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McDevitt T, Durkie M, Arnold N, Burghel GJ, Butler S, Claes KBM, Logan P, Robinson R, Sheils K, Wolstenholme N, Hanson H, Turnbull C, Hume S. EMQN best practice guidelines for genetic testing in hereditary breast and ovarian cancer. Eur J Hum Genet 2024; 32:479-488. [PMID: 38443545 PMCID: PMC11061103 DOI: 10.1038/s41431-023-01507-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/07/2023] [Accepted: 11/21/2023] [Indexed: 03/07/2024] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) is a genetic condition associated with increased risk of cancers. The past decade has brought about significant changes to hereditary breast and ovarian cancer (HBOC) diagnostic testing with new treatments, testing methods and strategies, and evolving information on genetic associations. These best practice guidelines have been produced to assist clinical laboratories in effectively addressing the complexities of HBOC testing, while taking into account advancements since the last guidelines were published in 2007. These guidelines summarise cancer risk data from recent studies for the most commonly tested high and moderate risk HBOC genes for laboratories to refer to as a guide. Furthermore, recommendations are provided for somatic and germline testing services with regards to clinical referral, laboratory analyses, variant interpretation, and reporting. The guidelines present recommendations where 'must' is assigned to advocate that the recommendation is essential; and 'should' is assigned to advocate that the recommendation is highly advised but may not be universally applicable. Recommendations are presented in the form of shaded italicised statements throughout the document, and in the form of a table in supplementary materials (Table S4). Finally, for the purposes of encouraging standardisation and aiding implementation of recommendations, example report wording covering the essential points to be included is provided for the most common HBOC referral and reporting scenarios. These guidelines are aimed primarily at genomic scientists working in diagnostic testing laboratories.
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Affiliation(s)
- Trudi McDevitt
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland.
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children's NHS Foundation Trust Western Bank, Sheffield, UK
| | - Norbert Arnold
- UKSH Campus Kiel, Gynecology and Obstetrics, Institut of Clinical Chemistry, Institut of Clinical Molecular Biology, Kiel, Germany
| | - George J Burghel
- Manchester University NHS Foundation Trust, North West Genomic Laboratory Hub, Manchester, UK
| | - Samantha Butler
- Central and South Genomic Laboratory Hub, West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Peter Logan
- HSCNI / Belfast Trust Laboratories, Regional Molecular Diagnostics Service, Belfast, Northern Ireland
| | - Rachel Robinson
- Leeds Teaching Hospitals NHS Trust, Genetics Department, Leeds, UK
| | | | | | - Helen Hanson
- St George's University Hospitals NHS Foundation Trust, Clinical Genetics, London, UK
| | | | - Stacey Hume
- University of British Columbia, Pathology and Laboratory Medicine, Vancouver, British Columbia, Canada
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Ratnaparkhi R, Javellana M, Jewell A, Spoozak L. Evaluation of Homologous Recombination Deficiency in Ovarian Cancer. Curr Treat Options Oncol 2024; 25:237-260. [PMID: 38300479 DOI: 10.1007/s11864-024-01176-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2024] [Indexed: 02/02/2024]
Abstract
OPINION STATEMENT Homologous recombination deficiency (HRD) is an important biomarker guiding selection of ovarian cancer patients who will derive the most benefit from poly(ADP-ribose) polymerase inhibitors (PARPi). HRD prevents cells from repairing double-stranded DNA damage with high fidelity, PARPis limit single-stranded repair, and together these deficits induce synthetic lethality. Germline or somatic BRCA mutations represent the narrowest definition of HRD, but do not reflect all patients who will have a durable PARPi response. HRD can also be defined by its downstream consequences, which are measured by different metrics depending on the test used. Ideally, all patients will undergo genetic counseling and germline testing shortly after diagnosis and have somatic testing sent once an adequate tumor sample is available. Should barriers to one test be higher, pursuing germline testing with reflex to somatic testing for BRCA wildtype patients or somatic testing first strategies are both evidence-based. Ultimately both tests offer complementary information, germline testing should be pursued for any patient with a history of ovarian cancer, and somatic testing is valuable at recurrence if not performed in the upfront setting. There is a paucity of data to suggest superiority of one germline or somatic assay; therefore, selection should optimize turnaround time, cost to patients, preferred result format, and logistical burden. Each clinic should implement a standard testing strategy for all ovarian cancer patients that ensures HRD status is known at the time of upfront chemotherapy completion to facilitate comprehensive counseling about anticipated maintenance PARPi benefit.
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Affiliation(s)
- Rubina Ratnaparkhi
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, USA.
| | - Melissa Javellana
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrea Jewell
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Lori Spoozak
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, USA
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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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Barbero G, Zuntini R, Magini P, Desiderio L, Bonaguro M, Perrone AM, Rubino D, Grippa M, De Leo A, Ceccarelli C, Godino L, Miccoli S, Ferrari S, Santini D, De Iaco P, Zamagni C, Innella G, Turchetti D. Characterization of BRCA Deficiency in Ovarian Cancer. Cancers (Basel) 2023; 15:cancers15051530. [PMID: 36900320 PMCID: PMC10001116 DOI: 10.3390/cancers15051530] [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: 01/31/2023] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
BRCA testing is recommended in all Ovarian Cancer (OC) patients, but the optimal approach is debated. The landscape of BRCA alterations was explored in 30 consecutive OC patients: 6 (20.0%) carried germline pathogenic variants, 1 (3.3%) a somatic mutation of BRCA2, 2 (6.7%) unclassified germline variants in BRCA1, and 5 (16.7%) hypermethylation of the BRCA1 promoter. Overall, 12 patients (40.0%) showed BRCA deficit (BD), due to inactivation of both alleles of either BRCA1 or BRCA2, while 18 (60.0%) had undetected/unclear BRCA deficit (BU). Regarding sequence changes, analysis performed on Formalin-Fixed-Paraffin-Embedded tissue through a validated diagnostic protocol showed 100% accuracy, compared with 96.3% for Snap-Frozen tissue and 77.8% for the pre-diagnostic Formalin-Fixed-Paraffin-Embedded protocol. BD tumors, compared to BU, showed a significantly higher rate of small genomic rearrangements. After a median follow-up of 60.3 months, the mean PFS was 54.9 ± 27.2 months in BD patients and 34.6 ± 26.7 months in BU patients (p = 0.055). The analysis of other cancer genes in BU patients identified a carrier of a pathogenic germline variant in RAD51C. Thus, BRCA sequencing alone may miss tumors potentially responsive to specific treatments (due to BRCA1 promoter methylation or mutations in other genes) while unvalidated FFPE approaches may yield false-positive results.
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Affiliation(s)
- Giovanna Barbero
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Roberta Zuntini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Laura Desiderio
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Michela Bonaguro
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Anna Myriam Perrone
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Daniela Rubino
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Mina Grippa
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Antonio De Leo
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Claudio Ceccarelli
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Lea Godino
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Sara Miccoli
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Simona Ferrari
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Donatella Santini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Pierandrea De Iaco
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Claudio Zamagni
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
| | - Giovanni Innella
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Correspondence:
| | - Daniela Turchetti
- Medical Genetics Unit, IRCCS Azienda Ospedaliero—Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
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Catalano M, Generali D, Gatti M, Riboli B, Paganini L, Nesi G, Roviello G. DNA repair deficiency as circulating biomarker in prostate cancer. Front Oncol 2023; 13:1115241. [PMID: 36793600 PMCID: PMC9922904 DOI: 10.3389/fonc.2023.1115241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
Deleterious aberrations in DNA repair genes are actionable in approximately 25% of metastatic castration-resistant prostate cancers (mCRPC) patients. Homology recombination repair (HRR) is the DNA damage repair (DDR) mechanism most frequently altered in prostate cancer; of note BRCA2 is the most frequently altered DDR gene in this tumor. Poly ADP-ribose polymerase inhibitors showed antitumor activity with a improvement in overall survival in mCRPC carrying somatic and/or germline alterations of HHR. Germline mutations are tested on peripheral blood samples using DNA extracted from peripheral blood leukocytes, while the somatic alterations are assessed by extracting DNA from a tumor tissue sample. However, each of these genetic tests have some limitations: the somatic tests are related to the sample availability and tumor heterogeneity, while the germline testing are mainly related to the inability to detect somatic HRR mutations. Therefore, the liquid biopsy, a non-invasive and easily repeatable test compared to tissue test, could identified somatic mutation detected on the circulating tumor DNA (ctDNA) extracted from a plasma. This approach should better represent the heterogeneity of the tumor compared to the primary biopsy and maybe helpful in monitoring the onset of potential mutations involved in treatment resistance. Furthermore, ctDNA may inform about timing and potential cooperation of multiple driver genes aberration guiding the treatment options in patients with mCRPC. However, the clinical use of ctDNA test in prostate cancer compared to blood and tissue testing are currently very limited. In this review, we summarize the current therapeutic indications in prostate cancer patients with DDR deficiency, the recommendation for germline and somatic-genomic testing in advanced PC and the advantages of the use liquid biopsy in clinical routine for mCRPC.
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Affiliation(s)
- Martina Catalano
- School of Human Health Sciences, University of Florence, Florence, Italy
| | - Daniele Generali
- Department of Medical, Surgical and Health Sciences, University of Trieste, Cattinara Hospital Trieste, Trieste, Italy
| | - Marta Gatti
- Servizio di Citogenetica e Genetica - Azienda Socio-Sanitaria Territoriale (ASST) di Cremona, Cremona, Italy
| | - Barbara Riboli
- Servizio di Citogenetica e Genetica - Azienda Socio-Sanitaria Territoriale (ASST) di Cremona, Cremona, Italy
| | - Leda Paganini
- Servizio di Citogenetica e Genetica - Azienda Socio-Sanitaria Territoriale (ASST) di Cremona, Cremona, Italy
| | - Gabriella Nesi
- Department of Health Sciences, University of Florence, Florence, Italy
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Laboratory Cross-Comparison and Ring Test Trial for Tumor BRCA Testing in a Multicenter Epithelial Ovarian Cancer Series: The BORNEO GEICO 60-0 Study. J Pers Med 2022; 12:jpm12111842. [PMID: 36579549 PMCID: PMC9698073 DOI: 10.3390/jpm12111842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022] Open
Abstract
Germline and tumor BRCA testing constitutes a valuable tool for clinical decision-making in the management of epithelial ovarian cancer (EOC) patients. Tissue testing is able to identify both germline (g) and somatic (s) BRCA variants, but tissue preservation methods and the widespread implementation of NGS represent pre-analytical and analytical challenges that need to be managed. This study was carried out on a multicenter prospective GEICO cohort of EOC patients with known gBRCA status in order to determine the inter-laboratory reproducibility of tissue sBRCA testing. The study consisted of two independent experimental approaches, a bilateral comparison between two reference laboratories (RLs) testing 82 formalin-paraffin-embedded (FFPE) EOC samples each, and a Ring Test Trial (RTT) with five participating clinical laboratories (CLs) evaluating the performance of tissue BRCA testing in a total of nine samples. Importantly, labs employed their own locally adopted next-generation sequencing (NGS) analytical approach. BRCA mutation frequency in the RL sub-study cohort was 23.17%: 12 (63.1%) germline and 6 (31.6%) somatic. Concordance between the two RLs with respect to BRCA status was 84.2% (gBRCA 100%). The RTT study distributed a total of nine samples (three commercial synthetic human FFPE references, three FFPE, and three OC DNA) among five CLs. The median concordance detection rate among them was 64.7% (range: 35.3-70.6%). Analytical discrepancies were mainly due to the minimum variant allele frequency thresholds, bioinformatic pipeline filters, and downstream variant interpretation, some of them with consequences of clinical relevance. Our study demonstrates a wide range of concordance in the identification and interpretation of BRCA sequencing data, highlighting the relevance of establishing standard criteria for detecting, interpreting, and reporting BRCA variants.
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Chiu PKF, Lee EKC, Chan MTY, Chan WHC, Cheung MH, Lam MHC, Ma ESK, Poon DMC. Genetic Testing and Its Clinical Application in Prostate Cancer Management: Consensus Statements from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology. Front Oncol 2022; 12:962958. [PMID: 35924163 PMCID: PMC9339641 DOI: 10.3389/fonc.2022.962958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background In recent years, indications for genetic testing in prostate cancer (PC) have expanded from patients with a family history of prostate and/or related cancers to those with advanced castration-resistant disease, and even to early PC patients for determination of the appropriateness of active surveillance. The current consensus aims to provide guidance to urologists, oncologists and pathologists working with Asian PC patients on who and what to test for in selected populations. Methods A joint consensus panel from the Hong Kong Urological Association and Hong Kong Society of Uro-Oncology was convened over a series of 5 physical and virtual meetings. A background literature search on genetic testing in PC was performed in PubMed, ClinicalKey, EBSCOHost, Ovid and ProQuest, and three working subgroups were formed to review and present the relevant evidence. Meeting agendas adopted a modified Delphi approach to ensure that discussions proceed in a structured, iterative and balanced manner, which was followed by an anonymous voting on candidate statements. Of 5 available answer options, a consensus statement was accepted if ≥ 75% of the panelists chose “Accept Completely” (Option A) or “Accept with Some Reservation” (Option B). Results The consensus was structured into three parts: indications for testing, testing methods, and therapeutic implications. A list of 35 candidate statements were developed, of which 31 were accepted. The statements addressed questions on the application of PC genetic testing data and guidelines to Asian patients, including patient selection for germline testing, selection of gene panel and tissue sample, provision of genetic counseling, and use of novel systemic treatments in metastatic castration-resistant PC patients. Conclusion This consensus provides guidance to urologists, oncologists and pathologists working with Asian patients on indications for genetic testing, testing methods and technical considerations, and associated therapeutic implications.
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Affiliation(s)
- Peter K. F. Chiu
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eric K. C. Lee
- Department of Clinical Oncology, Tuen Mun Hospital, Hong Kong SAR, China
| | - Marco T. Y. Chan
- Division of Urology, Department of Surgery, Tuen Mun Hospital, Hong Kong SAR, China
| | - Wilson H. C. Chan
- Division of Urology, Department of Surgery, United Christian Hospital, Hong Kong SAR, China
| | - M. H. Cheung
- Division of Urology, Department of Surgery, Tseung Kwan O Hospital, Hong Kong SAR, China
| | - Martin H. C. Lam
- Department of Oncology, United Christian Hospital, Hong Kong SAR, China
| | - Edmond S. K. Ma
- Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
| | - Darren M. C. Poon
- Department of Clinical Oncology, State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
- Comprehensive Oncology Centre, Hong Kong Sanatorium and Hospital, Hong Kong SAR, China
- *Correspondence: Darren M. C. Poon,
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De Paolis E, Marchetti C, Concolino P, Scambia G, Urbani A, Fagotti A, Minucci A. A commentary on the discrepancy between blood and tumour BRCA testing: An open question. BJOG 2022; 129:1422-1426. [PMID: 35319826 PMCID: PMC9543799 DOI: 10.1111/1471-0528.17158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/08/2022] [Accepted: 03/20/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Elisa De Paolis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Paola Concolino
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Andrea Urbani
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Anna Fagotti
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Bekos C, Grimm C, Kranawetter M, Polterauer S, Oberndorfer F, Tan Y, Müllauer L, Singer CF. Reliability of Tumor Testing Compared to Germline Testing for Detecting BRCA1 and BRCA2 Mutations in Patients with Epithelial Ovarian Cancer. J Pers Med 2021; 11:jpm11070593. [PMID: 34202525 PMCID: PMC8305542 DOI: 10.3390/jpm11070593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/09/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background: BRCA 1/2 mutation status has become one of the most important parameters for treatment decision in patients with epithelial ovarian cancer (EOC). The aim of this study was to compare tumor DNA with blood DNA sequencing to evaluate the reliability of BRCA tumor testing results. Methods: Patients who were treated for EOC between 2003 and 2019 at the Medical University of Vienna and underwent both germline (gBRCA) and tumor (tBRCA) testing for BRCA mutations were identified. We calculated the concordance rate and further analyzed discordant cases. Results: Out of 140 patients with EOC, gBRCA mutation was found in 47 (33.6%) and tBRCA mutation in 53 (37.9%) patients. Tumor testing identified an additional 9/140 (6.4%) patients with somatic BRCA mutation and negative germline testing. The comparison of germline testing with tumor testing revealed a concordance rate of 93.5% and a negative predictive value of tumor testing of 96.0%. After BRCA variants of uncertain significance were included in the analysis, concordance rate decreased to 90.9%. Conclusion: Tumor testing identified the majority of pathogenic germline BRCA mutations but missed three (2.1%) patients. In contrast, nine (6.4%) patients harboring a somatic BRCA mutation would have been missed by gBRCA testing only.
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Affiliation(s)
- Christine Bekos
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
| | - Christoph Grimm
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
| | - Marlene Kranawetter
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
| | - Stephan Polterauer
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
| | | | - Yen Tan
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, A-1090 Vienna, Austria;
- Correspondence:
| | - Christian F. Singer
- Comprehensive Cancer Center, Gynecologic Cancer Unit, Department of Obstetrics and Gynecology, Division of General Gynecology and Gynecologic Oncology, Medical University of Vienna, A-1090 Vienna, Austria; (C.B.); (C.G.); (M.K.); (S.P.); (Y.T.); (C.F.S.)
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Cimadamore A, Cheng L, Massari F, Santoni M, Pepi L, Franzese C, Scarpelli M, Lopez-Beltran A, Galosi AB, Montironi R. Circulating Tumor DNA Testing for Homology Recombination Repair Genes in Prostate Cancer: From the Lab to the Clinic. Int J Mol Sci 2021; 22:5522. [PMID: 34073818 PMCID: PMC8197269 DOI: 10.3390/ijms22115522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Approximately 23% of metastatic castration-resistant prostate cancers (mCRPC) harbor deleterious aberrations in DNA repair genes. Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) therapy has shown improvements in overall survival in patients with mCRPC who harbor somatic and/or germline alterations of homology recombination repair (HRR) genes. Peripheral blood samples are typically used for the germline mutation analysis test using the DNA extracted from peripheral blood leucocytes. Somatic alterations can be assessed by extracting DNA from a tumor tissue sample or using circulating tumor DNA (ctDNA) extracted from a plasma sample. Each of these genetic tests has its own benefits and limitations. The main advantages compared to the tissue test are that liquid biopsy is a non-invasive and easily repeatable test with the value of better representing tumor heterogeneity than primary biopsy and of capturing changes and/or resistance mutations in the genetic tumor profile during disease progression. Furthermore, ctDNA can inform about mutation status and guide treatment options in patients with mCRPC. Clinical validation and test implementation into routine clinical practice are currently very limited. In this review, we discuss the state of the art of the ctDNA test in prostate cancer compared to blood and tissue testing. We also illustrate the ctDNA testing workflow, the available techniques for ctDNA extraction, sequencing, and analysis, describing advantages and limits of each techniques.
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Affiliation(s)
- Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, School of Medicine, Indiana University, Indianapolis, IN 46202, USA;
| | - Francesco Massari
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, 40138 Bologna, Italy;
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Laura Pepi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Carmine Franzese
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Marina Scarpelli
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
| | - Antonio Lopez-Beltran
- Department of Morphological Sciences, Cordoba University Medical School, 14071 Cordoba, Spain;
| | - Andrea Benedetto Galosi
- Department of Specialist Clinical Science and Odontostomatology, Urology Division, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (C.F.); (A.B.G.)
| | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, Polytechnic University of the Marche Region, United Hospitals, 60126 Ancona, Italy; (A.C.); (L.P.); (M.S.)
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11
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Care M, McCuaig J, Clarke B, Grenier S, Kim RH, Rouzbahman M, Stickle N, Bernardini M, Stockley TL. Tumor and germline next generation sequencing in high grade serous cancer: experience from a large population-based testing program. Mol Oncol 2020; 15:80-90. [PMID: 33030818 PMCID: PMC7782089 DOI: 10.1002/1878-0261.12817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to determine the prevalence of somatic and germline pathogenic variants (PVs) in high‐grade serous cancer (HGSC) and to demonstrate the technical feasibility and effectiveness of a large‐scale, population‐based tumor testing program. It involved a retrospective review of genetic test results in 600 consecutive HGSC tumor samples and a subsequent comparison of germline and tumor results in a subset of 200 individuals. Tumor testing was successful in 95% of samples (570/600) with at least one BRCA1/2 PV identified in 16% (93/570) of cases. Among the 200 paired cases, BRCA1/2 PVs were detected in 38 tumors (19%); 58% were somatic (22/38); and 42% were germline (16/38). There was 100% concordance between germline and tumor test results. This is the largest series of BRCA1/2 testing in HGSC (tumor‐only and paired cohorts), reported to date, and our data show that an effectively designed and validated population‐based tumor testing program can be used to determine both treatment eligibility and hereditary cancer risk.
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Affiliation(s)
- Melanie Care
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jeanna McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, University Health Network, Toronto, Canada.,Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Toronto, Canada
| | - Blaise Clarke
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Sylvie Grenier
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, University Health Network, Toronto, Canada.,Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, Canada
| | - Marjan Rouzbahman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Natalie Stickle
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Marcus Bernardini
- Department of Gynecologic Oncology, Princess Margaret Hospital Cancer Centre, Toronto, Canada
| | - Tracy L Stockley
- Laboratory Medicine Program, Division of Clinical Laboratory Genetics, University Health Network, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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12
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Fumagalli C, Guerini-Rocco E, Buttitta F, Iapicca P, You W, Mauri M, Felicioni L, Troncone G, Malapelle U, Scarpa A, Zamboni G, Calistri D, Barberis M, Marchetti A. Reliability and reproducibility among different platforms for tumour BRCA testing in ovarian cancer: a study of the Italian NGS Network. J Clin Pathol 2020; 74:668-672. [PMID: 33020174 DOI: 10.1136/jclinpath-2020-206800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/18/2020] [Accepted: 09/19/2020] [Indexed: 11/03/2022]
Abstract
INTRODUCTION BRCA tumour testing is a crucial tool for personalised therapy of patients with ovarian cancer. Since different next-generation sequencing (NGS) platforms and BRCA panels are available, the NGS Italian Network proposed to assess the robustness of different technologies. METHODS Six centres, using four different technologies, provided raw data of 284 cases, including 75 cases with pathogenic/likely pathogenic variants, for a revision blindly performed by an external bioinformatic platform. RESULTS The third-party revision assessed that all the 284 raw data reached good quality parameters. The variant calling analysis confirmed all the 75 pathogenic/likely pathogenic variants, including challenging variants, achieving a concordance rate of 100% regardless of the panel, instrument and bioinformatic pipeline adopted. No additional variants were identified in the reanalysis of a subset of 41 cases. CONCLUSIONS BRCA tumour testing performed with different technologies in different centres, may achieve the realibility and reproducibility required for clinical diagnostic procedures.
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Affiliation(s)
- Caterina Fumagalli
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Elena Guerini-Rocco
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Fiamma Buttitta
- Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), University of Chieti, Chieti, Italy.,Department of Medical and Oral Sciences and Biotechnologies, University of Chieti, Chieti, Italy
| | | | - Wenqi You
- SOPHiA GENETICS SA, Headquarters, Saint Sulpice, Switzerland
| | - Michela Mauri
- SOPHiA GENETICS SA, Headquarters, Saint Sulpice, Switzerland
| | - Lara Felicioni
- Department of Pathology, SS Annunziata Clinical Hospital, Chieti, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.,ARC-Net Centre for Applied Research on Cancer, Verona, Italy
| | - Giuseppe Zamboni
- Department of Diagnostics and Public Health, Section of Pathology, University of Verona, Verona, Italy.,Department of Pathology, IRCCS Sacro Cuore - Don Calabria-Negrar, Negrar, Italy
| | - Daniele Calistri
- Laboratory of Biosciences, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori Srl, Meldola, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Antonio Marchetti
- Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), University of Chieti, Chieti, Italy.,Department of Medical and Oral Sciences and Biotechnologies, University of Chieti, Chieti, Italy
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13
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Prevalence of tumor BRCA1 and BRCA2 dysfunction in unselected patients with ovarian cancer. Obstet Gynecol Sci 2020; 63:643-654. [PMID: 32872764 PMCID: PMC7494761 DOI: 10.5468/ogs.20033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Objective The therapeutic benefits of poly(ADP-ribose) polymerase inhibitors highlight the need to evaluate BRCA1/2 defects in tubal/ovarian cancer (OC). We sought to determine the pattern and disease characteristics associated with tumor BRCA1/2 mutations and BRCA1 methylation in women with OC. Methods We obtained 111 OC specimens from 2 university hospitals and assessed BRCA1/2 mutations and BRCA1 methylation in tumor DNA. The frequency and pattern of BRCA1/2 defects were examined. Associations between patient/disease characteristics and BRCA1/2 defects were ascertained (Fisher’s exact test). Platinum-free interval (PFI), progression-free survival (PFS), and overall survival (OS) based on the underlying BRCA1/2 defect were determined (Kaplan-Meier analysis [log-rank test]). Results We observed a BRCA1/2 dysfunction rate of 40% (28/70) in high-grade serous tubal/ovarian cancer (HGSC), including 14.3% BRCA1 methylation (n=10), 7.1% BRCA1 mutation (n=5), and 18.6% BRCA2 mutation (n=13). Defects in BRCA1/2 genes were associated with stage III/IV HGSC (BRCA1 methylation: P=0.005 [stage III/IV] and P=0.004 [HGSC]; BRCA1/2 mutation: P=0.03 [stage III/IV] and P<0.001 [HGSC]). Patients with BRCA1/2-mutated cancers showed improved OS (hazard ratio [HR], 0.65; 95% confidence interval [CI], 0.43–0.99; P=0.045) and a trend toward improved PFI (HR, 0.48; 95% CI, 0.22–1.06; P=0.07) and PFS (HR, 0.72; 95% CI, 0.51–1.03; P=0.07). No survival differences were observed between BRCA1-methylated and BRCA1/2 wild-type non-BRCA1-methylated cancers. Conclusion We observed a high tumor BRCA1/2 dysfunction rate in HGSC with a unique predominance of BRCA2 over BRCA1 mutations. While BRCA1/2 mutations conferred survival benefits in OC, no such association was observed with BRCA1 methylation.
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14
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Berrino E, Annaratone L, Miglio U, Maldi E, Piccinelli C, Peano E, Balmativola D, Cassoni P, Pisacane A, Sarotto I, Venesio T, Sapino A, Marchiò C. Cold Formalin Fixation Guarantees DNA Integrity in Formalin Fixed Paraffin Embedded Tissues: Premises for a Better Quality of Diagnostic and Experimental Pathology With a Specific Impact on Breast Cancer. Front Oncol 2020; 10:173. [PMID: 32140450 PMCID: PMC7042205 DOI: 10.3389/fonc.2020.00173] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/31/2020] [Indexed: 11/29/2022] Open
Abstract
Formalin fixation and paraffin embedding (FFPE) represent the standard method to preserve tissue specimens for diagnostic pathology, however formalin fixation induces severe fragmentation of nucleic acids. We investigated whether formalin fixation at 4°C could preserve DNA integrity in FFPE specimens. Paired samples from 38 specimens were formalin fixed at room temperature (stdFFPE) and at 4°C (coldFFPE), respectively. Two independent cohorts were prospectively collected, cohort A (collected 6 years prior to the study, n = 21), cohort B (collected at time of the study, n = 17). DNA was extracted and its integrity evaluated with a qPCR-based assay that produces a normalized integrity index, the QC score (ratio between the quantity of a long and a short amplicon of the same gene). We observed higher QC scores in coldFFPE compared to stdFFPE samples (mean values: 0.69 vs. 0.36, p < 0.0001) and stdFFPE breast cancer specimens showed the most detrimental effect overall. Comparable QC scores were obtained between coldFFPE tissues of both cohorts; conversely, DNA integrity of stdFFPE was significantly lower in cohort A compared to cohort B (p < 0.0001). Of note, QC scores of stdFFPE (but not of coldFFPE) samples were significantly reduced following 6 months of storage (p = 0.0001). Monitored formalin fixation at 4°C outperforms standard fixation in ensuring high-quality DNA, which is key to feasibility of downstream high-throughput molecular analyses. An important effect was observed over storage time, thus suggesting a likely better preservation of archival samples when this cold fixation protocol is used.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Umberto Miglio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Elena Maldi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Chiara Piccinelli
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Erica Peano
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Paola Cassoni
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Città Della Salute e Della Scienza di Torino, Turin, Italy
| | - Alberto Pisacane
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy.,Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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15
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Pietragalla A, Minucci A, Marchetti C, Scambia G, Fagotti A. Can somatic BRCA2 status solve a case of olaparib monotherapy resistance? Int J Gynecol Cancer 2019; 29:1440-1445. [DOI: 10.1136/ijgc-2019-000757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 01/04/2023] Open
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16
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Hauke J, Hahnen E, Schneider S, Reuss A, Richters L, Kommoss S, Heimbach A, Marmé F, Schmidt S, Prieske K, Gevensleben H, Burges A, Borde J, De Gregorio N, Nürnberg P, El-Balat A, Thiele H, Hilpert F, Altmüller J, Meier W, Dietrich D, Kimmig R, Schoemig-Markiefka B, Kast K, Braicu E, Baumann K, Jackisch C, Park-Simon TW, Ernst C, Hanker L, Pfisterer J, Schnelzer A, du Bois A, Schmutzler RK, Harter P. Deleterious somatic variants in 473 consecutive individuals with ovarian cancer: results of the observational AGO-TR1 study (NCT02222883). J Med Genet 2019; 56:574-580. [PMID: 30979843 DOI: 10.1136/jmedgenet-2018-105930] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/26/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND For individuals with ovarian cancer (OC), therapy options mainly depend on BRCA1/2 germline status. What is the prevalence of deleterious somatic variants, that is, does genetic tumour testing identify subgroups of individuals who also might benefit from targeted therapy? METHODS Paired analysis of tumour-derived versus blood-derived DNA to determine the prevalence of deleterious somatic variants in OC predisposition genes (ATM, BRCA1/2, BRIP1, MSH2/6, PALB2, RAD51C/D and TP53) and the PIK3CA and PTEN genes in individuals with OC (AGO-TR1 study, NCT02222883). Results were complemented by BRCA1, PALB2 and RAD51C promoter methylation analyses and stratified by histological subtype; 473 individuals were included. RESULTS The combined analyses revealed that deleterious germline variants in established OC predisposition genes (all: 125/473, 26.4%; BRCA1/2: 97/473, 20.5%), deleterious somatic variants in established OC predisposition genes excluding TP53 (all: 39/473, 8.2%; BRCA1/2: 30/473, 6.3%) and promoter methylation (all: 67/473, 14.2%; BRCA1: 57/473, 12.1%; RAD51C: 10/473, 2.1%; PALB2: 0/473) were mutually exclusive, with a few exceptions. The same holds true for deleterious somatic PIK3CA and/or PTEN variants (33/473, 7.0%) found to be enriched in endometrioid and clear cell OC (16/35, 45.7%); 84.3 % of the deleterious single-nucleotide/indel germline variants in established OC predisposition genes showed significantly higher variant fractions (VFs) in the tumour-derived versus blood-derived DNA, indicating a loss of the wild-type alleles. CONCLUSION Tumour sequencing of the BRCA1, BRCA2, PIK3CA and PTEN genes along with BRCA1 and RAD51C promoter methylation analyses identified large subgroups of germline mutation-negative individuals who may be addressed in interventional studies using PARP or PI3K/AKT/mTOR inhibitors. TRIAL REGISTRATION NUMBER NCT02222883.
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Affiliation(s)
- Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stephanie Schneider
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Alexander Reuss
- Coordinating Center for Clinical Trials, Philipps-University of Marburg, Marburg, Germany
| | - Lisa Richters
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Stefan Kommoss
- Department of Women's Health, University Hospital Tuebingen, Tuebingen, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederik Marmé
- National Center for Tumor Disease, Department of Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Sandra Schmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Katharina Prieske
- Department of Gynecology and Gynecologic Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Alexander Burges
- Department of Gynecology, University Hospital Munich-Großhadern, Munich, Germany
| | - Julika Borde
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Nikolaus De Gregorio
- Department of Gynecology and Obstetrics, University Hospital, Universität Ulm, Ulm, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Ahmed El-Balat
- Department of Gynecology, University of Frankfurt, Frankfurt, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Felix Hilpert
- Department of Gynecology, University of Kiel, Kiel, Germany.,Onkologisches Therapiezentrum, Krankenhaus Jerusalem, Hamburg, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG) & Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Cologne, Germany
| | - Werner Meier
- Department of Gynecology and Obstetrics, University Hospital Duesseldorf, Duesseldorf, Germany
| | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Rainer Kimmig
- Department of Gynecology, University of Essen, Essen, Germany
| | | | - Karin Kast
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Partner Site Dresden, Heidelberg, Germany
| | - Elena Braicu
- Department of Gynecology and Gynecological Oncology, Charité, Berlin, Germany
| | - Klaus Baumann
- Department of Gynecology, Gynecologic Endocrinology and Oncology, University of Gießen and Marburg GmbH, Marburg, Germany.,Department of Gynecology and Obstetrics, Klinikum Ludwigshafen, Ludwigshafen, Germany
| | - Christian Jackisch
- Department of Gynecology and Obstetrics, Sana Klinikum, Offenbach, Germany
| | | | - Corinna Ernst
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Lars Hanker
- Department of Gynecology & Obstetrics, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | | | - Andreas Schnelzer
- Department of Obstetrics and Gynecology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.,Department of Obstetrics and Gynecology, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte Evangelische Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
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17
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Kechin A, Khrapov E, Boyarskikh U, Kel A, Filipenko M. BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes. Comput Biol Chem 2018; 77:297-306. [PMID: 30408727 DOI: 10.1016/j.compbiolchem.2018.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 09/14/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
The use of targeted next-generation sequencing (NGS) provides great new opportunities for molecular and medical genetics. However, in order to take advantage of these opportunities, we need to have reliable tools for extracting the necessary information from the huge amount of data generated by NGS. Here we present our automatic multithreaded workflow for processing NGS data of BRCA1 and BRCA2 genes obtained with NGS technology named BRCA-analyzer. Optimizing it on the sequencing data of 899 samples from 693 patients, we were able to find the most reliable tools and adjust their parameters in such a way that all pathogenic variants found were confirmed by Sanger's sequencing. For 82 and 24 DNA samples from blood and formalin-fixed paraffin-embedded blocks, NGS libraries were prepared with GeneRead BRCA panel v2 (Qiagen). The reads obtained were processed with BRCA-analyzer and Qiagen GeneRead Data analysis workflow. In total 27 pathogenic variants were found and confirmed by Sanger's sequencing, with all of them determined with BRCA-analyzer. Qiagen GeneRead Data analysis discarded 5 true pathogenic variants due to their location in homopolymeric sequence stretches. For other 793 samples, libraries were prepared by the in-house method, and NGS data were analyzed by BRCA-analyzer in comparison to another free automatic amplicon NGS workflow Canary. From total 137 pathogenic variations, BRCA-analyzer found 135 and Canary 123. Mutations were missed by BRCA-analyzer due to the trimming primer sequences from reads before mapping to be fixed in the next version. On the freely available NGS data, we showed that BRCA-analyzer could also be used for hybrid capture gene panels, although it needs more extensive testing on such library preparation methods. Thus, BRCA-analyzer is an automatic workflow for processing NGS data of BRCA1/2 genes with variant filters adapted to amplicon-based targeted NGS data. BRCA-analyzer can be used to identify germline as well as somatic mutations. BRCA-analyzer is freely available at https://github.com/aakechin/BRCA-analyzer.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Uljana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
| | - Alexander Kel
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia; geneXplain GmbH, Wolfenbüttel, 38302, Germany; biosoft.ru, Novosibirsk, 630058, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia
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18
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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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19
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Capoluongo E, Scambia G, Nabholtz JM. Main implications related to the switch to BRCA1/2 tumor testing in ovarian cancer patients: a proposal of a consensus. Oncotarget 2018. [PMID: 29731958 DOI: 10.18632/oncotarget.24728]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Since the approval of the first poly (adenosine diphosphate [ADP]) ribose polymerase inhibitor (PARPi; olaparib [Lynparza™]) for platinum-sensitive relapsed high grade ovarian cancer, with either germline or somatic BRCA1/2 deleterious variants, the strategies for BRCA1/2 are dynamically changing. Along with germline testing within the context of familial or sporadic ovarian cancer, patients are now being referred for BRCA1/2 genetic assay above all for treatment decisions: in this setting tumour BRCA assay can allow to identify an estimated 3-9% of patients with peculiar somatic BRCA1/2 mutations. These women could also benefit from PARPi therapy. This new type of approach is really challenging, in particular due to the technical and analytical difficulties regarding low quality DNA deriving from formalin-fixed, paraffin-embedded (FFPE) specimens. AIM in this manuscript, we try to a) underline many issues related to BRCA1/2 analysis by next generation sequencing technologies (NGS), b) provide some responses to many questions regarding this new paradigm related to OvCa patients' management. Some considerations for incorporating genetic analysis of ovarian tumour samples into the patient pathway and ethical requirements are also provided. METHODS we used our retrospective data based on thousands of ovarian cancer women sequenced for BRCA1/2 genes. DISCUSSION tumor BRCA1/2 assay should be rapidly introduced in routine laboratory practice as first line testing by using harmonized pipelines based on consensus guidelines.
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Affiliation(s)
- Ettore Capoluongo
- Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy.,Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Giovanni Scambia
- Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Jean-Marc Nabholtz
- Cancer Research Oncology Centre, King Saud University Medical City, Riyadh, KSA
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20
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Capoluongo E, Scambia G, Nabholtz JM. Main implications related to the switch to BRCA1/2 tumor testing in ovarian cancer patients: a proposal of a consensus. Oncotarget 2018. [PMID: 29731958 DOI: 10.18632/oncotarget.24728] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background Since the approval of the first poly (adenosine diphosphate [ADP]) ribose polymerase inhibitor (PARPi; olaparib [Lynparza™]) for platinum-sensitive relapsed high grade ovarian cancer, with either germline or somatic BRCA1/2 deleterious variants, the strategies for BRCA1/2 are dynamically changing. Along with germline testing within the context of familial or sporadic ovarian cancer, patients are now being referred for BRCA1/2 genetic assay above all for treatment decisions: in this setting tumour BRCA assay can allow to identify an estimated 3-9% of patients with peculiar somatic BRCA1/2 mutations. These women could also benefit from PARPi therapy. This new type of approach is really challenging, in particular due to the technical and analytical difficulties regarding low quality DNA deriving from formalin-fixed, paraffin-embedded (FFPE) specimens. Aim in this manuscript, we try to a) underline many issues related to BRCA1/2 analysis by next generation sequencing technologies (NGS), b) provide some responses to many questions regarding this new paradigm related to OvCa patients' management. Some considerations for incorporating genetic analysis of ovarian tumour samples into the patient pathway and ethical requirements are also provided. Methods we used our retrospective data based on thousands of ovarian cancer women sequenced for BRCA1/2 genes. Discussion tumor BRCA1/2 assay should be rapidly introduced in routine laboratory practice as first line testing by using harmonized pipelines based on consensus guidelines.
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Affiliation(s)
- Ettore Capoluongo
- Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy.,Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Giovanni Scambia
- Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Jean-Marc Nabholtz
- Cancer Research Oncology Centre, King Saud University Medical City, Riyadh, KSA
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21
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Capoluongo E, Scambia G, Nabholtz JM. Main implications related to the switch to BRCA1/2 tumor testing in ovarian cancer patients: a proposal of a consensus. Oncotarget 2018; 9:19463-19468. [PMID: 29731958 PMCID: PMC5929401 DOI: 10.18632/oncotarget.24728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/06/2018] [Indexed: 12/20/2022] Open
Abstract
Background Since the approval of the first poly (adenosine diphosphate [ADP]) ribose polymerase inhibitor (PARPi; olaparib [Lynparza™]) for platinum-sensitive relapsed high grade ovarian cancer, with either germline or somatic BRCA1/2 deleterious variants, the strategies for BRCA1/2 are dynamically changing. Along with germline testing within the context of familial or sporadic ovarian cancer, patients are now being referred for BRCA1/2 genetic assay above all for treatment decisions: in this setting tumour BRCA assay can allow to identify an estimated 3–9% of patients with peculiar somatic BRCA1/2 mutations. These women could also benefit from PARPi therapy. This new type of approach is really challenging, in particular due to the technical and analytical difficulties regarding low quality DNA deriving from formalin-fixed, paraffin-embedded (FFPE) specimens. Aim in this manuscript, we try to a) underline many issues related to BRCA1/2 analysis by next generation sequencing technologies (NGS), b) provide some responses to many questions regarding this new paradigm related to OvCa patients’ management. Some considerations for incorporating genetic analysis of ovarian tumour samples into the patient pathway and ethical requirements are also provided. Methods we used our retrospective data based on thousands of ovarian cancer women sequenced for BRCA1/2 genes. Discussion tumor BRCA1/2 assay should be rapidly introduced in routine laboratory practice as first line testing by using harmonized pipelines based on consensus guidelines.
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Affiliation(s)
- Ettore Capoluongo
- Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy.,Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Giovanni Scambia
- Catholic University of The Sacred Heart, Rome, Italy.,Molipharma Srl, a Spinoff of Catholic University, Campobasso, Italy
| | - Jean-Marc Nabholtz
- Cancer Research Oncology Centre, King Saud University Medical City, Riyadh, KSA
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22
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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: 18] [Impact Index Per Article: 2.6] [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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23
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Löser H, Heydt C, Büttner R, Markiefka B. [BRCA diagnostics of ovarian cancer : Molecular tumor testing since the introduction of PARP inhibitor therapy]. DER PATHOLOGE 2017; 38:117-126. [PMID: 28258387 DOI: 10.1007/s00292-017-0274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Approximately 9000 women are diagnosed with ovarian cancer in Germany each year. The most common subtype is high-grade serous ovarian cancer. A relevant proportion of these tumors are associated with mutations in the breast and ovarian cancer susceptibility genes (BRCA1 and BRCA2) representing highly penetrant tumor suppressor genes with autosomal inheritance and play a crucial role in DNA repair mechanisms. These patients have predominantly germline mutations and less frequently have somatic BRCA mutations. Tumors harboring BRCA mutations show a significant improvement in progression-free survival under therapy with poly(adenosine diphosphate ribose) polymerase (PARP) inhibitors. In 2015 the first PARP inhibitor was approved for the therapy of high-grade serous ovarian cancer with BRCA mutations. Mutation analysis can be performed on formalin-fixed paraffin-embedded (FFPE) tumor tissue within a few days.
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Affiliation(s)
- H Löser
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - C Heydt
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - R Büttner
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - B Markiefka
- Institut für Pathologie, Uniklinik Köln, Kerpener Str. 62, 50937, Köln, Deutschland.
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