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Davidson AL, Michailidou K, Parsons MT, Fortuno C, Bolla MK, Wang Q, Dennis J, Naven M, Abubakar M, Ahearn TU, Alonso MR, Andrulis IL, Antoniou AC, Auvinen P, Behrens S, Bermisheva MA, Bogdanova NV, Bojesen SE, Brüning T, Byers HJ, Camp NJ, Campbell A, Castelao JE, Cessna MH, Chang-Claude J, Chanock SJ, Chenevix-Trench G, Collée JM, Czene K, Dörk T, Eriksson M, Evans DG, Fasching PA, Figueroa JD, Flyger H, Gago-Dominguez M, García-Closas M, Glendon G, González-Neira A, Grassmann F, Gronwald J, Guénel P, Hadjisavvas A, Haeberle L, Hall P, Hamann U, Hartman M, Ho PJ, Hooning MJ, Hoppe R, Howell A, Jakubowska A, Khusnutdinova EK, Kristensen VN, Li J, Lim J, Lindblom A, Liu J, Lophatananon A, Mannermaa A, Mavroudis DA, Mensenkamp AR, Milne RL, Muir KR, Newman WG, Obi N, Panayiotidis MI, Park SK, Park-Simon TW, Peterlongo P, Radice P, Rashid MU, Rhenius V, Saloustros E, Sawyer EJ, Schmidt MK, Seibold P, Shah M, Southey MC, Teo SH, Tomlinson I, Torres D, Truong T, van de Beek I, van der Hout AH, Wendt CC, Dunning AM, Pharoah PDP, Devilee P, Easton DF, James PA, Spurdle AB. Co-observation of germline pathogenic variants in breast cancer predisposition genes: Results from analysis of the BRIDGES sequencing dataset. Am J Hum Genet 2024; 111:2059-2069. [PMID: 39096911 PMCID: PMC11393698 DOI: 10.1016/j.ajhg.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/05/2024] Open
Abstract
Co-observation of a gene variant with a pathogenic variant in another gene that explains the disease presentation has been designated as evidence against pathogenicity for commonly used variant classification guidelines. Multiple variant curation expert panels have specified, from consensus opinion, that this evidence type is not applicable for the classification of breast cancer predisposition gene variants. Statistical analysis of sequence data for 55,815 individuals diagnosed with breast cancer from the BRIDGES sequencing project was undertaken to formally assess the utility of co-observation data for germline variant classification. Our analysis included expected loss-of-function variants in 11 breast cancer predisposition genes and pathogenic missense variants in BRCA1, BRCA2, and TP53. We assessed whether co-observation of pathogenic variants in two different genes occurred more or less often than expected under the assumption of independence. Co-observation of pathogenic variants in each of BRCA1, BRCA2, and PALB2 with the remaining genes was less frequent than expected. This evidence for depletion remained after adjustment for age at diagnosis, study design (familial versus population-based), and country. Co-observation of a variant of uncertain significance in BRCA1, BRCA2, or PALB2 with a pathogenic variant in another breast cancer gene equated to supporting evidence against pathogenicity following criterion strength assignment based on the likelihood ratio and showed utility in reclassification of missense BRCA1 and BRCA2 variants identified in BRIDGES. Our approach has applicability for assessing the value of co-observation as a predictor of variant pathogenicity in other clinical contexts, including for gene-specific guidelines developed by ClinGen Variant Curation Expert Panels.
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Affiliation(s)
- Aimee L Davidson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Cristina Fortuno
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Marc Naven
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - M Rosario Alonso
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, 70210 Kuopio, Finland; Institute of Clinical Medicine, Oncology, University of Eastern Finland, 70210 Kuopio, Finland; Department of Oncology, Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina A Bermisheva
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany; Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany; N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk 223040, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, 44789 Bochum, Germany
| | - Helen J Byers
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS) Foundation, Complejo Hospitalario Universitario de Santiago, SERGAS, 36312 Vigo, Spain
| | - Melissa H Cessna
- Department of Pathology, Intermountain Health, Murray, UT, USA; Intermountain Biorepository, Intermountain Health, Murray, UT, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA
| | - Georgia Chenevix-Trench
- Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - D Gareth Evans
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Jonine D Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA; Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh, Edinburgh EH16 4UX, UK; Cancer Research UK Edinburgh Centre, The University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Manuela Gago-Dominguez
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Gallega de IDIS, Cancer Genetics and Epidemiology Group, Genomic Medicine Group, 15706 Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20850, USA; The Division of Genetics and Epidemiology, The Institute of Cancer Research, London SM2 5NG, UK
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden; Health and Medical University, Potsdam, Germany
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, 70-115 Szczecin, Poland
| | - Pascal Guénel
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussay, CESP, 94805 Villejuif, France
| | - Andreas Hadjisavvas
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Lothar Haeberle
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65 Stockholm, Sweden; Department of Oncology, Södersjukhuset, 118 83 Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Department of Surgery, National University Hospital and National University Health System, Singapore City 119228, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore City 119228, Singapore
| | - Peh Joo Ho
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A(∗)STAR), Singapore City 138672, Singapore
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, the Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; University of Tübingen, 72074 Tübingen, Germany
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, 70-115 Szczecin, Poland; Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 171-252 Szczecin, Poland
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa 450054, Russia; Federal State Budgetary Educational Institution of Higher Education, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Vessela N Kristensen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0379 Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Jingmei Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A(∗)STAR), Singapore City 138672, Singapore
| | - Joanna Lim
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Jenny Liu
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore City 117549, Singapore; Department of General Surgery, Ng Teng Fong General Hospital, Singapore City 609606, Singapore
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, 70210 Kuopio, Finland; Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210 Kuopio, Finland; Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Dimitrios A Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10 Heraklion, Greece
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, 6525 Nijmegen GA, the Netherlands
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
| | - Kenneth R Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
| | - William G Newman
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Nadia Obi
- Institute for Occupational and Maritime Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Mihalis I Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 03080, Korea; Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul 03080, Korea; Cancer Research Institute, Seoul National University, Seoul 03080, Korea
| | | | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS - the AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Paolo Radice
- Predictive Medicine: Molecular Bases of Genetic Risk, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), 20133 Milan, Italy
| | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore 54000, Pakistan
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Emmanouil Saloustros
- Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Elinor J Sawyer
- School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands; Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Petra Seibold
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia; Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia; Department of Surgery, Faculty of Medicine, University of Malaya, UM Cancer Research Institute, Kuala Lumpur 50603, Malaysia
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford OX3 7LF, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota 110231, Colombia
| | - Thérèse Truong
- Paris-Saclay University, UVSQ, INSERM, Gustave Roussay, CESP, 94805 Villejuif, France
| | - Irma van de Beek
- Department of Clinical Genetics, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Annemieke H van der Hout
- Department of Genetics, University Medical Center Groningen, University Groningen, 9713 GZ Groningen, the Netherlands
| | - Camilla C Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 118 83 Stockholm, Sweden
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul D P Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90069, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul A James
- Parkville Familial Cancer Centre, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia.
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Dong Z, Wang Y, Zhang J, Zhu F, Liu Z, Kang Y, Lin M, Shi H. Analyzing the effects of BRCA1/2 variants on mRNA splicing by minigene assay. J Hum Genet 2023; 68:65-71. [PMID: 36446827 DOI: 10.1038/s10038-022-01077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022]
Abstract
As BRCA1/2 gene sequencing become more extensive, a large number VUS (variants of uncertain significance) emerge rapidly. Verifying the splicing effect is an effective means for VUS reclassification. The Minigene Assay platform was established and its reliability was verified in this article. 47 BRCA1 or BRCA2 variants were selected and performed to validate their effect on mRNA splicing. The results showed that, a total of 16 variants were experimentally proved to have effects on mRNA splicing, among which 14 variants were shown to cause truncated proteins by Sanger sequencing. While the other two variants, BRCA2 c.7976 + 3 A > G and BRCA1 c.5152 + 3_5152 + 4insT was analyzed to cause 57 bp and 26 bp base in-frame deletion, respectively. The remaining 31 variants were not shown to cause mRNA splicing abnormity, including several sites at the edge of exons, which were predicted to affect splicing of mRNA by multiple bioinformatic software. Based on our experimental results, 37 variants were reclassified by ACMG rules. Our study showed that experimental splicing analysis was effectual for variants classification, and multiple functional assay or clinical data were also necessary for comprehensive judgment of variants.
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Affiliation(s)
- Zhouhuan Dong
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Yun Wang
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Jing Zhang
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Fengwei Zhu
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China
| | - Zhiyuan Liu
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Yajun Kang
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Mingyuan Lin
- Amoy Diagnostics Co., Ltd., Xiamen, 361027, PR China
| | - Huaiyin Shi
- The First Medical Center, Chinese PLA General Hospital & PLA Medical School, Beijing, 100853, PR China.
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Identification of a Splice Variant (c.5074+3A>C) of BRCA1 by RNA Sequencing and TOPO Cloning. Genes (Basel) 2021; 12:genes12060810. [PMID: 34073420 PMCID: PMC8229931 DOI: 10.3390/genes12060810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022] Open
Abstract
Grading the pathogenicity of BRCA1/2 variants has great clinical importance in patient treatment as well as in the prevention and screening of hereditary breast and ovarian cancer (HBOC). For accurate evaluation, confirming the splicing effect of a possible splice site variant is crucial. We report a significant splicing variant (c.5074+3A>C) in BRCA1 in a patient with recurrent ovarian cancer. Next-generation sequencing (NGS) of BRCA1/2 from patient’s peripheral blood identified the variant, which was strongly suspected of being a splicing mutation based on in silico predictions. Direct RNA analysis yielded multiple transcripts, and TOPO cloning of the complementary DNA (cDNA) and Sanger sequencing revealed an aberrant transcript with an insertion of the first 153 bp of intron 17, and another transcript with the 153 bp insertion along with an exon 18 deletion. A premature termination codon was presumed to be formed by the 153 bp partial intron retention common to the two transcripts. Therefore, BRCA1 c.5074+3A>C was classified as a likely pathogenic variant. Our findings show that active use of functional studies of variants suspected of altered splicing are of great help in classifying them.
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Lu K, Smith M, Kanderi T, Verbiar J, Laspe J, Bair L, Torp L. Genetic Variation and the Role of Multigene Panel Testing for Hereditary Breast Cancer: A Single-Institution Experience. Cureus 2021; 13:e14637. [PMID: 34046273 PMCID: PMC8140759 DOI: 10.7759/cureus.14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Breast cancer is the second leading cause of cancer death in women. There are multiple pathogenic mutations in addition to BRCA1/2 that are implicated in causing hereditary breast cancer. Methods and results We conducted a retrospective analysis of 1568 patients with breast cancer diagnosed between January 1, 2015, and December 31, 2018. The age range is 23-87. Among the study population, 26% had genetic testing and 8% of those were found to carry a pathogenic variant, as designated in NCCN (National Comprehensive Cancer Network) Guidelines. Of that 8%, 3.4% were BRCA1 and BRCA2 mutations, and the rest were other prevalent pathogenic variants. Discussion Expanded panel testing has the potential to increase the detection rate of pathogenic variants compared to testing for BRCA1/2 alone. Diagnostic accuracy of genetic causes of breast cancer has a significant clinical impact on patients and their families in terms of targeted treatment and prevention strategies. There is a strong need for further understanding of genetic patterns and variations in hereditary breast cancer. Awareness of the possibility of moderate to low penetrance genes and variants of uncertain significance (VUS) is important to assist with appropriate genetic counseling. We believe that physicians should consider re-testing with an expanded panel if patients previously had BRCA1 and BRCA2 testings only with a negative result as it may identify additional mutations.
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Affiliation(s)
- Kit Lu
- Medical Oncology, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
| | - Meagan Smith
- Genetics, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
| | - Tejaswi Kanderi
- Internal Medicine, University of Pittsburgh Medical Center Harrisburg, Harrisburg, USA
| | - Julia Verbiar
- Genetics, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
| | - Jennifer Laspe
- Medicine, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
| | - Latesha Bair
- Medicine, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
| | - Lisa Torp
- Breast Care Center, University of Pittsburgh Medical Center Hillman Cancer Center, Harrisburg, USA
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Improving Genetic Testing in Hereditary Cancer by RNA Analysis: Tools to Prioritize Splicing Studies and Challenges in Applying American College of Medical Genetics and Genomics Guidelines. J Mol Diagn 2020; 22:1453-1468. [PMID: 33011440 DOI: 10.1016/j.jmoldx.2020.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 11/23/2022] Open
Abstract
RNA analyses are a potent tool to identify spliceogenic effects of DNA variants, although they are time-consuming and cannot always be performed. We present splicing assays of 20 variants that represent a variety of mutation types in 10 hereditary cancer genes and attempt to incorporate these results into American College of Medical Genetics and Genomics (ACMG) classification guidelines. Sixteen single-nucleotide variants, 3 exon duplications, and 1 single-exon deletion were selected and prioritized by in silico algorithms. RNA was extracted from short-term lymphocyte cultures to perform RT-PCR and Sanger sequencing, and allele-specific expression was assessed whenever possible. Aberrant transcripts were detected in 14 variants (70%). Variant interpretation was difficult, especially comparing old classification standards to generic ACMG guidelines and a proposal was devised to weigh functional analyses at RNA level. According to the ACMG guidelines, only 12 variants were reclassified as pathogenic/likely pathogenic because the other two variants did not gather enough evidence. This study highlights the importance of RNA studies to improve variant classification. However, it also indicates the challenge of incorporating these results into generic ACMG guidelines and the need to refine these criteria gene specifically. Nevertheless, 60% of variants were reclassified, thus improving genetic counseling and surveillance for carriers of these variants.
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The yield of full BRCA1/2 genotyping in Israeli Arab high-risk breast/ovarian cancer patients. Breast Cancer Res Treat 2019; 178:231-237. [PMID: 31368036 DOI: 10.1007/s10549-019-05379-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE While the spectrum of germline mutations in BRCA1/2 genes in the Israeli Jewish population has been extensively studied, there is a paucity of data pertaining to Israeli Arab high-risk cases. METHODS Consecutive Israeli Arab breast and/or ovarian cancer patients were recruited using an ethically approved protocol from January 2012 to February 2019. All ovarian cancer cases were referred for BRCA genotyping. Breast cancer patients were offered BRCA sequencing and deletion/duplication analysis after genetic counseling, if the calculated risk for carrying a BRCA mutation by risk prediction algorithms was ≥10%. RESULTS Overall, 188 patients participated; 150 breast cancer cases (median age at diagnosis: 40 years, range 22-67) and 38 had ovarian cancer (median age at diagnosis: 52.5 years, range 26-79). Of genotyped cases, 18 (10%) carried one of 12 pathogenic or likely-pathogenic variants, 12 in BRCA1, 6 in BRCA2. Only one was a rearrangement. Three variants recurred in more than one case; one was detected in five seemingly unrelated families. The detection rate for all breast cancer cases was 4%, 5% in bilateral breast cancer cases and 3% if breast cancer was diagnosed < 40 years. Of patients with ovarian cancer, 12/38 (32%) were carriers; the detection rate reached 75% (3/4) among patients diagnosed with both breast and ovarian cancer. CONCLUSIONS The overall yield of comprehensive BRCA1/2 testing in high-risk Israeli Arab individuals is low in breast cancer patients, and much higher in ovarian cancer patients. These results may guide optimal cancer susceptibility testing strategy in the Arab-Israeli population.
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7
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Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel) 2019; 11:cancers11030295. [PMID: 30832263 PMCID: PMC6468917 DOI: 10.3390/cancers11030295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Highly penetrant variants of BRCA1/2 genes are involved in hereditary predisposition to breast and ovarian cancer. The detection of pathogenic BRCA variants has a considerable clinical impact, allowing appropriate cancer-risk management. However, a major drawback is represented by the identification of variants of uncertain significance (VUS). Many VUS potentially affect mRNA splicing, making transcript analysis an essential step for the definition of their pathogenicity. Here, we characterize the impact on splicing of ten BRCA1/2 variants. Aberrant splicing patterns were demonstrated for eight variants whose alternative transcripts were fully characterized. Different events were observed, including exon skipping, intron retention, and usage of de novo and cryptic splice sites. Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. Partial/complete splicing effect and quantitative contribution of different isoforms were assessed, leading to variant classification according to Evidence-based Network for the Interpretation of Mutant Alleles (ENIGMA) consortium guidelines. Two variants could be classified as pathogenic and two as likely benign, while due to a partial splicing effect, six variants remained of uncertain significance. The association with an undefined tumor risk justifies caution in recommending aggressive risk-reduction treatments, but prevents the possibility of receiving personalized therapies with potential beneficial effect. This indicates the need for applying additional approaches for the analysis of variants resistant to classification by gene transcript analyses.
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8
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Baert A, Machackova E, Coene I, Cremin C, Turner K, Portigal-Todd C, Asrat MJ, Nuk J, Mindlin A, Young S, MacMillan A, Van Maerken T, Trbusek M, McKinnon W, Wood ME, Foulkes WD, Santamariña M, de la Hoya M, Foretova L, Poppe B, Vral A, Rosseel T, De Leeneer K, Vega A, Claes KBM. Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11. Hum Mutat 2018; 39:515-526. [PMID: 29280214 DOI: 10.1002/humu.23390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/03/2017] [Accepted: 12/17/2017] [Indexed: 12/31/2022]
Abstract
For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies.
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Affiliation(s)
- Annelot Baert
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ilse Coene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Carol Cremin
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | - Jennifer Nuk
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- BC Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andree MacMillan
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland and Labrador, Canada
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Wendy McKinnon
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - Marie E Wood
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - William D Foulkes
- Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
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9
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Jarhelle E, Riise Stensland HMF, Mæhle L, Van Ghelue M. Characterization of BRCA1 and BRCA2 variants found in a Norwegian breast or ovarian cancer cohort. Fam Cancer 2017; 16:1-16. [PMID: 27495310 DOI: 10.1007/s10689-016-9916-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Molecular screening of these two genes in patients with a family history of breast or ovarian cancer has revealed pathogenic variants as well as genetic variants of unknown significance (VUS). These VUS may cause a challenge in the genetic counseling process regarding clinical management of the patient and the family. We investigated 32 variants previously detected in 33 samples from patients with a family history of breast or ovarian cancer. cDNA was analyzed for alternative transcripts and selected missense variants located in the BRCT domains of BRCA1 were assessed for their trans-activation ability. Although an extensive cDNA analysis was done, only three of the 32 variants appeared to affect the splice-process (BRCA1 c.213-5T>A, BRCA1 c.5434C>G and BRCA2 c.68-7T>A). In addition, two variants located in the BRCT domains of BRCA1 (c.5075A>C p.Asp1692Ala and c.5513T>G p.Val1838Gly) were shown to abolish the BRCT domain trans-activation ability, whereas BRCA1 c.5125G>A p.Gly1709Arg exhibited equal trans-activation capability as the WT domain. These functional studies may offer further insights into the pathogenicity of certain identified variants; however, this assay is only applicable for a subset of missense variants.
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Affiliation(s)
- Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Hilde Monica Frostad Riise Stensland
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway.
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10
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Rodríguez-Balada M, Roig B, Martorell L, Melé M, Salvat M, Vilella E, Borràs J, Gumà J. In silico, in vitro and case-control analyses as an effective combination for analyzing BRCA1 and BRCA2 unclassified variants in a population-based sample. Cancer Genet 2016; 209:487-492. [PMID: 27886673 DOI: 10.1016/j.cancergen.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/12/2016] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
Ascertaining the clinical consequences of BRCA1 and BRCA2 variants of uncertain significance (VUS) is currently indispensable for providing effective genetic counseling and preventive actions for families with hereditary breast and ovarian cancer (HBOC). To this end, we conducted a combination of in silico prediction and cDNA splicing analyses of 13 BRCA1 and 10 BRCA2 VUS identified in our cohort as well as a case-control analysis in a population-based sample of 10 recurrent VUS. We observed consistent results between the in silico predictions and sequencing analyses for all analyzed VUS. An abnormal cDNA pattern was observed for variants c.212+1G>A and c.5278-1G>A in BRCA1 and c.516+2T>A and c.8168A>G in BRCA2 according to in silico splicing prediction. A case-control study of VUS confirmed the polymorphisms of the c.67+62A>G, c.7008-62A>G and c.8851G>A BRCA2 variants previously published. c.4068G>A in the BRCA2 gene can also be considered a polymorphism due to its occurrence at a frequency greater than 1% in our population. Our study shows that employing population-based analysis and a combination of several in silico methods yields highly accurate information, resulting in a reliable tool for selecting variants for cDNA sequencing analysis in routine cancer genetic counseling units.
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Affiliation(s)
- Marta Rodríguez-Balada
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Bàrbara Roig
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, C/Sant Llorenç, Reus, Spain
| | - Mireia Melé
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Mònica Salvat
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, C/Sant Llorenç, Reus, Spain
| | - Joan Borràs
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Josep Gumà
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain.
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11
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de Juan I, Palanca S, Domenech A, Feliubadaló L, Segura Á, Osorio A, Chirivella I, de la Hoya M, Sánchez AB, Infante M, Tena I, Díez O, Garcia-Casado Z, Vega A, Teulé À, Barroso A, Pérez P, Durán M, Carrasco E, Juan-Fita MJ, Murria R, Llop M, Barragan E, Izquierdo Á, Benítez J, Caldés T, Salas D, Bolufer P. BRCA1 and BRCA2 mutations in males with familial breast and ovarian cancer syndrome. Results of a Spanish multicenter study. Fam Cancer 2016; 14:505-13. [PMID: 26026974 DOI: 10.1007/s10689-015-9814-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Male breast cancer (MBC) is a rare disease that represents <1% of all breast cancers (BCs). We analyze the results of a multicenter study performed in Spanish familial MBC including family history of hereditary breast and ovarian cancer syndrome (HBOCS) and clinicopathological features. We also study the relationship between BRCA1/BRCA2 mutational status in male relatives affected with cancer (MAC) and, family history and tumor types. The study included 312 men index cases with family history of HBOCS and 61 MAC BRCA1/2 mutation-carriers. Family history, histological grade (HG), clinicopathological and immunohistochemistry data were collected. BRCA1/2 mutation analyses were performed by direct sequencing or screening methods and the large rearrangements by multiplex ligation dependent probe amplification. We found 49 mutation-carriers (15.7%), 95.9% with BRCA2 mutations. BRCA2 mutation-carriers were associated with families with at least one MBC and one BC in female (type II; p = 0.05). Strong association were found between the presence of pathogenic mutations in MBCs and the advanced HG (p = 0.003). c.658_659delTG, c.2808_2811delACAA, c.6275_6276delTT and c.9026_9030delATCAT were the most prevalent mutations. In 61 MAC we found 20 mutations in BRCA1 and 41 in BRCA2. For MAC we show that mutational status was differentially associated with family history (p = 0.018) and tumor type, being BRCA2 mutations linked with BC and prostatic cancer (p = 0.018). MBC caused by BRCA1/2 mutations define two types of MBCs. The most frequent caused by BRCA2 mutation linked to type II families and the rarest one attributed to BRCA1 mutation. Tumor associated with MAC suggest that only BRCA2 mutations have to do with a specific type of cancer (BC and prostatic cancer); but the linkage to tumors is questionable for BRCA1 mutations .
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Affiliation(s)
- Inmaculada de Juan
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain.
| | - Sarai Palanca
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain
| | - Asunción Domenech
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat (Barcelona), Spain
| | - Ángel Segura
- Unit of Genetic Counseling in Cancer, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre and Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Isabel Chirivella
- Unit of Genetic Counseling in Cancer, Hospital Clínico, Valencia, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, IdISSC, Hospital Clínico San Carlos, Madrid, Spain
| | - Ana Beatriz Sánchez
- Unit of Genetic Counseling in Cancer, Hospital General de Elche, Elche, Spain
| | - Mar Infante
- Cancer Genetic Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Valladolid, Spain
| | - Isabel Tena
- Unit of Genetic Counseling in Cancer, Hospital General de Castellón, Castellón, Spain
| | - Orland Díez
- Oncogenetics Laboratory, University Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Zaida Garcia-Casado
- Laboratory of Molecular Biology, Valencian Institute of Oncology (IVO), Valencia, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela, Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat (Barcelona), Spain
| | - Alicia Barroso
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre and Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Pedro Pérez
- Department of Oncology, IdISSC, Hospital Clínico San Carlos, Madrid, Spain
| | - Mercedes Durán
- Cancer Genetic Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Valladolid, Spain
| | - Estela Carrasco
- High Risk and Prevention Unit, University Hospital Vall d'Hebron, Barcelona, Spain
| | | | - Rosa Murria
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain
| | - Marta Llop
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain
| | - Eva Barragan
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain
| | - Ángel Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat (Barcelona), Spain
| | - Javier Benítez
- Human Genetics Group and Genotyping Unit, Human Cancer Genetics Programme, Spanish National Cancer Research Centre and Spanish Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, IdISSC, Hospital Clínico San Carlos, Madrid, Spain
| | - Dolores Salas
- General Directorate Public Health and Centre for Public Health Research (CSISP), Valencia Genetic Counseling in Cancer Programme, Valencia, Spain
| | - Pascual Bolufer
- Laboratory of Molecular Biology, Service of Clinical Analysis, University and Polytechnic Hospital La Fe, Escuela de Enfermería 7ª planta. Avd. Campanar 21, Valencia, 46009, Spain.
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12
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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13
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Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. BMC Med Genomics 2016; 9:19. [PMID: 27067391 PMCID: PMC4828881 DOI: 10.1186/s12920-016-0178-5] [Citation(s) in RCA: 22] [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: 08/11/2015] [Accepted: 03/15/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Sequencing of both healthy and disease singletons yields many novel and low frequency variants of uncertain significance (VUS). Complete gene and genome sequencing by next generation sequencing (NGS) significantly increases the number of VUS detected. While prior studies have emphasized protein coding variants, non-coding sequence variants have also been proven to significantly contribute to high penetrance disorders, such as hereditary breast and ovarian cancer (HBOC). We present a strategy for analyzing different functional classes of non-coding variants based on information theory (IT) and prioritizing patients with large intragenic deletions. METHODS We captured and enriched for coding and non-coding variants in genes known to harbor mutations that increase HBOC risk. Custom oligonucleotide baits spanning the complete coding, non-coding, and intergenic regions 10 kb up- and downstream of ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, and TP53 were synthesized for solution hybridization enrichment. Unique and divergent repetitive sequences were sequenced in 102 high-risk, anonymized patients without identified mutations in BRCA1/2. Aside from protein coding and copy number changes, IT-based sequence analysis was used to identify and prioritize pathogenic non-coding variants that occurred within sequence elements predicted to be recognized by proteins or protein complexes involved in mRNA splicing, transcription, and untranslated region (UTR) binding and structure. This approach was supplemented by in silico and laboratory analysis of UTR structure. RESULTS 15,311 unique variants were identified, of which 245 occurred in coding regions. With the unified IT-framework, 132 variants were identified and 87 functionally significant VUS were further prioritized. An intragenic 32.1 kb interval in BRCA2 that was likely hemizygous was detected in one patient. We also identified 4 stop-gain variants and 3 reading-frame altering exonic insertions/deletions (indels). CONCLUSIONS We have presented a strategy for complete gene sequence analysis followed by a unified framework for interpreting non-coding variants that may affect gene expression. This approach distills large numbers of variants detected by NGS to a limited set of variants prioritized as potential deleterious changes.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada
- Cytognomix Inc., London, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada.
- Department of Computer Science, Faculty of Science, Western University, London, N6A 2C1, Canada.
- Cytognomix Inc., London, Canada.
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, N6A 2C1, Canada.
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14
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Investigating the effect of 28 BRCA1 and BRCA2 mutations on their related transcribed mRNA. Breast Cancer Res Treat 2016; 155:253-60. [PMID: 26780556 DOI: 10.1007/s10549-015-3676-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/31/2015] [Indexed: 01/25/2023]
Abstract
Germline inactivating mutations in the BRCA1 and BRCA2 genes are responsible for hereditary breast and ovarian cancer syndrome (HBOCS). Genetic testing of these genes identifies a significant proportion of variants of uncertain significance (VUS). Elucidation of the clinical impact of these variants is an important challenge in genetic diagnostics and counseling. In this study, we assess the RNA effect of 28 BRCA1 and BRCA2 VUS identified in our set of HBOCS families with the aim of gaining insight into their clinical relevance. mRNA was extracted from VUS carriers and controls lymphocytes cultured for 5-6 days and treated with puromycin. RNA was reverse transcribed to perform transcriptional analysis for the study of splicing aberrations. In silico prediction tools were used to select those variants most likely to affect the RNA splicing process. Six out of the 28 variants analyzed showed an aberrant splicing pattern and could therefore be classified as probably pathogenic mutations. Reclassification of VUS improves the genetic counseling and clinical surveillance of carriers of these mutations and highlights the importance of RNA studies in routine diagnostic laboratories.
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Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer. Sci Rep 2014; 4:7063. [PMID: 25394353 PMCID: PMC4231324 DOI: 10.1038/srep07063] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/29/2014] [Indexed: 12/22/2022] Open
Abstract
Somatic mutations reported in large-scale breast cancer (BC) sequencing studies primarily consist of protein coding mutations. mRNA splicing mutation analyses have been limited in scope, despite their prevalence in Mendelian genetic disorders. We predicted splicing mutations in 442 BC tumour and matched normal exomes from The Cancer Genome Atlas Consortium (TCGA). These splicing defects were validated by abnormal expression changes in these tumours. Of the 5,206 putative mutations identified, exon skipping, leaky or cryptic splicing was confirmed for 988 variants. Pathway enrichment analysis of the mutated genes revealed mutations in 9 NCAM1-related pathways, which were significantly increased in samples with evidence of lymph node metastasis, but not in lymph node-negative tumours. We suggest that comprehensive reporting of DNA sequencing data should include non-trivial splicing analyses to avoid missing clinically-significant deleterious splicing mutations, which may reveal novel mutated pathways present in genetic disorders.
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Santos C, Peixoto A, Rocha P, Pinto P, Bizarro S, Pinheiro M, Pinto C, Henrique R, Teixeira MR. Pathogenicity evaluation of BRCA1 and BRCA2 unclassified variants identified in Portuguese breast/ovarian cancer families. J Mol Diagn 2014; 16:324-34. [PMID: 24607278 DOI: 10.1016/j.jmoldx.2014.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 01/14/2014] [Accepted: 01/24/2014] [Indexed: 01/18/2023] Open
Abstract
Hereditary breast/ovarian cancer syndrome is caused by germline deleterious mutations in BRCA1 and BRCA2. A major problem of genetic testing and counseling is the finding of variants of uncertain significance (VUS). We sought to ascertain the pathogenicity of 25 BRCA1 and BRCA2 VUS identified in Portuguese families during genetic testing. We performed cosegregation analysis of VUS with cancer in families, evaluated their frequency in unaffected controls, and looked for loss of heterozygosity in tumors. In addition, three different bioinformatic algorithms were used (Interactive Biosoftware, ESEfinder, and PolyPhen). Finally, six VUS located in exon-intron boundaries were analyzed by RT-PCR. We found that seven variants segregated with the disease, six variants co-occurred with a pathogenic mutation in the same gene, and four variants co-occurred with a deleterious mutation in the other BRCA gene. By RT-PCR, we observed that four variants (BRCA1 c.4484G>T, BRCA2 c.682-2A>C, BRCA2 c.8488-1G>A, and BRCA2 c.8954-5A>G) disrupted splicing. After the combined analysis, we were able to classify 4 splicing variants as pathogenic mutations, 16 variants as neutral, and 3 variants as polymorphisms; only 2 variants remained classified as VUS. This work highlights the contribution of DNA, RNA, and in silico data to assess the pathogenicity of BRCA1/2 VUS, which, in turn, allows more accurate genetic counseling and clinical management of the families carrying them.
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Affiliation(s)
- Catarina Santos
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Patrícia Rocha
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Pedro Pinto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Susana Bizarro
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Manuela Pinheiro
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute, Porto, Portugal; Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal; Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal.
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Whiley PJ, de la Hoya M, Thomassen M, Becker A, Brandão R, Pedersen IS, Montagna M, Menéndez M, Quiles F, Gutiérrez-Enríquez S, De Leeneer K, Tenés A, Montalban G, Tserpelis D, Yoshimatsu T, Tirapo C, Raponi M, Caldes T, Blanco A, Santamariña M, Guidugli L, de Garibay GR, Wong M, Tancredi M, Fachal L, Ding YC, Kruse T, Lattimore V, Kwong A, Chan TL, Colombo M, De Vecchi G, Caligo M, Baralle D, Lázaro C, Couch F, Radice P, Southey MC, Neuhausen S, Houdayer C, Fackenthal J, Hansen TVO, Vega A, Diez O, Blok R, Claes K, Wappenschmidt B, Walker L, Spurdle AB, Brown MA. Comparison of mRNA splicing assay protocols across multiple laboratories: recommendations for best practice in standardized clinical testing. Clin Chem 2013; 60:341-52. [PMID: 24212087 DOI: 10.1373/clinchem.2013.210658] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Accurate evaluation of unclassified sequence variants in cancer predisposition genes is essential for clinical management and depends on a multifactorial analysis of clinical, genetic, pathologic, and bioinformatic variables and assays of transcript length and abundance. The integrity of assay data in turn relies on appropriate assay design, interpretation, and reporting. METHODS We conducted a multicenter investigation to compare mRNA splicing assay protocols used by members of the ENIGMA (Evidence-Based Network for the Interpretation of Germline Mutant Alleles) consortium. We compared similarities and differences in results derived from analysis of a panel of breast cancer 1, early onset (BRCA1) and breast cancer 2, early onset (BRCA2) gene variants known to alter splicing (BRCA1: c.135-1G>T, c.591C>T, c.594-2A>C, c.671-2A>G, and c.5467+5G>C and BRCA2: c.426-12_8delGTTTT, c.7988A>T, c.8632+1G>A, and c.9501+3A>T). Differences in protocols were then assessed to determine which elements were critical in reliable assay design. RESULTS PCR primer design strategies, PCR conditions, and product detection methods, combined with a prior knowledge of expected alternative transcripts, were the key factors for accurate splicing assay results. For example, because of the position of primers and PCR extension times, several isoforms associated with BRCA1, c.594-2A>C and c.671-2A>G, were not detected by many sites. Variation was most evident for the detection of low-abundance transcripts (e.g., BRCA2 c.8632+1G>A Δ19,20 and BRCA1 c.135-1G>T Δ5q and Δ3). Detection of low-abundance transcripts was sometimes addressed by using more analytically sensitive detection methods (e.g., BRCA2 c.426-12_8delGTTTT ins18bp). CONCLUSIONS We provide recommendations for best practice and raise key issues to consider when designing mRNA assays for evaluation of unclassified sequence variants.
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Affiliation(s)
- Phillip J Whiley
- Genetics & Computational Biology Division, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
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de Garibay GR, Acedo A, García-Casado Z, Gutiérrez-Enríquez S, Tosar A, Romero A, Garre P, Llort G, Thomassen M, Díez O, Pérez-Segura P, Díaz-Rubio E, Velasco EA, Caldés T, de la Hoya M. Capillary electrophoresis analysis of conventional splicing assays: IARC analytical and clinical classification of 31 BRCA2 genetic variants. Hum Mutat 2013; 35:53-7. [PMID: 24123850 DOI: 10.1002/humu.22456] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 09/23/2013] [Indexed: 11/07/2022]
Abstract
Rare sequence variants in "high-risk" disease genes, often referred as unclassified variants (UVs), pose a serious challenge to genetic testing. However, UVs resulting in splicing alterations can be readily assessed by in vitro assays. Unfortunately, analytical and clinical interpretation of these assays is often challenging. Here, we explore this issue by conducting splicing assays in 31 BRCA2 genetic variants. All variants were assessed by RT-PCR followed by capillary electrophoresis and direct sequencing. If assays did not produce clear-cut outputs (Class-2 or Class-5 according to analytical International Agency for Research on Cancer guidelines), we performed qPCR and/or minigene assays. The latter were performed with a new splicing vector (pSAD) developed by authors of the present manuscript (patent #P201231427 CSIC). We have identified three clinically relevant Class-5 variants (c.682-2A>G, c.7617+1G>A, and c.8954-5A>G), and 27 analytical Class-2 variants (not inducing splicing alterations). In addition, we demonstrate that rs9534262 (c.7806-14T>C) is a BRCA2 splicing quantitative trait locus.
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Affiliation(s)
- Gorka Ruiz de Garibay
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
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Apostolou P, Fostira F. Hereditary breast cancer: the era of new susceptibility genes. BIOMED RESEARCH INTERNATIONAL 2013; 2013:747318. [PMID: 23586058 PMCID: PMC3618918 DOI: 10.1155/2013/747318] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/21/2013] [Indexed: 12/20/2022]
Abstract
Breast cancer is the most common malignancy among females. 5%-10% of breast cancer cases are hereditary and are caused by pathogenic mutations in the considered reference BRCA1 and BRCA2 genes. As sequencing technologies evolve, more susceptible genes have been discovered and BRCA1 and BRCA2 predisposition seems to be only a part of the story. These new findings include rare germline mutations in other high penetrant genes, the most important of which include TP53 mutations in Li-Fraumeni syndrome, STK11 mutations in Peutz-Jeghers syndrome, and PTEN mutations in Cowden syndrome. Furthermore, more frequent, but less penetrant, mutations have been identified in families with breast cancer clustering, in moderate or low penetrant genes, such as CHEK2, ATM, PALB2, and BRIP1. This paper will summarize all current data on new findings in breast cancer susceptibility genes.
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Affiliation(s)
- Paraskevi Apostolou
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research “Demokritos”, Athens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research “Demokritos”, Athens, Greece
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Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations. PLoS One 2013; 8:e57173. [PMID: 23451180 PMCID: PMC3579815 DOI: 10.1371/journal.pone.0057173] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022] Open
Abstract
Several unclassified variants (UVs) have been identified in splicing regions of disease-associated genes and their characterization as pathogenic mutations or benign polymorphisms is crucial for the understanding of their role in disease development. In this study, 24 UVs located at BRCA1 and BRCA2 splice sites were characterized by transcripts analysis. These results were used to evaluate the ability of nine bioinformatics programs in predicting genetic variants causing aberrant splicing (spliceogenic variants) and the nature of aberrant transcripts. Eleven variants in BRCA1 and 8 in BRCA2, including 8 not previously characterized at transcript level, were ascertained to affect mRNA splicing. Of these, 16 led to the synthesis of aberrant transcripts containing premature termination codons (PTCs), 2 to the up-regulation of naturally occurring alternative transcripts containing PTCs, and one to an in-frame deletion within the region coding for the DNA binding domain of BRCA2, causing the loss of the ability to bind the partner protein DSS1 and ssDNA. For each computational program, we evaluated the rate of non-informative analyses, i.e. those that did not recognize the natural splice sites in the wild-type sequence, and the rate of false positive predictions, i.e., variants incorrectly classified as spliceogenic, as a measure of their specificity, under conditions setting sensitivity of predictions to 100%. The programs that performed better were Human Splicing Finder and Automated Splice Site Analyses, both exhibiting 100% informativeness and specificity. For 10 mutations the activation of cryptic splice sites was observed, but we were unable to derive simple criteria to select, among the different cryptic sites predicted by the bioinformatics analyses, those actually used. Consistent with previous reports, our study provides evidences that in silico tools can be used for selecting splice site variants for in vitro analyses. However, the latter remain mandatory for the characterization of the nature of aberrant transcripts.
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Acedo A, Sanz DJ, Durán M, Infante M, Pérez-Cabornero L, Miner C, Velasco EA. Comprehensive splicing functional analysis of DNA variants of the BRCA2 gene by hybrid minigenes. Breast Cancer Res 2012; 14:R87. [PMID: 22632462 PMCID: PMC3446350 DOI: 10.1186/bcr3202] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/15/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
Introduction The underlying pathogenic mechanism of a large fraction of DNA variants of disease-causing genes is the disruption of the splicing process. We aimed to investigate the effect on splicing of the BRCA2 variants c.8488-1G > A (exon 20) and c.9026_9030del (exon 23), as well as 41 BRCA2 variants reported in the Breast Cancer Information Core (BIC) mutation database. Methods DNA variants were analyzed with the splicing prediction programs NNSPLICE and Human Splicing Finder. Functional analyses of candidate variants were performed by lymphocyte RT-PCR and/or hybrid minigene assays. Forty-one BIC variants of exons 19, 20, 23 and 24 were bioinformatically selected and generated by PCR-mutagenesis of the wild type minigenes. Results Lymphocyte RT-PCR of c.8488-1G > A showed intron 19 retention and a 12-nucleotide deletion in exon 20, whereas c.9026_9030del did not show any splicing anomaly. Minigene analysis of c.8488-1G > A displayed the aforementioned aberrant isoforms but also exon 20 skipping. We further evaluated the splicing outcomes of 41 variants of four BRCA2 exons by minigene analysis. Eighteen variants presented splicing aberrations. Most variants (78.9%) disrupted the natural splice sites, whereas four altered putative enhancers/silencers and had a weak effect. Fluorescent RT-PCR of minigenes accurately detected 14 RNA isoforms generated by cryptic site usage, exon skipping and intron retention events. Fourteen variants showed total splicing disruptions and were predicted to truncate or eliminate essential domains of BRCA2. Conclusions A relevant proportion of BRCA2 variants are correlated with splicing disruptions, indicating that RNA analysis is a valuable tool to assess the pathogenicity of a particular DNA change. The minigene system is a straightforward and robust approach to detect variants with an impact on splicing and contributes to a better knowledge of this gene expression step.
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Affiliation(s)
- Alberto Acedo
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Valladolid, Sanz y Forés 3, Valladolid 47003, Spain
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