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Daly GR, Naidoo S, Alabdulrahman M, McGrath J, Dowling GP, AlRawashdeh MM, Hill ADK, Varešlija D, Young L. Screening and Testing for Homologous Recombination Repair Deficiency (HRD) in Breast Cancer: an Overview of the Current Global Landscape. Curr Oncol Rep 2024; 26:890-903. [PMID: 38822929 PMCID: PMC11300621 DOI: 10.1007/s11912-024-01560-3] [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] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
PURPOSE OF REVIEW Homologous recombination repair deficiency (HRD) increases breast cancer susceptibility and influences both prophylactic and active management of breast cancer. This review evaluates HRD testing and the therapeutic implications of HRD in a global context. RECENT FINDINGS Ongoing research efforts have highlighted the importance of HRD beyond BRCA1/2 as a potential therapeutic target in breast cancer. However, despite the improved affordability of next-generation sequencing (NGS) and the discovery of PARP inhibitors, economic and geographical barriers in access to HRD testing and breast cancer screening do not allow all patients to benefit from the personalized treatment approach they provide. Advancements in HRD testing modalities and targeted therapeutics enable tailored breast cancer management. However, inequalities in access to testing and optimized treatments are contributing to widening health disparities globally.
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Affiliation(s)
- Gordon R Daly
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland.
| | - Sindhuja Naidoo
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Mohammad Alabdulrahman
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Jason McGrath
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Gavin P Dowling
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Maen M AlRawashdeh
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Arnold D K Hill
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- The Department of Surgery, Beaumont Hospital, Dublin, Ireland
| | - Damir Varešlija
- School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
| | - Leonie Young
- The Department of Surgery, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Beaumont RCSI Cancer Centre, Beaumont Hospital, Dublin, Ireland
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Al-Shamsi HO, Alwbari A, Azribi F, Calaud F, Thuruthel S, Tirmazy SHH, Kullab S, Ostomane S, Abulkhair O. BRCA testing and management of BRCA-mutated early-stage breast cancer: a comprehensive statement by expert group from GCC region. Front Oncol 2024; 14:1358982. [PMID: 38725624 PMCID: PMC11080009 DOI: 10.3389/fonc.2024.1358982] [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: 12/20/2023] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
BReast CAncer (BRCA)1 and BRCA2 gene pathogenic variants account for most hereditary breast cancers (BC). Identification of BRCA mutations can significantly influence both prognosis and treatment outcomes. Furthermore, it enables the identification of individuals who are at heightened risk of developing BC due to inherited genetic mutations. Many developing countries rely on western guidelines for BRCA testing and BC management; however, there exist wide disparities in the prevalence of risk factors, availability of medical resources, and practice patterns. Guidelines tailored to specific regions can help mitigate healthcare variations, promote consistency in treatment, and aid healthcare providers in identifying effective therapies for improving patient outcomes. Hence, oncologists from the Gulf Cooperation Council (GCC) congregated virtually in March 2023 and reviewed existing data on the epidemiology of BC, BRCA mutations, practices and challenges associated with BRCA testing and management of BRCA mutated early-stage BC in the GCC region. They also provided insights on the real-world diagnostic and treatment practices and challenges in the GCC region in the BRCA-mutated early-stage BC domain and suggested some variations to international guidelines to aid their uptake in this region.
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Affiliation(s)
- Humaid O. Al-Shamsi
- Burjeel Medical City, Burjeel Holding, Abu Dhabi, United Arab Emirates
- Gulf Medical University, Ajman, United Arab Emirates
- Emirates Oncology Society, Dubai, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Gulf Cancer Society, Alsafa, Kuwait
| | - Ahmed Alwbari
- Almoosa Specialist Hospital Cancer Center, Al Ahsa, Saudi Arabia
| | | | | | | | | | - Sharif Kullab
- King Khalid University Hospital, Riyadh, Saudi Arabia
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Knoedler L, Huelsboemer L, Hollmann K, Alfertshofer M, Herfeld K, Hosseini H, Boroumand S, Stoegner VA, Safi AF, Perl M, Knoedler S, Pomahac B, Kauke-Navarro M. From standard therapies to monoclonal antibodies and immune checkpoint inhibitors - an update for reconstructive surgeons on common oncological cases. Front Immunol 2024; 15:1276306. [PMID: 38715609 PMCID: PMC11074450 DOI: 10.3389/fimmu.2024.1276306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 04/05/2024] [Indexed: 05/23/2024] Open
Abstract
Malignancies represent a persisting worldwide health burden. Tumor treatment is commonly based on surgical and/or non-surgical therapies. In the recent decade, novel non-surgical treatment strategies involving monoclonal antibodies (mAB) and immune checkpoint inhibitors (ICI) have been successfully incorporated into standard treatment algorithms. Such emerging therapy concepts have demonstrated improved complete remission rates and prolonged progression-free survival compared to conventional chemotherapies. However, the in-toto surgical tumor resection followed by reconstructive surgery oftentimes remains the only curative therapy. Breast cancer (BC), skin cancer (SC), head and neck cancer (HNC), and sarcoma amongst other cancer entities commonly require reconstructive surgery to restore form, aesthetics, and functionality. Understanding the basic principles, strengths, and limitations of mAB and ICI as (neo-) adjuvant therapies and treatment alternatives for resectable or unresectable tumors is paramount for optimized surgical therapy planning. Yet, there is a scarcity of studies that condense the current body of literature on mAB and ICI for BC, SC, HNC, and sarcoma. This knowledge gap may result in suboptimal treatment planning, ultimately impairing patient outcomes. Herein, we aim to summarize the current translational endeavors focusing on mAB and ICI. This line of research may serve as an evidence-based fundament to guide targeted therapy and optimize interdisciplinary anti-cancer strategies.
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Affiliation(s)
- Leonard Knoedler
- Department of Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Lioba Huelsboemer
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Katharina Hollmann
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Faculty of Medicine, University of Wuerzbuerg, Wuerzburg, Germany
| | - Michael Alfertshofer
- Division of Hand, Plastic and Aesthetic Surgery, Ludwig-Maximilians University Munich, Munich, Germany
| | - Konstantin Herfeld
- Department of Internal Medicine III (Oncology and Haematology), University Hospital Regensburg, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Helia Hosseini
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Sam Boroumand
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Viola A. Stoegner
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
- Department of Plastic, Aesthetic, Hand and Reconstructive Surgery, Burn Center, Hannover Medical School, Hannover, Germany
| | - Ali-Farid Safi
- Craniologicum, Center for Cranio-Maxillo-Facial Surgery, Bern, Switzerland
- Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Markus Perl
- Department of Internal Medicine III (Oncology and Haematology), University Hospital Regensburg, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Samuel Knoedler
- Department of Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg, Regensburg, Germany
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Bohdan Pomahac
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
| | - Martin Kauke-Navarro
- Division of Plastic Surgery, Department of Surgery, Yale New Haven Hospital, Yale School of Medicine, New Haven, CT, United States
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Kechin A, Boyarskikh U, Borobova V, Khrapov E, Subbotin S, Filipenko M. BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data. Int J Mol Sci 2023; 24:16630. [PMID: 38068953 PMCID: PMC10706169 DOI: 10.3390/ijms242316630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Viktoriya Borobova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Sergey Subbotin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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Dinneen K, Arora R. Molecular Testing in Ovarian Tumours: Challenges from the Pathologist's Perspective. Diagnostics (Basel) 2023; 13:2072. [PMID: 37370967 DOI: 10.3390/diagnostics13122072] [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: 05/07/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The use of molecular testing to direct diagnosis and treatment options in ovarian tumours has rapidly expanded in recent years, in particular with regard to the recommendation for routine homologous recombination deficiency (HRD) testing in all patients with high-grade ovarian epithelial tumours. The implications of this increased level of testing upon the pathologist is significant in terms of increased workload, the provision of adequate tumour samples for molecular testing, and the interpretation of complex molecular pathology reports. In order to optimise the quality of reports generated, it is important to establish clear pathways of communication on both a local and national level between clinicians, pathology lab staff, and medical scientists. On a national level, in the United Kingdom, Genomic Laboratory Hubs (GLHs) have been established to provide a uniform high-quality molecular diagnostics service to all patients with ovarian tumours within the National Health services in the country. On a local level, there are a number of small steps that can be taken to improve the quality of tissues available for testing and to streamline the processes involved in generating requests for molecular testing. This article discusses these factors from the perspective of the clinical histopathologist.
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Affiliation(s)
- Kate Dinneen
- Department of Cellular Pathology, University College London NHS Trust, 60 Whitfield Street, London W1T 4E, UK
| | - Rupali Arora
- Department of Cellular Pathology, University College London NHS Trust, 60 Whitfield Street, London W1T 4E, UK
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Janíková K, Váňová B, Grendár M, Samec M, Loderer D, Kašubová I, Škereňová M, Farkašová A, Scheerová K, Slávik P, Lasabová Z, Danková Z, Strnádel J, Halašová E, Plank L. Small-scale variants and large deletions in BRCA1/2 genes in Slovak high-grade serous ovarian cancer. Pathol Res Pract 2023; 246:154475. [PMID: 37121054 DOI: 10.1016/j.prp.2023.154475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/02/2023]
Abstract
The role of PARP inhibitors is to prevent the polymerase from repairing the single-strand break that occurred due to tumor growth and thus induce cell apoptosis when the homologous recombination deficiency (HRD) system is disabled. The eliminated system can be monitored especially in patients with serous ovarian epithelial tumors. Current studies still show the highest progression-free survival (PFS) in the examined groups with BRCA mutant status, even though they are also effective in the case of a disrupted HRD system, apart from BRCA genes. The study cohort consists of women diagnosed with high-grade serous ovarian cancer (HGSOC), after at least two lines of chemotherapy and after relapse of the disease, as determined by ESMO standards and guidelines. The commercially available tool SOPHIA DDM™ (SophiaGenetics, Switzerland) was used to classify the variants after sequencing. The most common variants (pathogenic or likely pathogenic) were in BRCA1 c.1067 A>G (rs1799950) and c.5266dupC (rs80357906) and in BRCA2 c.9976 A>T (rs11571833). Large deletions were detected in one and three cases in the BRCA1 and BRCA2 genes, respectively. A mutation in the BRCA1/2 genes was confirmed in 50% of the examined patients. In the study, we focused on the identification of mutated BRCA genes by a commercially available Sophia DDM™ system to identify a pathogenic or probable pathogenic variant in a cohort of patients with HGSOC in the Slovak population, which could result in better management and stratification of the individual.
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Affiliation(s)
- Katarína Janíková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Barbora Váňová
- Martin´s Immunology Center, Ltd., 03601 Martin, Slovakia.
| | - Marián Grendár
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Marek Samec
- Department of Pathological Physiology, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital in Martin, 03601 Martin, Slovakia.
| | - Dušan Loderer
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Ivana Kašubová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Mária Škereňová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | | | | | - Pavol Slávik
- Department of Pathological Anatomy, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital in Martin, 03601 Martin, Slovakia.
| | - Zora Lasabová
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Zuzana Danková
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Ján Strnádel
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Erika Halašová
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; Department of Biology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia.
| | - Lukáš Plank
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, 03601 Martin, Slovakia; Martin´s Biopsy Center, Ltd., 03601 Martin, Slovakia; Department of Pathological Anatomy, Comenius University in Bratislava, Jessenius Faculty of Medicine and University Hospital in Martin, 03601 Martin, Slovakia.
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Kim ET, Jeong HE, Yoon HJ, Kim KH, Suh DS. Validation of multi-gene panel next-generation sequencing for the detection of BRCA mutation in formalin-fixed, paraffin-embedded epithelial ovarian cancer tissues. Taiwan J Obstet Gynecol 2023; 62:66-70. [PMID: 36720553 DOI: 10.1016/j.tjog.2022.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVE The therapeutic effect of poly (ADP-ribose) polymerase (PARP) inhibitors in patients with epithelial ovarian cancer (EOC) with somatic BRCA mutations is consistent with that observed in patients with germline BRCA mutations, indicating the importance of detecting both germline and somatic BRCA mutations concurrently. We compared the efficacy of multi-gene panel next generation sequencing (NGS) in EOC patients' formalin-fixed, paraffin-embedded (FFPE) tissue to that of conventional Sanger sequencing in blood samples. MATERIALS AND METHODS This study included 48 patients with EOC, and both blood Sanger sequencing and FFPE tissue NGS were conducted in all of them. Clinical and pathological data were reviewed, including age at diagnosis, histology, and stage. Blood Sanger sequencing was performed using peripheral blood leukocytes. The target regions of 90 cancer-related genes were identified using FFPE tissue. RESULTS The median age of patients was 56.1 years, with serous carcinoma (n = 40, 83.3%) and stage III (n = 37, 77.1%) being the most common histology and International Federation of Gynecology and Obstetrics (FIGO) stage, respectively. FFPE tissue NGS identified ten pathogenic variants, including all eight pathogenic variants identified by blood Sanger sequencing and two additional pathogenic variants. Furthermore, FFPE tissue NGS identified 19 variants of uncertain significance (VUS), including all ten VUS identified by blood Sanger sequencing and nine additional VUS. CONCLUSION The FFPE tissue multi-gene panel NGS had 100% sensitivity for detecting BRCA germline mutations and could detect additional somatic mutations. Furthermore, performing FFPE tissue multi-gene panel NGS followed by blood Sanger sequencing sequentially may help differentiate germline from somatic BRCA mutations for genetic counseling.
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Affiliation(s)
- Eun Taeg Kim
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ha Eun Jeong
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Hyung Joon Yoon
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Ki Hyung Kim
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Dong Soo Suh
- Department of Obstetrics and Gynecology, Pusan National University School of Medicine, Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea.
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Chu DT, Vu Ngoc Suong M, Vu Thi H, Vu TD, Nguyen MH, Singh V. The expression and mutation of BRCA1/2 genes in ovarian cancer: a global systematic study. Expert Rev Mol Diagn 2023; 23:53-61. [PMID: 36634123 DOI: 10.1080/14737159.2023.2168190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION This systematic review was designed to summarize the findings on expression and mutation of BRCA1/2 genes in ovarian cancer (OC) patients, focusing on mutation detection technology and taking clinical decisions for better treatment. AREAS COVERED We conducted a systematic review by following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses document selection guidelines for the document selection process and the PICOT standard for developing the keywords to search for. A total of 5729 publications were included, and 50 articles were put into the final screening. The results showed that Next-Generation Sequencing was a breakthrough technology in detecting Breast Cancer 1/2 (BRCA1/2) gene mutations because of its efficacy and affordability. Other technologies are also being applied now for mutation detection. The most prominent associations of BRCA1/2 gene mutations were age, heredity, and family history. Furthermore, mutations of BRCA1/2 could improve survival rate and overall survival. There is no sufficient study available to conclude a systematic analysis for the expression of BRCA1/2 gene in OC. EXPERT OPINION Research will continue to develop more diagnostic techniques based on the expression and mutation of BCRA1/2 genes for OC in the near future.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Mai Vu Ngoc Suong
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam.,Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Manh-Hung Nguyen
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, India
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Challenges in next generation sequencing of homology recombination repair genomic variants in prostate cancer: A nationwide survey and calibration project in China. Prostate Int 2022; 10:181-187. [PMID: 36570645 PMCID: PMC9747577 DOI: 10.1016/j.prnil.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 12/27/2022] Open
Abstract
Background Homologous Recombination Repair (HRR) is the most reliable and important signaling pathway for repairing DNA damage. We initiated a calibration project to better understand the NGS landscape for HRR gene testing in China, provide indications for testing standardization, and guide clinical practice. Methods A questionnaire was used to collect laboratory information, panel design for HRR gene testing, tissue sample test parameters, plasma ctDNA sample test parameters, and procedures for variant interpretation. The testing quality of the participating laboratories was further evaluated by external quality assessment (EQA), which provided 5 FFPE slices and 5 mimic ctDNA samples as standard references for evaluation. Test results and reports were collected to assess laboratory performance. Results Our results showed that different laboratories had significant differences in sequencing platforms, library construction technologies, genes in the testing panel, detectable mutation types, probe coverage regions, sequencing parameters, variants interpretation guidelines, and positive test rates. For the EQA test, the overall pass rate was about 60%. The average accuracy for tissue samples and ctDNA samples was 79.55% and 74.13%, respectively. It is worth noting that variants in tandem repetition regions and splice sites, and those with low allele frequency were more prone to misdetection. The most common reasons for misdetection were as follows: the testing panel did not cover the genes or the whole exon and splice sites of the genes; the variants were misclassified as benign or likely benign, and the variants failed the QC criteria. Conclusions The discrepancies observed in our survey and EQA test affect the authenticity of HRR gene test results for prostate cancer, underlining the need to establish guidelines for HRR gene testing and variant interpretation in China, and to optimize HRR gene testing in clinical practice to improve management and patient care.
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Nunziato M, Di Maggio F, Pensabene M, Esposito MV, Starnone F, De Angelis C, Calabrese A, D’Aiuto M, Botti G, De Placido S, D’Argenio V, Salvatore F. Multi-gene panel testing increases germline predisposing mutations’ detection in a cohort of breast/ovarian cancer patients from Southern Italy. Front Med (Lausanne) 2022; 9:894358. [PMID: 36035419 PMCID: PMC9403188 DOI: 10.3389/fmed.2022.894358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is the most common neoplasia in females worldwide, about 10% being hereditary/familial and due to DNA variants in cancer-predisposing genes, such as the highly penetrant BRCA1/BRCA2 genes. However, their variants explain up to 25% of the suspected hereditary/familial cases. The availability of NGS methodologies has prompted research in this field. With the aim to improve the diagnostic sensitivity of molecular testing, a custom designed panel of 44 genes, including also non-coding regions and 5’ and 3’ UTR regions, was set up. Here, are reported the results obtained in a cohort of 64 patients, including also few males, from Southern Italy. All patients had a positive personal and/or familial history for breast and other cancers, but tested negative to routine BRCA analysis. After obtaining their written informed consent, a genomic DNA sample/patient was used to obtain an enriched DNA library, then analyzed by NGS. Sequencing data analysis allowed the identification of pathogenic variants in 12 of tested patients (19%). Interestingly, MUTYH was the most frequently altered gene, followed by RNASEL, ATM, MSH6, MRE11A, and PALB2 genes. The reported resultsreinforce the need for enlarged molecular testing beyond BRCA genes, at least in patients with a personal and familial history, strongly suggestive for a hereditary/familial form. This gives also a hint to pursue more specific precision oncology therapy.
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Affiliation(s)
- Marcella Nunziato
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Federica Di Maggio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Matilde Pensabene
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Maria Valeria Esposito
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Flavio Starnone
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Alessandra Calabrese
- Division of Breast Surgery, Department of Breast Disease, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Massimiliano D’Aiuto
- Clinica Villa Fiorita, Aversa, Italy
- Division of Breast Oncology, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Gerardo Botti
- Scientific Directorate, National Cancer Institute, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) “Fondazione G. Pascale,”Naples, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
- Department of Oncology and Hematology, Regional Reference Center for Rare Tumors, Azienda Ospedaliera Universitaria (AOU) Federico II of Naples, Naples, Italy
| | - Valeria D’Argenio
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy
- *Correspondence: Valeria D’Argenio,
| | - Francesco Salvatore
- CEINGE–Biotecnologie Avanzate, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
- Francesco Salvatore,
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11
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Goh JC, Gourley C, Tan DSP, Nogueira-Rodrigues A, Elghazaly H, Edy Pierre M, Giornelli G, Kim BG, Morales–Vasquez F, Tyulyandina A. Optimizing treatment selection and sequencing decisions for first-line maintenance therapy of newly diagnosed advanced ovarian cancer – International considerations amongst upper middle- and high-income countries (UMIC and HIC). Gynecol Oncol Rep 2022; 42:101028. [PMID: 35813356 PMCID: PMC9263863 DOI: 10.1016/j.gore.2022.101028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/04/2022] [Accepted: 06/11/2022] [Indexed: 11/30/2022] Open
Abstract
Early BRCA testing is crucial and enables personalized treatment approach. BRCA mutation analysis is essential and should be utilized at the time of diagnosis. Single-agent PARP inhibitors seem most beneficial in BRCA mutations or HRD. Evidence suggests bevacizumab or niraparib-alone benefits for HRD-negative patients. HRD-tailored treatment should be explored further.
The incidence and mortality rates of ovarian cancer are increasing globally. Ovarian cancer is diagnosed at an advanced stage in 80% of women. After standard, platinum-based, front-line chemotherapy, poly (ADP-ribose) polymerase (PARP) inhibitors and antiangiogenic agents are successfully employed as maintenance strategies for newly diagnosed, advanced ovarian cancer patients. Landmark clinical studies, including SOLO-1, PAOLA-1, PRIMA, and VELIA, have provided crucial insights on optimizing first-line maintenance treatment using PARP inhibitors. A group of ovarian cancer experts, primarily from low- and middle-income countries, met in September 2019 to discuss new developments for the first-line treatment of ovarian cancer and its implications. Key implications of the evolving clinical data included: (1) olaparib or niraparib maintenance therapy appears to be the preferred choice for patients with BRCA1/2 mutations; hence, BRCA testing is beneficial in identifying these patients; (2) niraparib monotherapy and olaparib in combination with bevacizumab have demonstrated significant benefit in progression-free survival (PFS) in homologous recombination deficiency (HRD)-positive patients; (3) bevacizumab, niraparib alone, or observation can be an alternative for HRD-negative patients; (4) further data is warranted to explore the role of PARP inhibitors in treating HRD-negative, ovarian cancer patients to confirm findings of the exploratory analysis of PRIMA; (5) PARP inhibitors may be beneficial for stage IV ovarian cancer patients with inoperable disease and patients with prior neoadjuvant chemotherapy; and (6) there is an urgent need to increase awareness in both clinicians and patients on BRCA and HRD testing for optimizing treatment decision-making and improving clinical outcomes in newly diagnosed, advanced ovarian cancer patients. In clinical medicine, the limited availability of family history (FH) information and the complexity of FH criteria has hampered the implementation of BRCA testing. Moreover, many cancer patients with BRCA mutations are not tested because they do not meet the criteria for FH. Consequently, BRCA testing in many high income countries, including the US and Australia, is underused and used inappropriately, which has resulted in the loss of valuable opportunities for better cancer management and cancer prevention.
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Affiliation(s)
- Jeffrey C.H. Goh
- Department of Oncology – Cancer Care Services, Level 5, Joyce Tweddell Building, Royal Brisbane & Women’s Hospital, Butterfield Street, Herston, Queensland 4029, University of Queensland, St Lucia, Australia
- Corresponding author at: Department of Oncology – Cancer Care Services, Level 5, Joyce Tweddell Building, Royal Brisbane & Women’s Hospital, Butterfield Street, Herston, Queensland 4029, Australia.
| | - Charlie Gourley
- Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South Edinburgh, EH4 2XR, UK
| | - David S P Tan
- Department of Haematology-Oncology, National University Cancer Institute, Singapore
| | - Angélica Nogueira-Rodrigues
- Federal University of Minas Gerais, DOM Oncologia, Grupo Oncoclınicas, EVA Brazilian Group of Gynecologic Cancer, LACOG, Porto Alegre, Brazil
| | - Hesham Elghazaly
- Clinical Oncology Head of Medical Research Center MASRI, Ain Shams University, Cairo, Egypt
| | - Marc Edy Pierre
- Gynecology Oncology Unit, Luis Carlos Samiento Angulo Cancer Treatment and Research Center - CTIC,Bogotá, Colombia
| | - Gonzalo Giornelli
- Department of Oncology, Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Alexandra Tyulyandina
- Department of Clinical Pharmacology And Chemotherapy, N. N. Blokhin Russian Cancer Research Center, Moscow, Russia
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12
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Secondino A, Starnone F, Veneruso I, Di Tella MA, Conato S, De Angelis C, De Placido S, D’Argenio V. Evaluation of a Four-Gene Panel for Hereditary Cancer Risk Assessment. Genes (Basel) 2022; 13:genes13040682. [PMID: 35456488 PMCID: PMC9024623 DOI: 10.3390/genes13040682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 02/01/2023] Open
Abstract
BRCA1/2 are tumor suppressor genes involved in DNA double-strand break repair. They are the most penetrant genes for hereditary breast and ovarian cancers, but pathogenic variants in these two genes can be identified only in a fraction of hereditary cases. Following the diffusion of BRCA molecular testing and the availability of specific therapeutic strategies for the management of pathogenic variant carriers, the demand for the analysis of additional predisposing genetic factors has increased. Indeed, there is accumulating evidence regarding the role of other genes, including CHEK2 and PALB2. Both of them are involved in the same molecular pathway as BRCA genes, with CHEK2 being responsible for cell cycle stopping to allow the repair of DNA double-strand breaks and PALB2 being able to interact with BRCA1 and activate BRCA2. Thus, their role as additional hereditary cancer predisposing factors is intriguing. Accordingly, guidelines for hereditary cancer risk assessment have been updated to include the criteria for additional genes testing. In this context, we validated a commercially available kit allowing for the simultaneous analysis of BRCA1, BRCA2, CHEK2 and PALB2. Forty-eight patients, already tested for BRCA mutational status, were re-analyzed in the present study. Results comparison showed that the tested method was able to correctly identify all the variants previously detected in the same patients. In particular, all single-nucleotide variants and small indels were correctly identified. Moreover, two copy number variants, included to assess the software’s performance in detecting this kind of gene alteration, were also detected. Even if copy number variant estimation still requires confirmation by a molecular technique to avoid false positive results, it is able to reduce the number of patients requiring multiplex ligation probe amplification analysis, positively impacting the test’s turnaround time. Finally, since the time and costs of the analysis are similar to those required just for BRCA genes, this strategy may be affordable for providing a more comprehensive test for hereditary cancer risk assessment.
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Affiliation(s)
- Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy; (A.S.); (I.V.)
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
| | - Flavio Starnone
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy; (A.S.); (I.V.)
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
| | - Maria Antonietta Di Tella
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
| | - Serena Conato
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy; (C.D.A.); (S.D.P.)
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy; (C.D.A.); (S.D.P.)
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate, Via G. Salvatore 486, 80145 Napoli, Italy; (F.S.); (M.A.D.T.); (S.C.)
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
- Correspondence:
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13
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Lavoro A, Scalisi A, Candido S, Zanghì GN, Rizzo R, Gattuso G, Caruso G, Libra M, Falzone L. Identification of the most common BRCA alterations through analysis of germline mutation databases: Is droplet digital PCR an additional strategy for the assessment of such alterations in breast and ovarian cancer families? Int J Oncol 2022; 60:58. [PMID: 35383859 PMCID: PMC8997337 DOI: 10.3892/ijo.2022.5349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Breast and ovarian cancer represent two of the most common tumor types in females worldwide. Over the years, several non‑modifiable and modifiable risk factors have been associated with the onset and progression of these tumors, including age, reproductive factors, ethnicity, socioeconomic status and lifestyle factors, as well as family history and genetic factors. Of note, BRCA1 and BRCA2 are two tumor suppressor genes with a key role in DNA repair processes, whose mutations may induce genomic instability and increase the risk of cancer development. Specifically, females with a family history of breast or ovarian cancer harboring BRCA1/2 germline mutations have a 60‑70% increased risk of developing breast cancer and a 15‑40% increased risk for ovarian cancer. Different databases have collected the most frequent germline mutations affecting BRCA1/2. Through the analysis of such databases, it is possible to identify frequent hotspot mutations that may be analyzed with next‑generation sequencing (NGS) and novel innovative strategies. In this context, NGS remains the gold standard method for the assessment of BRCA1/2 mutations, while novel techniques, including droplet digital PCR (ddPCR), may improve the sensitivity to identify such mutations in the hereditary forms of breast and ovarian cancer. On these bases, the present study aimed to provide an update of the current knowledge on the frequency of BRCA1/2 mutations and cancer susceptibility, focusing on the diagnostic potential of the most recent methods, such as ddPCR.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aurora Scalisi
- Italian League Against Cancer, Section of Catania, I‑95122 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Guido Nicola Zanghì
- Department of General Surgery and Medical‑Surgical Specialties, Policlinico‑Vittorio Emanuele Hospital, University of Catania, I‑95123 Catania, Italy
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute IRCCS Fondazione 'G. Pascale', I‑80131 Naples, Italy
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14
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Ebner S, Winkelmann R, Martin S, Köllermann J, Wild PJ, Demes M. Sequencing of BRCA1/2-alterations using NGS-based technology: annotation as a challenge. Oncotarget 2022; 13:464-475. [PMID: 35251494 PMCID: PMC8893798 DOI: 10.18632/oncotarget.28213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
In this study, the molecular profile of different BRCA-associated tumor types was assessed with regard to the classification and annotation of detected BRCA1/2 variants. The aim was to establish guidelines in order to facilitate the interpretation of BRCA1/2 alterations in routine diagnostics. Annotation of detected variants was evaluated compared to background mutations found in normal tissue samples and manually reviewed according to distinct online databases. This retrospective study included 48 samples (45 tumors, three non-tumors), which were sequenced with the GeneReader (QIAGEN). Thereof ten samples were additionally analyzed with the Ion S5™ (Thermo Fisher) and 20 samples with the MiSeq™ (Illumina®) to compare the different NGS devices, as well as the sequencing results and their quality. The analysis showed that the individual NGS platforms detected different numbers of BRCA1/2 alterations in the respective tumor sample. In addition, the GeneReader revealed variability in the detection and classification of pathogenic alterations within the platform itself as well as in comparison with the other platforms or online databases. The study concluded that the Ion S5™ in combination with the Oncomine™ Comprehensive Assay v3 is most recommendable for current and prospective requirements of molecular analysis in routine diagnostics. In addition to the two BRCA1/2 genes, a broad number of other genes (BRCAness genes and genes involved in the repair pathway) is covered by the panel, which may open up new treatment options for patients depending on the respective eligibility criteria.
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Affiliation(s)
- Silvana Ebner
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Saskia Martin
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Jens Köllermann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt am Main, Germany
| | - Melanie Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany.,Wildlab, University Hospital MVZ GmbH, Frankfurt am Main, Germany
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15
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Feasibility of targeted cascade genetic testing in the family members of BRCA1/2 gene pathogenic variant/likely pathogenic variant carriers. Sci Rep 2022; 12:1842. [PMID: 35115620 PMCID: PMC8813990 DOI: 10.1038/s41598-022-05931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenic variant (PV) or likely pathogenic variant (LPV) BRCA1/2 gene is strongly associated with hereditary breast or ovarian cancer. Therefore, it is important to screen blood relatives to establish preventive modalities and surveillance. This study evaluated the feasibility of targeted cascade genetic testing for family members of BRCA1/2 gene PV or LPV carriers. We screened 18 families for BRCA1/2 gene status via the conventional cascade genetic test (n = 9) and targeted cascade genetic test (n = 9), which targeted the exon region wherein the index patient showed PV or LPV. The pedigree and clinicopathologic characteristics were reviewed and analyzed. All index patients were diagnosed with breast cancer, while the third family members were all healthy. In the conventional cascade test group, 3 index patients and 3 family members had the BRCA1/2 gene PV or LPV. In the targeted cascade test group, 5 family members had same type of BRCA1/2 gene PV or LPV as their index patients. Two families had an identical string of BRCA1/2 gene PV or LPV. Although the targeted cascade genetic test cannot completely characterize the BRCA1/2 gene, it is sufficient for determining its PV or LPV status. This limited genetic test can be used for family members of PV or LPV carriers.
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16
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Li J, Wang P, Zhang C, Han S, Xiao H, Liu Z, Wang X, Liu W, Wei B, Ma J, Li H, Guo Y. Characterization of Synonymous BRCA1:c.132C>T as a Pathogenic Variant. Front Oncol 2022; 11:812656. [PMID: 35087763 PMCID: PMC8789006 DOI: 10.3389/fonc.2021.812656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
Breast cancer gene 1 (BRCA1) and BRCA2 are tumor suppressors involved in DNA damage response and repair. Carriers of germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2 have significantly increased lifetime risks of breast cancer, ovarian cancer, and other cancer types; this phenomenon is known as hereditary breast and ovarian cancer (HBOC) syndrome. Accurate interpretation of BRCA1 and BRCA2 variants is important not only for disease management in patients, but also for determining preventative measures for their families. BRCA1:c.132C>T (p.Cys44=) is a synonymous variant recorded in the ClinVar database with “conflicting interpretations of its pathogenicity”. Here, we report our clinical tests in which we identified this variant in two unrelated patients, both of whom developed breast cancer at an early age with ovarian presentation a few years later and had a family history of relevant cancers. Minigene assay showed that this change caused a four-nucleotide loss at the end of exon 3, resulting in a truncated p.Cys44Tyrfs*5 protein. Reverse transcription-polymerase chain reaction identified two fragments (123 and 119 bp) using RNA isolated from patient blood samples, in consistency with the results of the minigene assay. Collectively, we classified BRCA1:c.132C>T (p.Cys44=) as a pathogenic variant, as evidenced by functional studies, RNA analysis, and the patients’ family histories. By analyzing variants recorded in the BRCA Exchange database, we found synonymous changes at the ends of exons could potentially influence splicing; meanwhile, current in silico tools could not predict splicing changes efficiently if the variants were in the middle of an exon, or in the deep intron region. Future studies should attempt to identify variants that influence gene expression and post-transcription modifications to improve our understanding of BRCA1 and BRCA2, as well as their related cancers.
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Affiliation(s)
- Jun Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Ping Wang
- Department of Pathophysiology, School of Basic Medical Science, Zhengzhou University, Zhengzhou, China
| | - Cuiyun Zhang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Sile Han
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Han Xiao
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiyuan Liu
- Amoy Diagnostics Co., Ltd. (AmoyDx), Xiamen, China
| | - Xiaoyan Wang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Weiling Liu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzou, China
| | - Bing Wei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Hongle Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
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17
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SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction. BIOCHIP JOURNAL 2022; 16:41-48. [PMID: 35096279 PMCID: PMC8790009 DOI: 10.1007/s13206-021-00044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/02/2022]
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18
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Correlation between the number of false positive variants and the quality of results using Ion Torrent PGM™ sequencing to screen BRCA genes. BIOMÉDICA 2021; 41:773-786. [PMID: 34936260 PMCID: PMC8768485 DOI: 10.7705/biomedica.5663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Indexed: 11/21/2022]
Abstract
Introduction: Next Generation Sequencing (NGS) is cost-effective and a faster method to study genes, but its protocol is challenging. Objective: To analyze different adjustments to the protocol for screening the BRCA genes using Ion Torrent PGM sequencing and correlate the results with the number of false positive (FP) variants. Material and methods: We conducted a library preparation process and analyzed the number of FP InDels, the library concentration, the number of cycles in the target amplification step, the purity of the nucleic acid, the input, and the number of samples/Ion 314 chips in association with the results obtained by NGS. Results: We carried out 51 reactions and nine adjustments of protocols and observed eight FP InDels in homopolymer regions. No FP Single-Nucleotide Polymorphism variant was observed; 67.5% of protocol variables were jointly associated with the quality of the results obtained (p<0.05). The number of FP InDels decreased when the quality of results increased. Conclusion: The Ion AmpliSeq BRCA1/BRCA2 Community Panel had a better performance using four samples per Ion-314 chip instead of eight and the optimum number of cycles in the amplification step, even when using high-quality DNA, was 23. We observed better results with the manual equalization process and not using the Ion Library Equalizer kit. These adjustments provided a higher coverage of the variants and fewer artifacts (6.7-fold). Laboratories must perform internal validation because FP InDel variants can vary according to the quality of results while the NGS assay should be validated with Sanger.
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19
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Chandrasekaran D, Sobocan M, Blyuss O, Miller RE, Evans O, Crusz SM, Mills-Baldock T, Sun L, Hammond RFL, Gaba F, Jenkins LA, Ahmed M, Kumar A, Jeyarajah A, Lawrence AC, Brockbank E, Phadnis S, Quigley M, El Khouly F, Wuntakal R, Faruqi A, Trevisan G, Casey L, Burghel GJ, Schlecht H, Bulman M, Smith P, Bowers NL, Legood R, Lockley M, Wallace A, Singh N, Evans DG, Manchanda R. Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study. Cancers (Basel) 2021; 13:cancers13174344. [PMID: 34503154 PMCID: PMC8431198 DOI: 10.3390/cancers13174344] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/09/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline BRCA1/BRCA2/RAD51C/RAD51D/BRIP1 and parallel somatic BRCA1/BRCA2 testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97.7%. Counselling by clinical-nurse-specialist more frequently needed >1 consultation (53.6% (30/56)) compared to a medical (15.0% (21/137)) or surgical oncologist (15.3% (17/110)) (p < 0.001). The median age was 54 (IQR = 51-62) years in germline pathogenic-variant (PV) versus 61 (IQR = 51-71) in BRCA wild-type (p = 0.001). There was no significant difference in distribution of PVs by ethnicity, stage, surgery timing or resection status. A total of 15.5% germline and 7.8% somatic BRCA1/BRCA2 PVs were identified. A total of 2.3% patients had RAD51C/RAD51D/BRIP1 PVs. A total of 11% germline PVs were large-genomic-rearrangements and missed by somatic testing. A total of 20% germline PVs are missed by somatic first BRCA-testing approach and 55.6% germline PVs missed by family history ascertainment. The somatic testing failure rate is higher (23%) for patients undergoing diagnostic biopsies. Our findings favour a prospective parallel somatic and germline panel testing approach as a clinically efficient strategy to maximise variant identification. UK Genomics test-directory criteria should be expanded to include a panel of OC genes.
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Affiliation(s)
- Dhivya Chandrasekaran
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Monika Sobocan
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Divison for Gynaecology and Perinatology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Oleg Blyuss
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield AL10 9AB, UK;
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow 119991, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow 119991, Russia
| | - Rowan E. Miller
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Olivia Evans
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Shanthini M. Crusz
- Department of Medical Oncology, Barts Health NHS Trust, London EC1A 7BE, UK; (R.E.M.); (S.M.C.)
| | - Tina Mills-Baldock
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Li Sun
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Rory F. L. Hammond
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Faiza Gaba
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
| | - Lucy A. Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Munaza Ahmed
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK; (L.A.J.); (M.A.); (A.K.)
| | - Arjun Jeyarajah
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Alexandra C. Lawrence
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Elly Brockbank
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Saurabh Phadnis
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
| | - Mary Quigley
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Fatima El Khouly
- Department of Medical Oncology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK; (T.M.-B.); (M.Q.); (F.E.K.)
| | - Rekha Wuntakal
- Department of Gynaecology, Barking, Havering & Redbridge University Hospitals, Essex RM7 0AG, UK;
| | - Asma Faruqi
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Giorgia Trevisan
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - Laura Casey
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - George J. Burghel
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Philip Smith
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naomi L. Bowers
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Rosa Legood
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
| | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK;
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Naveena Singh
- Department of Pathology, Barts Health NHS Trust, London E1 1FR, UK; (R.F.L.H.); (A.F.); (G.T.); (L.C.); (N.S.)
| | - D. Gareth Evans
- Manchester Centre for Genomic Medicine, Saint Marys Hospital, Manchester M13 9WL, UK; (G.J.B.); (H.S.); (M.B.); (P.S.); (N.L.B.); (A.W.); (D.G.E.)
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Barts CRUK Cancer Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; (D.C.); (M.S.); (O.E.); (L.S.); (F.G.)
- Department of Gynaecological Oncology, Barts Health NHS Trust, London EC1 1BB, UK; (A.J.); (A.C.L.); (E.B.); (S.P.)
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London WC1H 9SH, UK;
- Correspondence:
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20
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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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21
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Vietri MT, D'Elia G, Caliendo G, Casamassimi A, Federico A, Passariello L, Cioffi M, Molinari AM. Prevalence of mutations in BRCA and MMR genes in patients affected with hereditary endometrial cancer. Med Oncol 2021; 38:13. [PMID: 33484353 PMCID: PMC7826304 DOI: 10.1007/s12032-021-01454-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/01/2021] [Indexed: 10/29/2022]
Abstract
Endometrial cancer (EC) is the fifth most common cancer in women from developed countries, accounting for 4.8% of new cases and 2.1% of deaths. The genetic basis for the familial risk of endometrial cancer has not been completely defined. Mostly, hereditary EC is part of two syndromes as Lynch syndrome (LS) and Hereditary Breast and Ovarian Cancer syndrome (HBOC). LS is the prototypical hereditary cancer syndrome in EC and accounts for 2-6% of all endometrial cancers. This disease is caused by autosomal dominant mutations in DNA mismatch repair (MMR) genes. Patients carrying a germline mutation in one of the MMR genes have a cumulative lifetime risk to develop EC of 20-70%. HBOC is an autosomal dominantly inherited disease, which mostly predisposes to breast and ovarian cancers, but it can be also associated with other malignancies. HBOC results from germline mutations in BRCA1/2 genes. The aim of this study was to determine the mutational status of a cohort of 40 EC patients, 19 belonging to families with LS and 21 to HBOC. Mutation analysis of MLH1, MSH2, BRCA1 and BRCA2 genes showed pathogenic variants in 17/40 (42.5%) patients. Out of 19 patients belonging to LS families, 8 (42.1%) showed a pathogenic variant. Out of 21 patients belonging to HBOC families, 9 (42.8%) showed a pathogenic variant. 1/21 (4.8%) patient report 1 variant of unknown significance (UV), c.599 C > T (p.T200I), in BRCA2. Moreover, in 1/21 (4.8%) patient we identified a novel missense variant in BRCA2, c.9541A > T (p.Met3181Leu). Mutational analysis was extended to family members, both healthy and cancer affected, of mutated patients; all the tested relatives affected with cancer displayed the pathogenic variant. Our data suggest that patients with hereditary EC have a high percentage of mutations in the LS and HBOC main susceptibility genes; therefore, the surveillance for EC, already indicated in LS patients, should also be recommended for patients with HBOC.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy. .,U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Giovanna D'Elia
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Gemma Caliendo
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Alessandro Federico
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.,U.O.C. Hepato-Gastroenterology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Luana Passariello
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Michele Cioffi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.,U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Anna Maria Molinari
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.,U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
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22
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Incorvaia L, Fanale D, Bono M, Calò V, Fiorino A, Brando C, Corsini LR, Cutaia S, Cancelliere D, Pivetti A, Filorizzo C, La Mantia M, Barraco N, Cusenza S, Badalamenti G, Russo A, Bazan V. BRCA1/2 pathogenic variants in triple-negative versus luminal-like breast cancers: genotype-phenotype correlation in a cohort of 531 patients. Ther Adv Med Oncol 2020; 12:1758835920975326. [PMID: 33403015 PMCID: PMC7747114 DOI: 10.1177/1758835920975326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/29/2020] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Several available data suggest the association between specific molecular subtypes and BRCA1/2 mutational status. Previous investigations showed the association between BRCA1/2 pathogenic variants (PVs) in specific genomic regions and phenotypic variations of cancer relative risk, while the role of PV type and location in determining the breast cancer (BC) phenotypic features remains still unclear. The aim of this research was to describe the germline BRCA1/2 PVs in triple-negative breast cancer (TNBC) versus luminal-like BC and their potential leverage on BC phenotype. PATIENTS & METHODS We retrospectively collected and analyzed all clinical information of 531 patients with BC genetically tested for germline BRCA1/2 PVs by Next-Generation Sequencing analysis at University Hospital Policlinico "P. Giaccone" of Palermo (Sicily) from January 2016 to February 2020. RESULTS Our results corroborate the evidence that BRCA1-related tumors often have a profile which resembles the TNBC subtype, whereas BRCA2-associated tumors have a profile that resembles luminal-like BC, especially the Luminal B subtype. Interestingly, our findings suggest that the PVs identified in TNBC were not largely overlapping with those in luminal-like tumors. Differences in the frequency of two PVs potentially associated with different molecular tumor subtypes were observed. BRCA1-633delC was detected with relatively higher prevalence in patients with TNBC, whereas BRCA2-1466delT was found mainly in Luminal B tumors, but in no TNBC patient. CONCLUSION Future studies examining the type and location of BRCA1/2 PVs within different molecular subtypes are required to verify our hypothesis and could provide an interesting insight into the complex topic of genotype-phenotype correlations. Additionally, a more in-depth understanding of the potential correlations between BRCA PVs and clinical and phenotypic features of hereditary BC syndrome patients could be the key to develop better strategies of prevention and surveillance in BRCA-positive carriers without disease.
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Affiliation(s)
- Lorena Incorvaia
- Section of Medical Oncology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, Palermo, Italy
| | - Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valentina Calò
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Lidia Rita Corsini
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Sofia Cutaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Clarissa Filorizzo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Maria La Mantia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Stefania Cusenza
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Giuseppe Badalamenti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Via del Vespro 129, Palermo, 90127, Italy
| | - Viviana Bazan
- Section of Medical Oncology, Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), University of Palermo, Palermo, Italy
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23
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Five Italian Families with Two Mutations in BRCA Genes. Genes (Basel) 2020; 11:genes11121451. [PMID: 33287145 PMCID: PMC7761639 DOI: 10.3390/genes11121451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Double heterozygosity (DH) in BRCA1 and BRCA2 genes and double mutation (DM) in BRCA1 or BRCA2 are extremely rare events in the general population, and few cases have been reported worldwide so far. Here, we describe five probands, all women, with breast and/or ovarian cancer and their families. Particularly, we identified two probands with DH in the BRCA1/2 genes with a frequency of 0.3% and three probands with DM in the BRCA2 gene with a frequency of 0.5%. The DH BRCA1 c.547+2T>A (IVS8+2T>A)/BRCA2 c.2830A>T (p.Lys944Ter) and BRCA1 c.3752_3755GTCT (p.Ser1253fs)/BRCA2 c.425+2T>C (IVS4+2T>C) have not been described together so far. The DM in BRCA2, c.631G>A (p.Val211Ile) and c.7008-2A>T (IVS13-2A>T), found in three unrelated probands, was previously reported in further unrelated patients. Due to its peculiarity, it is likely that both pathogenic variants descend from a common ancestor and, therefore, are founder mutations. Interestingly, analyzing the tumor types occurring in DH and DM families, we observed ovarian cancer only in DH families, probably due to the presence in DH patients of BRCA1 pathogenic variants, which predispose one more to ovarian cancer onset. Furthermore, male breast cancer and pancreatic cancer ensued in families with DM but not with DH. These data confirm that BRCA2 pathogenic variants have greater penetrance to develop breast cancer in men and are associated with an increased risk of pancreatic cancer.
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24
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Tumor BRCA Testing in High Grade Serous Carcinoma: Mutation Rates and Optimal Tissue Requirements. Cancers (Basel) 2020; 12:cancers12113468. [PMID: 33233347 PMCID: PMC7700467 DOI: 10.3390/cancers12113468] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Approximately 25% of women diagnosed with tubo-ovarian high-grade serous carcinoma have germline deleterious mutations in BRCA1 or BRCA2, characteristic of hereditary breast and ovarian cancer syndrome, while somatic mutations have been detected in 3–7%. We set out to determine the mutation rates and optimal tissue requirements for tumor BRCA testing in 291 tissue samples. Initial testing was successful in 78% and deemed indeterminate in 13%. Repeat testing was successful in 67% of retested samples, with an overall success rate of 86%. Clinically significant BRCA variants were identified in 17% of patients. Successful sequencing was dependent on sample type, tumor cellularity and size (p ≤ 0.001) but not on neoadjuvant chemotherapy or age of blocks. In summary, our study shows a 17% tumor BRCA mutation rate, with an overall success rate of 86%. Biopsy and cytology samples and post-chemotherapy specimens can be used, and optimal tumors measure ≥5 mm in size with at least 20% cellularity. Abstract Background: Approximately 25% of women diagnosed with tubo-ovarian high-grade serous carcinoma have germline deleterious mutations in BRCA1 or BRCA2, characteristic of hereditary breast and ovarian cancer syndrome, while somatic mutations have been detected in 3–7%. We set out to determine the BRCA mutation rates and optimal tissue requirements for tumor BRCA testing in patients diagnosed with tubo-ovarian high-grade serous carcinoma. Methods: Sequencing was performed using a multiplexed polymerase chain reaction-based approach on 291 tissue samples, with a minimum sequencing depth of 500X and an allele frequency of >5%. Results: There were 253 surgical samples (87%), 35 biopsies (12%) and 3 cytology cell blocks (1%). The initial failure rate was 9% (25/291), including 9 cases (3%) with insufficient tumor, and 16 (6%) with non-amplifiable DNA. Sequencing was successful in 78% (228/291) and deemed indeterminate due to failed exons or variants below the limit of detection in 13% (38/291). Repeat testing was successful in 67% (28/42) of retested samples, with an overall success rate of 86% (251/291). Clinically significant (pathogenic, likely pathogenic) variants were identified in 17% (48/276) of complete and indeterminate cases. Successful sequencing was dependent on sample type, tumor cellularity and size (p ≤ 0.001) but not on neoadjuvant chemotherapy or age of blocks (p > 0.05). Conclusions: Our study shows a 17% tumor BRCA mutation rate, with an overall success rate of 86%. Biopsy and cytology samples and post-chemotherapy specimens can be used for tumor BRCA testing, and optimal tumors measure ≥5 mm in size with at least 20% cellularity.
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25
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Kassem N, Stout LA, Hunter C, Schneider B, Radovich M. Precision Prevention: The Current State and Future of Genomically Guided Cancer Prevention. JCO Precis Oncol 2020; 4:96-108. [PMID: 35050732 DOI: 10.1200/po.19.00278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The identification of cancer-predisposing germline variants has potentially substantial clinical impact for patients and their families. Although management guidelines have been proposed for some genes, guidelines for other genes are lacking. This review focuses on the current surveillance and management guidelines for the most common hereditary cancer syndromes and discusses some of the most pivotal studies supporting the available guidelines. We also highlight the gaps in the identification of germline carriers, the cascade testing of at-risk relatives, and the challenges impeding the proper follow-up and optimal management of pathogenic germline carriers. The anticipated surge in the number of identified germline carriers, deficient management guidelines, poor cascade testing uptake, and long-term follow-up necessitate the development of multidisciplinary clinics as an obligatory step toward the improvement of cancer prevention.
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Affiliation(s)
- Nawal Kassem
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Leigh Anne Stout
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Cynthia Hunter
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Bryan Schneider
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
| | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN.,Indiana University Health Precision Genomics, Indianapolis, IN
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26
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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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Roberts JL, Foulkes AL. GENETIC DUTIES. WILLIAM AND MARY LAW REVIEW 2020; 62:143-211. [PMID: 37654734 PMCID: PMC10471136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Most of our genetic information does not change, yet the results of our genetic tests might. Labs reclassify genetic variants in response to advances in genetic science. As a result, a person who took a test in 2010 could take the same test with the same lab in 2020 and get a different result. However, no legal duty requires labs or physicians to inform patients when a lab reclassifies a variant, even if the reclassification communicates clinically actionable information. This Article considers the need for such duties and their potential challenges. In so doing, it offers much-needed guidance to physicians and labs, who may face liability, and to courts, which will hear these cases.
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Cao Y, Chen H, Huang Y, Hu H. Real-world clinical outcomes of olaparib therapy in Chinese patients with advanced serous ovarian cancer treated in Macau. Cancer Rep (Hoboken) 2020; 2:e1180. [PMID: 32721133 PMCID: PMC7941423 DOI: 10.1002/cnr2.1180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/21/2019] [Accepted: 03/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Olaparib has been approved as an active and maintenance therapy for patients with platinum-sensitive, BRCA-mutated high-grade serous ovarian cancer (SOC). However, the efficacy and safety data is lack among Chinese ovarian cancer patients. AIM This real-world study aimed to evaluate the effectiveness and safety profile of olaparib in patients from mainland China, where olaparib is currently unavailable. METHODS AND RESULTS This single-center, observational study included 65 patients with pathologically confirmed advanced serous ovarian cancer from Kiang Wu Hospital in Macau between December 2015 and September 2017. Progression-free survival (PFS) and other endpoints (treatment response, disease progression, and adverse events) were evaluated. PFS was estimated using the Kaplan-Meier method. The median treatment duration was 4 months (range, 1-15). The median PFS for the overall population was 4.2 months (95% CI 2.7-5.2), while those for patients with wild-type BRCA1/2 and BRCA1/2 mutations were 3.1 months (95% CI 1.3-4.6) and 5.3 months (95% CI 2.8-7.1), respectively. The median PFS tended to be longer for patients on maintenance therapy (between 9.0 months [95% CI 1.4-17.5] and 10.0 months [95% CI 2.5-18.1]) than for those on active therapy (between 3.1 months [95% CI 2.1-3.8] and 3.0 months [95% CI 1.4-4.5]). Most patients (87.0%) experienced low-grade adverse events; the most common of which were fatigue (49.0%) and nausea (35.0%). CONCLUSION Our findings demonstrate clinical benefit of olaparib to mainland Chinese patients with high-grade SOC, particularly for patients with BRCA mutations and who require maintenance therapy.
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Affiliation(s)
- Yabing Cao
- Department of Oncology, Kiang Wu Hospital, Macau SAR, China
| | - Hongtao Chen
- Department of Laboratory, the Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Yaobin Huang
- Department of Oncology, Kiang Wu Hospital, Macau SAR, China
| | - Hao Hu
- Department of Oncology, Kiang Wu Hospital, Macau SAR, China
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Malhotra H, Kowtal P, Mehra N, Pramank R, Sarin R, Rajkumar T, Gupta S, Bapna A, Bhattacharyya GS, Gupta S, Maheshwari A, Mannan AU, Reddy Kundur R, Sekhon R, Singhal M, Smruti B, SP S, Suryavanshi M, Verma A. Genetic Counseling, Testing, and Management of HBOC in India: An Expert Consensus Document from Indian Society of Medical and Pediatric Oncology. JCO Glob Oncol 2020; 6:991-1008. [PMID: 32628584 PMCID: PMC7392772 DOI: 10.1200/jgo.19.00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Hereditary breast and ovarian cancer (HBOC) syndrome is primarily characterized by mutations in the BRCA1/2 genes. There are several barriers to the implementation of genetic testing and counseling in India that may affect clinical decisions. These consensus recommendations were therefore convened as a collaborative effort to improve testing and management of HBOC in India. DESIGN Recommendations were developed by a multidisciplinary group of experts from the Indian Society of Medical and Pediatric Oncology and some invited experts on the basis of graded evidence from the literature and using a formal Delphi process to help reach consensus. PubMed and Google Scholar databases were searched to source relevant articles. RESULTS This consensus statement provides practical insight into identifying patients who should undergo genetic counseling and testing on the basis of assessments of family and ancestry and personal history of HBOC. It discusses the need and significance of genetic counselors and medical professionals who have the necessary expertise in genetic counseling and testing. Recommendations elucidate requirements of pretest counseling, including discussions on genetic variants of uncertain significance and risk reduction options. The group of experts recommended single-site mutation testing in families with a known mutation and next-generation sequencing coupled with multiplex ligation probe amplification for the detection of large genomic rearrangements for unknown mutations. Recommendations for surgical and lifestyle-related risk reduction approaches and management using poly (ADP-ribose) polymerase inhibitors are also detailed. CONCLUSION With rapid strides being made in the field of genetic testing/counseling in India, more oncologists are expected to include genetic testing/counseling as part of their clinical practice. These consensus recommendations are anticipated to help homogenize genetic testing and management of HBOC in India for improved patient care.
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Affiliation(s)
- Hemant Malhotra
- Department of Medical Oncology, Sri Ram Cancer Center, Mahatma Gandhi Medical College Hospital, Jaipur, India
| | - Pradnya Kowtal
- Sarin Laboratory and OIC Sanger Sequencing Facility, Advanced Centre for Treatment Research, and Education in Cancer, Navi Mumbai, India
| | - Nikita Mehra
- Department of Medical Oncology, Cancer Institute (WIA), Chennai, India
| | - Raja Pramank
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajiv Sarin
- Radiation Oncology, Cancer Genetics Unit, Tata Memorial Centre and PI Sarin Laboratory, Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | | | - Sudeep Gupta
- Tata Memorial Centre Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ajay Bapna
- Department of Medical Oncology, Bhagwan Mahavir Cancer Hospital Research Center, Jaipur, India
| | | | - Sabhyata Gupta
- Department of Gynae Oncology, Medanta-The Medicity, Gurgaon, India
| | - Amita Maheshwari
- Department of Gynecologic Oncology, Tata Memorial Centre, Mumbai, India
| | - Ashraf U. Mannan
- Clinical Diagnostics, Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India
| | | | - Rupinder Sekhon
- Gynae Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | | | - B.K. Smruti
- Bombay Hospital and Medical Research Centre, Mumbai, India
| | - Somashekhar SP
- Manipal Comprehensive Cancer Center, Manipal Hospital, Bengaluru, India
| | - Moushumi Suryavanshi
- Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
| | - Amit Verma
- Molecular Oncology and Cancer Genetics, Max Hospital, New Delhi, India
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Minucci A, Mazzuccato G, Marchetti C, Pietragalla A, Scambia G, Fagotti A, Urbani A. Detecting Large Germline Rearrangements of BRCA1 by Next Generation Tumor Sequencing. Mol Biol 2020. [DOI: 10.1134/s0026893320030127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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BRCA testing in a genomic diagnostics referral center during the COVID-19 pandemic. Mol Biol Rep 2020; 47:4857-4860. [PMID: 32388698 PMCID: PMC7210797 DOI: 10.1007/s11033-020-05479-3] [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: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/22/2022]
Abstract
The first person-to-person transmission of the 2019-novel coronavirus in Italy on 21 February 2020 led to an infection chain that represents one of the largest known COVID-19 outbreaks outside Asia. Hospitals have been forced to reorganized their units in response to prepare for an unforeseen healthcare emergency. In this context, our laboratory (Molecular and Genomic Diagnostics Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS) re-modulated its priorities by temporarily interrupting most of the molecular tests guaranteeing only those considered “urgent” and not postponable. In particular, this paper details changes regarding the execution of germline BRCA (gBRCA) testing in our laboratory. A substantial reduction in gBRCA testing (about 60%) compared to the first 2 months of the current year was registered, but the requests have not been reset. The requesting physicians were mainly gynaecologists and oncologists. These evidences further emphasize the new era of gBRCA testing in the management of cancer patients and confirms definitively the integration of gBRCA testing/Next Generation Sequencing (NGS) into clinical oncology. Finally, a re-organization of gBRCA testing in our Unit, mainly related to delayed and reduced arrival of tests was necessary, ensuring, however, a high-quality standard and reliability, mandatory for gBRCA testing in a clinical setting.
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Vietri MT, D'Elia G, Caliendo G, Casamassimi A, Resse M, Passariello L, Cioffi M, Molinari AM. Double mutation of APC and BRCA1 in an Italian family. Cancer Genet 2020; 244:32-35. [PMID: 32388397 DOI: 10.1016/j.cancergen.2020.04.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/11/2020] [Accepted: 04/12/2020] [Indexed: 12/30/2022]
Abstract
Familial adenomatous polyposis (FAP) is a rare genetic disorder caused mainly by monoallelic mutations of APC gene. The hereditary breast and ovarian cancer (HBOC) syndrome is an autosomal dominantly inherited disease, which mostly predisposes to breast and ovarian cancers as a result of germline mutations in BRCA1 or BRCA2 genes. In a family, mutations in two cancer susceptibility genes are extremely rare. We studied a family with a case of a 46 years-old woman affected with FAP and ovarian cancer. The patient was affected with profuse FAP since the age of 18 years and a serous ovarian cancer was diagnosed at the age of 45 years. She reported other FAP cases and one case of breast cancer in maternal family. Initially, she was tested for FAP predisposition with mutational analysis of APC gene that revealed the presence of a frameshift mutation, c.3927_3931delAAAGA (p.Glu1309AspfsX4). The presence of ovarian cancer in the patient and of a breast cancer case in the maternal family, suggested an extended analysis to HBOC susceptibility genes that led to the detection of a frameshift mutation, c.3756_3759delGTCT (p.Ser1253Argfs), in BRCA1 gene. The genetic analysis was extended also to family members. The occurrence of the double mutation in APC and BRCA1 genes in the patient was responsible for the onset of FAP and ovarian cancer respectively. The genetic counselling in hereditary cancer with a careful analysis of the pedigree allows identifying the gene to be analyzed. The development of multi-gene panels testing for cancer predisposition, with next generation sequencing (NGS), may reveal mutations in genes of high and moderate penetrance for cancer, although at a low frequency and allows diagnosing a possible double heterozygosity. This enables an adjusted treatment for the affected patient and is critical as it allows initiation of early risk-reducing measures for identified mutation carriers among family members.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy.
| | - Giovanna D'Elia
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Gemma Caliendo
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy
| | - Marianna Resse
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy
| | - Luana Passariello
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Michele Cioffi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Anna Maria Molinari
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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Han E, Yoo J, Chae H, Lee S, Kim DH, Kim KJ, Kim Y, Kim M. Detection of BRCA1/2 large genomic rearrangement including BRCA1 promoter-region deletions using next-generation sequencing. Clin Chim Acta 2020; 505:49-54. [PMID: 32092317 DOI: 10.1016/j.cca.2020.02.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Germline mutations in BRCA1 and BRCA2 (BRCA1/2) have been conventionally analyzed by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). Nowadays, next-generation sequencing (NGS) is increasingly being used in clinical genetics. The aim of this study was to evaluate the performance of NGS BRCA1/2 assays by comparing them with the conventional method. MATERIALS AND METHODS We did BRCA1/2 NGS assays of 108 breast and/or ovarian cancer patients whose BRCA1/2 mutation had been previously analyzed by Sanger sequencing and MLPA using TruSeq Custom Amplicon Design AFP2. Single-nucleotide variations (SNVs) and small insertions or deletions (InDels) were evaluated. In addition, we analyzed large genomic rearrangements (LGRs) using a coverage-based algorithm as well as a revised BRCA1/2 NGS assay (BRCAaccuTest PLUS), which additionally covered a BRCA1 promoter region. RESULTS The NGS BRCA1/2 assay detected all 20 SNVs and 21 small InDels in 56 patients. Among seven LGRs detected by MLPA, six exonic LGRs were well identified by both NGS BRCA1/2 assays. One pathogenic LGR, located on a BRCA1 promoter region, was successfully identified using revised BRCAaccuTestPLUS. CONCLUSIONS These results indicated that an NGS BRCA1/2 assay could detect most LGRs including BRCA1 promoter-region deletion as well as SNVs and small InDels. Therefore, it was applicable to clinical BRCA1/2 mutation tests.
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Affiliation(s)
- Eunhee Han
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Jaeeun Yoo
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Hyojin Chae
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Seungok Lee
- Department of Laboratory Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Do-Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | | | - Yonggoo Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea
| | - Myungshin Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea; Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Republic of Korea.
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Vietri MT, Caliendo G, D'Elia G, Resse M, Casamassimi A, Minucci PB, Cioffi M, Molinari AM. BRCA and PALB2 mutations in a cohort of male breast cancer with one bilateral case. Eur J Med Genet 2020; 63:103883. [PMID: 32058061 DOI: 10.1016/j.ejmg.2020.103883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Male Breast Cancer (MBC) is a rare disease, about 1% of all breast cancers worldwide and less than 1% of cancers occurring in men. The bilateral male breast cancer (bMBC) is extremely rare. Germline mutations of BRCA1/BRCA2 genes are associated with a significantly increased risk of cancer in MBC; the role of PALB2 remains to be clarified. Our main goal was to provide contribution on characterization of BRCA1/BRCA2 and PALB2 mutations in MBC patients. METHODS We observed 28 MBC cases; one of them was a bMBC. Screening for BRCA1, BRCA2 and PALB2 genes was performed on all 28 MBC patients. Mutational analysis was extended to family members of mutated patients. RESULTS In our study, the MBC incidence was 5.2% and for bMBC was 3.6%. Mutation analysis showed pathogenic mutations in 11/28 (39.3%) patients; 2/28 (7.1%) displayed a mutation in BRCA1, 8/28 (28.6%) in BRCA2 and 1/28 (3.6%) in PALB2. Out of 11 mutated patients, one (9.1%) reported a double mutation in BRCA2. Personal history of other cancers was reported in 2/28 (7.1%) patients affected by bladder cancer. A first/second degree family history of breast/ovarian and other cancers occurred in 23/28 (82.1%) patients. CONCLUSION Our findings indicate BRCA2 as the main MBC susceptibility gene and describe an increased risk of bMBC and bladder cancer in mutated patients. The identification of mutations in MBC susceptibility genes supports the usage of oncology prevention programs in affected patients and their relatives carrying the mutation.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy.
| | - Gemma Caliendo
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Giovanna D'Elia
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Marianna Resse
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | | | - Michele Cioffi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
| | - Anna Maria Molinari
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138, Naples, Italy; U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania "Luigi Vanvitelli", 80138, Naples, Italy
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Germline mutations of multiple breast cancer-related genes are differentially associated with triple-negative breast cancers and prognostic factors. J Hum Genet 2020; 65:577-587. [PMID: 32029870 DOI: 10.1038/s10038-020-0729-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/30/2022]
Abstract
Genetic testing for BRCA1/2 mutations has become the standard clinical practice. Recent findings suggest the clinical significance of multigene panel testing of BRCA1/2 and other cancer-related genes. However, the clinical features of patients with breast cancer with germline mutations identified using multigene panels remain unclear. In this study, DNA samples from 583 Chinese women with breast cancer were subjected to target sequencing for 54 cancer-related genes using a pre-capture pooling method followed by next-generation sequencing. We identified 79 pathogenic germline mutations in 21 cancer-related genes. Forty-five patients (7.7%) harbored BRCA1/2 mutations, and 38 patients (6.5%) carried pathogenic mutations in the remaining 19 genes. PALB2 was the most commonly (1.2%) mutated gene other than BRCA1/2. Most of the identified pathogenic mutations were novel, suggesting mutation screening by using multigene panel testing is important particularly for non-European populations. Mutations in BRCA1/2 and the other cancer-related genes were differentially associated with clinical features. BRCA1 mutation carriers were strongly associated with triple-negative breast cancer (TNBC), whereas BRCA2 mutation carriers were not. Tumors in BRCA1-mutation carriers had a high histological grade. Patients with BRCA2-mutated breast cancers were likely to develop E-cadherin-negative tumors with bone metastases. Furthermore, mutations in PALB2 were strongly associated with TNBC. We demonstrated the usefulness of multigene panel testing and observed that a substantial proportion of patients with breast cancer had hereditary risk factors. Identifying differential associations between mutation status and clinical features will advance our understanding regarding the pathologies of this heterogeneous disease.
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Tendl KA, Bago-Horvath Z. Molecular profiling in breast cancer—ready for clinical routine? MEMO - MAGAZINE OF EUROPEAN MEDICAL ONCOLOGY 2020. [DOI: 10.1007/s12254-020-00578-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SummaryThe herald of genomic testing opened novel diagnostic and therapeutic possibilities for many tumor entities. For breast cancer, molecular profiling has become an integral part of disease management on multiple levels. Genetic testing allows for the identification of hereditary cancer syndromes in patients with a family history of malignancies and contributes to the successful prevention of breast cancer. In early breast cancer, several prospective randomized trials demonstrated the prognostic significance of commercially available mRNA-based gene expression analyses, which now have become part of standard of care in the adjuvant setting. In advanced breast cancer, testing for targetable mutations ensures personalized cancer treatment. Poly-ADP-ribose polymerase (PARP) inhibitors provide the first targeted alternative for patients with BRCA 1/2-associated breast cancer. In advanced breast cancer of luminal type, the detection of Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) mutations provides a novel treatment option with alpelisib, a PIK3CA inhibitor. Further targetable mutations include NTRK3 in rare cases of secretory breast carcinoma and human epidermal growth factor receptor 2 (HER2). Recent data support the importance of the analysis of circulating tumor cells and cell-free DNA. These “liquid biopsies” open novel possibilities of molecular profiling. However, clinical benefit of such analyses remains to be confirmed.
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Zelli V, Compagnoni C, Cannita K, Capelli R, Capalbo C, Di Vito Nolfi M, Alesse E, Zazzeroni F, Tessitore A. Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. High Throughput 2020; 9:ht9010001. [PMID: 31936873 PMCID: PMC7151204 DOI: 10.3390/ht9010001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 12/24/2022] Open
Abstract
Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Katia Cannita
- Medical Oncology Unit, St Salvatore Hospital, Via L. Natali 1, 67100 L’Aquila, Italy;
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Rome “La Sapienza”, Viale Regina Elena 324, 00161 Rome, Italy;
| | - Mauro Di Vito Nolfi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito 2, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (M.D.V.N.); (E.A.); (F.Z.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence:
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38
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Gallardo-Rincón D, Álvarez-Gómez RM, Montes-Servín E, Toledo-Leyva A, Montes-Servín E, Michel-Tello D, Alamilla-García G, Bahena-González A, Hernández-Nava E, Fragoso-Ontiveros V, Espinosa-Romero R, Cetina-Pérez L. Clinical Evaluation of BRCA1/2 Mutation in Mexican Ovarian Cancer Patients. Transl Oncol 2019; 13:212-220. [PMID: 31869745 PMCID: PMC6931216 DOI: 10.1016/j.tranon.2019.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 11/30/2022] Open
Abstract
Ovarian cancer (OC) is an important cause of gynecologic cancer-related deaths. In Mexico, around 4700 new cases of OC are diagnosed per year and it represents the second cause of gynecological cancer mortality with more than 2700 deaths. Germline mutations in BRCA1/2 genes are present in 13–18% of OC cases. Few studies have evaluated the presence of mutations in BRCA genes in a population of OC Mexican patients and their relationship with clinical response and survival rates. A total of 179 OC patients were studied by molecular testing for BRCA1/2 through next-generation sequencing and multiplex ligation-dependent probe amplification. Recurrence-free survival (RFS) was estimated by the Kaplan–Meier method. BRCA mutation was detected in 33% of patients. A percentage of 66.1% were BRCA1 mutated and 33.9% were BRCA2 mutated. BRCA1 mutation carriers had a worst RFS compared with BRCA2 mutation carriers (37.6 [29–46.2] vs 72.7 [38.4–107.2]; P = 0.030). The most common mutation for BRCA1 was ex9-12del (28.2%) (Mexican founder mutation). The Mexican founder mutation had a better RFS than other BRCA1 mutations (86.1 [37.2–135.1] vs 34.5 [20.7–48.2]; P = 0.033). The presence of BRCA2 mutations in the ovarian cancer cluster region (OCCR) had a significantly better RFS than mutations in breast cancer cluster regions (BCCR) and not-related risk region (NRR) (NR vs 72.8 [39–106.6] vs 25.8 [8.3–43.2]; P = 0.013). These results demonstrate that the prevalence of BRCA1/2 positive patients in OC Mexican patients are the highest reported. Patients with mutations in BRCA2 have a better prognosis than those mutated in BRCA1. The Mexican founder mutation has an important role in clinical outcomes. These results highlight the importance to test all the HGSP (high-grade serous papillary) OC patients with or without cancer family history (CFH) in Mexican population.
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Affiliation(s)
- Dolores Gallardo-Rincón
- Ovarian Cancer Program, Instituto Nacional de Cancerología, Mexico City, Mexico; Department of Medical Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico.
| | | | - Edgar Montes-Servín
- Ovarian Cancer Program, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | | | - David Michel-Tello
- Ovarian Cancer Program, Instituto Nacional de Cancerología, Mexico City, Mexico
| | | | | | | | | | | | - Lucely Cetina-Pérez
- Department of Medical Oncology, Instituto Nacional de Cancerología, Mexico City, Mexico
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39
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Kim Y, Cho CH, Ha JS, Kim DH, Kwon SY, Oh SC, Lee KA. An optimized BRCA1/2 next-generation sequencing for different clinical sample types. J Gynecol Oncol 2019; 31:e9. [PMID: 31788999 PMCID: PMC6918881 DOI: 10.3802/jgo.2020.31.e9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 02/04/2023] Open
Abstract
Objective A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. Methods We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. Results The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. Conclusions On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation.
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Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Do Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Seoung Chul Oh
- Department of Laboratory Medicine, Gangnam Severance Hospital, Seoul, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
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40
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Akras Z, Bungo B, Leach BH, Marquard J, Ahluwalia M, Carraway H, Grivas P, Sohal DP, Funchain P. Primer on Hereditary Cancer Predisposition Genes Included Within Somatic Next-Generation Sequencing Panels. JCO Precis Oncol 2019; 3:1-11. [DOI: 10.1200/po.18.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
PURPOSE It has been estimated that 5% to 10% of cancers are due to hereditary causes. Recent data sets indicate that the incidence of hereditary cancer may be as high as 17.5% in patients with cancer, and a notable subset is missed if screening is solely by family history and current syndrome-based testing guidelines. Identification of germline variants has implications for both patients and their families. There is currently no comprehensive overview of cancer susceptibility genes or inclusion of these genes in commercially available somatic testing. We aimed to summarize genes linked to hereditary cancer and the somatic and germline panels that include such genes. METHODS Germline predisposition genes were chosen if commercially available for testing. Penetrance was defined as low, moderate, or high according to whether the gene conferred a 0% to 20%, 20% to 50%, or 50% to 100% lifetime risk of developing the cancer or, when percentages were not available, was estimated on the basis of existing literature descriptions. RESULTS We identified a total of 89 genes linked to hereditary cancer predisposition, and we summarized these genes alphabetically and by organ system. We considered four germline and six somatic commercially available panel tests and quantified the coverage of germline genes across them. Comparison between the number of genes that had germline importance and the number of genes included in somatic testing showed that many but not all germline genes are tested by frequently used somatic panels. CONCLUSION The inclusion of cancer-predisposing genes in somatic variant testing panels makes incidental germline findings likely. Although somatic testing can be used to screen for germline variants, this strategy is inadequate for comprehensive screening. Access to genetic counseling is essential for interpretation of germline implications of somatic testing and implementation of appropriate screening and follow-up.
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41
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Nicolussi A, Belardinilli F, Silvestri V, Mahdavian Y, Valentini V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Di Giulio S, Fabretti F, Fratini B, Gradilone A, Ottini L, Giannini G, Coppa A, Capalbo C. Identification of novel BRCA1 large genomic rearrangements by a computational algorithm of amplicon-based Next-Generation Sequencing data. PeerJ 2019; 7:e7972. [PMID: 31741787 PMCID: PMC6859874 DOI: 10.7717/peerj.7972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/30/2022] Open
Abstract
Background Genetic testing for BRCA1/2 germline mutations in hereditary breast/ovarian cancer patients requires screening for single nucleotide variants, small insertions/deletions and large genomic rearrangements (LGRs). These studies have long been run by Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). The recent introduction of next-generation sequencing (NGS) platforms dramatically improved the speed and the efficiency of DNA testing for nucleotide variants, while the possibility to correctly detect LGRs by this mean is still debated. The purpose of this study was to establish whether and to which extent the development of an analytical algorithm could help us translating NGS sequencing via an Ion Torrent PGM platform into a tool suitable to identify LGRs in hereditary breast-ovarian cancer patients. Methods We first used NGS data of a group of three patients (training set), previously screened in our laboratory by conventional methods, to develop an algorithm for the calculation of the dosage quotient (DQ) to be compared with the Ion Reporter (IR) analysis. Then, we tested the optimized pipeline with a consecutive cohort of 85 uncharacterized probands (validation set) also subjected to MLPA analysis. Characterization of the breakpoints of three novel BRCA1 LGRs was obtained via long-range PCR and direct sequencing of the DNA products. Results In our cohort, the newly defined DQ-based algorithm detected 3/3 BRCA1 LGRs, demonstrating 100% sensitivity and 100% negative predictive value (NPV) (95% CI [87.6–99.9]) compared to 2/3 cases detected by IR (66.7% sensitivity and 98.2% NPV (95% CI [85.6–99.9])). Interestingly, DQ and IR shared 12 positive results, but exons deletion calls matched only in five cases, two of which confirmed by MLPA. The breakpoints of the 3 novel BRCA1 deletions, involving exons 16–17, 21–22 and 20, have been characterized. Conclusions Our study defined a DQ-based algorithm to identify BRCA1 LGRs using NGS data. Whether confirmed on larger data sets, this tool could guide the selection of samples to be subjected to MLPA analysis, leading to significant savings in time and money.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Valentina Silvestri
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science @ Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Francesca Fabretti
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Beatrice Fratini
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
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42
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Cao CX, Sharib JM, Blanco AM, Goldberg D, Bracci P, Mukhtar RA, Esserman LJ, Kirkwood KS. Abdominal Imaging of Pancreatic Cysts and Cyst-Associated Pancreatic Cancer in BRCA1/2 Mutation Carriers: A Retrospective Cross-Sectional Study. J Am Coll Surg 2019; 230:53-63.e1. [PMID: 31672679 DOI: 10.1016/j.jamcollsurg.2019.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/30/2019] [Accepted: 09/16/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Direct-to-consumer BRCA testing will increase BRCA diagnoses and subsequent abdominal imaging. It is unclear whether BRCA carriers are at higher risk of developing pancreatic cysts (PCs) or cyst-associated pancreatic ductal adenocarcinoma (PDAC). We investigated the prevalence of PCs in BRCA-tested patients, and whether BRCA-carriers have higher rates of PDAC when PCs are found. STUDY DESIGN This is a retrospective cross-sectional study of patients with BRCA testing and abdominal imaging between 1996 and 2018. Pancreatic cysts were identified on original imaging reports. Prevalence and risk characteristics of PCs, as well as incidence of PDAC, were compared between BRCA+, BRCA-, and BRCA-untested patients. RESULTS Pancreatic cysts were identified in 4,045 patients among 128,164 unique patients with abdominal imaging, including 33 patients with PCs in 1,113 BRCA-tested patients. There was no difference in PC prevalence between BRCA+, BRCA-, and untested patients (3.6%, 2.6%, 3.2%, respectively; p = 0.64). Pancreatic cysts were diagnosed in BRCA+ patients at a younger age (57.1 vs 65.3 years, p < 0.001); however, there was no difference in risk stratification compared with BRCA- or untested patients by consensus criteria. Across the population of imaged patients, patients with PCs had significantly higher rates of PDAC compared with those without PCs (18.2% vs 2.4%, p < 0.001). Incidence of cyst-associated PDAC was similar in BRCA+ and BRCA- patients (13.3% vs 22.2%, p = 0.84). CONCLUSIONS BRCA+ patients have similar rates of PCs, high-risk features in their cysts, and PDAC as BRCA- and untested patients. BRCA+ patients likely do not require dedicated abdominal imaging to evaluate for PCs and should follow management guidelines similar to those as the untested general population if an incidental PC is identified.
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Affiliation(s)
- Carrie X Cao
- Department of Surgery, University of California San Francisco, San Francisco, CA
| | - Jeremy M Sharib
- Department of Surgery, University of California San Francisco, San Francisco, CA.
| | - Amie M Blanco
- University of California San Francisco Cancer Genetics and Prevention Program, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Dena Goldberg
- University of California San Francisco Cancer Genetics and Prevention Program, San Francisco, CA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA
| | - Rita A Mukhtar
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Laura J Esserman
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Kimberly S Kirkwood
- Department of Surgery, University of California San Francisco, San Francisco, CA; University of California San Francisco Heller Diller Family Comprehensive Cancer Center, San Francisco, CA
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43
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Tumor BRCA Test for Patients with Epithelial Ovarian Cancer: The Role of Molecular Pathology in the Era of PARP Inhibitor Therapy. Cancers (Basel) 2019; 11:cancers11111641. [PMID: 31653094 PMCID: PMC6896171 DOI: 10.3390/cancers11111641] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/01/2019] [Accepted: 10/21/2019] [Indexed: 01/05/2023] Open
Abstract
The PARP inhibitor olaparib has been approved in the maintenance setting of platinum-sensitive epithelial ovarian cancer patients with germline or somatic BRCA1/2 mutation. Therefore, the availability of a tumor BRCA test has become a clinical need. We report the results of the clinical implementation of a tumor BRCA test within the frame of an institutional workflow for the management of patients with nonmucinous and nonborderline epithelial ovarian cancer. In total, 223 patients with epithelial ovarian cancer were prospectively analyzed. BRCA1/2 status was evaluated on formalin-fixed, paraffin-embedded tumor specimens using next-generation sequencing technology. The tumor BRCA test had a success rate of 99.1% (221 of 223 successfully analyzed cases) and a median turnaround time of 17 calendar days. Among the 221 cases, BRCA1 or BRCA2 pathogenic/likely pathogenic mutations were found in 62 (28.1%) cases and variants of uncertain significance in 25 (11.3%) cases. The concordance rate between tumor BRCA test results and germline BRCA1/2 status was 87%, with five cases harboring pathogenic/likely pathogenic somatic-only mutations. The next-generation, sequencing-based tumor BRCA test showed a high success rate and a turnaround time compatible with clinical purposes. The tumor BRCA test could be implemented in a molecular diagnostic setting and it may guide the clinical management of patients with epithelial ovarian cancer.
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44
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Montalban G, Bonache S, Moles-Fernández A, Gadea N, Tenés A, Torres-Esquius S, Carrasco E, Balmaña J, Diez O, Gutiérrez-Enríquez S. Incorporation of semi-quantitative analysis of splicing alterations for the clinical interpretation of variants in BRCA1 and BRCA2 genes. Hum Mutat 2019; 40:2296-2317. [PMID: 31343793 DOI: 10.1002/humu.23882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
BRCA1 and BRCA2 (BRCA1/2) genetic variants that disrupt messenger RNA splicing are commonly associated with increased risks of developing breast/ovarian cancer. The majority of splicing studies published to date rely on qualitative methodologies (i.e., Sanger sequencing), but it is necessary to incorporate semi-quantitative or quantitative approaches to accurately interpret the clinical significance of spliceogenic variants. Here, we characterize the splicing impact of 31 BRCA1/2 variants using semi-quantitative capillary electrophoresis of fluorescent amplicons (CE), Sanger sequencing and allele-specific assays. A total of 14 variants were found to disrupt splicing. Allelic-specific assays could be performed for BRCA1 c.302-1G>A and BRCA2 c.516+2T>A, c.1909+1G>A, c.8332-13T>G, c.8332-2A>G, c.8954-2A>T variants, showing a monoallelic contribution to full-length transcript expression that was concordant with semi-quantitative data. The splicing fraction of alternative and aberrant transcripts was also measured by CE, facilitating variant interpretation. Following Evidence-based Network for the Interpretation of Germline Mutant Alleles criteria, we successfully classified eight variants as pathogenic (Class 5), five variants as likely pathogenic (Class 4), and 14 variants as benign (Class 1). We also provide splicing data for four variants classified as uncertain (Class 3), which produced a "leaky" splicing effect or introduced a missense change in the protein sequence, that will require further assessment to determine their clinical significance.
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Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Neus Gadea
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Sara Torres-Esquius
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
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45
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Qu S, Chen Q, Yi Y, Shao K, Zhang W, Wang Y, Bai J, Li X, Liu Z, Wang X, Jing R, Guan Y, Yi X, Yan M, Cao B, Chen F, Zhu S, Yang X, Wu Y, Huang J. A Reference System for BRCA Mutation Detection Based on Next-Generation Sequencing in the Chinese Population. J Mol Diagn 2019; 21:677-686. [DOI: 10.1016/j.jmoldx.2019.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/17/2019] [Accepted: 03/13/2019] [Indexed: 12/12/2022] Open
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46
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Nicolussi A, Belardinilli F, Mahdavian Y, Colicchia V, D'Inzeo S, Petroni M, Zani M, Ferraro S, Valentini V, Ottini L, Giannini G, Capalbo C, Coppa A. Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer. PeerJ 2019; 7:e6661. [PMID: 31065452 PMCID: PMC6482939 DOI: 10.7717/peerj.6661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Background Conventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment. Methods We first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set). Results By minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis. Discussion Our experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches.
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Affiliation(s)
- Arianna Nicolussi
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
| | | | - Yasaman Mahdavian
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Valeria Colicchia
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sonia D'Inzeo
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy.,U.O.C. Microbiology and Virology Laboratory, A.O. San Camillo Forlanini, Roma, Italy
| | - Marialaura Petroni
- Istituto Italiano di Tecnologia, Center for Life Nano Science@Sapienza, Roma, Italy
| | - Massimo Zani
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Sergio Ferraro
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Virginia Valentini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Laura Ottini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy.,Istituto Pasteur-Fondazione Cenci Bolognetti, Roma, Italy
| | - Carlo Capalbo
- Department of Molecular Medicine, University of Roma "La Sapienza", Roma, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University of Roma "La Sapienza", Roma, Italy
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47
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O'Brien O, Wright MC, O'Brien C, Geoghegan O, Leonard N, Nicholson S, Cuffe S, Fabre A, Jochum W, Joerger M, Gray SG, Finn SP. Cost-Efficient and Easy to Perform PCR-Based Assay to Identify Met Exon 14 Skipping in Formalin-Fixed Paraffin-Embedded (FFPE) Non-Small Cell Lung Cancer (NSCLC) Samples. Diagnostics (Basel) 2019; 9:diagnostics9010013. [PMID: 30669306 PMCID: PMC6468531 DOI: 10.3390/diagnostics9010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 01/03/2023] Open
Abstract
MET is a receptor tyrosine kinase (RTK) that plays important roles in carcinogenesis. Despite being frequently overexpressed in cancer, clinical responses to targeting this receptor have been limited. Recently novel splicing mutations involving the loss of exon 14 (called METex14 skipping) have emerged as potential biomarkers to predict for responsiveness to targeted therapies with Met inhibitors in non-small cell lung cancer (NSCLC). Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. In this report, we examine three different methodologies to detect METex14 and assess their potential utility for use as a diagnostic assay for both the identification of METex14 and intra-tumoural distribution in NSCLC.
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Affiliation(s)
- Odharnaith O'Brien
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Mark C Wright
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Cathal O'Brien
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Orla Geoghegan
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
| | - Niamh Leonard
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Sinéad Cuffe
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- HOPE Directorate, St. James's Hospital, D08 RT2X Dublin, Ireland.
| | - Aurelie Fabre
- Department of Pathology, St. Vincent's University Hospital, University College Dublin School of Medicine, D04 T6F4 Dublin, Ireland.
| | - Wolfram Jochum
- Department of Pathology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Markus Joerger
- Department of Medical Oncology & Hematology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, D08 NF82 Dublin, Ireland.
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D08 X4RX Dublin, Ireland.
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48
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Rutgers E, Balmana J, Beishon M, Benn K, Evans DG, Mansel R, Pharoah P, Perry Skinner V, Stoppa-Lyonnet D, Travado L, Wyld L. European Breast Cancer Council manifesto 2018: Genetic risk prediction testing in breast cancer. Eur J Cancer 2019; 106:45-53. [PMID: 30471647 DOI: 10.1016/j.ejca.2018.09.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 12/17/2022]
Abstract
European Breast Cancer Council manifesto and supporting article on genetic risk prediction testing in breast cancer, presented at the 11th European Breast Cancer Conference in Barcelona, Spain.
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Affiliation(s)
- Emiel Rutgers
- Department of Surgery, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith Balmana
- Medical Oncology Department, University Hospital Vall D'Hebron, Barcelona, Spain
| | | | - Karen Benn
- Europa Donna - The European Breast Cancer Coalition, Milan, Italy
| | - D Gareth Evans
- Department of Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, St Mary's Hospital, Manchester, United Kingdom
| | - Robert Mansel
- School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Paul Pharoah
- Department of Oncology, Cambridge, United Kingdom; Department of Public Health and Primary Care, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Victoria Perry Skinner
- Department of Surgery, Netherlands Cancer Institute/Antoni van Leeuwenhoek, Amsterdam, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France; University Paris Descartes, Paris, France
| | - Luzia Travado
- Psycho-Oncology, Champalimaud Clinical Center, Lisbon, Portugal
| | - Lynda Wyld
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom; Doncaster and Bassetlaw Teaching Hospitals NHS Foundation Trust, Doncaster, United Kingdom
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49
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Carvalho JP, Baracat EC, Carvalho FM. Ovarian Cancer Previvors: How to manage these patients? Clinics (Sao Paulo) 2019; 74:e1343. [PMID: 31340254 PMCID: PMC6636587 DOI: 10.6061/clinics/2019/e1343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jesus Paula Carvalho
- Disciplina de Ginecologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | - Edmund Chada Baracat
- Disciplina de Ginecologia, Instituto do Cancer do Estado de Sao Paulo (ICESP), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Filomena Marino Carvalho
- Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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50
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Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline. Oncotarget 2018; 9:33648-33655. [PMID: 30263092 PMCID: PMC6154752 DOI: 10.18632/oncotarget.26000] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/04/2018] [Indexed: 01/29/2023] Open
Abstract
Molecular analysis of BRCA1 (MIM# 604370) and BRCA2 (MIM #600185) genes is essential for familial breast and ovarian cancer prevention and treatment. An efficient, rapid, cost-effective accurate strategy for the detection of pathogenic variants is crucial. Mutations detection of BRCA1/2 genes includes screening for single nucleotide variants (SNVs), small insertions or deletions (indels), and Copy Number Variations (CNVs). Sanger sequencing is unable to identify CNVs and therefore Multiplex Ligation Probe amplification (MLPA) or Multiplex Amplicon Quantification (MAQ) is used to complete the BRCA1/2 genes analysis. The rapid evolution of Next Generation Sequencing (NGS) technologies allows the search for point mutations and CNVs with a single platform and workflow. In this study we test the possibilities of NGS technology to simultaneously detect point mutations and CNVs in BRCA1/2 genes, using the OncomineTM BRCA Research Assay on Personal Genome Machine (PGM) Platform with Ion Reporter Software for sequencing data analysis (Thermo Fisher Scientific). Comparison between the NGS-CNVs, MLPA and MAQ results shows how the NGS approach is the most complete and fast method for the simultaneous detection of all BRCA mutations, avoiding the usual time consuming multistep approach in the routine diagnostic testing of hereditary breast and ovarian cancers.
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