1
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Grigore LG, Radoi VE, Serban A, Mihai AD, Stoica I. The Molecular Detection of Germline Mutations in the BRCA1 and BRCA2 Genes Associated with Breast and Ovarian Cancer in a Romanian Cohort of 616 Patients. Curr Issues Mol Biol 2024; 46:4630-4645. [PMID: 38785549 PMCID: PMC11119367 DOI: 10.3390/cimb46050281] [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: 04/15/2024] [Revised: 05/07/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
The objective of this study was to identify and classify the spectrum of mutations found in the BRCA1 and BRCA2 genes associated with breast and ovarian cancer in female patients in Romania. Germline BRCA1 and BRCA2 mutations were investigated in a cohort of 616 female patients using NGS and/or MLPA methods followed by software-based data analysis and classification according to international guidelines. Out of the 616 female patients included in this study, we found that 482 patients (78.2%) did not have any mutation present in the two genes investigated; 69 patients (11.2%) had a BRCA1 mutation, 34 (5.5%) had a BRCA2 mutation, and 31 (5%) presented different type of mutations with uncertain clinical significance, moderate risk or a large mutation in the BRCA1 gene. Our investigation indicates the most common mutations in the BRCA1 and BRCA2 genes, associated with breast and ovarian cancer in the Romanian population. Our results also bring more data in support of the frequency of the c.5266 mutation in the BRCA1 gene, acknowledged in the literature as a founder mutation in Eastern Europe. We consider that the results of our study will provide necessary data regarding BRCA1 and BRCA2 mutations that would help to create a genetic database for the Romanian population.
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Affiliation(s)
- Liliana-Georgiana Grigore
- Doctoral School of Biology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
- Personal Genetics, 010987 Bucharest, Romania
| | - Viorica-Elena Radoi
- Department of Medical Genetics, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- “Alessandrescu-Rusescu” National Institute for Maternal and Child Health, 20382 Bucharest, Romania
| | | | | | - Ileana Stoica
- Department of Genetics, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania
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2
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Andaluz S, Zhao B, Sinha S, Lagniton PNP, Costa DA, Ding X, Brito M, Wang SM. Using Portuguese BRCA pathogenic variation as a model to study the impact of human admixture on human health. BMC Genomics 2024; 25:416. [PMID: 38671360 PMCID: PMC11055274 DOI: 10.1186/s12864-024-10311-4] [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: 08/13/2023] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Admixture occurs between different ethnic human populations. The global colonization in recent centuries by Europeans led to the most significant admixture in human history. While admixture may enhance genetic diversity for better fitness, it may also impact on human health by transmitting genetic variants for disease susceptibility in the admixture population. The admixture by Portuguese global exploration initiated in the 15th century has reached over 20 million of Portuguese-heritage population worldwide. It provides a valuable model to study the impact of admixture on human health. BRCA1 and BRCA2 (BRCA) are two of the important tumor suppressor genes. The pathogenic variation (PV) in BRCA is well determined to cause high risk of hereditary breast and ovarian cancer. Tracing the distribution of Portuguese BRCA PV in Portuguese-heritage population will help to understand the impact of admixture on cancer susceptibility in modern humans. In this study, we analyzed the distribution of the Portuguese-originated BRCA variation in Brazilian population, which has high degree Portuguese-heritage. METHODS By comprehensive data mining, standardization and annotation, we generated a Portuguese-derived BRCA variation dataset and a Brazilian-derived BRCA variation dataset. We compared the two BRCA variation datasets to identify the BRCA variants shared between the two populations. RESULTS The Portuguese-derived BRCA variation dataset consists of 220 BRCA variants including 78 PVs from 11,482 Portuguese cancer patients, 93 (42.2%) in BRCA1 and 127 (57.7%) in BRCA2. Of the 556 Portuguese BRCA PV carriers carrying the 78 PVs, 331 (59.5%) carried the three Portuguese-BRCA founder PVs of BRCA1 c.2037delinsCC, BRCA1 c.3331_3334del and BRCA2 c.156_157insAlu. The Brazilian-derived BRCA variation dataset consists of 255 BRCA PVs from 7,711 cancer patients, 136 (53.3%) in BRCA1 and 119 (46.6%) in BRCA2. We developed an open database named dbBRCA-Portuguese ( https://genemutation.fhs.um.edu.mo/dbbrca-portuguese/ ) and an open database named dbBRCA-Brazilian ( https://genemutation.fhs.um.edu.mo/dbbrca-brazilian ) to host the BRCA variation data from Portuguese and Brazilian populations. We compared the BRCA PV datasets between Portuguese and Brazilian populations, and identified 29 Portuguese-specific BRCA PVs shared between Portuguese and Brazilian populations, 14 in BRCA1 including the Portuguese founder BRCA1 c.3331_3334del and BRCA1 c.2037delinsCC, and 15 in BRCA2 including the Portuguese founder BRCA2 c.156_157insAlu. Searching the 78 Portuguese BRCA PVs in over 5,000 ancient human genomes identified evolution origin for only 8 PVs in Europeans dated between 37,470 and 3,818 years before present, confirming the Portuguese-specificity of Portuguese BRCA PVs; comparing the 78 Portuguese BRCA PVs Portuguese, 255 Brazilian BRCA PVs, and 134 African BRCA PVs showed little overlapping, ruling out the possibility that the BRCA PVs shared between Portuguese and Brazilian may also be contributed by African. CONCLUSION Our study provides evidence that the admixture in recent human history contributed to cancer susceptibility in modern humans.
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Affiliation(s)
- Stephanie Andaluz
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Philip Naderev Panuringan Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Diogo Alpuim Costa
- Medical Oncology Department, Hospital de Cascais, Cascais; Haematology and Oncology Department, CUF Oncologia, Lisbon; NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Xiaofan Ding
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China
| | - Miguel Brito
- Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Lisbon, Portugal.
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macao SRA, China.
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3
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Romey M, Rodepeter F, Hattesohl A, Kaiser K, Teply-Szymanski J, Heitz F, Staebler A, Serra V, Grass A, Marmé F, Timms KM, Harter P, Llop-Guevara A, Kommoss S, Boekhoff J, Denkert C. Systematic Analysis of Homologous Recombination Deficiency Testing in Ovarian Cancer-Development of Recommendations for Optimal Assay Performance. Mod Pathol 2024; 37:100445. [PMID: 38341130 DOI: 10.1016/j.modpat.2024.100445] [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: 09/08/2023] [Revised: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Homologous recombination deficiency (HRD) assays are an important element of personalized oncology in ovarian carcinomas, but the optimal tissue requirements for these complex molecular assays remain unclear. As a result, a considerable percentage of assays are not successful, leading to suboptimal diagnoses for these patients. In this study, we have systematically analyzed tumor and tissue parameters for HRD analysis in a large cohort of real-world cancer samples. The aim of this study is to give recommendations for pathologists and gynecologic oncologists for selection of tissue samples to maximize the success rate of HRD analyses. Tumor samples from 2702 patients were sent to the Institute of Pathology of the Philipps-University Marburg between October 2020 and September 2022, of which 2654 were analyzed using the Myriad MyChoice HRD+ CDx assay. A total of 2396 of 2654 samples (90.3%) were successfully tested, of which 984 of 2396 (41.1%) were HRD positive and 1412 (58.9%) were HRD negative. Three hundred sixty-three of 2396 samples (15.2%) were BRCA1/2-mutated; 27 samples had a BRCA1/2 mutation and a genomic instability score (GIS) < 42. Twenty-two samples (0.9%) failed GIS measurement but displayed a BRCA1/2 mutation. BRCA1/2-mutated samples showed significantly (P < .0001) higher GIS values than those with a wild-type BRCA1/2 status. Tumor cell content, tumor area, and histology significantly (P < .0001) affected the probability of successfully analyzing a sample. Based on a systematic analysis of tumor cell content and tumor area, we recommend selecting patient high-grade serous ovarian cancer samples that display a tumor cell content ≥30% and a tumor area ≥0.5 cm2 (based on their hematoxylin and eosin) for HRD testing to allow for optimal chances of a successful analysis and conclusive results. Considering histologic and sample conditions, success rates of up to 98% can be achieved. Our comprehensive evaluation contributes to further standardization of recommendations on HRD testing in ovarian cancer, which will have a large impact on personalized therapeutic strategies in this highly aggressive tumor type.
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Affiliation(s)
- Marcel Romey
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany
| | - Fiona Rodepeter
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany
| | - Akira Hattesohl
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany
| | | | - Julia Teply-Szymanski
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Ev. Kliniken Essen-Mitte, Essen, Germany; Department of Gynecology with the Centre of Oncologic Surgery Charite Campus, Virchow Klinikum, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Staebler
- Institute of Pathology and Neuropathology, Tübingen University Hospital, Tubingen, Germany
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Albert Grass
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany
| | - Frederik Marmé
- Medical Faculty Mannheim, Department of Obstetrics and Gynaecology, Heidelberg University, University Hospital Mannheim, Mannheim, Germany
| | | | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Ev. Kliniken Essen-Mitte, Essen, Germany
| | | | - Stefan Kommoss
- Department of Women's Health, Tübingen University Hospital, Tubingen, Germany; Clinic for Gynecology, Diakonie-Klinikum Schwäbisch Hall, Schwabisch Hall, Germany
| | - Jelena Boekhoff
- Institute of Gynecology, Philipps-University Marburg and Marburg University Hospital, Marburg, Germany
| | - Carsten Denkert
- Institute of Pathology, Philipps-University Marburg, Marburg University Hospital, and University Cancer Center Frankfurt-Marburg, Marburg, Germany.
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4
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Paulo P, Cardoso M, Brandão A, Pinto P, Falconi A, Pinheiro M, Cerveira N, Silva R, Santos C, Pinto C, Peixoto A, Maia S, Teixeira MR. Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients. Genes Chromosomes Cancer 2023; 62:710-720. [PMID: 37436117 DOI: 10.1002/gcc.23190] [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: 03/28/2023] [Revised: 06/19/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Prostate cancer (PrCa) is one of the three most frequent and deadliest cancers worldwide. The discovery of PARP inhibitors for the treatment of tumors with deleterious variants in homologous recombination repair (HRR) genes has placed PrCa on the roadmap of precision medicine. However, the overall contribution of HRR genes to the 10%-20% of carcinomas arising in men with early-onset/familial PrCa has not been fully clarified. We used targeted next-generation sequencing (T-NGS) covering eight HRR genes (ATM, BRCA1, BRCA2, BRIP1, CHEK2, NBN, PALB2, and RAD51C) and an analysis pipeline querying both small and large genomic variations to clarify their global and relative contribution to hereditary PrCa predisposition in a series of 462 early-onset/familial PrCa cases. Deleterious variants were found in 3.9% of the patients, with CHEK2 and ATM being the most frequently mutated genes (38.9% and 22.2% of the carriers, respectively), followed by PALB2 and NBN (11.1% of the carriers, each), and finally by BRCA2, RAD51C, and BRIP1 (5.6% of the carriers, each). Using the same NGS data, exonic rearrangements were found in two patients, one pathogenic in BRCA2 and one of unknown significance in BRCA1. These results contribute to clarify the genetic heterogeneity that underlies PrCa predisposition in the early-onset and familial disease, respectively.
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Affiliation(s)
- Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Marta Cardoso
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ariane Falconi
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Nuno Cerveira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Rui Silva
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ana Peixoto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Sofia Maia
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Medical Genetics Unit, Hospital Pediátrico de Coimbra, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP) /RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) /Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
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5
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González-Martín A, Matulonis UA, Korach J, Mirza MR, Moore KN, Wu X, York W, Gupta D, Lechpammer S, Monk BJ. Niraparib treatment for patients with BRCA-mutated ovarian cancer: review of clinical data and therapeutic context. Future Oncol 2022; 18:2505-2536. [PMID: 35791804 DOI: 10.2217/fon-2022-0206] [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] [Indexed: 12/15/2022] Open
Abstract
We reviewed clinical data for niraparib monotherapy in BRCA-mutated (BRCAm) epithelial ovarian cancer (OC), contextualizing results with data from other poly(ADP-ribose) polymerase inhibitors (PARPis). Niraparib reduced the likelihood of progression or death by 60% as first-line maintenance therapy and by 73-78% in recurrent disease. In heavily pretreated OC, efficacy was greater in the BRCAm versus non-BRCAm cohort. Quality-of-life (QoL) was maintained throughout treatment. Adverse events were consistent with the known niraparib safety profile. Cumulative efficacy, safety and QoL evidence demonstrate niraparib maintenance monotherapy has a positive benefit:risk ratio in BRCAm OC. Niraparib significantly improved progression-free survival as first-line maintenance therapy in all patients with OC (i.e., of any biomarker status).
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Affiliation(s)
- Antonio González-Martín
- Grupo Español de Investigación en Cáncer de Ovario (GEICO) and Medical Oncology Department, Clínica Universidad de Navarra, Madrid, Spain & Program in Solid Tumors, Center for Applied Medical Research (CIMA), Madrid, 31008, Spain
| | - Ursula A Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jacob Korach
- Gynecologic Oncology Department, Chaim Sheba Medical Center, Tel-Hashomer, Sackler School of Medicine, Tel Aviv University, 69978, Israel
| | - Mansoor R Mirza
- Department of Oncology, Rigshospitalet Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | - Kathleen N Moore
- Department of Gynecologic Oncology, Stephenson Cancer Center at the University of Oklahoma Health Science Center, Oklahoma City, OK 73104 & Sarah Cannon Research Institute, Nashville, TN 37203, USA
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Whitney York
- GlaxoSmithKline, Upper Providence, PA 19426, USA
| | | | | | - Bradley J Monk
- HonorHealth Research Institute & Department of Obstetrics and Gynecology, University of Arizona, Creighton University, Phoenix, AZ 85258, USA
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6
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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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7
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Barbosa A, Pinto P, Peixoto A, Guerra J, Pinheiro M, Santos C, Pinto C, Escudeiro C, Bartosch C, Santos R, Brandão A, Silva J, Teixeira MR. Next Generation Sequencing of Tumor and Matched Plasma Samples: Identification of Somatic Variants in ctDNA From Ovarian Cancer Patients. Front Oncol 2021; 11:754094. [PMID: 34660321 PMCID: PMC8515058 DOI: 10.3389/fonc.2021.754094] [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: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022] Open
Abstract
Genetic testing to detect somatic alterations is usually performed on formalin-fixed paraffin-embedded tumor samples. However, tumor molecular profiling through ctDNA analysis may be particularly interesting with the emergence of targeted therapies for ovarian cancer (OC), mainly when tumor is not available and biopsy is not viable, also allowing representation of multiple neoplastic subclones. Using a custom panel of 27 genes, next-generation sequencing (NGS) was performed on tumor and matched plasma samples from 96 OC patients, which were combined in two groups (treatment naive and post-treatment). Overall, at least one somatic variant present in the tumor sample was also detected in the matched plasma sample in 35.6% of the patients, a percentage that increased to 69.6% of the treatment naive patients and 83.3% of those with stage IV disease, showing the potential of ctDNA analysis as an alternative to identify somatic variants in these patients, namely those that have predictive value for targeted therapy. In fact, of the two treatment-naive patients with somatic BRCA1 variants identified in tumor samples, in one of them we detected in ctDNA a BRCA1 somatic variant that was present in the tumor with a VAF of 53%, but not in the one that had a VAF of 5.4%. We also showed that ctDNA analysis has a complementary role to molecular unraveling of inter- and intra-tumor heterogeneity, as exemplified by one patient diagnosed with bilateral OC in which different somatic variants from both tumors were detected in ctDNA. Interestingly, as these bilateral tumors shared a rare combination of two of the three variants identified in ctDNA, we could conclude that these morphologically different tumors were clonally related and not synchronous independent neoplasias. Moreover, in the post-treatment group of patients with plasma samples collected after surgery, those with detectable somatic variants had poor prognosis when compared with patients with no detectable somatic variants, highlighting the potential of ctDNA analysis to identify patients at higher risk of recurrence. Concluding, this study demonstrated that somatic variants can be detected in plasma samples of a significant proportion of OC patients, supporting the use of NGS-based ctDNA testing for noninvasive tumor molecular profiling and to stratify patients according to prognosis.
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Affiliation(s)
- Ana Barbosa
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Ana Peixoto
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carla Escudeiro
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Rui Santos
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Andreia Brandão
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - João Silva
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Manuel R Teixeira
- Cancer Genetics Group, Instituto Português de Oncologia (IPO)-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Department of Genetics, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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8
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Frugtniet B, Morgan S, Murray A, Palmer-Smith S, White R, Jones R, Hanna L, Fuller C, Hudson E, Mullard A, Quinton AE. The detection of germline and somatic BRCA1/2 genetic variants through parallel testing of patients with high-grade serous ovarian cancer: a national retrospective audit. BJOG 2021; 129:433-442. [PMID: 34657373 PMCID: PMC9298909 DOI: 10.1111/1471-0528.16975] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/11/2021] [Accepted: 09/12/2021] [Indexed: 12/05/2022]
Abstract
Objective To determine the frequency of germline and somatic pathogenic BRCA1 and BRCA2 variants in patients with high‐grade serous ovarian cancer tested by next‐generation sequencing (NGS), with the aim of defining the best strategy to be implemented in future routine testing. Design National retrospective audit. Setting The All Wales Medical Genomics Service (AWMGS). Population Patients with high‐grade serous ovarian/fallopian tube/peritoneal cancer referred by oncologists to the AWMGS between February 2015 and February 2021 for germline and/or tumour testing of the BRCA1 and BRCA2 genes by NGS. Methods Analysis of NGS data from germline and/or tumour testing. Main outcome measures Frequency of BRCA1 and BRCA2 pathogenic variants. Results The overall observed germline/somatic pathogenic variant detection rate was 11.6% in the 844 patients included in this study, with a 9.2% (73/791) germline pathogenic variant detection rate. Parallel tumour and germline testing was carried out for 169 patients and the overall pathogenic variant detection rate for this cohort was 14.8%, with 6.5% (11/169) shown to have a somatic pathogenic variant. Two BRCA1 dosage variants were found during germline screens, representing 2.0% (2/98) of patients with a pathogenic variant that would have been missed through tumour testing alone. Conclusions Parallel germline and tumour BRCA1 and BRCA2 testing maximises the detection of pathogenic variants in patients with high‐grade serous ovarian cancer. Tweetable abstract Parallel germline and tumour testing maximises BRCA pathogenic variant detection in ovarian cancer. Parallel germline and tumour testing maximises BRCA pathogenic variant detection in ovarian cancer. Linked article This article is commented on by C Gourley, p. 443 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16978.
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Affiliation(s)
- B Frugtniet
- All Wales Medical Genomics Laboratory, University Hospital of Wales, Cardiff, UK
| | - S Morgan
- All Wales Medical Genomics Laboratory, University Hospital of Wales, Cardiff, UK
| | - A Murray
- All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - S Palmer-Smith
- All Wales Medical Genomics Laboratory, University Hospital of Wales, Cardiff, UK
| | - R White
- All Wales Medical Genomics Laboratory, University Hospital of Wales, Cardiff, UK
| | - R Jones
- South West Wales Cancer Centre, Singleton Hospital, Swansea, UK
| | - L Hanna
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
| | - C Fuller
- Bwrdd Iechyd Prifysgol Betsi Cadwaladr University Health Board, Bangor, UK
| | - E Hudson
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
| | - A Mullard
- Bwrdd Iechyd Prifysgol Betsi Cadwaladr University Health Board, Bangor, UK
| | - A E Quinton
- Velindre Cancer Centre, Velindre University NHS Trust, Cardiff, UK
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Grabenstetter A, Lazaro C, Turashvili G. Editorial: Hereditary Breast and Ovarian Cancer: Current Concepts of Prevention and Treatment. Front Oncol 2020; 10:618369. [PMID: 33344261 PMCID: PMC7738629 DOI: 10.3389/fonc.2020.618369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anne Grabenstetter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Barcelona, Spain
| | - Gulisa Turashvili
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Mount Sinai Hospital, Toronto, ON, Canada
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10
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Barbosa A, Pinto P, Peixoto A, Guerra J, Pinto C, Santos C, Pinheiro M, Escudeiro C, Bartosch C, Silva J, Teixeira MR. Gene Panel Tumor Testing in Ovarian Cancer Patients Significantly Increases the Yield of Clinically Actionable Germline Variants beyond BRCA1/ BRCA2. Cancers (Basel) 2020; 12:cancers12102834. [PMID: 33008098 PMCID: PMC7650720 DOI: 10.3390/cancers12102834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 01/13/2023] Open
Abstract
Simple Summary Germline and somatic variant testing of the BRCA1 and BRCA2 genes are important to predict treatment response to PARP inhibitors in ovarian cancer patients. However, germline variants in other genes besides BRCA1 and BRCA2 are associated with ovarian cancer predisposition, which would be missed by a genetic testing aimed only at treatment decision. We aimed to evaluate the yield of clinically actionable germline variants using next-generation sequencing of a customized panel of 10 genes for the analysis of pathology samples of ovarian carcinomas. We identified clinically actionable germline variants in a significantly higher proportion of ovarian cancer patients when compared with genetic testing focused only on BRCA1 and BRCA2. This strategy increases the chance to make available genetic counseling, presymptomatic genetic testing, and gynecological cancer prophylaxis to female relatives who turn out to be healthy carriers of deleterious germline variants. Abstract Since the approval of PARP inhibitors for the treatment of high-grade serous ovarian cancer, in addition to cancer risk assessment, BRCA1 and BRCA2 genetic testing also has therapeutic implications (germline and somatic variants) and should be offered to these patients at diagnosis, irrespective of family history. However, variants in other genes besides BRCA1 and BRCA2 are associated with ovarian cancer predisposition, which would be missed by a genetic testing aimed only at indication for PARP inhibitor treatment. In this study, we aimed to evaluate the yield of clinically actionable germline variants using next-generation sequencing of a customized panel of 10 genes for the analysis of formalin-fixed paraffin-embedded samples from 96 ovarian carcinomas, a strategy that allows the detection of both somatic and germline variants in a single test. In addition to 13.7% of deleterious germline BRCA1/BRCA2 carriers, we identified 7.4% additional patients with pathogenic germline variants in other genes predisposing for ovarian cancer, namely RAD51C, RAD51D, and MSH6, representing 35% of all pathogenic germline variants. We conclude that the strategy of reflex gene-panel tumor testing enables the identification of clinically actionable germline variants in a significantly higher proportion of ovarian cancer patients, which may be valuable information in patients with advanced disease that have run out of approved therapeutic options. Furthermore, this approach increases the chance to make available genetic counseling, presymptomatic genetic testing, and gynecological cancer prophylaxis to female relatives who turn out to be healthy carriers of deleterious germline variants.
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Affiliation(s)
- Ana Barbosa
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
| | - Pedro Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
| | - Ana Peixoto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
| | - Carla Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Catarina Santos
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
| | - Carla Escudeiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal;
| | - João Silva
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Manuel R. Teixeira
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.); (A.P.); (J.G.); (C.P.); (C.S.); (M.P.); (C.E.); (J.S.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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