijn Jl Ligtenberg
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marco Loddo
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Jose Carlos Machado
- i3S Instituto de Investigação e Inovação em Saúde/IPATIMUP Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, CeSI-MeT, University of Chieti, Chieti, Italy
| | - Katherine Marquis
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Joanne Mason
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London, EC1M 6BQ, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumouri "Fondazione Giovanni Pascale" IRCCS, Naples, Italy
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Genetic and Pathology Molecular Service, Gustave Roussy, 114 Rue Edouard Vaillant, 94800, Villejuif, France
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center of Groningen, Groningen, The Netherlands
| | - Keeda-Marie Snelson
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Erik Thunnissen
- Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Bastiaan Tops
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gareth Williams
- Oncologica UK Ltd, Suite 15-16, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Han van Krieken
- Department of Pathology and Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacqueline A Hall
- International Quality Network for Pathology (IQN Path) Association Sans But Lucratif (A.S.B.L), 17 Boulevard Royal, L2449, Luxembourg City, Luxembourg
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
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A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. Int J Genomics 2016; 2016:7983236. [PMID: 28070503 PMCID: PMC5192301 DOI: 10.1155/2016/7983236] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/26/2016] [Indexed: 12/31/2022] Open
Abstract
Whole Exome Sequencing (WES) is the application of the next-generation technology to determine the variations in the exome and is becoming a standard approach in studying genetic variants in diseases. Understanding the exomes of individuals at single base resolution allows the identification of actionable mutations for disease treatment and management. WES technologies have shifted the bottleneck in experimental data production to computationally intensive informatics-based data analysis. Novel computational tools and methods have been developed to analyze and interpret WES data. Here, we review some of the current tools that are being used to analyze WES data. These tools range from the alignment of raw sequencing reads all the way to linking variants to actionable therapeutics. Strengths and weaknesses of each tool are discussed for the purpose of helping researchers make more informative decisions on selecting the best tools to analyze their WES data.
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40
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Badoer C, Garrec C, Goossens D, Ellison G, Mills J, Dzial M, Housni HE, Berwouts S, Concolino P, Guevellou VGL, Delnatte C, Favero JD, Capoluongo E, Bézieau S. Performance of multiplicom's BRCA MASTR Dx kit on the detection of BRCA1 and BRCA2 mutations in fresh frozen ovarian and breast tumor samples. Oncotarget 2016; 7:81357-81366. [PMID: 27793035 PMCID: PMC5348397 DOI: 10.18632/oncotarget.12877] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/08/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing (NGS) has enabled new approaches for detection of mutations in the BRCA1 and BRCA2 genes responsible for hereditary breast and ovarian cancer (HBOC). The search for germline mutations in the BRCA1 and BRCA2 genes is of importance with respect to oncogenetic and surgical (bilateral mastectomy, ovariectomy) counselling. Testing tumor material for BRCA mutations is of increasing importance for therapeutic decision making as the poly ADP ribose polymerase (PARP) inhibitor, olaparib, is now available to treat patients with specific forms of ovarian cancer and BRCA mutations. Molecular genetics laboratories should develop reliable and sensitive techniques for the complete analysis of the BRCA1 and BRCA2 genes. This is a challenge due to the size of the coding sequence of the BRCA1/2 genes, the absence of hot spot mutations, and particularly by the lower DNA quality obtained from Formalin-Fixed Paraffin-Embedded (FFPE) tissue. As a result, a number of analyses are uninterpretable and do not always provide a result to the clinician, limiting the optimal therapeutic management of patients. The availability of Fresh Frozen Tissue (FFT) for some laboratories and the excellent quality of the DNA extracted from it offers an alternative. For this reason, we evaluated Multiplicom's BRCA MASTR Dx assay on a set of 97 FFT derived DNA samples, in combination with the MID for Illumina MiSeq for BRCA1 and BRCA2 mutation detection. We obtained interpretable NGS results for all tested samples and showed > 99,7% sensitivity, specificity and accuracy.
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Affiliation(s)
- Cindy Badoer
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | - Céline Garrec
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Gillian Ellison
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield, UK
| | - John Mills
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield, UK
| | - Mélina Dzial
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | - Hakim El Housni
- Laboratoire de Génétique Moléculaire, Clinique Universitaire de Bruxelles-Hôpital Erasme-Université Libre de Bruxelles (CUB-Erasme-ULB), Brussels, Belgium
| | | | - Paola Concolino
- Laboratory of Clinical Molecular and Personalized Diagnostics, Foundation Policlinico Gemelli and Catholic University of Rome, Italy
| | - Virginie Guibert-Le Guevellou
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Capucine Delnatte
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Ettore Capoluongo
- Laboratory of Clinical Molecular and Personalized Diagnostics, Foundation Policlinico Gemelli and Catholic University of Rome, Italy
- Molipharma and Giovanni Paolo II Foundation, Campobasso, Italy
| | - Stéphane Bézieau
- Institut de Biologie, Laboratoire de Génétique Moléculaire, Service de Génétique Médicale, CHU Nantes, Nantes, France
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41
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Weren RDA, Mensenkamp AR, Simons M, Eijkelenboom A, Sie AS, Ouchene H, van Asseldonk M, Gomez-Garcia EB, Blok MJ, de Hullu JA, Nelen MR, Hoischen A, Bulten J, Tops BBJ, Hoogerbrugge N, Ligtenberg MJL. Novel BRCA1 and BRCA2 Tumor Test as Basis for Treatment Decisions and Referral for Genetic Counselling of Patients with Ovarian Carcinomas. Hum Mutat 2016; 38:226-235. [PMID: 27767231 PMCID: PMC5248611 DOI: 10.1002/humu.23137] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/05/2016] [Accepted: 10/14/2016] [Indexed: 11/08/2022]
Abstract
With the recent introduction of Poly(ADP‐ribose) polymerase inhibitors, a promising novel therapy has become available for ovarian carcinoma (OC) patients with inactivating BRCA1 or BRCA2 mutations in their tumor. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumor is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin‐fixed, paraffin‐embedded (FFPE) tissue, we have developed a single‐molecule molecular inversion probe (smMIP)‐based targeted next‐generation sequencing (NGS) approach. Our smMIP‐based NGS approach provides analysis of both strands of the open reading frame of BRCA1 and BRCA2, enabling the discrimination between real variants and formalin‐induced artefacts. The single molecule tag enables compilation of unique reads leading to a high analytical sensitivity and enabling assessment of the reliability of mutation‐negative results. Multiplex ligation‐dependent probe amplification (MLPA) and Methylation‐specific multiplex ligation‐dependent probe amplification (MS‐MLPA) were used to detect exon deletions of BRCA1 and methylation of the BRCA1 promoter, respectively. Here, we show that this combined approach allows the rapid and reliable detection of both germline and somatic aberrations affecting BRCA1 and BRCA2 in DNA derived from FFPE OCs, enabling improved hereditary cancer risk assessment and clinical treatment of ovarian cancer patients.
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Affiliation(s)
- Robbert D A Weren
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michiel Simons
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Aisha S Sie
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hicham Ouchene
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Monique van Asseldonk
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Encarna B Gomez-Garcia
- Department of Clinical Genetics, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, GROW - School for Oncology & Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Joanne A de Hullu
- Department of Obstetrics & Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johan Bulten
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bastiaan B J Tops
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
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42
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Abstract
Increased demand for BRCA testing is placing pressures on diagnostic laboratories to raise their mutation screening capacity and handle the challenges associated with classifying BRCA sequence variants for clinical significance, for example interpretation of pathogenic mutations or variants of unknown significance, accurate determination of large genomic rearrangements and detection of somatic mutations in DNA extracted from formalin-fixed, paraffin-embedded tumour samples. Many diagnostic laboratories are adopting next-generation sequencing (NGS) technology to increase their screening capacity and reduce processing time and unit costs. However, migration to NGS introduces complexities arising from choice of components of the BRCA testing workflow, such as NGS platform, enrichment method and bioinformatics analysis process. An efficient, cost-effective accurate mutation detection strategy and a standardised, systematic approach to the reporting of BRCA test results is imperative for diagnostic laboratories. This review covers the challenges of BRCA testing from the perspective of a diagnostics laboratory.
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Affiliation(s)
- Andrew J Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
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43
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Lim D, Ngeow J. Evaluation of the methods to identify patients who may benefit from PARP inhibitor use. Endocr Relat Cancer 2016; 23:R267-85. [PMID: 27226207 DOI: 10.1530/erc-16-0116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022]
Abstract
The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in treating cancers associated with BRCA1/2 mutations hinges upon the concept of synthetic lethality and exemplifies the principles of precision medicine. Currently, most clinical trials are recruiting patients based on pathological subtypes or have included BRCA mutation analysis (germ line and/or somatic) as part of the selection criteria. Mounting evidence, however, suggests that these drugs may also be efficacious in tumors with defects in other genes involved in the homologous recombination repair pathway. Advances in molecular profiling techniques together with increased research efforts have led to a better understanding of the molecular aberrations underlying this BRCA-like phenotype and helped broaden the concept of BRCAness. Hence, it is likely that the list of predictive biomarkers for PARPi therapy will increase in future. There is currently no gold standard method of testing for PARPi response and no universal guidelines are in place on how to incorporate biomarker testing into routine clinical diagnostics. In this review, we explore the concept of BRCAness and highlight the different methods that have been used to identify patients who may benefit from the use of these anticancer agents. The identification of predictive biomarkers is crucial in improving patient selection and expanding the clinical applications of PARPi therapy.
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Affiliation(s)
- Diana Lim
- Department of PathologyNational University Health System, Singapore, Singapore
| | - Joanne Ngeow
- Lee Kong Chian School of MedicineNanyang Technological University, Singapore, Singapore Cancer Genetics ServiceDivision of Medical Oncology, National Cancer Centre, Singapore, Singapore
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44
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Endris V, Stenzinger A, Pfarr N, Penzel R, Möbs M, Lenze D, Darb-Esfahani S, Hummel M, Sabine-Merkelbach-Bruse, Jung A, Lehmann U, Kreipe H, Kirchner T, Büttner R, Jochum W, Höfler G, Dietel M, Weichert W, Schirmacher P. NGS-based BRCA1/2 mutation testing of high-grade serous ovarian cancer tissue: results and conclusions of the first international round robin trial. Virchows Arch 2016; 468:697-705. [PMID: 27003155 DOI: 10.1007/s00428-016-1919-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/17/2015] [Accepted: 02/25/2016] [Indexed: 01/03/2023]
Abstract
With the approval of olaparib as monotherapy treatment in platinum-sensitive, relapsed high-grade serous ovarian cancer by the European Medical Agency (EMA), comprehensive genotyping of BRCA1 and BRCA2 in tumor tissue has become a mandatory pre-therapeutic test. This requires significant advances in routine tumor test methodologies due to the large size of both genes and the lack of mutational hot spots. Classical focused screening approaches, like Sanger sequencing, do not allow for a sensitive, rapid, and economic analysis of tumor tissue. Next-generation sequencing (NGS) approaches employing targeted panels for BRCA1/2 to interrogate formalin-fixed and paraffin-embedded tumor samples from either surgical resection or biopsy specimens can overcome these limitations. Although focused NGS methods have been implemented by few centers in routine molecular diagnostics for the analysis of some druggable oncogenic mutations, the reliable diagnostic testing of the entire coding regions of BRCA1 and BRCA2 was a new challenge requiring extensive technological improvement and quality management. Here, we describe the implementation and results of the first round robin trial for BRCA1/2 mutation testing in tumor tissue that was conducted in central Europe on May 2015, shortly after the approval and prior to the official release of olaparib. The high success rate of 81 % (21/26 test centers) demonstrates that BRCA1/2 multicenter mutation testing is well feasible in FFPE tumor tissue, extending to other tumor entities beyond ovarian cancer. The high number of test centers passing the trial demonstrates the success of the concerted efforts by German, Swiss, and Austrian pathology centers to ensure quality-controlled NGS-based testing and proves the potential of this technology in routine molecular pathology. On the basis of our results, we provide recommendations for predictive testing of tumor tissue for BRCA1/2 to clinical decision making in ovarian cancer patients.
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Affiliation(s)
- Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany
| | - Nicole Pfarr
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitaetsmedizin Berlin, Berlin, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitaetsmedizin Berlin, Berlin, Germany
| | | | - Michael Hummel
- Institute of Pathology, Charité Universitaetsmedizin Berlin, Berlin, Germany
| | | | - Andreas Jung
- Institute of Pathology, Ludwig-Maximilians University (LMU), Munich, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Thomas Kirchner
- Institute of Pathology, Ludwig-Maximilians University (LMU), Munich, Germany
| | | | - Wolfram Jochum
- Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Gerald Höfler
- Institute of Pathology, Medical University Graz, Graz, Austria
| | - Manfred Dietel
- Institute of Pathology, Charité Universitaetsmedizin Berlin, Berlin, Germany
| | - Wilko Weichert
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld, 224, Heidelberg, Germany.
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45
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Petersen AH, Aagaard MM, Nielsen HR, Steffensen KD, Waldstrøm M, Bojesen A. Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling. Eur J Hum Genet 2016; 24:1104-11. [PMID: 26733283 PMCID: PMC4970683 DOI: 10.1038/ejhg.2015.268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/30/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022] Open
Abstract
Accurate estimation of cancer risk in HBOC families often requires BRCA1/2 testing, but this may be impossible in deceased family members. Previous, testing archival formalin-fixed, paraffin-embedded (FFPE) tissue for germline BRCA1/2 variants was unsuccessful, except for the Jewish founder mutations. A high-throughput method to systematically test for variants in all coding regions of BRCA1/2 in archival FFPE samples of non-tumor tissue is described, using HaloPlex target enrichment and next-generation sequencing. In a validation study, correct identification of variants or wild-type was possible in 25 out of 30 (83%) FFPE samples (age range 1–14 years), with a known variant status in BRCA1/2. No false positive was found. Unsuccessful identification was due to highly degraded DNA or presence of large intragenic deletions. In clinical use, a total of 201 FFPE samples (aged 0–43 years) were processed. Thirty-six samples were rejected because of highly degraded DNA or failed library preparation. Fifteen samples were investigated to search for a known variant. In the remaining 150 samples (aged 0–38 years), three variants known to affect function and one variant likely to affect function in BRCA1, six variants known to affect function and one variant likely to affect function in BRCA2, as well as four variants of unknown significance (VUS) in BRCA1 and three VUS in BRCA2 were discovered. It is now possible to test for germline BRCA1/2 variants in deceased persons, using archival FFPE samples from non-tumor tissue. Accurate genetic counseling is achievable in families where variant testing would otherwise be impossible.
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Affiliation(s)
| | - Mads Malik Aagaard
- Department of Clinical Genetics, Vejle Hospital, Lillebaelt Hospital, Vejle, Denmark
| | | | - Karina Dahl Steffensen
- Department of Clinical Oncology, Vejle Hospital, Lillebaelt Hospital, Vejle, Denmark.,Faculty of Health Sciences, Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
| | - Marianne Waldstrøm
- Faculty of Health Sciences, Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark.,Department of Pathology, Vejle Hospital, Lillebaelt Hospital, Vejle, Denmark
| | - Anders Bojesen
- Department of Clinical Genetics, Vejle Hospital, Lillebaelt Hospital, Vejle, Denmark.,Faculty of Health Sciences, Institute of Regional Health Services Research, University of Southern Denmark, Odense, Denmark
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