1
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Mishra AP, Hartford S, Chittela RK, Sahu S, Kharat SS, Alvaro-Aranda L, Contreras-Perez A, Sullivan T, Martin BK, Albaugh M, Southon E, Burkett S, Karim B, Carreira A, Tessarollo L, Sharan SK. Characterization of BRCA2 R3052Q variant in mice supports its functional impact as a low-risk variant. Cell Death Dis 2023; 14:753. [PMID: 37980415 PMCID: PMC10657400 DOI: 10.1038/s41419-023-06289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Pathogenic variants in BRCA2 are known to significantly increase the lifetime risk of developing breast and ovarian cancers. Sequencing-based genetic testing has resulted in the identification of thousands of BRCA2 variants that are considered to be variants of uncertain significance (VUS) because the disease risk associated with them is unknown. One such variant is p.Arg3052Gln, which has conflicting interpretations of pathogenicity in the ClinVar variant database. Arginine at position 3052 in BRCA2 plays an important role in stabilizing its C-terminal DNA binding domain. We have generated a knock-in mouse model expressing this variant to examine its role on growth and survival in vivo. Homozygous as well as hemizygous mutant mice are viable, fertile and exhibit no overt phenotype. While we did not observe any hematopoietic defects in adults, we did observe a marked reduction in the in vitro proliferative ability of fetal liver cells that were also hypersensitive to PARP inhibitor, olaparib. In vitro studies performed on embryonic and adult fibroblasts derived from the mutant mice showed significant reduction in radiation induced RAD51 foci formation as well as increased genomic instability after mitomycin C treatment. We observed mis-localization of a fraction of R3052Q BRCA2 protein to the cytoplasm which may explain the observed in vitro phenotypes. Our findings suggest that BRCA2 R3052Q should be considered as a hypomorphic variant.
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Affiliation(s)
- Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne Hartford
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Rajani Kant Chittela
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Applied Genomics Section, Bhabha Atomic Research Center, Trombay, Mumbai, 400085, India
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Lucia Alvaro-Aranda
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Aida Contreras-Perez
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Betty K Martin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Aura Carreira
- Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid, Spain
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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2
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Shinde S, Satpute DP, Behera SK, Kumar D. Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification. ACS OMEGA 2022; 7:30447-30461. [PMID: 36061650 PMCID: PMC9434626 DOI: 10.1021/acsomega.2c03851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Male breast cancer (MBC) is a relatively rare disease, but emerging data recommend the development of novel therapeutics considering its alarming threats. Compared to female breast cancer (FBC), MBC is reportedly associated with inferior outcomes (poor survival) owing to their late diagnosis and lack of adequate treatment. Treatment typically correlates with FBC, involving surgical removal of the breast tissue along with chemo/hormonal/radiation therapy, the tamoxifen being a standard adjuvant. Considering the distinct immunophenotypic (implying different pathogenesis and progression) differences from FBC, the identification of diagnostics, prognostics, and therapeutics for MBC is highly desirable. In this context, we have analyzed the most deleterious nsSNPs of BRCA2, a human tumor suppressor gene constituting the potential biomarker for tumors including MBC, to predict the structural changes associated with the mutants hampering the normal protein-protein and protein-ligand interactions, resulting in MBC progression. Among 27 nsSNPs confined to 21 rsIDs pertaining to MBC, the 19 nsSNPs constituting 14 rsIDs have been predicted as highly deleterious. We believe that these nsSNPs could serve as potential biomarkers for diagnostic and prognostic purposes and could be the pivotal target for MBC drug discovery. Subsequently, the study highlights the exploration of the key nsSNPs (of BRCA2 associated with the MBC) and its applications toward the identification of therapeutic hit TIP006136 following the homology modeling, virtual screening of 5284 phytochemicals retrieved from the TIPdb (a database of phytochemicals from indigenous plants in Taiwan) database, molecular docking (against native and mutant BRCA2), dynamic simulations (against native and mutant BRCA2), density functional theory (DFT), and molecular electrostatic potential. To the best of our knowledge, this is the first report to use diverse computational modules to investigate the important nsSNPs of BRCA2 related to MBC, implying that TIP006136 could be a potential hit and must be studied further (in vitro and in vivo) to establish its anticancer property and efficacy against MBC.
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Affiliation(s)
- Sangita
Dattatray Shinde
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Parshuram Satpute
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Santosh Kumar Behera
- Department
of Biotechnology, National Institute of
Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
| | - Dinesh Kumar
- Department
of Medicinal Chemistry, National Institute
of Pharmaceutical Education and Research (NIPER) − Ahmadabad, Palaj, Gandhinagar 382355, Gujarat, India
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3
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Jimenez-Sainz J, Krysztofiak A, Garbarino J, Rogers F, Jensen RB. The Pathogenic R3052W BRCA2 Variant Disrupts Homology-Directed Repair by Failing to Localize to the Nucleus. Front Genet 2022; 13:884210. [PMID: 35711920 PMCID: PMC9197106 DOI: 10.3389/fgene.2022.884210] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
The BRCA2 germline missense variant, R3052W, resides in the DNA binding domain and has been previously classified as a pathogenic allele. In this study, we sought to determine how R3052W alters the cellular functions of BRCA2 in the DNA damage response. The BRCA2 R3052W mutated protein exacerbates genome instability, is unable to rescue homology-directed repair, and fails to complement cell survival following exposure to PARP inhibitors and crosslinking drugs. Surprisingly, despite anticipated defects in DNA binding or RAD51-mediated DNA strand exchange, the BRCA2 R3052W protein mislocalizes to the cytoplasm precluding its ability to perform any DNA repair functions. Rather than acting as a simple loss-of-function mutation, R3052W behaves as a dominant negative allele, likely by sequestering RAD51 in the cytoplasm.
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Affiliation(s)
| | | | | | | | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, United States
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4
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Khan MA, Siddiqui MQ, Kuligina E, Varma AK. Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. Int J Biol Macromol 2022; 209:716-724. [PMID: 35413318 DOI: 10.1016/j.ijbiomac.2022.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair mechanism of DNA double-strand breaks and interstrand cross-links by Homologous recombination. Germline mutations identified in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer. Missense mutations are identified all over the gene, including the DNA binding region of BRCA2 that interacts with FANCD2. However, the majority of these missense mutations are classified as 'Variants of Uncertain Significance' due to a lack of structural, functional and clinical correlations. Therefore, multi-disciplinary in-silico, in-vitro and biophysical approaches have been explored to characterize an unclassified missense mutation, BRCA2 Arg2502Cys, identified from a case-control study. Circular-dichroism and Fluorescence spectroscopy show that the Arg2502Cys mutation in hBRCA2 (residues 2350-2545) decreases the α-helical/β-sheet propensity of the wild-type protein and perturb the tertiary structure conformation. Molecular dynamics simulations revealed alteration in the intramolecular H-bonds, overall compactness and stability of the hydrophobic core were observed in the mutant protein. Principle component analysis indicated that Arg2502Cys mutant exhibited comparatively large conformational transitions and periodic fluctuation. Therefore, to our conclusion, BRCA2 Arg2502Cys mutant perturbed the structural integrity and conformational dynamics of BRCA2.
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Affiliation(s)
- Mudassar Ali Khan
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Present address: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Ekaterina Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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5
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Jimenez-Sainz J, Jensen RB. Imprecise Medicine: BRCA2 Variants of Uncertain Significance (VUS), the Challenges and Benefits to Integrate a Functional Assay Workflow with Clinical Decision Rules. Genes (Basel) 2021; 12:genes12050780. [PMID: 34065235 PMCID: PMC8161351 DOI: 10.3390/genes12050780] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Pathological mutations in homology-directed repair (HDR) genes impact both future cancer risk and therapeutic options for patients. HDR is a high-fidelity DNA repair pathway for resolving DNA double-strand breaks throughout the genome. BRCA2 is an essential protein that mediates the loading of RAD51 onto resected DNA breaks, a key step in HDR. Germline mutations in BRCA2 are associated with an increased risk for breast, ovarian, prostate, and pancreatic cancer. Clinical findings of germline or somatic BRCA2 mutations in tumors suggest treatment with platinum agents or PARP inhibitors. However, when genetic analysis reveals a variant of uncertain significance (VUS) in the BRCA2 gene, precision medicine-based decisions become complex. VUS are genetic changes with unknown pathological impact. Current statistics indicate that between 10–20% of BRCA sequencing results are VUS, and of these, more than 50% are missense mutations. Functional assays to determine the pathological outcome of VUS are urgently needed to provide clinical guidance regarding cancer risk and treatment options. In this review, we provide a brief overview of BRCA2 functions in HDR, describe how BRCA2 VUS are currently assessed in the clinic, and how genetic and biochemical functional assays could be integrated into the clinical decision process. We suggest a multi-step workflow composed of robust and accurate functional assays to correctly evaluate the potential pathogenic or benign nature of BRCA2 VUS. Success in this precision medicine endeavor will offer actionable information to patients and their physicians.
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Affiliation(s)
- Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
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6
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Sullivan T, Thirthagiri E, Chong CE, Stauffer S, Reid S, Southon E, Hassan T, Ravichandran A, Wijaya E, Lim J, Taib NAM, Fadzli F, Yip CH, Hartman M, Li J, van Dam RM, North SL, Das R, Easton DF, Biswas K, Teo SH, Sharan SK. Epidemiological and ES cell-based functional evaluation of BRCA2 variants identified in families with breast cancer. Hum Mutat 2021; 42:200-212. [PMID: 33314489 PMCID: PMC7919386 DOI: 10.1002/humu.24154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/29/2020] [Accepted: 11/28/2020] [Indexed: 01/06/2023]
Abstract
The discovery of high-risk breast cancer susceptibility genes, such as Breast cancer associated gene 1 (BRCA1) and Breast cancer associated gene 2 (BRCA2) has led to accurate identification of individuals for risk management and targeted therapy. The rapid decline in sequencing costs has tremendously increased the number of individuals who are undergoing genetic testing world-wide. However, given the significant differences in population-specific variants, interpreting the results of these tests can be challenging especially for novel genetic variants in understudied populations. Here we report the characterization of novel variants in the Malaysian and Singaporean population that consist of different ethnic groups (Malays, Chinese, Indian, and other indigenous groups). We have evaluated the functional significance of 14 BRCA2 variants of uncertain clinical significance by using multiple in silico prediction tools and examined their frequency in a cohort of 7840 breast cancer cases and 7928 healthy controls. In addition, we have used a mouse embryonic stem cell (mESC)-based functional assay to assess the impact of these variants on BRCA2 function. We found these variants to be functionally indistinguishable from wild-type BRCA2. These variants could fully rescue the lethality of Brca2-null mESCs and exhibited no sensitivity to six different DNA damaging agents including a poly ADP ribose polymerase inhibitor. Our findings strongly suggest that all 14 evaluated variants are functionally neutral. Our findings should be valuable in risk assessment of individuals carrying these variants.
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Affiliation(s)
- Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eswary Thirthagiri
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Servier, Kuala Lumpur, Malaysia.,Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Chan-Eng Chong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Tiara Hassan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Aravind Ravichandran
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India.,SASTRA University, Thirumalaisamudram, Thanjavur, Tamil Nadu, India
| | | | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | - Farhana Fadzli
- Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | | | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Jingmei Li
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore.,Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Susan L North
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ranabir Das
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, UM Cancer Research Institute, University of Malaya Medical Center, Kuala Lumpur, Malaysia
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
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7
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Yang Y, Hong C, Liang JW, Gruber S, Parmigiani G, Idos G, Braun D. A likelihood-based approach to assessing frequency of pathogenicity among variants of unknown significance in susceptibility genes. Stat Med 2020; 40:593-606. [PMID: 33120437 DOI: 10.1002/sim.8791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 08/24/2020] [Accepted: 10/12/2020] [Indexed: 11/12/2022]
Abstract
Commercialized multigene panel testing brings unprecedented opportunities to understand germline genetic contributions to hereditary cancers. Most genetic testing companies classify the pathogenicity of variants as pathogenic, benign, or variants of unknown significance (VUSs). The unknown pathogenicity of VUSs poses serious challenges to clinical decision-making. This study aims to assess the frequency of VUSs that are likely pathogenic in disease-susceptibility genes. Using estimates of probands' probability of having a pathogenic mutation (ie, the carrier score) based on a family history probabilistic risk prediction model, we assume the carrier score distribution for probands with VUSs is a mixture of the carrier score distribution for probands with positive results and the carrier score distribution for probands with negative results. Under this mixture model, we propose a likelihood-based approach to assess the frequency of pathogenicity among probands with VUSs, while accounting for the existence of possible pathogenic mutations on genes not tested. We conducted simulations to assess the performance of the approach and show that under various settings, the approach performs well with very little bias in the estimated proportion of VUSs that are likely pathogenic. We also estimate the positive predictive value across the entire range of carrier scores. We apply our approach to the USC-Stanford Hereditary Cancer Panel Testing cohort, and estimate the proportion of probands that have VUSs in BRCA1/2 that are likely pathogenic to be 10.12% [95%CI: 0%, 43.04%]. This approach will enable clinicians to target high-risk patients who have VUSs, allowing for early prevention interventions.
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Affiliation(s)
- Yunqi Yang
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Christine Hong
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jane W Liang
- City of Hope National Medical Cente, Duarte, California, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Stephen Gruber
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Giovanni Parmigiani
- City of Hope National Medical Cente, Duarte, California, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gregory Idos
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Danielle Braun
- City of Hope National Medical Cente, Duarte, California, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Padilla N, Moles-Fernández A, Riera C, Montalban G, Özkan S, Ootes L, Bonache S, Díez O, Gutiérrez-Enríquez S, de la Cruz X. BRCA1- and BRCA2-specific in silico tools for variant interpretation in the CAGI 5 ENIGMA challenge. Hum Mutat 2019; 40:1593-1611. [PMID: 31112341 DOI: 10.1002/humu.23802] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 11/09/2022]
Abstract
BRCA1 and BRCA2 (BRCA1/2) germline variants disrupting the DNA protective role of these genes increase the risk of hereditary breast and ovarian cancers. Correct identification of these variants then becomes clinically relevant, because it may increase the survival rates of the carriers. Unfortunately, we are still unable to systematically predict the impact of BRCA1/2 variants. In this article, we present a family of in silico predictors that address this problem, using a gene-specific approach. For each protein, we have developed two tools, aimed at predicting the impact of a variant at two different levels: Functional and clinical. Testing their performance in different datasets shows that specific information compensates the small number of predictive features and the reduced training sets employed to develop our models. When applied to the variants of the BRCA1/2 (ENIGMA) challenge in the fifth Critical Assessment of Genome Interpretation (CAGI 5) we find that these methods, particularly those predicting the functional impact of variants, have a good performance, identifying the large compositional bias towards neutral variants in the CAGI sample. This performance is further improved when incorporating to our prediction protocol estimates of the impact on splicing of the target variant.
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Affiliation(s)
- Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR). Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Casandra Riera
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR). Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Selen Özkan
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR). Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Lars Ootes
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR). Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | | | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR). Universitat Autònoma de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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9
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Heczkova M, Machackova E, Macinga P, Gallmeier E, Cahova M, Spicak J, Jirsa M, Foretova L, Hucl T. Functional evaluation of variants of unknown significance in the BRCA2 gene identified in genetic testing. Cancer Biol Ther 2019; 20:633-641. [PMID: 30638113 DOI: 10.1080/15384047.2018.1550566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Heterozygous germline BRCA2 mutations predispose to breast, ovarian, pancreatic and other types of cancer. The presence of a pathogenic mutation in patients or their family members warrants close surveillance or prophylactic surgery. Besides clearly pathogenic mutations, variants leading only to a single amino acid substitution are often identified. The influence of such variants on cancer risk is often unknown, making their presence a major clinical problem. When genetic methods are insufficient to classify these variants, functional assays with various cellular models are performed. We developed and applied a new syngeneic model of human cancer cells to test all variants of unknown significance in exon 18 identified by genetic testing of high-risk cancer patients in the Czech Republic, via introduction of constructs containing each of these variants into the wild-type allele of BRCA2-heterozygous DLD1 cells (BRCA2wt/Δex11). We found unaffected DNA repair function of BRCA2 in cell lines BRCA27997G>C/Δex11, BRCA28111C>T/Δex11, BRCA28149G>T/Δex11, BRCA28182G>A/Δex11, and BRCA28182G>T/Δex11, whereas the cell line BRCA28168A>G/Δex11 and the nonsense mutation carrying line BRCA28305G>T/Δex11 did affect protein function. Targeting the BRCA2 wild-type allele with a construct carrying the variant c.7988A> G resulted in incorporation exclusively into the already defective allele in all viable clones, strongly suggesting a detrimental phenotype. Our model thus offers a valuable tool for the functional evaluation of unclassified variants in the BRCA2 gene and provides a stable and distributable cellular resource for further research.
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Affiliation(s)
- Marie Heczkova
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Eva Machackova
- b Department of Cancer Epidemiology and Genetics , Masaryk Memorial Cancer Institute , Brno , Czech Republic
| | - Peter Macinga
- c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Eike Gallmeier
- d Department of Internal Medicine , Philipps University of Marburg , Marburg , Germany
| | - Monika Cahova
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Julius Spicak
- c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Milan Jirsa
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
| | - Lenka Foretova
- b Department of Cancer Epidemiology and Genetics , Masaryk Memorial Cancer Institute , Brno , Czech Republic
| | - Tomas Hucl
- a Center for Experimental Medicine , Institute of Clinical and Experimental Medicine , Prague , Czech Republic.,c Department of Gastroenterology and Hepatology , Institute of Clinical and Experimental Medicine , Prague , Czech Republic
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10
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Lüscher B, Bütepage M, Eckei L, Krieg S, Verheugd P, Shilton BH. ADP-Ribosylation, a Multifaceted Posttranslational Modification Involved in the Control of Cell Physiology in Health and Disease. Chem Rev 2017; 118:1092-1136. [PMID: 29172462 DOI: 10.1021/acs.chemrev.7b00122] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Posttranslational modifications (PTMs) regulate protein functions and interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use nicotinamide adenine dinucleotide (NAD+) to modify target proteins with ADP-ribose. This modification can occur as mono- or poly-ADP-ribosylation. The latter involves the synthesis of long ADP-ribose chains that have specific properties due to the nature of the polymer. ADP-Ribosylation is reversed by hydrolases that cleave the glycosidic bonds either between ADP-ribose units or between the protein proximal ADP-ribose and a given amino acid side chain. Here we discuss the properties of the different enzymes associated with ADP-ribosylation and the consequences of this PTM on substrates. Furthermore, the different domains that interpret either mono- or poly-ADP-ribosylation and the implications for cellular processes are described.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany
| | - Brian H Shilton
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University , 52057 Aachen, Germany.,Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario , Medical Sciences Building Room 332, London, Ontario Canada N6A 5C1
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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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12
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Shimelis H, Mesman RLS, Von Nicolai C, Ehlen A, Guidugli L, Martin C, Calléja FMGR, Meeks H, Hallberg E, Hinton J, Lilyquist J, Hu C, Aalfs CM, Aittomäki K, Andrulis I, Anton-Culver H, Arndt V, Beckmann MW, Benitez J, Bogdanova NV, Bojesen SE, Bolla MK, Borresen-Dale AL, Brauch H, Brennan P, Brenner H, Broeks A, Brouwers B, Brüning T, Burwinkel B, Chang-Claude J, Chenevix-Trench G, Cheng CY, Choi JY, Collée JM, Cox A, Cross SS, Czene K, Darabi H, Dennis J, Dörk T, Dos-Santos-Silva I, Dunning AM, Fasching PA, Figueroa J, Flyger H, García-Closas M, Giles GG, Glendon G, Guénel P, Haiman CA, Hall P, Hamann U, Hartman M, Hogervorst FB, Hollestelle A, Hopper JL, Ito H, Jakubowska A, Kang D, Kosma VM, Kristensen V, Lai KN, Lambrechts D, Marchand LL, Li J, Lindblom A, Lophatananon A, Lubinski J, Machackova E, Mannermaa A, Margolin S, Marme F, Matsuo K, Miao H, Michailidou K, Milne RL, Muir K, Neuhausen SL, Nevanlinna H, Olson JE, Olswold C, Oosterwijk JJC, Osorio A, Peterlongo P, Peto J, Pharoah PDP, Pylkäs K, Radice P, Rashid MU, Rhenius V, Rudolph A, Sangrajrang S, Sawyer EJ, Schmidt MK, Schoemaker MJ, Seynaeve C, Shah M, Shen CY, Shrubsole M, Shu XO, Slager S, Southey MC, Stram DO, Swerdlow A, Teo SH, Tomlinson I, Torres D, Truong T, van Asperen CJ, van der Kolk LE, Wang Q, Winqvist R, Wu AH, Yu JC, Zheng W, Zheng Y, Leary J, Walker L, Foretova L, Fostira F, Claes KBM, Varesco L, Moghadasi S, Easton DF, Spurdle A, Devilee P, Vrieling H, Monteiro ANA, Goldgar DE, Carreira A, Vreeswijk MPG, Couch FJ. BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer. Cancer Res 2017; 77:2789-2799. [PMID: 28283652 PMCID: PMC5508554 DOI: 10.1158/0008-5472.can-16-2568] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/14/2016] [Accepted: 03/03/2017] [Indexed: 12/20/2022]
Abstract
Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case-control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789-99. ©2017 AACR.
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Affiliation(s)
- Hermela Shimelis
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Romy L S Mesman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Asa Ehlen
- Genotoxic Stress and Cancer, Institut Curie, Orsay, France
| | - Lucia Guidugli
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | | | | | - Huong Meeks
- Cancer Control and Population Sciences, University of Utah, Salt Lake City, Utah
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jamie Hinton
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cora M Aalfs
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene 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, California
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias W Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - 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
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Anne-Lise Borresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Barbara Brouwers
- Laboratory of Experimental Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, Bochum, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Ching-Yu Cheng
- Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - 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
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - 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, United Kingdom
| | - Alison M Dunning
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- Department of Medicine, Division of Hematology and Oncology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, United Kingdom
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - 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
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University Health System, Singapore, Singapore
| | - Frans B Hogervorst
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Antoinette Hollestelle
- 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
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Veli-Matti Kosma
- 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
| | | | - Kah-Nyin Lai
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | | | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, United Kingdom
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - 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
| | - 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
| | - Keitaro Matsuo
- Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - 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
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, United Kingdom
- Institute of Population Health, University of Manchester, Manchester, United Kingdom
| | - 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, University of Helsinki, Helsinki, Finland
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Jan J C Oosterwijk
- Department of Genetics, University of Groningen, Groningen, the Netherlands
| | - Ana Osorio
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - 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 IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Valerie Rhenius
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, United Kingdom
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mitul Shah
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Chen-Yang Shen
- School of Public Health, China Medical University, Taichung, Taiwan
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Martha Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
- Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
| | - Soo H Teo
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 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
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lizet E van der Kolk
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Qin Wang
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - 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
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jyh-Cherng Yu
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jennifer Leary
- Westmead Millenium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Logan Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, Institute of Radioisotopes and Radiodiagnostic Products (IRRP), Athens, Greece
| | | | - Liliana Varesco
- Unit of Hereditary Cancers, IRCCS AOU San Martino, Genova, Italy
| | - Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Amanda Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Science, University of South Florida, Tampa, Florida
| | - David E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah, Salt Lake City, Utah
| | - Aura Carreira
- Genotoxic Stress and Cancer, Institut Curie, Orsay, France
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
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13
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Lai KN, Ho WK, Kang IN, Kang PCE, Phuah SY, Mariapun S, Yip CH, Mohd Taib NA, Teo SH. Characterization of BRCA1 and BRCA2 variants in multi-ethnic Asian cohort from a Malaysian case-control study. BMC Cancer 2017; 17:149. [PMID: 28222693 PMCID: PMC5320733 DOI: 10.1186/s12885-017-3099-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Background Genetic testing for BRCA1 and BRCA2 has led to the accurate identification of individuals at higher risk of cancer and the development of new therapies. Approximately 10-20% of the genetic testing for BRCA1 and BRCA2 leads to the identification of variants of uncertain significance (VUS), with higher proportions in Asians. We investigated the functional significance of 7 BRCA1 and 25 BRCA2 variants in a multi-ethnic Asian cohort using a case-control approach. Methods The MassARRAY genotyping was conducted in 1,394 Chinese, 406 Malay and 310 Indian breast cancer cases and 1,071 Chinese, 167 Malay and 255 Indian healthy controls. The association of individual variant with breast cancer risk was analyzed using logistic regression model adjusted for ethnicity, age and family history. Results Our study confirmed BRCA2 p.Ile3412Val is presented in >2% of unaffected women and is likely benign, and BRCA2 p.Ala1996Thr which is predicted to be likely pathogenic by in-silico models is presented in 2% of healthy Indian women suggesting that it may not be associated with breast cancer risk. Single-variant analysis suggests that BRCA1 p.Arg762Ser may be associated with breast cancer risk (OR = 7.4; 95% CI, 0.9–62.3; p = 0.06). Conclusions Our study shows that BRCA2 p.Ile3412Val and p.Ala1996Thr are likely benign and highlights the need for population-specific studies to determine the likely functional significance of population-specific variants. Our study also suggests that BRCA1 p.Arg762Ser may be associated with increased risk of breast cancer but other methods or larger studies are required to determine a more precise estimate of breast cancer risk. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3099-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kah Nyin Lai
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Weang Kee Ho
- Department of Applied Mathematics, Faculty of Engineering, The University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
| | - In Nee Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Peter Choon Eng Kang
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Sze Yee Phuah
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Shivaani Mariapun
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Cheng-Har Yip
- Subang Jaya Medical Centre, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia
| | - Soo-Hwang Teo
- Cancer Research Malaysia, 1 Jalan SS12/1A, 47500, Subang Jaya, Selangor, Malaysia. .,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, 50603, Kuala Lumpur, Malaysia.
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14
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Pesaran T, Karam R, Huether R, Li S, Farber-Katz S, Chamberlin A, Chong H, LaDuca H, Elliott A. Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. Int J Breast Cancer 2016; 2016:2469523. [PMID: 27822389 PMCID: PMC5086358 DOI: 10.1155/2016/2469523] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 09/04/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022] Open
Abstract
Genetic testing for hereditary breast cancer is an integral part of individualized care in the new era of precision medicine. The accuracy of an assay is reliant on not only the technology and bioinformatics analysis utilized but also the experience and infrastructure required to correctly classify genetic variants as disease-causing. Interpreting the clinical significance of germline variants identified by hereditary cancer testing is complex and has a significant impact on the management of patients who are at increased cancer risk. In this review we give an overview of our clinical laboratory's integrated approach to variant assessment. We discuss some of the nuances that should be considered in the assessment of genomic variants. In addition, we highlight lines of evidence such as functional assays and structural analysis that can be useful in the assessment of rare and complex variants.
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Affiliation(s)
- T. Pesaran
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Karam
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Huether
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Li
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Farber-Katz
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Chamberlin
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. Chong
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. LaDuca
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Elliott
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
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15
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Miolo G, Viel A, Canzonieri V, Baresic T, Buonadonna A, Santeufemia DA, Lara DP, Corona G. Association of the germline BRCA2 missense variation Glu2663Lys with high sensitivity to trabectedin-based treatment in soft tissue sarcoma. Cancer Biol Ther 2016; 17:1017-1021. [PMID: 27561088 DOI: 10.1080/15384047.2016.1219812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We report an interesting clinical case of a patient carrying a specific BRCA2 germline variant affected by bone and hepatic metastases from a high grade uterine stromal sarcoma who obtained a complete metabolic response after only 3 cycles of trabectedin treatment (1.5 mg/m2 given intravenously over 24 hours every 21 days). Molecular investigations linked this outstanding positive pharmacological response with the loss of heterozygosity (LOH) of the mutated BRCA2 gene. These data support the hypothesis that the response to trabectedin may be positively conditioned by the different DNA repair defects present in the neoplasm and that BRCAness tumor genotype is important in determining the efficacy of trabectedin-based chemotherapy.
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Affiliation(s)
- Gianmaria Miolo
- a Division of Medical Oncology B , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
| | - Alessandra Viel
- b Division of Experimental Oncology 1 , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
| | - Vincenzo Canzonieri
- c Department of Diagnostic Laboratories and Cell Therapy, Division of Pathology , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
| | - Tania Baresic
- d Nuclear Medicine Unit, IRCCS National Cancer Institute (CRO) , Aviano , Italy
| | - Angela Buonadonna
- a Division of Medical Oncology B , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
| | | | - Della Puppa Lara
- b Division of Experimental Oncology 1 , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
| | - Giuseppe Corona
- f Department of Translational Research , IRCCS, National Cancer Institute (CRO) , Aviano , Italy
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16
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Palmero EI, Alemar B, Schüler-Faccini L, Hainaut P, Moreira-Filho CA, Ewald IP, dos Santos PK, Ribeiro PLI, de Oliveira CB, Kelm FLC, Tavtigian S, Cossio SL, Giugliani R, Caleffi M, Ashton-Prolla P. Screening for germline BRCA1, BRCA2, TP53 and CHEK2 mutations in families at-risk for hereditary breast cancer identified in a population-based study from Southern Brazil. Genet Mol Biol 2016; 39:210-22. [PMID: 27223485 PMCID: PMC4910552 DOI: 10.1590/1678-4685-gmb-2014-0363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 11/24/2015] [Indexed: 01/22/2023] Open
Abstract
In Brazil, breast cancer is a public health care problem due to its high incidence and mortality rates. In this study, we investigated the prevalence of hereditary breast cancer syndromes (HBCS) in a population-based cohort in Brazils southernmost capital, Porto Alegre. All participants answered a questionnaire about family history (FH) of breast, ovarian and colorectal cancer and those with a positive FH were invited for genetic cancer risk assessment (GCRA). If pedigree analysis was suggestive of HBCS, genetic testing of the BRCA1, BRCA2, TP53, and CHEK2 genes was offered. Of 902 women submitted to GCRA, 214 had pedigrees suggestive of HBCS. Fifty of them underwent genetic testing: 18 and 40 for BRCA1/BRCA2 and TP53 mutation screening, respectively, and 7 for CHEK2 1100delC testing. A deleterious BRCA2 mutation was identified in one of the HBOC probands and the CHEK2 1100delC mutation occurred in one of the HBCC families. No deleterious germline alterations were identified in BRCA1 or TP53. Although strict inclusion criteria and a comprehensive testing approach were used, the suspected genetic risk in these families remains unexplained. Further studies in a larger cohort are necessary to better understand the genetic component of hereditary breast cancer in Southern Brazil.
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Affiliation(s)
- Edenir Inêz Palmero
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de
Barretos, Barretos, SP, Brazil
- Faculdade de Ciências da Saúde Dr. Paulo Prata, São Paulo, SP,
Brazil
| | - Bárbara Alemar
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | - Lavínia Schüler-Faccini
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
| | - Pierre Hainaut
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Carlos Alberto Moreira-Filho
- Centro de Pesquisa Experimental, Instituto de Educação e Pesquisa
Albert Einstein, São Paulo, SP, Brazil
- Departmento de Imunologia, Instituto de Ciências Biomédicas,
Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ingrid Petroni Ewald
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | - Patricia Koehler dos Santos
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
| | | | | | - Florence Le Calvez Kelm
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Sean Tavtigian
- Cluster of Molecular Carcinogenesis, International Agency for
Research on Cancer, Lyon, France
| | - Silvia Liliana Cossio
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Gastroenterologia, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto Giugliani
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
| | - Maira Caleffi
- Nucleo Mama Porto Alegre e Associação Hospitalar Moinhos de Vento,
Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós Graduação em Genética e Biologia Molecular,
Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório de Medicina Genômica, Hospital de Clinicas de Porto
Alegre, Porto Alegre, RS, Brazil
- Serviço de Genética Médica, Hospital de Clinicas de Porto Alegre,
Porto Alegre, RS, Brazil
- Departmento de Genética, Universidade Federal do Rio Grande do Sul,
Porto Alegre, RS, Brazil
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17
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Dodgshun AJ, Sexton-Oates A, Saffery R, Sullivan MJ. Biallelic FANCD1/BRCA2 mutations predisposing to glioblastoma multiforme with multiple oncogenic amplifications. Cancer Genet 2015; 209:53-6. [PMID: 26740091 DOI: 10.1016/j.cancergen.2015.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 11/18/2015] [Accepted: 11/20/2015] [Indexed: 12/16/2022]
Abstract
Fanconi anaemia (FA) caused by biallelic mutation in FANCD1/BRCA2 is rare but carries a high risk of early onset cancer. Medulloblastoma is well described in this cohort but reports of other brain tumours are uncommon. The molecular profile of tumours from FA patients is not well reported. A glioblastoma multiforme (GBM) from a 3-year-old patient with FA and confirmed biallelic BRCA2 mutations was submitted for methylation analysis. This revealed strong clustering with the K27 mutation subgroup and copy number analysis showed gains of chromosomes 1q, 4q, part of 7q, part of 8q and 17q with resultant amplifications of MDM4, CDK6, MET, MYC and PPM1D (WIP1). We also describe for the first time the germline mutation in BRCA2 c.8057T > C resulting in p.Leu2686Pro in our patient with confirmed FA. Biallelic BRCA2 mutations have predisposed to an aggressive and universally fatal subtype of childhood GBM in our patient. Copy number alterations and multiple oncogenic amplifications may be secondary to inherent chromosomal instability and this raises the question of what role BRCA2 may play in the development of GBM in children without FA.
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Affiliation(s)
- Andrew J Dodgshun
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia.
| | - Alexandra Sexton-Oates
- Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Michael J Sullivan
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria 3052, Australia; Murdoch Children's Research Institute, Melbourne, Victoria 3052, Australia
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18
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Zhang F, Shi J, Bian C, Yu X. Poly(ADP-Ribose) Mediates the BRCA2-Dependent Early DNA Damage Response. Cell Rep 2015; 13:678-689. [PMID: 26489468 DOI: 10.1016/j.celrep.2015.09.040] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/26/2015] [Accepted: 09/14/2015] [Indexed: 01/01/2023] Open
Abstract
Breast cancer susceptibility gene 2 (BRCA2) plays a key role in DNA damage repair for maintaining genomic stability. Previous studies have shown that BRCA2 contains three tandem oligonucleotide/oligosaccharide binding folds (OB-folds) that are involved in DNA binding during DNA double-strand break repair. However, the molecular mechanism of BRCA2 in DNA damage repair remains elusive. Unexpectedly, we found that the OB-folds of BRCA2 recognize poly(ADP-ribose) (PAR) and mediate the fast recruitment of BRCA2 to DNA lesions, which is suppressed by PARP inhibitor treatment. Cancer-associated mutations in the OB-folds of BRCA2 disrupt the interaction with PAR and abolish the fast relocation of BRCA2 to DNA lesions. The quickly recruited BRCA2 is important for the early recruitment of exonuclease 1(EXO1) and is involved in DNA end resection, the first step of homologous recombination (HR). Thus, these findings uncover a molecular mechanism by which BRCA2 participates in DNA damage repair.
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Affiliation(s)
- Feng Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Guilin Road 100, Shanghai 200234, China; Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA
| | - Jiazhong Shi
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA; Department of Cell Biology, the Third Military Medical University, Chongqing 400038, China
| | - Chunjing Bian
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA; Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91773, USA
| | - Xiaochun Yu
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, 1150 W. Medical Center Drive, 5560 MSRBII, Ann Arbor, MI 48109, USA; Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91773, USA.
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19
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Ronowicz A, Janaszak-Jasiecka A, Skokowski J, Madanecki P, Bartoszewski R, Bałut M, Seroczyńska B, Kochan K, Bogdan A, Butkus M, Pęksa R, Ratajska M, Kuźniacka A, Wasąg B, Gucwa M, Krzyżanowski M, Jaśkiewicz J, Jankowski Z, Forsberg L, Ochocka JR, Limon J, Crowley MR, Buckley PG, Messiaen L, Dumanski JP, Piotrowski A. Concurrent DNA Copy-Number Alterations and Mutations in Genes Related to Maintenance of Genome Stability in Uninvolved Mammary Glandular Tissue from Breast Cancer Patients. Hum Mutat 2015. [PMID: 26219265 DOI: 10.1002/humu.22845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Somatic mosaicism for DNA copy-number alterations (SMC-CNAs) is defined as gain or loss of chromosomal segments in somatic cells within a single organism. As cells harboring SMC-CNAs can undergo clonal expansion, it has been proposed that SMC-CNAs may contribute to the predisposition of these cells to genetic disease including cancer. Herein, the gross genomic alterations (>500 kbp) were characterized in uninvolved mammary glandular tissue from 59 breast cancer patients and matched samples of primary tumors and lymph node metastases. Array-based comparative genomic hybridization showed 10% (6/59) of patients harbored one to 359 large SMC-CNAs (mean: 1,328 kbp; median: 961 kbp) in a substantial portion of glandular tissue cells, distal from the primary tumor site. SMC-CNAs were partially recurrent in tumors, albeit with considerable contribution of stochastic SMC-CNAs indicating genomic destabilization. Targeted resequencing of 301 known predisposition and somatic driver loci revealed mutations and rare variants in genes related to maintenance of genomic integrity: BRCA1 (p.Gln1756Profs*74, p.Arg504Cys), BRCA2 (p.Asn3124Ile), NCOR1 (p.Pro1570Glnfs*45), PALB2 (p.Ser500Pro), and TP53 (p.Arg306*). Co-occurrence of gross SMC-CNAs along with point mutations or rare variants in genes responsible for safeguarding genomic integrity highlights the temporal and spatial neoplastic potential of uninvolved glandular tissue in breast cancer patients.
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Affiliation(s)
- Anna Ronowicz
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Jarosław Skokowski
- The Central Bank of Tissues and Genetic Specimens, Medical University of Gdansk, Gdansk, Poland.,Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Magdalena Bałut
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Barbara Seroczyńska
- The Central Bank of Tissues and Genetic Specimens, Medical University of Gdansk, Gdansk, Poland
| | - Kinga Kochan
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Adam Bogdan
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Krzyżanowski
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Janusz Jaśkiewicz
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | - Zbigniew Jankowski
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Lars Forsberg
- Department of Immunology, Genetics and Pathology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - J Renata Ochocka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Crowley
- Heflin Center for Genomic Sciences, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and SciLifeLab, Uppsala University, Uppsala, Sweden
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20
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Evaluation of BRCA1/2 mutational status among German and Austrian women with triple-negative breast cancer. J Cancer Res Clin Oncol 2015; 141:2005-12. [PMID: 25971625 DOI: 10.1007/s00432-015-1986-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/02/2015] [Indexed: 12/27/2022]
Abstract
PURPOSE Testing for BRCA1 and BRCA2 mutations in breast cancer patients is used to identify the risk of second primary cancers and the risk of cancer in the patients' family. Women with triple-negative breast cancer (TNBC) are thought to be more likely to be BRCA1/2 mutation carriers, but most national guidelines for genetic testing, including those used in Germany and Austria, do not consider receptor triple negativity. METHODS We determined the prevalence of BRCA1 and BRCA2 mutations within a cohort of 100 unselected TNBC cases, including patients from Germany and Austria to identify those BRCA-positive patients with a masked family history and who would have been missed due to respective current national guidelines. Double-stranded Sanger sequencing of all exons of BRCA1 and BRCA2, respectively, was performed. RESULTS We identified a total of 13 deleterious mutations in BRCA1 and a total of four deleterious mutations in BRCA2. The total rate of deleterious BRCA1/2 mutation carriers was 21 % in our cohort. Six novel mutations, including two deleterious mutations, have been identified, which have not been described in public mutation databases so far. According to current German and Austrian national guidelines for genetic testing, 38.1 and 52.4 %, respectively, of BRCA1/2 mutation carriers would have been overlooked. CONCLUSIONS We conclude that the prevalence of BRCA1 and BRCA2 mutations is high in TNBC patients and that BRCA1/2 mutations are not restricted to young women or patients with a positive family history. Receptor triple negativity should therefore be considered in BRCA1/2 genetic testing guidelines.
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21
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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22
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Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2014; 147:119-32. [PMID: 25085752 DOI: 10.1007/s10549-014-3065-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/15/2014] [Indexed: 02/06/2023]
Abstract
BRCA1 and BRCA2 sequencing analysis detects variants of uncertain clinical significance in approximately 2 % of patients undergoing clinical diagnostic testing in our laboratory. The reclassification of these variants into either a pathogenic or benign clinical interpretation is critical for improved patient management. We developed a statistical variant reclassification tool based on the premise that probands with disease-causing mutations are expected to have more severe personal and family histories than those having benign variants. The algorithm was validated using simulated variants based on approximately 145,000 probands, as well as 286 BRCA1 and 303 BRCA2 true variants. Positive and negative predictive values of ≥99 % were obtained for each gene. Although the history weighting algorithm was not designed to detect alleles of lower penetrance, analysis of the hypomorphic mutations c.5096G>A (p.Arg1699Gln; BRCA1) and c.7878G>C (p.Trp2626Cys; BRCA2) indicated that the history weighting algorithm is able to identify some lower penetrance alleles. The history weighting algorithm is a powerful tool that accurately assigns actionable clinical classifications to variants of uncertain clinical significance. While being developed for reclassification of BRCA1 and BRCA2 variants, the history weighting algorithm is expected to be applicable to other cancer- and non-cancer-related genes.
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23
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Clinical and molecular characterization of the BRCA2 p.Asn3124Ile variant reveals substantial evidence for pathogenic significance. Breast Cancer Res Treat 2014; 145:451-60. [DOI: 10.1007/s10549-014-2943-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/19/2022]
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24
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Jeyasekharan AD, Liu Y, Hattori H, Pisupati V, Jonsdottir AB, Rajendra E, Lee M, Sundaramoorthy E, Schlachter S, Kaminski C, Ofir-Rosenfeld Y, Sato K, Savill J, Ayoub N, Venkitaraman AR. A cancer-associated BRCA2 mutation reveals masked nuclear export signals controlling localization. Nat Struct Mol Biol 2013; 20:1191-8. [PMID: 24013206 PMCID: PMC3796201 DOI: 10.1038/nsmb.2666] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/25/2013] [Indexed: 02/02/2023]
Abstract
Germline missense mutations affecting a single BRCA2 allele predispose humans to cancer. Here we identify a protein-targeting mechanism that is disrupted by the cancer-associated mutation, BRCA2(D2723H), and that controls the nuclear localization of BRCA2 and its cargo, the recombination enzyme RAD51. A nuclear export signal (NES) in BRCA2 is masked by its interaction with a partner protein, DSS1, such that point mutations impairing BRCA2-DSS1 binding render BRCA2 cytoplasmic. In turn, cytoplasmic mislocalization of mutant BRCA2 inhibits the nuclear retention of RAD51 by exposing a similar NES in RAD51 that is usually obscured by the BRCA2-RAD51 interaction. Thus, a series of NES-masking interactions localizes BRCA2 and RAD51 in the nucleus. Notably, BRCA2(D2723H) decreases RAD51 nuclear retention even when wild-type BRCA2 is also present. Our findings suggest a mechanism for the regulation of the nucleocytoplasmic distribution of BRCA2 and RAD51 and its impairment by a heterozygous disease-associated mutation.
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Affiliation(s)
- Anand D Jeyasekharan
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Yang Liu
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Hiroyoshi Hattori
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Venkat Pisupati
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Asta Bjork Jonsdottir
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Eeson Rajendra
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Miyoung Lee
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | | | | | | | - Yaara Ofir-Rosenfeld
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Ko Sato
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Jane Savill
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Nabieh Ayoub
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
| | - Ashok R Venkitaraman
- The Medical Research Council Cancer Cell Unit, Hutchison-MRC Research Centre, Cambridge, UK
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25
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John AM, C GPD, Ebenazer A, Seshadri MS, Nair A, Rajaratnam S, Pai R. P.Arg82Leu von Hippel-Lindau (VHL) gene mutation among three members of a family with familial bilateral pheochromocytoma in India: molecular analysis and in silico characterization. PLoS One 2013; 8:e61908. [PMID: 23626751 PMCID: PMC3633967 DOI: 10.1371/journal.pone.0061908] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 03/14/2013] [Indexed: 11/18/2022] Open
Abstract
Various missense mutations in the VHL gene have been reported among patients with familial bilateral pheochromocytoma. However, the p.Arg82Leu mutation in the VHL gene described here among patients with familial bilateral pheochromocytoma, has never been reported previously in a germline configuration. Interestingly, long-term follow-up of these patients indicated that the mutation might have had little impact on the normal function of the VHL gene, since all of them have remained asymptomatic. We further attempted to correlate this information with the results obtained by in silico analysis of this mutation using SIFT, PhD-SNP SVM profile, MutPred, PolyPhen2, and SNPs&GO prediction tools. To gain, new mechanistic insight into the structural effect, we mapped the mutation on to 3D structure (PDB ID 1LM8). Further, we analyzed the structural level changes in time scale level with respect to native and mutant protein complexes by using 12 ns molecular dynamics simulation method. Though these methods predict the mutation to have a pathogenic potential, it remains to be seen if these patients will eventually develop symptomatic disease.
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Affiliation(s)
- Anulekha Mary John
- Department of Endocrinology, Christian Medical College, Vellore, Tamil Nadu, India
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26
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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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27
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Spugnesi L, Balia C, Collavoli A, Falaschi E, Quercioli V, Caligo MA, Galli A. Effect of the expression of BRCA2 on spontaneous homologous recombination and DNA damage-induced nuclear foci in Saccharomyces cerevisiae. Mutagenesis 2013; 28:187-95. [DOI: 10.1093/mutage/ges069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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28
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Becker AA, Graeser MK, Landwehr C, Hilger T, Baus W, Wappenschmidt B, Meindl A, Weber RG, Schmutzler RK. A 24-color metaphase-based radiation assay discriminates heterozygous BRCA2 mutation carriers from controls by chromosomal radiosensitivity. Breast Cancer Res Treat 2012; 135:167-75. [PMID: 22729890 DOI: 10.1007/s10549-012-2119-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/26/2012] [Indexed: 11/30/2022]
Abstract
Numerous allelic variants identified in the familial breast cancer and DNA repair genes BRCA1 and BRCA2 are of unknown impact on protein function or clinical relevance, referred to as unclassified variants (UCV). Lymphocytes from pathogenic BRCA1/2 mutation carriers exhibit an increased level of chromosomal damage after irradiation. We established a radiation assay for the discrimination of pathogenic BRCA2 variants versus controls based on the level of chromosomal damage upon irradiation (p < 0.001). As a consequence, lymphocytes from UCV carriers could be separated into two distinct groups with normal or diminished DNA double strand break repair capacity. Our results suggested that all five UCV tested were benign and that one family carried a putative mutation in an as yet undetected DNA-repair gene. Thus, our test may serve as a valuable tool that aids the classification of BRCA2 UCV, but very likely also of BRCA1 UCV or aberrations in other genes involved in the DNA-repair system.
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Affiliation(s)
- Alexandra A Becker
- Centre for Hereditary Breast and Ovarian Cancer, University Hospital Cologne, Kerpener Str. 62, 50931 Cologne, Germany
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29
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Biswas K, Das R, Eggington JM, Qiao H, North SL, Stauffer S, Burkett SS, Martin BK, Southon E, Sizemore SC, Pruss D, Bowles KR, Roa BB, Hunter N, Tessarollo L, Wenstrup RJ, Byrd RA, Sharan SK. Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay. Hum Mol Genet 2012; 21:3993-4006. [PMID: 22678057 DOI: 10.1093/hmg/dds222] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-nucleotide substitutions and small in-frame insertions or deletions identified in human breast cancer susceptibility genes BRCA1 and BRCA2 are frequently classified as variants of unknown clinical significance (VUS) due to the availability of very limited information about their functional consequences. Such variants can most reliably be classified as pathogenic or non-pathogenic based on the data of their co-segregation with breast cancer in affected families and/or their co-occurrence with a pathogenic mutation. Biological assays that examine the effect of variants on protein function can provide important information that can be used in conjunction with available familial data to determine the pathogenicity of VUS. In this report, we have used a previously described mouse embryonic stem (mES) cell-based functional assay to characterize eight BRCA2 VUS that affect highly conserved amino acid residues and map to the N-terminal PALB2-binding or the C-terminal DNA-binding domains. For several of these variants, very limited co-segregation information is available, making it difficult to determine their pathogenicity. Based on their ability to rescue the lethality of Brca2-deficient mES cells and their effect on sensitivity to DNA-damaging agents, homologous recombination and genomic integrity, we have classified these variants as pathogenic or non-pathogenic. In addition, we have used homology-based modeling as a predictive tool to assess the effect of some of these variants on the structural integrity of the C-terminal DNA-binding domain and also generated a knock-in mouse model to analyze the physiological significance of a residue reported to be essential for the interaction of BRCA2 with meiosis-specific recombinase, DMC1.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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30
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Masica DL, Sosnay PR, Cutting GR, Karchin R. Phenotype-optimized sequence ensembles substantially improve prediction of disease-causing mutation in cystic fibrosis. Hum Mutat 2012; 33:1267-74. [PMID: 22573477 DOI: 10.1002/humu.22110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 04/12/2012] [Indexed: 12/20/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) mutation is associated with a phenotypic spectrum that includes cystic fibrosis (CF). The disease liability of some common CFTR mutations is known, but rare mutations are seen in too few patients to categorize unequivocally, making genetic diagnosis difficult. Computational methods can predict the impact of mutation, but prediction specificity is often below that required for clinical utility. Here, we present a novel supervised learning approach for predicting CF from CFTR missense mutation. The algorithm begins by constructing custom multiple sequence alignments called phenotype-optimized sequence ensembles (POSEs). POSEs are constructed iteratively, by selecting sequences that optimize predictive performance on a training set of CFTR mutations of known clinical significance. Next, we predict CF disease liability from a different set of CFTR mutations (test-set mutations). This approach achieves improved prediction performance relative to popular methods recently assessed using the same test-set mutations. Of clinical significance, our method achieves 94% prediction specificity. Because databases such as HGMD and locus-specific mutation databases are growing rapidly, methods that automatically tailor their predictions for a specific phenotype may be of immediate utility. If the performance achieved here generalizes to other systems, the approach could be an excellent tool to help establish genetic diagnoses.
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Affiliation(s)
- David L Masica
- Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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31
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Levanat S, Musani V, Cvok ML, Susac I, Sabol M, Ozretic P, Car D, Eljuga D, Eljuga L, Eljuga D. Three novel BRCA1/BRCA2 mutations in breast/ovarian cancer families in Croatia. Gene 2012; 498:169-76. [PMID: 22366370 DOI: 10.1016/j.gene.2012.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 02/09/2012] [Indexed: 02/08/2023]
Abstract
BRCA1 and BRCA2 genes from 167 candidates (145 families) were scanned for mutations. We identified 14 pathogenic point mutations in 17 candidates, 9 in BRCA1 and 5 in BRCA2. Of those, 11 have been previously described and 3 were novel (c.5335C>T in BRCA1 and c.4139_4140dupTT and c.8175G>A in BRCA2). No large deletions or duplications involving BRCA1 and BRCA2 genes were identified. No founder mutations were detected for the Croatian population. Croatia shares most of the mutations with neighboring Slovenia and also with Germany, Austria and Poland. Two common sequence variants in BRCA1, c.2077G>A and c.4956G>A, were found more frequently in mutation carriers compared to healthy controls. No difference in BRCA2 variants was detected between the groups. Haplotype inference showed no difference in haplotype distributions between deleterious mutation carriers and non-carriers in neither BRCA1 nor BRCA2. In silico analyses identified one BRCA1 sequence variant (c.4039A>G) and two BRCA2 variants (c.5986G>A and c.6884G>C) as harmful with high probability, and inconclusive results were obtained for our novel BRCA2 variant c.3864_3866delTAA. Combination of QMPSF and HRMA methods provides high detection rate and complete coverage of BRCA1/2 genes. Benefit of BRCA1/2 mutation testing is clear, since we detected mutations in young unaffected women, who will be closely monitored for breast and ovarian cancer.
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Affiliation(s)
- Sonja Levanat
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia.
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32
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Caputo S, Benboudjema L, Sinilnikova O, Rouleau E, Béroud C, Lidereau R. Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases. Nucleic Acids Res 2011; 40:D992-1002. [PMID: 22144684 PMCID: PMC3245050 DOI: 10.1093/nar/gkr1160] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BRCA1 and BRCA2 are the two main genes responsible for predisposition to breast and ovarian cancers, as a result of protein-inactivating monoallelic mutations. It remains to be established whether many of the variants identified in these two genes, so-called unclassified/unknown variants (UVs), contribute to the disease phenotype or are simply neutral variants (or polymorphisms). Given the clinical importance of establishing their status, a nationwide effort to annotate these UVs was launched by laboratories belonging to the French GGC consortium (Groupe Génétique et Cancer), leading to the creation of the UMD-BRCA1/BRCA2 databases (http://www.umd.be/BRCA1/ and http://www.umd.be/BRCA2/). These databases have been endorsed by the French National Cancer Institute (INCa) and are designed to collect all variants detected in France, whether causal, neutral or UV. They differ from other BRCA databases in that they contain co-occurrence data for all variants. Using these data, the GGC French consortium has been able to classify certain UVs also contained in other databases. In this article, we report some novel UVs not contained in the BIC database and explore their impact in cancer predisposition based on a structural approach.
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Affiliation(s)
- Sandrine Caputo
- Institut Curie-Hôpital René Huguenin, Service d'Oncogénétique, U735 INSERM-Saint-Cloud, France.
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33
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Cote S, Arcand SL, Royer R, Nolet S, Mes-Masson AM, Ghadirian P, Foulkes WD, Tischkowitz M, Narod SA, Provencher D, Tonin PN. The BRCA2 c.9004G>A (E2003K) variant is likely pathogenic and recurs in breast and/or ovarian cancer families of French Canadian descent. Breast Cancer Res Treat 2011; 131:333-40. [DOI: 10.1007/s10549-011-1796-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 09/16/2011] [Indexed: 12/14/2022]
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34
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Théry JC, Krieger S, Gaildrat P, Révillion F, Buisine MP, Killian A, Duponchel C, Rousselin A, Vaur D, Peyrat JP, Berthet P, Frébourg T, Martins A, Hardouin A, Tosi M. Contribution of bioinformatics predictions and functional splicing assays to the interpretation of unclassified variants of the BRCA genes. Eur J Hum Genet 2011; 19:1052-8. [PMID: 21673748 DOI: 10.1038/ejhg.2011.100] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A large fraction of sequence variants of unknown significance (VUS) of the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2 may induce splicing defects. We analyzed 53 VUSs of BRCA1 or BRCA2, detected in consecutive molecular screenings, by using five splicing prediction programs, and we classified them into two groups according to the strength of the predictions. In parallel, we tested them by using functional splicing assays. A total of 10 VUSs were predicted by two or more programs to induce a significant reduction of splice site strength or activation of cryptic splice sites or generation of new splice sites. Minigene-based splicing assays confirmed four of these predictions. Five additional VUSs, all at internal exon positions, were not predicted to induce alterations of splice sites, but revealed variable levels of exon skipping, most likely induced by the modification of exonic splicing regulatory elements. We provide new data in favor of the pathogenic nature of the variants BRCA1 c.212+3A>G and BRCA1 c.5194-12G>A, which induced aberrant out-of-frame mRNA forms. Moreover, the novel variant BRCA2 c.7977-7C>G induced in frame inclusion of 6 nt from the 3' end of intron 17. The novel variants BRCA2 c.520C>T and BRCA2 c.7992T>A induced incomplete skipping of exons 7 and 18, respectively. This work highlights the contribution of splicing minigene assays to the assessment of pathogenicity, not only when patient RNA is not available, but also as a tool to improve the accuracy of bioinformatics predictions.
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Affiliation(s)
- Jean Christophe Théry
- Inserm U614, IFRMP, Faculty of Medicine and Department of Genetics, University Hospital, Institute for Biomedical Research and Innovation, Rouen, France
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35
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Hicks S, Wheeler DA, Plon SE, Kimmel M. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 2011; 32:661-8. [PMID: 21480434 PMCID: PMC4154965 DOI: 10.1002/humu.21490] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 02/09/2011] [Indexed: 01/10/2023]
Abstract
Multiple algorithms are used to predict the impact of missense mutations on protein structure and function using algorithm-generated sequence alignments or manually curated alignments. We compared the accuracy with native alignment of SIFT, Align-GVGD, PolyPhen-2, and Xvar when generating functionality predictions of well-characterized missense mutations (n = 267) within the BRCA1, MSH2, MLH1, and TP53 genes. We also evaluated the impact of the alignment employed on predictions from these algorithms (except Xvar) when supplied the same four alignments including alignments automatically generated by (1) SIFT, (2) Polyphen-2, (3) Uniprot, and (4) a manually curated alignment tuned for Align-GVGD. Alignments differ in sequence composition and evolutionary depth. Data-based receiver operating characteristic curves employing the native alignment for each algorithm result in area under the curve of 78-79% for all four algorithms. Predictions from the PolyPhen-2 algorithm were least dependent on the alignment employed. In contrast, Align-GVGD predicts all variants neutral when provided alignments with a large number of sequences. Of note, algorithms make different predictions of variants even when provided the same alignment and do not necessarily perform best using their own alignment. Thus, researchers should consider optimizing both the algorithm and sequence alignment employed in missense prediction.
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Affiliation(s)
- Stephanie Hicks
- Department of Statistics, Rice University, Houston, Texas, USA
| | | | - Sharon E. Plon
- Human Genome Sequencing Center, Houston, Texas, USA
- Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, Texas, USA
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36
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Abstract
PURPOSE Lynch syndrome is a genetic disease that predisposes to colorectal tumors, caused by mutation in mismatch repair genes. The use of genetic tests to identify mutation carriers does not always give perfectly clear results, as happens when an unclassified variant is found. This study aimed to define the pathogenic role of 35 variants present in MSH2, MLH1, MSH6, and PMS2 genes identified in our 15-year case study. METHODS We collected clinical and molecular data of all carriers, and then we analyzed the variants pathogenic role with web tools and molecular analyses. Using a Bayesian approach, we derived a posterior probability of pathogenicity and classified each variant according to a standardized five-class system. RESULTS The MSH2 p.Pro349Arg, p.Met688Arg, the MLH1 p.Gly67Arg, p.Thr82Ala, p.Lys618Ala, the MSH6 p.Ala1236Pro, and the PMS2 p.Arg20Gln were classified as pathogenic, and the MSH2 p.Cys697Arg and the PMS2 p.Ser46Ile were classified as likely pathogenic. Seven variants were likely nonpathogenic, 3 were nonpathogenic, and 16 remained uncertain. CONCLUSION Quantitative assessment of several parameters and their integration in a multifactorial likelihood model is the method of choice for classifying the variants. As such classifications can be associated with surveillance and testing recommendations, the results and the method developed in our study can be useful for helping laboratory geneticists in evaluation of genetic tests and clinicians in the management of carriers.
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37
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Radice P, De Summa S, Caleca L, Tommasi S. Unclassified variants in BRCA genes: guidelines for interpretation. Ann Oncol 2011; 22 Suppl 1:i18-23. [PMID: 21285146 DOI: 10.1093/annonc/mdq661] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In the last few years, several studies have focused on the interpretation of unclassified variants (UVs) of BRCA1 and BRCA2 genes. Analysis of UVs through a unique approach is not sufficient to understand their role in the development of tumors. Thus, it is clear that assembling results from different sources (genetic and epidemiological data, histopathological features, and in vitro and in silico analyses) represents a powerful way to classify such variants. Building reliable integrated models for UV classification requires the joining of many working groups to collaborative consortia, allowing data exchange and improvements of methods. This will lead to improvement in the predictivity of gene testing in BRCA1 and BRCA2 and, consequently, to an increase in the number of families that can be correctly classified as linked or unlinked to these genes, allowing more accurate genetic counseling and clinical management.
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Affiliation(s)
- P Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
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38
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Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Sci 2011; 19:2110-21. [PMID: 20799350 DOI: 10.1002/pro.491] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human ATP-binding cassette (ABC) transporter superfamily consists of 48 integral membrane proteins that couple the action of ATP binding and hydrolysis to the transport of diverse substrates across cellular membranes. Defects in 18 transporters have been implicated in human disease. In hundreds of cases, disease phenotypes and defects in function can be traced to nonsynonymous single nucleotide polymorphisms (nsSNPs). The functional impact of the majority of ABC transporter nsSNPs has yet to be experimentally characterized. Here, we combine experimental mutational studies with sequence and structural analysis to describe the impact of nsSNPs in human ABC transporters. First, the disease associations of 39 nsSNPs in 10 transporters were rationalized by identifying two conserved loops and a small α-helical region that may be involved in interdomain communication necessary for transport of substrates. Second, an approach to discriminate between disease-associated and neutral nsSNPs was developed and tailored to this superfamily. Finally, the functional impact of 40 unannotated nsSNPs in seven ABC transporters identified in 247 ethnically diverse individuals studied by the Pharmacogenetics of Membrane Transporters consortium was predicted. Three predictions were experimentally tested using human embryonic kidney epithelial (HEK) 293 cells stably transfected with the reference multidrug resistance transporter 4 and its variants to examine functional differences in transport of the antiviral drug, tenofovir. The experimental results confirmed two predictions. Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily.
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Affiliation(s)
- Libusha Kelly
- Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA
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39
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Bodd TL, Van Ghelue M, Eiklid K, Ruud E, Møller P, Mæhle L. Fanconi anaemia, BRCA2 and familial considerations - follow up on a previous case report. Acta Paediatr 2010; 99:1741-3. [PMID: 20608899 DOI: 10.1111/j.1651-2227.2010.01929.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Trine Levin Bodd
- Section for Inherited Cancer, Department of Medical Genetics, Radiumhospitalet, Oslo University Hospital, Oslo, Norway
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40
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Clinical relevance of rare germline sequence variants in cancer genes: evolution and application of classification models. Curr Opin Genet Dev 2010; 20:315-23. [PMID: 20456937 DOI: 10.1016/j.gde.2010.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 12/11/2022]
Abstract
Multifactorial models developed for BRCA1/2 variant classification have proved very useful for delineating BRCA1/2 variants associated with very high risk of cancer, or with little clinical significance. Recent linkage of this quantitative assessment of risk to clinical management guidelines has provided a basis to standardize variant reporting, variant classification and management of families with such variants, and can theoretically be applied to any disease gene. As proof of principle, the multifactorial approach already shows great promise for application to the evaluation of mismatch repair gene variants identified in families with suspected Lynch syndrome. However there is need to be cautious of the noted limitations and caveats of the current model, some of which may be exacerbated by differences in ascertainment and biological pathways to disease for different cancer syndromes.
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Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti CB, Rosenquist R, Suthers G, Borg A, Radice P, Grist SA, Monteiro ANA, Billack B. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutat Res 2008; 660:1-11. [PMID: 18992264 DOI: 10.1016/j.mrfmmm.2008.09.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 08/12/2008] [Accepted: 09/27/2008] [Indexed: 12/19/2022]
Abstract
Germline mutations that inactivate BRCA1 are responsible for breast and ovarian cancer susceptibility. One possible outcome of genetic testing for BRCA1 is the finding of a genetic variant of uncertain significance for which there is no information regarding its cancer association. This outcome leads to problems in risk assessment, counseling and preventive care. The purpose of the present study was to functionally evaluate seven unclassified variants of BRCA1 including a genomic deletion that leads to the in-frame loss of exons 16/17 (Delta exons 16/17) in the mRNA, an insertion that leads to a frameshift and an extended carboxy-terminus (5673insC), and five missense variants (K1487R, S1613C, M1652I, Q1826H and V1833M). We analyzed the variants using a functional assay based on the transcription activation property of BRCA1 combined with supervised learning computational models. Functional analysis indicated that variants S1613C, Q1826H, and M1652I are likely to be neutral, whereas variants V1833M, Delta exons 16/17, and 5673insC are likely to represent deleterious variants. In agreement with the functional analysis, the results of the computational analysis also indicated that the latter three variants are likely to be deleterious. Taken together, a combined approach of functional and bioinformatics analysis, plus structural modeling, can be utilized to obtain valuable information pertaining to the effect of a rare variant on the structure and function of BRCA1. Such information can, in turn, aid in the classification of BRCA1 variants for which there is a lack of genetic information needed to provide reliable risk assessment.
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Affiliation(s)
- Marcelo Carvalho
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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