1
|
Sadowski CE, Kohlstedt D, Meisel C, Keller K, Becker K, Mackenroth L, Rump A, Schröck E, Wimberger P, Kast K. BRCA1/2 missense mutations and the value of in-silico analyses. Eur J Med Genet 2017; 60:572-577. [PMID: 28807866 DOI: 10.1016/j.ejmg.2017.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants. METHODS We conducted mutation analysis of BRCA1/2 in 523 index patients with suspected hereditary breast and ovarian cancer (HBOC). Classification of the genetic variants was performed according to the German Consortium (GC)-HBOC database. Additionally, all missense variants were classified by the following three in-silico prediction tools: SIFT, Mutation Taster (MT2) and PolyPhen2 (PPH2). RESULTS Overall 201 different variants, 68 of which constituted missense variants were ranked as pathogenic, neutral, or unknown. The classification of missense variants by in-silico tools resulted in a higher amount of pathogenic mutations (25% vs. 13.2%) compared to the GC-HBOC-classification. Altogether, more than fifty percent (38/68, 55.9%) of missense variants were ranked differently. Sensitivity of in-silico-tools for mutation prediction was 88.9% (PPH2), 100% (SIFT) and 100% (MT2). CONCLUSION We found a relevant discrepancy in variant classification by using in-silico prediction tools, resulting in potential overestimation and/or underestimation of cancer risk. More reliable, notably gene-specific, prediction tools and functional tests are needed to improve clinical counseling.
Collapse
Affiliation(s)
- Carolin E Sadowski
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Kohlstedt
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelia Meisel
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katja Keller
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Becker
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Luisa Mackenroth
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Andreas Rump
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Evelin Schröck
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karin Kast
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
2
|
Baert A, Depuydt J, Van Maerken T, Poppe B, Malfait F, Van Damme T, De Nobele S, Perletti G, De Leeneer K, Claes KBM, Vral A. Analysis of chromosomal radiosensitivity of healthy BRCA2 mutation carriers and non-carriers in BRCA families with the G2 micronucleus assay. Oncol Rep 2017; 37:1379-1386. [PMID: 28184943 PMCID: PMC5364849 DOI: 10.3892/or.2017.5407] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/03/2016] [Indexed: 01/07/2023] Open
Abstract
Breast cancer risk drastically increases in individuals with a heterozygous germline BRCA1 or BRCA2 mutation, while it is estimated to equal the population risk for relatives without the familial mutation (non-carriers). The aim of the present study was to use a G2 phase-specific micronucleus assay to investigate whether lymphocytes of healthy BRCA2 mutation carriers are characterized by increased radiosensitivity compared to controls without a family history of breast/ovarian cancer and how this relates to healthy non-carrier relatives. BRCA2 is active in homologous recombination, a DNA damage repair pathway, specifically active in the late S/G2 phase of the cell cycle. We found a significantly increased radiosensitivity in a cohort of healthy BRCA2 mutation carriers compared to individuals without a familial history of breast cancer (P=0.046; Mann-Whitney U test). At the individual level, 50% of healthy BRCA2 mutation carriers showed a radiosensitive phenotype (radiosensitivity score of 1 or 2), whereas 83% of the controls showed no radiosensitivity (P=0.038; one-tailed Fishers exact test). An odds ratio of 5 (95% CI, 1.07–23.47) indicated an association between the BRCA2 mutation and radiosensitivity in healthy mutation carriers. These results indicate the need for the gentle use of ionizing radiation for either diagnostic or therapeutic use in BRCA2 mutation carriers. We detected no increased radiosensitivity in the non-carrier relatives.
Collapse
Affiliation(s)
- Annelot Baert
- Department of Basic Medical Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Julie Depuydt
- Department of Basic Medical Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Tom Van Maerken
- Department of Pediatrics and Medical Genetics, Ghent University, B-9000 Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Tim Van Damme
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Sylvia De Nobele
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Gianpaolo Perletti
- Department of Basic Medical Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Kathleen B M Claes
- Center for Medical Genetics, Ghent University Hospital, B-9000 Ghent, Belgium
| | - Anne Vral
- Department of Basic Medical Sciences, Ghent University, B-9000 Ghent, Belgium
| |
Collapse
|
4
|
Guidugli L, Carreira A, Caputo SM, Ehlen A, Galli A, Monteiro ANA, Neuhausen SL, Hansen TVO, Couch FJ, Vreeswijk MPG. Functional assays for analysis of variants of uncertain significance in BRCA2. Hum Mutat 2013; 35:151-64. [PMID: 24323938 DOI: 10.1002/humu.22478] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/28/2013] [Indexed: 01/11/2023]
Abstract
Missense variants in the BRCA2 gene are routinely detected during clinical screening for pathogenic mutations in patients with a family history of breast and ovarian cancer. These subtle changes frequently remain of unknown clinical significance because of the lack of genetic information that may help establish a direct correlation with cancer predisposition. Therefore, alternative ways of predicting the pathogenicity of these variants are urgently needed. Since BRCA2 is a protein involved in important cellular mechanisms such as DNA repair, replication, and cell cycle control, functional assays have been developed that exploit these cellular activities to explore the impact of the variants on protein function. In this review, we summarize assays developed and currently utilized for studying missense variants in BRCA2. We specifically depict details of each assay, including variants of uncertain significance analyzed, and describe a validation set of (genetically) proven pathogenic and neutral missense variants to serve as a golden standard for the validation of each assay. Guidelines are proposed to enable implementation of laboratory-based methods to assess the impact of the variant on cancer risk.
Collapse
Affiliation(s)
- Lucia Guidugli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|