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Tuncer SB, Celik B, Erciyas SK, Erdogan OS, Gültaslar BK, Odemis DA, Avsar M, Sen F, Saip PM, Yazici H. Germline mutational variants of Turkish ovarian cancer patients suspected of Hereditary Breast and Ovarian Cancer (HBOC) by next-generation sequencing. Pathol Res Pract 2024; 254:155075. [PMID: 38219492 DOI: 10.1016/j.prp.2023.155075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 01/16/2024]
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) syndrome is characterized by an increased risk of developing breast cancer (BC) and ovarian cancer (OC) due to inherited genetic mutations. Understanding the genetic variants associated with HBOC is crucial for identifying individuals at high risk and implementing appropriate preventive measures. The study included 630 Turkish OC patients with confirmed diagnostic criteria of The National Comprehensive Cancer Network (NCCN) concerning HBOC. Genomic DNA was extracted from peripheral blood samples, and targeted Next-generation sequencing (NGS) was performed. Bioinformatics analysis and variant interpretation were conducted to identify pathogenic variants (PVs). Our analysis revealed a spectrum of germline pathogenic variants associated with HBOC in Turkish OC patients. Notably, several pathogenic variants in BRCA1, BRCA2, and other DNA repair genes were identified. Specifically, we observed germline PVs in 130 individuals, accounting for 20.63% of the total cohort. 76 distinct PVs in genes, BRCA1 (40 PVs), BRCA2 (29 PVs), ATM (1 PV), CHEK2 (2 PVs), ERCC2 (1 PV), MUTYH (1 PV), RAD51C (1 PV), and TP53 (1PV) and also, two different PVs (i.e., c.135-2 A>G p.? in BRCA1 and c.6466_6469delTCTC in BRCA2) were detected in a 34-year-old OC patient. In conclusion, our study contributes to a better understanding of the genetic variants underlying HBOC in Turkish OC patients. These findings provide valuable insights into the genetic architecture of HBOC in the Turkish population and shed light on the potential contribution of specific germline PVs to the increased risk of OC.
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Affiliation(s)
- Seref Bugra Tuncer
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye.
| | - Betul Celik
- Erzincan Binali Yıldırım University, Department of Molecular Biology, Erzincan, Türkiye
| | - Seda Kilic Erciyas
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Ozge Sukruoglu Erdogan
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Busra Kurt Gültaslar
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Demet Akdeniz Odemis
- Department of Cancer Genetics, Istanbul Faculty of Medicine, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Mukaddes Avsar
- Health Services Vocational of Higher Education, T.C. Istanbul Aydın University, Istanbul, Türkiye
| | - Fatma Sen
- Clinic of Medical Oncology, Avrasya Hospital, Istanbul, Türkiye
| | - Pınar Mualla Saip
- Department of Medical Oncology, Oncology Institute, Istanbul University, Istanbul, Türkiye
| | - Hulya Yazici
- Istanbul Arel University, Arel Medical Faculty, Department of Medical Biology and Genetics, Istanbul, Türkiye
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Bu R, Siraj AK, Al-Rasheed M, Iqbal K, Azam S, Qadri Z, Haqawi W, Tulbah A, Al-Dayel F, Almalik O, Al-Kuraya KS. Identification and characterization of ATM founder mutation in BRCA-negative breast cancer patients of Arab ethnicity. Sci Rep 2023; 13:20924. [PMID: 38017116 PMCID: PMC10684510 DOI: 10.1038/s41598-023-48231-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
Breast cancer (BC) is the most prevalent malignancy among women worldwide with germline pathogenic variants/likely pathogenic variants (PVs/LPVs) in BRCA1/2 accounting for a large portion of hereditary cases. Recently, heterozygous PVs/LPVs in the ATM serine/threonine kinase or Ataxia-telangiectasia mutated gene (ATM) has been identified as a moderate susceptibility factor for BC in diverse ethnicities. However, the prevalence of ATM PVs/LPVs in BC susceptibility in Arab populations remains largely unexplored. This study investigated the prevalence of ATM PVs/LPVs among BC patients from Saudi Arabia, employing capture-sequencing technology for ATM PVs/LPVs screening in a cohort of 715 unselected BC patients without BRCA1/2 PVs/LPVs. In addition, founder mutation analysis was conducted using the PHASE program. In our entire cohort, four unique PVs/LPVs in the ATM gene were identified in six cases (0.8%). Notably, one recurrent LPV, c.6115G > A:p.Glu2039Lys was identified in three cases, for which haplotype analysis confirmed as a novel putative founder mutation traced back to 13 generations on average. This founder mutation accounted for half of all identified mutant cases and 0.4% of total screened cases. This study further reveals a significant correlation between the presence of ATM mutation and family history of BC (p = 0.0127). These findings underscore an approximate 0.8% prevalence of ATM germline PVs/LPVs in Arab BC patients without BRCA1/2 PVs/LPVs and suggest a founder effect of specific recurrent ATM mutation. These insights can help in the design of a genetic testing strategy tailored to the local population in Saudi Arabia, thereby, enabling more accurate clinical management and risk prediction.
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Affiliation(s)
- Rong Bu
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Abdul K Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Wael Haqawi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Osama Almalik
- Department of Surgery, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia
| | - Khawla S Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, 11211, Riyadh, Saudi Arabia.
- Research Centre at KFNCCC, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
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3
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Stolarova L, Kleiblova P, Zemankova P, Stastna B, Janatova M, Soukupova J, Achatz MI, Ambrosone C, Apostolou P, Arun BK, Auer P, Barnard M, Bertelsen B, Blok MJ, Boddicker N, Brunet J, Burnside ES, Calvello M, Campbell I, Chan SH, Chen F, Chiang JB, Coppa A, Cortesi L, Crujeiras-González A, De Leeneer K, De Putter R, DePersia A, Devereux L, Domchek S, Efremidis A, Engel C, Ernst C, Evans DGR, Feliubadaló L, Fostira F, Fuentes-Ríos O, Gómez-García EB, González S, Haiman C, Hansen TVO, Hauke J, Hodge J, Hu C, Huang H, Ishak NDB, Iwasaki Y, Konstantopoulou I, Kraft P, Lacey J, Lázaro C, Li N, Lim WK, Lindstrom S, Lori A, Martinez E, Martins A, Matsuda K, Matullo G, McInerny S, Michailidou K, Montagna M, Monteiro AN, Mori L, Nathanson K, Neuhausen SL, Nevanlinna H, Olson JE, Palmer J, Pasini B, Patel A, Piane M, Poppe B, Radice P, Renieri A, Resta N, Richardson ME, Rosseel T, Ruddy KJ, Santamariña M, Dos Santos ES, Teras L, Toland AE, Trentham-Dietz A, Vachon CM, Volk AE, Weber-Lassalle N, Weitzel JN, Wiesmuller L, Winham S, Yadav S, Yannoukakos D, Yao S, Zampiga V, Zethoven M, Zhang ZW, Zima T, Spurdle AB, Vega A, Rossing M, Del Valle J, De Nicolo A, Hahnen E, Claes KB, Ngeow J, Momozawa Y, James PA, Couch FJ, Macurek L, Kleibl Z. ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk. Clin Cancer Res 2023; 29:3037-3050. [PMID: 37449874 PMCID: PMC10425727 DOI: 10.1158/1078-0432.ccr-23-0212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). EXPERIMENTAL DESIGN We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. RESULTS A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)-like (N = 226). We then examined their association with breast cancer risk in the case-control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35-3.41), 1.57 (95% CI, 1.41-1.75), and 1.19 (95% CI, 1.08-1.31), respectively. The meta-analysis of population-specific datasets showed similar results. CONCLUSIONS We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.
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Affiliation(s)
- Lenka Stolarova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Barbora Stastna
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Maria Isabel Achatz
- A.C. Camargo Cancer Center and Oncology Center, Hospital Sirio-Libanes, Sao Paulo, Brazil
| | - Christine Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Cancer Center, Buffalo, New York
- WCHS Inc., Baltimore, Maryland
| | - Paraskevi Apostolou
- Human Molecular Genetics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin
- WHI, USA
| | - Mollie Barnard
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marinus J. Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Nicholas Boddicker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- CARRIERS, USA
| | - Joan Brunet
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Elizabeth S. Burnside
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin
- WWHS, Charlotte, North Carolina
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Ian Campbell
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Sock Hoai Chan
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Fei Chen
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Jian Bang Chiang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Anna Coppa
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Laura Cortesi
- Department of Oncology and Haematology, Modena University Hospital, Modena, Italy
| | - Ana Crujeiras-González
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robin De Putter
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Allison DePersia
- Center for Medical Genetics, NorthShore University Health System, Evanston, Illinois
| | - Lisa Devereux
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Susan Domchek
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anna Efremidis
- Clinical Cancer Genetics and Family Consultants, CLINICAGENE, Athens Medical Center, Athens, Greece
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - D. Gareth R. Evans
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Lidia Feliubadaló
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Olivia Fuentes-Ríos
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Encarna B. Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Sara González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, California
- MEC, USA
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - James Hodge
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- CPS3, Kennesaw, Georgia
| | - Chunling Hu
- CARRIERS, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Hongyan Huang
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | | | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Cambridge, Massachusetts
- NHS, Reston, Virginia
| | - James Lacey
- Beckman Research Institute, City of Hope Cancer Center, Duarte, California
- CTS, USA
| | - Conxi Lázaro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Na Li
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Sara Lindstrom
- WHI, USA
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Adriana Lori
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
- American Cancer Society, Atlanta, Georgia
| | - Elana Martinez
- Duke-NUS Medical School, Singapore, Singapore
- Department of Family Medicine and Public Health, University of California San Diego, San Diego, California
| | - Alexandra Martins
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, Padua, Italy
| | - Alvaro N.A. Monteiro
- Cancer Epidemiology Program, Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Luigi Mori
- Endocrine and Metabolic Disease Unit, ASST Spedali Civili of Brescia, Brescia, Italia
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Katherine Nathanson
- CARRIERS, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Janet E. Olson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
- MCBCS, USA
| | - Julie Palmer
- Slone Epidemiology Center, Boston University, Boston, Massachusetts
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Alpa Patel
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Maria Piane
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Paolo Radice
- Department of Experimental Oncology, Molecular Bases of Genetic Risk and Genetic Testing Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Nicoletta Resta
- Department of Precision and Regenerative Medicine and Ionian Area, Medical Genetics Unit, University of Bari, Bari, Italy
| | | | - Toon Rosseel
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kathryn J. Ruddy
- MCBCS, USA
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Marta Santamariña
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | | | - Lauren Teras
- Department of Population Science, American Cancer Society, Atlanta, Georgia
- CPS-II, USA
| | - Amanda E. Toland
- Department of Cancer Biology & Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Amy Trentham-Dietz
- WWHS, Charlotte, North Carolina
- University of Wisconsin, Madison, Wisconsin
| | | | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Lisa Wiesmuller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Stacey Winham
- MMHS, USA
- Department Quantitative Sciences, Mayo Clinic, Rochester, Minnesota
| | - Siddhartha Yadav
- CARRIERS, USA
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRaSTES, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Song Yao
- WCHS Inc., Baltimore, Maryland
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Valentina Zampiga
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori," Meldola, Italy
| | - Magnus Zethoven
- Cancer Genomics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ze Wen Zhang
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
| | - Tomas Zima
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Amanda B. Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenomica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain
| | - Maria Rossing
- Center for Genomic Medicine, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jesús Del Valle
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL-IGTP-IDIBGI, L'Hospitalet, Barcelona, Spain
| | - Arcangela De Nicolo
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Joanne Ngeow
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
- Inserm UMR1245, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Normandie University, Rouen, France
| | - Fergus J. Couch
- CARRIERS, USA
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Pathophysiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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4
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Zhu JW, Charkhchi P, Adekunte S, Akbari MR. What Is Known about Breast Cancer in Young Women? Cancers (Basel) 2023; 15:cancers15061917. [PMID: 36980802 PMCID: PMC10047861 DOI: 10.3390/cancers15061917] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer-related death in women under the age of 40 years worldwide. In addition, the incidence of breast cancer in young women (BCYW) has been rising. Young women are not the focus of screening programs and BC in younger women tends to be diagnosed in more advanced stages. Such patients have worse clinical outcomes and treatment complications compared to older patients. BCYW has been associated with distinct tumour biology that confers a worse prognosis, including poor tumour differentiation, increased Ki-67 expression, and more hormone-receptor negative tumours compared to women >50 years of age. Pathogenic variants in cancer predisposition genes such as BRCA1/2 are more common in early-onset BC compared to late-onset BC. Despite all these differences, BCYW remains poorly understood with a gap in research regarding the risk factors, diagnosis, prognosis, and treatment. Age-specific clinical characteristics or outcomes data for young women are lacking, and most of the standard treatments used in this subpopulation currently are derived from older patients. More age-specific clinical data and treatment options are required. In this review, we discuss the epidemiology, clinicopathologic characteristics, outcomes, treatments, and special considerations of breast cancer in young women. We also underline future directions and highlight areas that require more attention in future studies.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Shadia Adekunte
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
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5
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Graffeo R, Rana H, Conforti F, Bonanni B, Cardoso M, Paluch-Shimon S, Pagani O, Goldhirsch A, Partridge A, Lambertini M, Garber J. Moderate penetrance genes complicate genetic testing for breast cancer diagnosis: ATM, CHEK2, BARD1 and RAD51D. Breast 2022; 65:32-40. [PMID: 35772246 PMCID: PMC9253488 DOI: 10.1016/j.breast.2022.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Breast cancer risk associated with germline likely pathogenic/pathogenic variants (PV) varies by gene, often by penetrance (high >50% or moderate 20–50%), and specific locus. Germline PVs in BRCA1 and BRCA2 play important roles in the development of breast and ovarian cancer in particular, as well as in other cancers such as pancreatic and prostate cancers and melanoma. Recent studies suggest that other cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C and RAD51D confer differential risks of breast and other specific cancers. In the era of multigene panel testing, advances in next-generation sequencing technologies have notably reduced costs in the United States (US) and enabled sequencing of BRCA1/2 concomitantly with additional genes. The use of multigene-panel testing is beginning to expand in Europe as well. Further research into the clinical implications of variants in moderate penetrance genes, particularly in unaffected carriers, is needed for appropriate counselling and risk management with data-driven plans for surveillance and/or risk reduction. For individuals at high risk without any pathogenic or likely pathogenic variant in cancer susceptibility genes or some carriers of pathogenic variants in moderate-risk genes such as ATM and CHEK2, polygenic risk scores offer promise to help stratify breast cancer risk and guide appropriate risk management options. Cancer patients whose tumours are driven by the loss of function of both copies of a predisposition gene may benefit from therapies targeting the biological alterations induced by the dysfunctional gene e.g. poly ADP ribose polymerase (PARP) inhibitors and other novel pathway agents in cancers with DNA repair deficiencies. A better understanding of mechanisms by which germline variants drive various malignancies may lead to improvements in both therapeutic and preventive management options. The interpretation of genetic testing results requires careful attention. ATM, CHEK2, RAD51D and BARD1 correlated with breast and other cancers risk. European and American guidelines discrepancies. Support European healthcare providers in interpreting and managing female carriers.
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6
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Paduano F, Colao E, Fabiani F, Rocca V, Dinatolo F, Dattola A, D’Antona L, Amato R, Trapasso F, Baudi F, Perrotti N, Iuliano R. Germline Testing in a Cohort of Patients at High Risk of Hereditary Cancer Predisposition Syndromes: First Two-Year Results from South Italy. Genes (Basel) 2022; 13:genes13071286. [PMID: 35886069 PMCID: PMC9319682 DOI: 10.3390/genes13071286] [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: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Germline pathogenic variants (PVs) in oncogenes and tumour suppressor genes are responsible for 5 to 10% of all diagnosed cancers, which are commonly known as hereditary cancer predisposition syndromes (HCPS). A total of 104 individuals at high risk of HCPS were selected by genetic counselling for genetic testing in the past 2 years. Most of them were subjects having a personal and family history of breast cancer (BC) selected according to current established criteria. Genes analysis involved in HCPS was assessed by next-generation sequencing (NGS) using a custom cancer panel with high- and moderate-risk susceptibility genes. Germline PVs were identified in 17 of 104 individuals (16.3%) analysed, while variants of uncertain significance (VUS) were identified in 21/104 (20.2%) cases. Concerning the germline PVs distribution among the 13 BC individuals with positive findings, 8/13 (61.5%) were in the BRCA1/2 genes, whereas 5/13 (38.4%) were in other high- or moderate-risk genes including PALB2, TP53, ATM and CHEK2. NGS genetic testing showed that 6/13 (46.1%) of the PVs observed in BC patients were detected in triple-negative BC. Interestingly, the likelihood of carrying the PVs in the moderate-to-high-risk genes calculated by the cancer risk model BOADICEA was significantly higher in pathogenic variant carriers than in negative subjects. Collectively, this study shows that multigene panel testing can offer an effective diagnostic approach for patients at high risk of hereditary cancers.
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Stem Cells and Medical Genetics Units, Tecnologica Research Institute and Marrelli Health, 88900 Crotone, Italy
- Correspondence: (F.P.); (R.I.)
| | - Emma Colao
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Fernanda Fabiani
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Valentina Rocca
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesca Dinatolo
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Adele Dattola
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Lucia D’Antona
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Francesco Trapasso
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesco Baudi
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Perrotti
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (F.P.); (R.I.)
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Vaidyanathan A, Kaklamani V. Understanding the Clinical Implications of Low Penetrant Genes and Breast Cancer Risk. Curr Treat Options Oncol 2021; 22:85. [PMID: 34424438 DOI: 10.1007/s11864-021-00887-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2021] [Indexed: 10/20/2022]
Abstract
OPINION STATEMENT Since the 2013 Supreme Court declaration, panel testing for hereditary cancer syndromes has evolved into the gold standard for oncology germline genetic testing. With the advent of next-generation sequencing, competitive pricing, and developing therapeutic options, panel testing is now well integrated into breast cancer management and surveillance. Although many established syndromes have well-defined cancer risks and management strategies, several breast cancer genes are currently classified as limited-evidence genes by the National Comprehensive Cancer Network (NCCN). Follow-up for individuals with mutations in these genes is a point of contention due to conflicting information in the literature. The most recent NCCN guidelines have stratified management based on gene-specific cancer risks indicating that expanding data will allow for better recommendations as research progresses. The evolving management for these genes emphasizes the clinicians' need for evidence-based understanding of low penetrance breast cancer genes and their implications for patient care. This article reviews current literature for limited evidence genes, detailing cancer risks, association with triple-negative breast cancer, and recommendations for surveillance. A brief review of the challenges and future directions is outlined to discuss the evolving nature of cancer genetics and the exciting opportunities that can impact management.
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Affiliation(s)
- Anusha Vaidyanathan
- UT Health Science Center San Antonio, 7979 Wurzbach Road, San Antonio, TX, 79229, USA.
| | - Virginia Kaklamani
- UT Health Science Center San Antonio, 7979 Wurzbach Road, San Antonio, TX, 79229, USA
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8
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Population-Based Estimates of the Age-Specific Cumulative Risk of Breast Cancer for Pathogenic Variants in CHEK2: Findings from the Australian Breast Cancer Family Registry. Cancers (Basel) 2021; 13:cancers13061378. [PMID: 33803639 PMCID: PMC8003064 DOI: 10.3390/cancers13061378] [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: 02/09/2021] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 02/03/2023] Open
Abstract
Simple Summary It is well established that women who carry pathogenic CHEK2 variants have about a 3-fold increased risk of developing breast cancer. CHEK2 is now commonly included in genetic tests for breast cancer predisposition and increasingly used to inform the clinical management of women who are identified to carry pathogenic variants. Important information for counselling these women includes knowing how breast cancer risk, due to having a pathogenic variant in CHEK2, changes over a woman’s lifetime. This information is currently not well established. By conducting a population-based case-control-family study of pathogenic CHEK2 variants we aimed to provide this information and estimated the penetrance (age-specific cumulative risk) of breast cancer to be 18% (95% CI 11–30%) to age 60 years and 33% (95% CI 21–48%) to age 80 years. These findings provide new and important information for the clinical management of breast cancer risk for women carrying pathogenic variants in CHEK2. Abstract Case-control studies of breast cancer have consistently shown that pathogenic variants in CHEK2 are associated with about a 3-fold increased risk of breast cancer. Information about the recurrent protein-truncating variant CHEK2 c.1100delC dominates this estimate. There have been no formal estimates of age-specific cumulative risk of breast cancer for all CHEK2 pathogenic (including likely pathogenic) variants combined. We conducted a population-based case-control-family study of pathogenic CHEK2 variants (26 families, 1071 relatives) and estimated the age-specific cumulative risk of breast cancer using segregation analysis. The estimated hazard ratio for carriers of pathogenic CHEK2 variants (combined) was 4.9 (95% CI 2.5–9.5) relative to non-carriers. The HR for carriers of the CHEK2 c.1100delC variant was estimated to be 3.5 (95% CI 1.02–11.6) and the HR for carriers of all other CHEK2 variants combined was estimated to be 5.7 (95% CI 2.5–12.9). The age-specific cumulative risk of breast cancer was estimated to be 18% (95% CI 11–30%) and 33% (95% CI 21–48%) to age 60 and 80 years, respectively. These findings provide important information for the clinical management of breast cancer risk for women carrying pathogenic variants in CHEK2.
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9
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Stolarova L, Kleiblova P, Janatova M, Soukupova J, Zemankova P, Macurek L, Kleibl Z. CHEK2 Germline Variants in Cancer Predisposition: Stalemate Rather than Checkmate. Cells 2020; 9:cells9122675. [PMID: 33322746 PMCID: PMC7763663 DOI: 10.3390/cells9122675] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Germline alterations in many genes coding for proteins regulating DNA repair and DNA damage response (DDR) to DNA double-strand breaks (DDSB) have been recognized as pathogenic factors in hereditary cancer predisposition. The ATM-CHEK2-p53 axis has been documented as a backbone for DDR and hypothesized as a barrier against cancer initiation. However, although CHK2 kinase coded by the CHEK2 gene expedites the DDR signal, its function in activation of p53-dependent cell cycle arrest is dispensable. CHEK2 mutations rank among the most frequent germline alterations revealed by germline genetic testing for various hereditary cancer predispositions, but their interpretation is not trivial. From the perspective of interpretation of germline CHEK2 variants, we review the current knowledge related to the structure of the CHEK2 gene, the function of CHK2 kinase, and the clinical significance of CHEK2 germline mutations in patients with hereditary breast, prostate, kidney, thyroid, and colon cancers.
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Affiliation(s)
- Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 12800 Prague, Czech Republic;
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, 12800 Prague, Czech Republic; (L.S.); (M.J.); (J.S.); (P.Z.)
- Correspondence: ; Tel.: +420-22496-745
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10
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Alenezi WM, Fierheller CT, Recio N, Tonin PN. Literature Review of BARD1 as a Cancer Predisposing Gene with a Focus on Breast and Ovarian Cancers. Genes (Basel) 2020; 11:E856. [PMID: 32726901 PMCID: PMC7464855 DOI: 10.3390/genes11080856] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Soon after the discovery of BRCA1 and BRCA2 over 20 years ago, it became apparent that not all hereditary breast and/or ovarian cancer syndrome families were explained by germline variants in these cancer predisposing genes, suggesting that other such genes have yet to be discovered. BRCA1-associated ring domain (BARD1), a direct interacting partner of BRCA1, was one of the earliest candidates investigated. Sequencing analyses revealed that potentially pathogenic BARD1 variants likely conferred a low-moderate risk to hereditary breast cancer, but this association is inconsistent. Here, we review studies of BARD1 as a cancer predisposing gene and illustrate the challenge of discovering additional cancer risk genes for hereditary breast and/or ovarian cancer. We selected peer reviewed research articles that focused on three themes: (i) sequence analyses of BARD1 to identify potentially pathogenic germline variants in adult hereditary cancer syndromes; (ii) biological assays of BARD1 variants to assess their effect on protein function; and (iii) association studies of BARD1 variants in family-based and case-control study groups to assess cancer risk. In conclusion, BARD1 is likely to be a low-moderate penetrance breast cancer risk gene.
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Affiliation(s)
- Wejdan M. Alenezi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medical Laboratory Technology, Taibah University, Medina 42353, Saudi Arabia
| | - Caitlin T. Fierheller
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Neil Recio
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Patricia N. Tonin
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada; (W.M.A.); (C.T.F.); (N.R.)
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Department of Medicine, McGill University, Montreal, QC H3A 0G4, Canada
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11
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Bharucha PP, Chiu KE, François FM, Scott JL, Khorjekar GR, Tirada NP. Genetic Testing and Screening Recommendations for Patients with Hereditary Breast Cancer. Radiographics 2020; 40:913-936. [PMID: 32469631 DOI: 10.1148/rg.2020190181] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Professionals who specialize in breast imaging may be the first to initiate the conversation about genetic counseling with patients who have a diagnosis of premenopausal breast cancer or a strong family history of breast and ovarian cancer. Commercial genetic testing panels have gained popularity and have become more affordable in recent years. Therefore, it is imperative for radiologists to be able to provide counseling and to identify those patients who should be referred for genetic testing. The authors review the process of genetic counseling and the associated screening recommendations for patients at high and moderate risk. Ultimately, genetic test results enable appropriate patient-specific screening, which allows improvement of overall survival by early detection and timely treatment. The authors discuss pretest counseling, which involves the use of various breast cancer risk assessment tools such as the Gail and Tyrer-Cuzick models. The most common high- and moderate-risk gene mutations associated with breast cancer are also reviewed. In addition to BRCA1 and BRCA2, several high-risk genes, including TP53, PTEN, CDH1, and STK11, are discussed. Moderate-risk genes include ATM, CHEK2, and PALB2. The imaging appearances of breast cancer typically associated with each gene mutation, as well as the other associated cancers, are described. ©RSNA, 2020 See discussion on this article by Butler (pp 937-940).
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Affiliation(s)
- Puja P Bharucha
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
| | - Kellie E Chiu
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
| | - Fabienne M François
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
| | - Jessica L Scott
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
| | - Gauri R Khorjekar
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
| | - Nikki P Tirada
- From the Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD 21201
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12
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13
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Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:46. [PMID: 32127026 PMCID: PMC7055088 DOI: 10.1186/s13046-020-01554-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
The promising expectations about personalized medicine have opened the path to routine large-scale sequencing and increased the importance of genetic counseling for hereditary cancers, among which hereditary breast and ovary cancers (HBOC) have a major impact. High-throughput sequencing, or Next-Generation Sequencing (NGS), has improved cancer patient management, ameliorating diagnosis and treatment decisions. In addition to its undeniable clinical utility, NGS is also unveiling a large number of variants that we are still not able to clearly define and classify, the variants of uncertain significance (VUS), which account for about 40% of total variants. At present, VUS use in the clinical context is challenging. Medical reports may omit this kind of data and, even when included, they limit the clinical utility of genetic information. This has prompted the scientific community to seek easily applicable tests to accurately classify VUS and increase the amount of usable information from NGS data. In this review, we will focus on NGS and classification systems for VUS investigation, with particular attention on HBOC-related genes and in vitro functional tests developed for ameliorating and accelerating variant classification in cancer.
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Dominguez-Valentin M, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Holth A, Capella G, Davidson B, Evans DG, Martins A, Møller P, Hovig E. Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing. Sci Rep 2019; 9:18555. [PMID: 31811167 PMCID: PMC6898579 DOI: 10.1038/s41598-019-54517-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023] Open
Abstract
We have surveyed 191 prospectively sampled familial cancer patients with no previously detected pathogenic variant in the BRCA1/2, PTEN, TP53 or DNA mismatch repair genes. In all, 138 breast cancer (BC) cases, 34 colorectal cancer (CRC) and 19 multiple early-onset cancers were included. A panel of 44 cancer-predisposing genes identified 5% (9/191) pathogenic or likely pathogenic variants and 87 variants of uncertain significance (VUS). Pathogenic or likely pathogenic variants were identified mostly in familial BC individuals (7/9) and were located in 5 genes: ATM (3), BRCA2 (1), CHEK2 (1), MSH6 (1) and MUTYH (1), followed by multiple early-onset (2/9) individuals, affecting the CHEK2 and ATM genes. Eleven of the 87 VUS were tested, and 4/11 were found to have an impact on splicing by using a minigene splicing assay. We here report for the first time the splicing anomalies using this assay for the variants ATM c.3806A > G and BUB1 c.677C > T, whereas CHEK1 c.61G > A did not result in any detectable splicing anomaly. Our study confirms the presence of pathogenic or likely pathogenic variants in genes that are not routinely tested in the context of the above-mentioned clinical phenotypes. Interestingly, more than half of the pathogenic germline variants were found in the moderately penetrant ATM and CHEK2 genes, where only truncating variants from these genes are recommended to be reported in clinical genetic testing practice.
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Affiliation(s)
- Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hélène Tubeuf
- Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Daniel Vodak
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anke M Nissen
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Arild Holth
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway
| | - Gabriel Capella
- Hereditary Cancer Program, Catalan Institute of Oncology, Insititut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain, and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway.,University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, N-, 0316, Oslo, Norway
| | - D Gareth Evans
- Department of Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, Manchester Academic Health Science Centre, St. Mary's Hospital, Manchester, United Kingdom.,Prevent Breast Cancer Centre, Wythenshawe Hospital, Southmoor Road, Manchester, United Kingdom
| | - Alexandra Martins
- Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Human Medicine, Universität Witten/Herdecke, Wuppertal, Germany
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
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15
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Sawyer L, Creswick H, Lewandowski R, Quillin J. Recontacting patients for multigene panel testing in hereditary cancer: Efficacy and insights. J Genet Couns 2019; 28:1198-1207. [PMID: 31553108 DOI: 10.1002/jgc4.1173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 01/15/2023]
Abstract
In hereditary cancer, multigene panel testing is currently replacing older single-gene approaches. Patients whose tests were previously uninformative could benefit from updated testing. Research suggests that patients desire to be recontacted about updated genetic testing, but few studies have tested the efficacy of recontact efforts. This study investigated the outcomes of a recontact effort in a hereditary cancer clinic and explored the impact of four different recontact letters, randomized in a 2X2 factorial design. Patients who had negative genetic testing for single genes or conditions were mailed letters inviting them to schedule an appointment to discuss updated testing. Patients were randomized to receive one of four letters and each letter emphasized different implications of updated multigene genetic testing: (a) personal medical management implications, (b) implications for family members, (c) both personal and family implications or (d) a control letter. The proportion of patients who arrived for appointments was assessed approximately 7 months after mailing along with associations with patient demographics and type of letter received. Letters were mailed to 586 patients who had initial testing between 2001 and 2015. Most patients were white (78%) and female (97%) with private insurance (65%). At 7 months, 25 patients (4.3%, 95% CI: 2.6% to 5.9%) had arrived for an appointment. Older age was significantly associated with response rate (p = .01), while type of recontact letter was not (p = .54). This study suggests that recontacting patients about updated genetic testing by mail does not yield a large response. It also suggests that personal and/or familial implications do not seem to be significant factors that determine response rate. Nevertheless, results provide meaningful information for cancer clinics about the outcomes of recontact efforts via informational letter.
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Affiliation(s)
- Lindsey Sawyer
- Department of Human Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Heather Creswick
- Department of Human Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Raymond Lewandowski
- Department of Human Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - John Quillin
- Department of Human Genetics, Virginia Commonwealth University, Richmond, VA, USA
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16
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Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, Sun Y, Shen Y, Garg A, Pal D, Yu Y, Huff CD, Tavtigian SV, Young E, Neuhausen SL, Ziv E, Pal LR, Andreoletti G, Brenner S, Kann MG. Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum Mutat 2019; 40:1612-1622. [PMID: 31241222 PMCID: PMC6744287 DOI: 10.1002/humu.23849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 01/22/2023]
Abstract
The availability of disease-specific genomic data is critical for developing new computational methods that predict the pathogenicity of human variants and advance the field of precision medicine. However, the lack of gold standards to properly train and benchmark such methods is one of the greatest challenges in the field. In response to this challenge, the scientific community is invited to participate in the Critical Assessment for Genome Interpretation (CAGI), where unpublished disease variants are available for classification by in silico methods. As part of the CAGI-5 challenge, we evaluated the performance of 18 submissions and three additional methods in predicting the pathogenicity of single nucleotide variants (SNVs) in checkpoint kinase 2 (CHEK2) for cases of breast cancer in Hispanic females. As part of the assessment, the efficacy of the analysis method and the setup of the challenge were also considered. The results indicated that though the challenge could benefit from additional participant data, the combined generalized linear model analysis and odds of pathogenicity analysis provided a framework to evaluate the methods submitted for SNV pathogenicity identification and for comparison to other available methods. The outcome of this challenge and the approaches used can help guide further advancements in identifying SNV-disease relationships.
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Affiliation(s)
- Alin Voskanian
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, U.S.A
- Department of Pharmacology, Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
- The eScience Institute, University of Washington, Seattle, Washington, U.S.A
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts, U.S.A
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, U.S.A
| | - Emidio Capriotti
- BioFolD Unit, Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, U.S.A
- Technical University of Munich Institute for Advanced Study, (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching/Munich, Germany
| | - Yanran Wang
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Max Miller
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, U.S.A
| | - Pier Luigi Martelli
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Castrense Savojardo
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Giulia Babbi
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Rita Casadio
- Biocomputing Group, BiGeA/Giorgio Prodi Interdepartmental Center for Cancer Research, University of Bologna, Via F. Selmi 3, Bologna, 40126, Italy
| | - Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, U.S.A
| | - Aditi Garg
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Debnath Pal
- Department of Computational and Data Sciences Indian Institute of Science, Bengaluru 560 012, India
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, U.S.A
| | - Sean V. Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Erin Young
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, U.S.A
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010 U.S.A
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA,U.S.A
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Maricel G. Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, MD, U.S.A
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17
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Kleiblova P, Stolarova L, Krizova K, Lhota F, Hojny J, Zemankova P, Havranek O, Vocka M, Cerna M, Lhotova K, Borecka M, Janatova M, Soukupova J, Sevcik J, Zimovjanova M, Kotlas J, Panczak A, Vesela K, Cervenkova J, Schneiderova M, Burocziova M, Burdova K, Stranecky V, Foretova L, Machackova E, Tavandzis S, Kmoch S, Macurek L, Kleibl Z. Identification of deleterious germline CHEK2 mutations and their association with breast and ovarian cancer. Int J Cancer 2019; 145:1782-1797. [PMID: 31050813 DOI: 10.1002/ijc.32385] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022]
Abstract
Germline mutations in checkpoint kinase 2 (CHEK2), a multiple cancer-predisposing gene, increase breast cancer (BC) risk; however, risk estimates differ substantially in published studies. We analyzed germline CHEK2 variants in 1,928 high-risk Czech breast/ovarian cancer (BC/OC) patients and 3,360 population-matched controls (PMCs). For a functional classification of VUS, we developed a complementation assay in human nontransformed RPE1-CHEK2-knockout cells quantifying CHK2-specific phosphorylation of endogenous protein KAP1. We identified 10 truncations in 46 (2.39%) patients and in 11 (0.33%) PMC (p = 1.1 × 10-14 ). Two types of large intragenic rearrangements (LGR) were found in 20/46 mutation carriers. Truncations significantly increased unilateral BC risk (OR = 7.94; 95%CI 3.90-17.47; p = 1.1 × 10-14 ) and were more frequent in patients with bilateral BC (4/149; 2.68%; p = 0.003), double primary BC/OC (3/79; 3.80%; p = 0.004), male BC (3/48; 6.25%; p = 8.6 × 10-4 ), but not with OC (3/354; 0.85%; p = 0.14). Additionally, we found 26 missense VUS in 88 (4.56%) patients and 131 (3.90%) PMC (p = 0.22). Using our functional assay, 11 variants identified in 15 (0.78%) patients and 6 (0.18%) PMC were scored deleterious (p = 0.002). Frequencies of functionally intermediate and neutral variants did not differ between patients and PMC. Functionally deleterious CHEK2 missense variants significantly increased BC risk (OR = 3.90; 95%CI 1.24-13.35; p = 0.009) and marginally OC risk (OR = 4.77; 95%CI 0.77-22.47; p = 0.047); however, carriers low frequency will require evaluation in larger studies. Our study highlights importance of LGR detection for CHEK2 analysis, careful consideration of ethnicity in both cases and controls for risk estimates, and demonstrates promising potential of newly developed human nontransformed cell line assay for functional CHEK2 VUS classification.
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Affiliation(s)
- Petra Kleiblova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Katerina Krizova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Filip Lhota
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Hojny
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ondrej Havranek
- BIOCEV, First Faculty of Medicine, Charles University, Prague, Czech Republic.,Department of Hematology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Michal Vocka
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Marta Cerna
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marianna Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Sevcik
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martina Zimovjanova
- Department of Oncology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jaroslav Kotlas
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Ales Panczak
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jana Cervenkova
- Department of Radiology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Michaela Schneiderova
- First Department of Surgery, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Monika Burocziova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Viktor Stranecky
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Spiros Tavandzis
- Department of Medical Genetics, AGEL Laboratories, AGEL Research and Training Institute, Novy Jicin, Czech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
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18
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Landscape of pathogenic variations in a panel of 34 genes and cancer risk estimation from 5131 HBOC families. Genet Med 2018; 20:1677-1686. [PMID: 29988077 DOI: 10.1038/s41436-018-0005-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Integration of gene panels in the diagnosis of hereditary breast and ovarian cancer (HBOC) requires a careful evaluation of the risk associated with pathogenic or likely pathogenic variants (PVs) detected in each gene. Here we analyzed 34 genes in 5131 suspected HBOC index cases by next-generation sequencing. METHODS Using the Exome Aggregation Consortium data sets plus 571 individuals from the French Exome Project, we simulated the probability that an individual from the Exome Aggregation Consortium carries a PV and compared it to the estimated frequency within the HBOC population. RESULTS Odds ratio conferred by PVs within BRCA1, BRCA2, PALB2, RAD51C, RAD51D, ATM, BRIP1, CHEK2, and MSH6 were estimated at 13.22 [10.01-17.22], 8.61 [6.78-10.82], 8.22 [4.91-13.05], 4.54 [2.55-7.48], 5.23 [1.46-13.17], 3.20 [2.14-4.53], 2.49 [1.42-3.97], 1.67 [1.18-2.27], and 2.50 [1.12-4.67], respectively. PVs within RAD51C, RAD51D, and BRIP1 were associated with ovarian cancer family history (OR = 11.36 [5.78-19.59], 12.44 [2.94-33.30] and 3.82 [1.66-7.11]). PALB2 PVs were associated with bilateral breast cancer (OR = 16.17 [5.48-34.10]) and BARD1 PVs with triple-negative breast cancer (OR = 11.27 [3.37-25.01]). Burden tests performed in both patients and the French Exome Project population confirmed the association of PVs of BRCA1, BRCA2, PALB2, and RAD51C with HBOC. CONCLUSION Our results validate the integration of PALB2, RAD51C, and RAD51D in the diagnosis of HBOC and suggest that the other genes are involved in an oligogenic determinism.
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19
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Young EL, Thompson BA, Neklason DW, Firpo MA, Werner T, Bell R, Berger J, Fraser A, Gammon A, Koptiuch C, Kohlmann WK, Neumayer L, Goldgar DE, Mulvihill SJ, Cannon-Albright LA, Tavtigian SV. Pancreatic cancer as a sentinel for hereditary cancer predisposition. BMC Cancer 2018; 18:697. [PMID: 29945567 PMCID: PMC6020441 DOI: 10.1186/s12885-018-4573-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genes associated with hereditary breast and ovarian cancer (HBOC) and colorectal cancer (CRC) predisposition have been shown to play a role in pancreatic cancer susceptibility. Growing evidence suggests that pancreatic cancer may be useful as a sentinel cancer to identify families that could benefit from HBOC or CRC surveillance, but to date pancreatic cancer is only considered an indication for genetic testing in the context of additional family history. METHODS Preliminary data generated at the Huntsman Cancer Hospital (HCH) included variants identified on a custom 34-gene panel or 59-gene panel including both known HBOC and CRC genes for respective sets of 66 and 147 pancreatic cancer cases, unselected for family history. Given the strength of preliminary data and corresponding literature, 61 sequential pancreatic cancer cases underwent a custom 14-gene clinical panel. Sequencing data from HCH pancreatic cancer cases, pancreatic cancer cases of the Cancer Genome Atlas (TCGA), and an unselected pancreatic cancer screen from the Mayo Clinic were combined in a meta-analysis to estimate the proportion of carriers with pathogenic and high probability of pathogenic variants of uncertain significance (HiP-VUS). RESULTS Approximately 8.6% of unselected pancreatic cancer cases at the HCH carried a variant with potential HBOC or CRC screening recommendations. A meta-analysis of unselected pancreatic cancer cases revealed that approximately 11.5% carry a pathogenic variant or HiP-VUS. CONCLUSION With the inclusion of both HBOC and CRC susceptibility genes in a panel test, unselected pancreatic cancer cases act as a useful sentinel cancer to identify asymptomatic at-risk relatives who could benefit from relevant HBOC and CRC surveillance measures.
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Affiliation(s)
- Erin L. Young
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Bryony A. Thompson
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Deborah W. Neklason
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
| | - Matthew A. Firpo
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Theresa Werner
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Oncology, Department of Medicine, University of Utah, Salt Lake City, United States
| | - Russell Bell
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
| | - Justin Berger
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Alison Fraser
- Population Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Amanda Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Cathryn Koptiuch
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Wendy K. Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Leigh Neumayer
- Department of Surgery and Arizona Cancer Center, University of Arizona, Tucson, United States
| | - David E. Goldgar
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, United States
| | - Sean J. Mulvihill
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, United States
| | - Lisa A. Cannon-Albright
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
- Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, United States
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, United States
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
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20
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Taylor A, Brady AF, Frayling IM, Hanson H, Tischkowitz M, Turnbull C, Side L. Consensus for genes to be included on cancer panel tests offered by UK genetics services: guidelines of the UK Cancer Genetics Group. J Med Genet 2018; 55:372-377. [PMID: 29661970 PMCID: PMC5992364 DOI: 10.1136/jmedgenet-2017-105188] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 01/26/2023]
Abstract
Genetic testing for hereditary cancer predisposition has evolved rapidly in recent years with the discovery of new genes, but there is much debate over the clinical utility of testing genes for which there are currently limited data regarding the degree of associated cancer risk. To address the discrepancies that have arisen in the provision of these tests across the UK, the UK Cancer Genetics Group facilitated a 1-day workshop with representation from the majority of National Health Service (NHS) clinical genetics services. Using a preworkshop survey followed by focused discussion of genes without prior majority agreement for inclusion, we achieved consensus for panels of cancer genes with sufficient evidence for clinical utility, to be adopted by all NHS genetics services. To support consistency in the delivery of these tests and advice given to families across the country, we also developed management proposals for individuals who are found to have pathogenic mutations in these genes. However, we fully acknowledge that the decision regarding what test is most appropriate for an individual family rests with the clinician, and will depend on factors including specific phenotypic features and the family structure.
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Affiliation(s)
- Amy Taylor
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park and St Mark's Hospitals, Harrow, UK
| | - Ian M Frayling
- All Wales Medical Genetics Service, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK.,Institute of Cancer & Genetics, Cardiff University, Cardiff, UK
| | - Helen Hanson
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Marc Tischkowitz
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.,South East Thames Regional Genetics Service, Guys and St Thomas NHS Foundation Trust, London, UK.,William Harvey Research Institute, Queen Mary University, London, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
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21
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Nakagomi H, Mochizuki H, Inoue M, Hirotsu Y, Amemiya K, Sakamoto I, Nakagomi S, Kubota T, Omata M. Combined annotation-dependent depletion score for BRCA1/2 variants in patients with breast and/or ovarian cancer. Cancer Sci 2018; 109:453-461. [PMID: 29215753 PMCID: PMC5797818 DOI: 10.1111/cas.13464] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/19/2017] [Accepted: 12/01/2017] [Indexed: 01/19/2023] Open
Abstract
Utility of combined annotation‐dependent depletion (CADD) score was recently reported to rank pathogenicity as C‐scores ranging 1‐99 for both confirmed deleterious mutation. Using C‐scores for BRCA1/2 variants, we tried to constitute the classification system for variant of uncertain significance (VUS), which had been a major problem of genetic testing for hereditary breast and/or ovarian cancer. We analyzed BRCA1/2 genes for 283 patients with breast and/or ovarian cancer. The deleterious mutation and missesne mutations, minor variant, and wild type of BRCA1 and ‐2 were 5, 27, 251 and 15, 85, 183, respectively. Meanwhile, the variants with C‐score ≥10 were involved in 19/283 (6.7%) in BRCA1 and 34/283 (12%) in BRCA2. All deleterious mutations were included in this group. Frequency of personal history and family history of ovarian cancer were significantly high, and frequency of serous adenocarcinoma of ovary and triple negative breast cancer was relatively high in the group with deleterious mutations. Similar findings were seen in patients with variants of C‐score ≥10. According to the C‐score and population frequency, we could define VUS for 11 patients out of 283 patients (3.9 CADD is useful to classify the variant of BRCA1/2 and selecting the patient who needs further segregation studies.
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Affiliation(s)
- Hiroshi Nakagomi
- Department of Breast Surgery, Yamanashi Central Hospital, Kofu, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Department of Gynecology, Yamanashi Central Hospital, Kofu, Japan
| | - Masayuki Inoue
- Department of Breast Surgery, Yamanashi Central Hospital, Kofu, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Department of Gynecology, Yamanashi Central Hospital, Kofu, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Department of Gynecology, Yamanashi Central Hospital, Kofu, Japan
| | - Ikuko Sakamoto
- Department of Gynecology, Yamanashi Central Hospital, Kofu, Japan
| | - Satoko Nakagomi
- Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Takeo Kubota
- Department of Child Studies, Seitoku University, Tokyo, Japan
| | - Masao Omata
- Genome Analysis Center, Department of Gynecology, Yamanashi Central Hospital, Kofu, Japan.,University of Tokyo, Tokyo, Japan
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22
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Park JS, Lee ST, Nam EJ, Han JW, Lee JY, Kim J, Kim TI, Park HS. Variants of cancer susceptibility genes in Korean BRCA1/2 mutation-negative patients with high risk for hereditary breast cancer. BMC Cancer 2018; 18:83. [PMID: 29338689 PMCID: PMC5769462 DOI: 10.1186/s12885-017-3940-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 12/19/2017] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND We evaluated the incidence and spectrum of pathogenic and likely pathogenic variants of cancer susceptibility genes in BRCA1/2 mutation-negative Korean patients with a high risk for hereditary breast cancer using a comprehensive multigene panel that included 35 cancer susceptibility genes. METHODS Samples from 120 patients who were negative for BRCA1/2 mutations, but had been diagnosed with breast cancer that was likely hereditary, were prospectively evaluated for the prevalence of high-penetrance and moderate-penetrance germline mutations. RESULTS Nine patients (7.5%) had at least one pathogenic or likely pathogenic variant. Ten variants were identified in these patients: TP53 in two patients, PALB2 in three patients, BARD1 in two patients, BRIP1 in two patients, and MRE11A in one patient. We also identified 30 types of 139 variants of unknown significance (VUS). High-penetrance germline mutations, including TP53 and PALB2, tended to occur with high frequency in young (< 35 years) breast cancer patients (4/19, 21.1%) than in those diagnosed with breast cancer at ≥35 years of age (1/101, 1.0%; p = 0.003). CONCLUSIONS These combined results demonstrate that multigene panels offer an alternative strategy for identifying veiled pathogenic and likely pathogenic mutations in breast cancer susceptibility genes.
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Affiliation(s)
- Ji Soo Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Ji Nam
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Women’s Cancer Clinic, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Woo Han
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung-Yun Lee
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Obstetrics and Gynecology, Institute of Women’s Life Medical Science, Women’s Cancer Clinic, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University School of Medicine, Seoul, Republic of Korea
| | - Tae Il Kim
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Division of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyung Seok Park
- Hereditary Cancer Clinic, Cancer Prevention Center, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Surgery, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722 Republic of Korea
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Decker B, Allen J, Luccarini C, Pooley KA, Shah M, Bolla MK, Wang Q, Ahmed S, Baynes C, Conroy DM, Brown J, Luben R, Ostrander EA, Pharoah PD, Dunning AM, Easton DF. Rare, protein-truncating variants in ATM, CHEK2 and PALB2, but not XRCC2, are associated with increased breast cancer risks. J Med Genet 2017; 54:732-741. [PMID: 28779002 PMCID: PMC5740532 DOI: 10.1136/jmedgenet-2017-104588] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 05/09/2017] [Accepted: 05/22/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Breast cancer (BC) is the most common malignancy in women and has a major heritable component. The risks associated with most rare susceptibility variants are not well estimated. To better characterise the contribution of variants in ATM, CHEK2, PALB2 and XRCC2, we sequenced their coding regions in 13 087 BC cases and 5488 controls from East Anglia, UK. METHODS Gene coding regions were enriched via PCR, sequenced, variant called and filtered for quality. ORs for BC risk were estimated separately for carriers of truncating variants and of rare missense variants, which were further subdivided by functional domain and pathogenicity as predicted by four in silico algorithms. RESULTS Truncating variants in PALB2 (OR=4.69, 95% CI 2.27 to 9.68), ATM (OR=3.26; 95% CI 1.82 to 6.46) and CHEK2 (OR=3.11; 95% CI 2.15 to 4.69), but not XRCC2 (OR=0.94; 95% CI 0.26 to 4.19) were associated with increased BC risk. Truncating variants in ATM and CHEK2 were more strongly associated with risk of oestrogen receptor (ER)-positive than ER-negative disease, while those in PALB2 were associated with similar risks for both subtypes. There was also some evidence that missense variants in ATM, CHEK2 and PALB2 may contribute to BC risk, but larger studies are necessary to quantify the magnitude of this effect. CONCLUSIONS Truncating variants in PALB2 are associated with a higher risk of BC than those in ATM or CHEK2. A substantial risk of BC due to truncating XRCC2 variants can be excluded.
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Affiliation(s)
- Brennan Decker
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jamie Allen
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Karen A Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Shahana Ahmed
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Don M Conroy
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Judith Brown
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Robert Luben
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Dp Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
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24
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Endometrial cancer gene panels: clinical diagnostic vs research germline DNA testing. Mod Pathol 2017; 30:1048-1068. [PMID: 28452373 DOI: 10.1038/modpathol.2017.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/12/2022]
Abstract
Endometrial cancer is the most common gynecological cancer, but is nevertheless uncommon enough to have value as a signature cancer for some hereditary cancer syndromes. Commercial multigene testing panels include up to 13 different genes annotated for germline DNA testing of patients with endometrial cancer. Many other genes have been reported as relevant to familial endometrial cancer from directed genome-wide sequencing studies or multigene panel testing, or research. This review assesses the evidence supporting association with endometrial cancer risk for 32 genes implicated in hereditary endometrial cancer, and presents a summary of rare germline variants in these 32 genes detected by analysis of quasi-population-based endometrial cancer patients from The Cancer Genome Atlas project. This comprehensive investigation has led to the conclusion that convincing evidence currently exists to support clinical testing of only six of these genes for diagnosis of hereditary endometrial cancer. Testing of endometrial cancer patients for the remaining genes should be considered in the context of research studies, as a means to better establish the level of endometrial cancer risk, if any, associated with genetic variants that are deleterious to gene or protein function. It is acknowledged that clinical testing of endometrial cancer patients for several genes included on commercial panels may provide actionable findings in relation to risk of other cancers, but these should be considered secondary or incidental findings and not conclusive evidence for diagnosis of inherited endometrial cancer. In summary, this review and analysis provides a comprehensive report of current evidence to guide the selection of genes for clinical and research gene testing of germline DNA from endometrial cancer patients.
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26
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Hamdi Y, Soucy P, Adoue V, Michailidou K, Canisius S, Lemaçon A, Droit A, Andrulis IL, Anton-Culver H, Arndt V, Baynes C, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brenner H, Broeks A, Burwinkel B, Chang-Claude J, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Dennis J, Devilee P, Dörk T, Dos-Santos-Silva I, Eriksson M, Fasching PA, Figueroa J, Flyger H, García-Closas M, Giles GG, Goldberg MS, González-Neira A, Grenaker-Alnæs G, Guénel P, Haeberle L, Haiman CA, Hamann U, Hallberg E, Hooning MJ, Hopper JL, Jakubowska A, Jones M, Kabisch M, Kataja V, Lambrechts D, Marchand LL, Lindblom A, Lubinski J, Mannermaa A, Maranian M, Margolin S, Marme F, Milne RL, Neuhausen SL, Nevanlinna H, Neven P, Olswold C, Peto J, Plaseska-Karanfilska D, Pylkäs K, Radice P, Rudolph A, Sawyer EJ, Schmidt MK, Shu XO, Southey MC, Swerdlow A, Tollenaar RA, Tomlinson I, Torres D, Truong T, Vachon C, Van Den Ouweland AMW, Wang Q, Winqvist R, Investigators KC, Zheng W, Benitez J, Chenevix-Trench G, Dunning AM, Pharoah PDP, Kristensen V, Hall P, Easton DF, Pastinen T, Nord S, Simard J. Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21. Oncotarget 2016; 7:80140-80163. [PMID: 27792995 PMCID: PMC5340257 DOI: 10.18632/oncotarget.12818] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/13/2016] [Indexed: 12/02/2022] Open
Abstract
There are significant inter-individual differences in the levels of gene expression. Through modulation of gene expression, cis-acting variants represent an important source of phenotypic variation. Consequently, cis-regulatory SNPs associated with differential allelic expression are functional candidates for further investigation as disease-causing variants. To investigate whether common variants associated with differential allelic expression were involved in breast cancer susceptibility, a list of genes was established on the basis of their involvement in cancer related pathways and/or mechanisms. Thereafter, using data from a genome-wide map of allelic expression associated SNPs, 313 genetic variants were selected and their association with breast cancer risk was then evaluated in 46,451 breast cancer cases and 42,599 controls of European ancestry ascertained from 41 studies participating in the Breast Cancer Association Consortium. The associations were evaluated with overall breast cancer risk and with estrogen receptor negative and positive disease. One novel breast cancer susceptibility locus on 4q21 (rs11099601) was identified (OR = 1.05, P = 5.6x10-6). rs11099601 lies in a 135 kb linkage disequilibrium block containing several genes, including, HELQ, encoding the protein HEL308 a DNA dependant ATPase and DNA Helicase involved in DNA repair, MRPS18C encoding the Mitochondrial Ribosomal Protein S18C and FAM175A (ABRAXAS), encoding a BRCA1 BRCT domain-interacting protein involved in DNA damage response and double-strand break (DSB) repair. Expression QTL analysis in breast cancer tissue showed rs11099601 to be associated with HELQ (P = 8.28x10-14), MRPS18C (P = 1.94x10-27) and FAM175A (P = 3.83x10-3), explaining about 20%, 14% and 1%, respectively of the variance inexpression of these genes in breast carcinomas.
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Affiliation(s)
- Yosr Hamdi
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
| | - Véronique Adoue
- Institut National de la Santé et de la Recherche Médicale U1043, Toulouse, France
- Centre National de la Recherche Scientifique, Toulouse, France
- Université de Toulouse, Université Paul Sabatier, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Audrey Lemaçon
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec – Université Laval, Faculté de Médecine, Département de Médecine Moléculaire, Université Laval, Quebec, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlevand Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Judith S. Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - NBCS Collaborators
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
- Section of Oncology, Institute of Medicine, University of Bergen, Bergen, Norway
- Department of Pathology, Akershus University Hospital, Lørenskog, Norway
- Department of Breast-Endocrine Surgery, Akershus University Hospital, Lørenskog, Norway
- Department of Breast and Endocrine Surgery, Oslo University Hospital, Ullevål, Oslo, Norway
- Department of Research, Vestre Viken, Drammen, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- National Advisory Unit on Late Effects after Cancer Treatment, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Oncology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Radiology and Nuclear Medicine, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | | | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Canada
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Grethe Grenaker-Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Michael Jones
- Division of Genetics and Epidemiology, the Institute of Cancer Research, London, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Vesa Kataja
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Central Finland Hospital District, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Arto Mannermaa
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mel Maranian
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Roger L. Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Multidisciplinary Breast Center, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov”, Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione Istituto Di Ricovero e Cura a Carattere, Scientifico, Istituto Nazionale Tumori, Milan, Italy
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Elinor J. Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology & Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rob A.E.M. Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, VilleJuif, France
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | | | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | | | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Vessela Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Silje Nord
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Quebec, Canada
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27
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Implementation of next-generation sequencing for molecular diagnosis of hereditary breast and ovarian cancer highlights its genetic heterogeneity. Breast Cancer Res Treat 2016; 159:245-56. [PMID: 27553368 DOI: 10.1007/s10549-016-3948-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/16/2016] [Indexed: 01/13/2023]
Abstract
Molecular diagnosis of hereditary breast and ovarian cancer (HBOC) by standard methodologies has been limited to the BRCA1 and BRCA2 genes. With the recent development of new sequencing methodologies, the speed and efficiency of DNA testing have dramatically improved. The aim of this work was to validate the use of next-generation sequencing (NGS) for the detection of BRCA1/BRCA2 point mutations in a diagnostic setting and to study the role of other genes associated with HBOC in Portuguese families. A cohort of 94 high-risk families was included in the study, and they were initially screened for the two common founder mutations with variant-specific methods. Fourteen index patients were shown to carry the Portuguese founder mutation BRCA2 c.156_157insAlu, and the remaining 80 were analyzed in parallel by Sanger sequencing for the BRCA1/BRCA2 genes and by NGS for a panel of 17 genes that have been described as involved in predisposition to breast and/or ovarian cancer. A total of 506 variants in the BRCA1/BRCA2 genes were detected by both methodologies, with a 100 % concordance between them. This strategy allowed the detection of a total of 39 deleterious mutations in the 94 index patients, namely 10 in BRCA1 (25.6 %), 21 in BRCA2 (53.8 %), four in PALB2 (10.3 %), two in ATM (5.1 %), one in CHEK2 (2.6 %), and one in TP53 (2.6 %), with 20.5 % of the deleterious mutations being found in genes other than BRCA1/BRCA2. These results demonstrate the efficiency of NGS for the detection of BRCA1/BRCA2 point mutations and highlight the genetic heterogeneity of HBOC.
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Maleva Kostovska I, Wang J, Bogdanova N, Schürmann P, Bhuju S, Geffers R, Dürst M, Liebrich C, Klapdor R, Christiansen H, Park-Simon TW, Hillemanns P, Plaseska-Karanfilska D, Dörk T. Rare ATAD5 missense variants in breast and ovarian cancer patients. Cancer Lett 2016; 376:173-7. [PMID: 27045477 DOI: 10.1016/j.canlet.2016.03.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/12/2022]
Abstract
ATAD5/ELG1 is a protein crucially involved in replication and maintenance of genome stability. ATAD5 has recently been identified as a genomic risk locus for both breast and ovarian cancer through genome-wide association studies. We aimed to investigate the spectrum of coding ATAD5 germ-line mutations in hospital-based series of patients with triple-negative breast cancer or serous ovarian cancer compared with healthy controls. The ATAD5 coding and adjacent splice site regions were analyzed by targeted next-generation sequencing of DNA samples from 273 cancer patients, including 114 patients with triple-negative breast cancer and 159 patients with serous epithelial ovarian cancer, and from 276 healthy females. Among 42 different variants identified, twenty-two were rare missense substitutions, of which 14 were classified as pathogenic by at least one in silico prediction tool. Three of four novel missense substitutions (p.S354I, p.H974R and p.K1466N) were predicted to be pathogenic and were all identified in ovarian cancer patients. Overall, rare missense variants with predicted pathogenicity tended to be enriched in ovarian cancer patients (14/159) versus controls (11/276) (p = 0.05, 2df). While truncating germ-line variants in ATAD5 were not detected, it remains possible that several rare missense variants contribute to genetic susceptibility toward epithelial ovarian carcinomas.
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Affiliation(s)
- Ivana Maleva Kostovska
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany; Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, Macedonia
| | - Jing Wang
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Natalia Bogdanova
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany; Clinics of Radiation Oncology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Peter Schürmann
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Sabin Bhuju
- Genome Analytics Group, Helmholtz Center for Infectious Diseases, Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Robert Geffers
- Genome Analytics Group, Helmholtz Center for Infectious Diseases, Inhoffenstraße 7, D-38124 Braunschweig, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University Jena, Bachstraße 18, D-07743 Jena, Germany
| | - Clemens Liebrich
- Clinics of Obstetrics and Gynecology, Sauerbruchstraße 7, D-38440 Wolfsburg, Germany
| | - Rüdiger Klapdor
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Hans Christiansen
- Clinics of Radiation Oncology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Tjoung-Won Park-Simon
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, Macedonia
| | - Thilo Dörk
- Clinics of Obstetrics and Gynecology, Hannover Medical School, Carl-Neuberg-Straße 1, D-30625 Hannover, Germany.
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