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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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: 0] [Impact Index Per Article: 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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3
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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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4
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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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5
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Mersch J, Brown N, Pirzadeh-Miller S, Mundt E, Cox HC, Brown K, Aston M, Esterling L, Manley S, Ross T. Prevalence of Variant Reclassification Following Hereditary Cancer Genetic Testing. JAMA 2018; 320:1266-1274. [PMID: 30264118 PMCID: PMC6233618 DOI: 10.1001/jama.2018.13152] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Variant reclassification is an important component of hereditary cancer genetic testing; however, there are few published data quantifying the prevalence of reclassification. OBJECTIVE Retrospective cohort study of individuals who had genetic testing from 2006 through 2016 at a single commercial laboratory. DESIGN, SETTING, AND PARTICIPANTS A retrospective cohort of individuals who had genetic testing between 2006 and 2016 at a single commercial laboratory was assessed. Variants were classified as benign, likely benign, variant of uncertain significance, likely pathogenic, or pathogenic. Retrospective chart reviews were conducted for patients from the University of Texas Southwestern (UTSW) Medical Center. EXPOSURES Hereditary cancer genetic testing. MAIN OUTCOMES AND MEASURES Frequency of and time to amended reports; frequency and types of variant reclassification. RESULTS From 2006 through 2018, 1.45 million individuals (median [interquartile range] age at testing, 49 years [40.69-58.31 years], 95.6% women) had genetic testing, and 56.6% (n = 821 724) had a personal history of cancer. A total of 1.67 million initial tests were reported and 59 955 amended reports were issued due to variant reclassification. Overall, 6.4% (2868 of 44 777) of unique variants were reclassified. Reclassification to a different clinical category was rare among unique variants initially classified as pathogenic or likely pathogenic (0.7%, 61 of 9112) or benign or likely benign (0.2%, 15 of 8995). However, 7.7% (2048 of 26 670) of unique variants of uncertain significance were reclassified: 91.2% (1867 of 2048) were downgraded to benign or likely benign (median time to amended report, 1.17 years), 8.7% (178 of 2048) were upgraded to pathogenic or likely pathogenic variants (median time to amended report, 1.86 years). Because most variants were observed in more than 1 individual, 24.9% (46 890 of 184 327) of all reported variants of uncertain significance were reclassified. CONCLUSIONS AND RELEVANCE Following hereditary cancer genetic testing at a single commercial laboratory, 24.9% of variants of uncertain significance were reclassified, which included both downgrades and upgrades. Further research is needed to assess generalizability of the findings for other laboratories, as well as the clinical consequences of the reclassification as a component of a genetic testing program.
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Affiliation(s)
| | - Nichole Brown
- University of Texas Southwestern Medical Center, Dallas
| | | | - Erin Mundt
- Myriad Genetic Laboratories Inc, Salt Lake City, Utah
| | - Hannah C. Cox
- Myriad Genetic Laboratories Inc, Salt Lake City, Utah
| | - Krystal Brown
- Myriad Genetic Laboratories Inc, Salt Lake City, Utah
| | - Melissa Aston
- Myriad Genetic Laboratories Inc, Salt Lake City, Utah
| | | | - Susan Manley
- Myriad Genetic Laboratories Inc, Salt Lake City, Utah
| | - Theodora Ross
- University of Texas Southwestern Medical Center, Dallas
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6
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Pedersen IS, Schmidt AY, Bertelsen B, Ernst A, Andersen CLT, Kruse T, Rossing M, Thomassen M. A Danish national effort of BRCA1/2 variant classification. Acta Oncol 2018; 57:159-162. [PMID: 29168416 DOI: 10.1080/0284186x.2017.1400693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Inge Søkilde Pedersen
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Ane Y. Schmidt
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Birgitte Bertelsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Anja Ernst
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | | | - Torben Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
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7
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Moghadasi S, Meeks HD, Vreeswijk MP, Janssen LA, Borg Å, Ehrencrona H, Paulsson-Karlsson Y, Wappenschmidt B, Engel C, Gehrig A, Arnold N, Hansen TVO, Thomassen M, Jensen UB, Kruse TA, Ejlertsen B, Gerdes AM, Pedersen IS, Caputo SM, Couch F, Hallberg EJ, van den Ouweland AM, Collée MJ, Teugels E, Adank MA, van der Luijt RB, Mensenkamp AR, Oosterwijk JC, Blok MJ, Janin N, Claes KB, Tucker K, Viassolo V, Toland AE, Eccles DE, Devilee P, Van Asperen CJ, Spurdle AB, Goldgar DE, García EG. The BRCA1 c. 5096G>A p.Arg1699Gln (R1699Q) intermediate risk variant: breast and ovarian cancer risk estimation and recommendations for clinical management from the ENIGMA consortium. J Med Genet 2017; 55:15-20. [PMID: 28490613 DOI: 10.1136/jmedgenet-2017-104560] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/11/2017] [Accepted: 04/17/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND We previously showed that the BRCA1 variant c.5096G>A p.Arg1699Gln (R1699Q) was associated with an intermediate risk of breast cancer (BC) and ovarian cancer (OC). This study aimed to assess these cancer risks for R1699Q carriers in a larger cohort, including follow-up of previously studied families, to further define cancer risks and to propose adjusted clinical management of female BRCA1*R1699Q carriers. METHODS Data were collected from 129 BRCA1*R1699Q families ascertained internationally by ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium members. A modified segregation analysis was used to calculate BC and OC risks. Relative risks were calculated under both monogenic model and major gene plus polygenic model assumptions. RESULTS In this cohort the cumulative risk of BC and OC by age 70 years was 20% and 6%, respectively. The relative risk for developing cancer was higher when using a model that included the effects of both the R1699Q variant and a residual polygenic component compared with monogenic model (for BC 3.67 vs 2.83, and for OC 6.41 vs 5.83). CONCLUSION Our results confirm that BRCA1*R1699Q confers an intermediate risk for BC and OC. Breast surveillance for female carriers based on mammogram annually from age 40 is advised. Bilateral salpingo-oophorectomy should be considered based on family history.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Huong D Meeks
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Maaike Pg Vreeswijk
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Linda Am Janssen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hans Ehrencrona
- Department of Clinical Genetics, Lund University, Lund, Sweden.,Department of Clinical Genetics, Laboratory Medicine, Office for Medical Services, Lund University, Lund, Sweden
| | | | - Barbara Wappenschmidt
- Centre of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany.,Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany.,Centre for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, University of Leipzig, Leipzig, Germany.,Department of Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, University Würzburg, Würzburg, Germany.,Department of Medical Genetics, University Würzburg, Würzburg, Germany.,Institute of Human Genetics, University Würzburg, Würzburg, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Thomas Van Overeem Hansen
- Center for Genomic Medicine, University of Copenhagen, Copenhagen, DenmarK.,Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Bent Ejlertsen
- Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK.,Department of Oncology, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Rigshospitalet, University of Copenhagen, Copenhagen, DenmarK.,Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark
| | - Inge Søkilde Pedersen
- Section of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | | | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Emily J Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Margriet J Collée
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Erik Teugels
- Familial Cancer Clinic and Medical Oncology, University Hospital Brussels, Belgium
| | - Muriel A Adank
- Department of Clinical Genetics, VU Medical Centre, Amsterdam, The Netherlands
| | - Rob B van der Luijt
- Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Jan C Oosterwijk
- Department of Genetics, University of Groningen, University Medical Centre, Groningen, The Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Nicolas Janin
- Department of Service de Génétique, Cliniques universitaires Saint-Luc, Bruxelles, Belgium
| | | | - Kathy Tucker
- Hereditary Cancer Service, Prince of Wales (and St George Hospitals) Hospital, Randwick, New South Wales, Australia
| | - Valeria Viassolo
- Department of Oncogenetics and Cancer Prevention Unit, Geneva University Hospitals, Geneva, Switzerland.,Division of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Diana E Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Christie J Van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - David E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine Salt Lake City, Salt Lake City, Utah, USA
| | - Encarna Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
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8
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Ryu JM, Kang G, Nam SJ, Kim SW, Yu J, Lee SK, Bae SY, Park S, Paik HJ, Kim JW, Park SS, Lee JE, Kim SW. Suggestion of BRCA1 c.5339T>C (p.L1780P) variant confer from 'unknown significance' to 'Likely pathogenic' based on clinical evidence in Korea. Breast 2017; 33:109-116. [PMID: 28364669 DOI: 10.1016/j.breast.2017.03.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 11/30/2022] Open
Abstract
PURPOSE We describe a rationale for the re-classification of the BRCA1 c.5539T>C (L1780P) variant using a clinical evidence. METHODS A retrospective review was conducted to identify all patients with breast or ovarian cancer and the L1780P variant between 2002 and 2015 at a single institution. RESULTS We identified the BRCA1/2 genetic mutation test results of 1223 breast cancer patients and 174 patients with ovarian cancer. Of the 160 BRCA 1/2 variant unknown significance, 16 (10.0%) patients were identified as having the L1780P variant. Among them, 10 had breast cancer, 4 had ovarian cancer, and 2 had both breast and ovarian cancer. Thirteen (81.3%) patients with this variant had family histories of breast or ovarian cancer. Two (16.7%) also had comorbid ovarian cancer. Two patients with this variant showed that co-segregation of the disease in multiple family members and family histories of breast and ovarian cancer. This variant was found to be either absent or at extremely low frequency in general population databases. CONCLUSION The L1780P variant might confer to "Likely pathogenic" according to a clinical evidence and the ACMG standards and guidelines. A nation-wide or global survey and a functional analysis are needed to confirm the pathogenicity of the L1780P variant.
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Affiliation(s)
- Jai Min Ryu
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Goeun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Seok Jin Nam
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Seok Won Kim
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jonghan Yu
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Se Kyung Lee
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Soo Youn Bae
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sungmin Park
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hyun-June Paik
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung-Shin Park
- Department of Pathology, Daerim St. Mary's Hospital, South Korea
| | - Jeong Eon Lee
- Division of Breast and Endocrine Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Sung-Won Kim
- Department of Surgery, Breast Care Center, Daerim St. Mary's Hospital, South Korea.
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9
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Flower KJ, Shenker NS, El-Bahrawy M, Goldgar DE, Parsons MT, Spurdle AB, Morris JR, Brown R, Flanagan JM. DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer. Epigenetics 2016; 10:1121-32. [PMID: 26727311 PMCID: PMC4844213 DOI: 10.1080/15592294.2015.1111504] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Germline pathogenic mutations in BRCA1 increase risk of developing breast cancer. Screening for mutations in BRCA1 frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate BRCA1-mutated from BRCA1-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 BRCA1 pathogenic mutation carriers, 65 BRCAx (BRCA1-wild type), 38 BRCA1 test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (BACH2, C8orf31, and LOC654342) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G>A (IVS 19-12 G>A) (P>0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of BRCA1 variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity.
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Affiliation(s)
- Kirsty J Flower
- a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK
| | - Natalie S Shenker
- a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK
| | - Mona El-Bahrawy
- b Department of Histopathology ; Hammersmith Hospital; Imperial College London ; UK
| | - David E Goldgar
- c Huntsman Cancer Institute; University of Utah ; Salt Lake City , UT , USA
| | - Michael T Parsons
- d QIMR Berghofer Medical Research Institute ; Brisbane , QLD , Australia
| | | | | | - Amanda B Spurdle
- d QIMR Berghofer Medical Research Institute ; Brisbane , QLD , Australia
| | - Joanna R Morris
- f Genome Stability Unit; School of Cancer Sciences; University of Birmingham ; UK
| | - Robert Brown
- a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK.,g Section of Molecular Pathology; Institute for Cancer Research ; Sutton , UK
| | - James M Flanagan
- a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK
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10
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Yoon KA, Park B, Lee BI, Yang MJ, Kong SY, Lee ES. Clinically Significant Unclassified Variants in BRCA1 and BRCA2 genes among Korean Breast Cancer Patients. Cancer Res Treat 2016; 49:627-634. [PMID: 27658390 PMCID: PMC5512368 DOI: 10.4143/crt.2016.292] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/13/2016] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Unclassified variants (UVs) of BRCA1 and BRCA2 genes are not defined as pathogenic for breast cancer, and their clinical significance currently remains undefined. Therefore, this study was conducted to identify potentially pathogenic UVs by comparing their prevalence between breast cancer patients and controls. MATERIALS AND METHODS A total of 328 breast cancer patients underwent BRCA1/2 genetic screening at the National Cancer Center of Korea. Genetic variants of BRCA genes that were categorized as unclassified according to the Breast Cancer Information Core database were selected based on allelic frequency, after which candidate variants were genotyped in 421 healthy controls. We also examined family members of the study participants. Finally, the effects of amino acid substitutions on protein structure and function were predicted in silico. RESULTS Genetic tests revealed 33 UVs in BRCA1 and 47 in BRCA2. Among 15 candidates genotyped in healthy controls, c.5339T>C in BRCA1 and c.6029T>G, c.7522G>A in BRCA2 were not detected. Moreover, the c.5339T>C variant in the BRCA1 gene was detected in four patients with a family history of breast cancer. This nonsynonymous variant (Leu1780Pro) in the BRCA1 C-terminal domain was predicted to have an effect on BRCA1 protein structure/function. CONCLUSION This study showed that comparison of genotype frequency between cases and controls could help identify UVs of BRCA genes that are potentially pathogenic. Moreover, ourfindings suggest that c.5339T>C in BRCA1 might be a pathogenic variant for patients and their families.
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Affiliation(s)
- Kyong-Ah Yoon
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea.,College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Boyoung Park
- Department of Cancer Control and Policy, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Byung Il Lee
- Biomolecular Function Research Branch, National Cancer Center, Goyang, Korea
| | - Moon Jung Yang
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- Genetic Counseling Clinic, Hospital, National Cancer Center, Goyang, Korea.,Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Translational Epidemiology Branch, National Cancer Center, Goyang, Korea
| | - Eun Sook Lee
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea.,Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Precision Medicine Branch, Research Institute, National Cancer Center, Goyang, Korea
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11
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Kerkhofs CHH, Spurdle AB, Lindsey PJ, Goldgar DE, Gómez-García EB. Assessing biases of information contained in pedigrees for the classification of BRCA-genetic variants: a study arising from the ENIGMA analytical working group. Hered Cancer Clin Pract 2016; 14:10. [PMID: 27134689 PMCID: PMC4851774 DOI: 10.1186/s13053-016-0050-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/24/2016] [Indexed: 11/07/2022] Open
Abstract
Purpose One way of evaluating family history (FH) for classifying BRCA1/2 variants of uncertain clinical significance (VUS) is to assess the “BRCA-ness” of a pedigree by comparing it to reference populations. The aim of this study was to assess if prediction of BRCA pathogenic variant (mutation) status based on pedigree information differed due to changes in FH since intake, both in families with a pathogenic variant (BRCAm) and in families with wild-type (BRCAwt). Patients and methods We compared the BRCA1/2 pathogenic variant detection probabilities between intake and most recent pedigree for BRCAm families (n = 64) and BRCAwt (n = 118) using the BRCAPRO software program. Results Follow-up time between intake and most recent pedigree was significantly longer (p < 0.001) in the BRCAm compared to the BRCAwt families. Among BRCAwt families, the probability to detect a pathogenic variant did not change over time. Conversely, among the BRCAm, this probability was significantly higher for most recent vs. intake pedigree (p = 0.006). Conclusion Clinical scores change significantly over time for BRCAm families. This may be due to differences in follow-up, but also to differences in cancer risks from carrying a pathogenic variant in a highly penetrant gene. To reduce bias, models for VUS classification should incorporate FH collected at intake.
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Affiliation(s)
- C H H Kerkhofs
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - P J Lindsey
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - D E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, USA
| | - E B Gómez-García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
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12
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Moghadasi S, Eccles DM, Devilee P, Vreeswijk MPG, van Asperen CJ. Classification and Clinical Management of Variants of Uncertain Significance in High Penetrance Cancer Predisposition Genes. Hum Mutat 2016; 37:331-6. [PMID: 26777316 DOI: 10.1002/humu.22956] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/13/2015] [Indexed: 11/12/2022]
Abstract
In 2008, the International Agency for Research on Cancer (IARC) proposed a system for classifying sequence variants in highly penetrant breast and colon cancer susceptibility genes, linked to clinical actions. This system uses a multifactorial likelihood model to calculate the posterior probability that an altered DNA sequence is pathogenic. Variants between 5%-94.9% (class 3) are categorized as variants of uncertain significance (VUS). This interval is wide and might include variants with a substantial difference in pathogenicity at either end of the spectrum. We think that carriers of class 3 variants would benefit from a fine-tuning of this classification. Classification of VUS to a category with a defined clinical significance is very important because for carriers of a pathogenic mutation full surveillance and risk-reducing surgery can reduce cancer incidence. Counselees who are not carriers of a pathogenic mutation can be discharged from intensive follow-up and avoid unnecessary risk-reducing surgery. By means of examples, we show how, in selected cases, additional data can lead to reclassification of some variants to a different class with different recommendations for surveillance and therapy. To improve the clinical utility of this classification system, we suggest a pragmatic adaptation to clinical practice.
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Affiliation(s)
- Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2333 ZA, The Netherlands
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333 ZC, The Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Centre, Leiden, 2333 ZC, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, 2333 ZA, The Netherlands
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13
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Acedo A, Hernández-Moro C, Curiel-García Á, Díez-Gómez B, Velasco EA. Functional classification of BRCA2 DNA variants by splicing assays in a large minigene with 9 exons. Hum Mutat 2015; 36:210-21. [PMID: 25382762 PMCID: PMC4371643 DOI: 10.1002/humu.22725] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/27/2014] [Indexed: 01/04/2023]
Abstract
Numerous pathogenic DNA variants impair the splicing mechanism in human genetic diseases. Minigenes are optimal approaches to test variants under the splicing viewpoint without the need of patient samples. We aimed to design a robust minigene construct of the breast cancer gene BRCA2 in order to investigate the impact of variants on splicing. BRCA2 exons 19-27 (MGBR2_ex19-27) were cloned in the new vector pSAD. It produced a large transcript of the expected size (2,174 nucleotides) and exon structure (V1-ex19-27-V2). Splicing assays showed that 18 (17 splice-site and 1 silencer variants) out of 40 candidate DNA variants induced aberrant patterns. Twenty-four anomalous transcripts were accurately detected by fluorescent-RT-PCR that were generated by exon-skipping, alternative site usage, and intron-retention events. Fourteen variants induced major anomalies and were predicted to disrupt protein function so they could be classified as pathogenic. Furthermore, minigene mimicked previously reported patient RNA outcomes of seven variants supporting the reproducibility of minigene assays. Therefore, a relevant fraction of variants are involved in breast cancer through splicing alterations. MGBR2_ex19-27 is the largest reported BRCA2 minigene and constitutes a valuable tool for the functional and clinical classification of sequence variations.
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Affiliation(s)
- Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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14
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Frey MK, Kim SH, Bassett RY, Martineau J, Dalton E, Chern JY, Blank SV. Rescreening for genetic mutations using multi-gene panel testing in patients who previously underwent non-informative genetic screening. Gynecol Oncol 2015; 139:211-5. [PMID: 26296696 DOI: 10.1016/j.ygyno.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The availability of next-generation sequencing and identification of multiple cancer-related genes has caused a shift away from single gene testing towards multi-gene panel testing for hereditary cancer syndromes. However, the utility of panels in individuals who previously underwent non-informative genetic screening has yet to be evaluated. We aim to evaluate the use of rescreening and results of multi-gene panels in this rescreened population. METHODS We reviewed the medical records for patients who had previously undergone genetic testing and then underwent multi-gene panel testing at a single institution between 9/2013 and 11/2014. RESULTS One hundred and twenty-seven patients with prior genetic testing underwent multi-gene panels. One hundred and four patients (82%) had a history of cancer and 118 (93%) had at least one family member with cancer. On primary testing, no pathogenic mutations were detected and 10 patients (8%) were found to have variants of uncertain significance (VUS). On repeat multi-gene panel testing, nine patients (7%) were found to have a pathogenic mutation and 53 patients (42%) were VUS not identified on prior testing. CONCLUSIONS Seven percent of patients with non-informative primary testing were found to have a pathogenic mutation with multi-gene panels, suggesting that there is a potential benefit to be gained from rescreening. However, 42% of patients were found to have new VUS with panels, a result that can cause patients anxiety without clear clinical implications.
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Affiliation(s)
- Melissa K Frey
- New York University Langone Medical Center, New York, NY, US.
| | - Sarah H Kim
- New York University Langone Medical Center, New York, NY, US
| | | | | | | | - Jing-Yi Chern
- New York University Langone Medical Center, New York, NY, US
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15
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The presentation of an asymptomatic ovarian carcinosarcoma caught by BRCA1 mutation surveillance program. Int Cancer Conf J 2014. [DOI: 10.1007/s13691-014-0155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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16
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Oosterwijk JC, de Vries J, Mourits MJ, de Bock GH. Genetic testing and familial implications in breast-ovarian cancer families. Maturitas 2014; 78:252-7. [PMID: 24894332 DOI: 10.1016/j.maturitas.2014.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/19/2022]
Abstract
DNA-testing for BRCA1 and BRCA2 has become incorporated in the diagnostic procedure of patients with breast and/or ovarian cancer. Since 1994 an immense amount of information has been gathered on mutation spectra, mutation risk assessment, cancer risks for mutation carriers, factors that modify these risks, unclassified DNA variants, surveillance strategies and preventive options. For the patient and family the main determinator still is whether a mutation is found or not. When a pathogenic mutation is detected in an index case, relatives can opt for pre-symptomatic DNA testing. However in the vast majority no mutation, or only unclear mutations are detectable yet. This means that a hereditary cause cannot be excluded, but pre-symptomatic DNA-testing is still unavailable for relatives. Surveillance for both index cases and relatives is based of the family history of cancer. Next generation genetic testing may help to elucidate genetic causes in these families.
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Affiliation(s)
- Jan C Oosterwijk
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands.
| | - Jakob de Vries
- Department of Surgery, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Marian J Mourits
- Department of Gynaecology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Geertruida H de Bock
- Department of Epidemiology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
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17
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Christou CM, Hadjisavvas A, Kyratzi M, Flouri C, Neophytou I, Anastasiadou V, Loizidou MA, Kyriacou K. The BRCA1 variant p.Ser36Tyr abrogates BRCA1 protein function and potentially confers a moderate risk of breast cancer. PLoS One 2014; 9:e93400. [PMID: 24695549 PMCID: PMC3973689 DOI: 10.1371/journal.pone.0093400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
The identification of variants of unknown clinical significance (VUS) in the BRCA1 gene complicates genetic counselling and causes additional anxiety to carriers. In silico approaches currently used for VUS pathogenicity assessment are predictive and often produce conflicting data. Furthermore, functional assays are either domain or function specific, thus they do not examine the entire spectrum of BRCA1 functions and interpretation of individual assay results can be misleading. PolyPhen algorithm predicted that the BRCA1 p.Ser36Tyr VUS identified in the Cypriot population was damaging, whereas Align-GVGD predicted that it was possibly of no significance. In addition the BRCA1 p.Ser36Tyr variant was found to be associated with increased risk (OR = 3.47, 95% CI 1.13-10.67, P = 0.02) in a single case-control series of 1174 cases and 1109 controls. We describe a cellular system for examining the function of exogenous full-length BRCA1 and for classifying VUS. We achieved strong protein expression of full-length BRCA1 in transiently transfected HEK293T cells. The p.Ser36Tyr VUS exhibited low protein expression similar to the known pathogenic variant p.Cys61Gly. Co-precipitation analysis further demonstrated that it has a reduced ability to interact with BARD1. Further, co-precipitation analysis of nuclear and cytosolic extracts as well as immunofluorescence studies showed that a high proportion of the p.Ser36Tyr variant is withheld in the cytoplasm contrary to wild type protein. In addition the ability of p.Ser36Tyr to co-localize with conjugated ubiquitin foci in the nuclei of S-phase synchronized cells following genotoxic stress with hydroxyurea is impaired at more pronounced levels than that of the p.Cys61Gly pathogenic variant. The p.Ser36Tyr variant demonstrates abrogated function, and based on epidemiological, genetic, and clinical data we conclude that the p.Ser36Tyr variant is probably associated with a moderate breast cancer risk.
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Affiliation(s)
- Charita M. Christou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Maria Kyratzi
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- The University of Cyprus, Department of Biological Sciences, Nicosia, Cyprus
| | - Christina Flouri
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Ioanna Neophytou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Violetta Anastasiadou
- The Cyprus Institute of Neurology and Genetics, Department of Clinical Genetics, Nicosia, Cyprus
| | - Maria A. Loizidou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- * E-mail:
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Guidugli L, Carreira A, Caputo SM, Ehlen A, Galli A, Monteiro ANA, Neuhausen SL, Hansen TVO, Couch FJ, Vreeswijk MPG. Functional assays for analysis of variants of uncertain significance in BRCA2. Hum Mutat 2013; 35:151-64. [PMID: 24323938 DOI: 10.1002/humu.22478] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/28/2013] [Indexed: 01/11/2023]
Abstract
Missense variants in the BRCA2 gene are routinely detected during clinical screening for pathogenic mutations in patients with a family history of breast and ovarian cancer. These subtle changes frequently remain of unknown clinical significance because of the lack of genetic information that may help establish a direct correlation with cancer predisposition. Therefore, alternative ways of predicting the pathogenicity of these variants are urgently needed. Since BRCA2 is a protein involved in important cellular mechanisms such as DNA repair, replication, and cell cycle control, functional assays have been developed that exploit these cellular activities to explore the impact of the variants on protein function. In this review, we summarize assays developed and currently utilized for studying missense variants in BRCA2. We specifically depict details of each assay, including variants of uncertain significance analyzed, and describe a validation set of (genetically) proven pathogenic and neutral missense variants to serve as a golden standard for the validation of each assay. Guidelines are proposed to enable implementation of laboratory-based methods to assess the impact of the variant on cancer risk.
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Affiliation(s)
- Lucia Guidugli
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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19
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Jankowitz RC, Knickelbein KZ. Editorial: BRCA1 and BRCA2 gene mutations screening in sporadic breast cancer patients in Kazakhstan. Cent Asian J Glob Health 2013; 2:41. [PMID: 29755873 PMCID: PMC5927764 DOI: 10.5195/cajgh.2013.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rachel C. Jankowitz
- University of Pittsburgh Cancer Institute, UPMC Magee Women’s Cancer Program
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20
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Spurdle AB, Whiley PJ, Thompson B, Feng B, Healey S, Brown MA, Pettigrew C, Van Asperen CJ, Ausems MGEM, Kattentidt-Mouravieva AA, van den Ouweland AMW, Lindblom A, Pigg MH, Schmutzler RK, Engel C, Meindl A, Caputo S, Sinilnikova OM, Lidereau R, Couch FJ, Guidugli L, Hansen TVO, Thomassen M, Eccles DM, Tucker K, Benitez J, Domchek SM, Toland AE, Van Rensburg EJ, Wappenschmidt B, Borg Å, Vreeswijk MPG, Goldgar DE. BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk. J Med Genet 2012; 49:525-32. [PMID: 22889855 DOI: 10.1136/jmedgenet-2012-101037] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Clinical classification of rare sequence changes identified in the breast cancer susceptibility genes BRCA1 and BRCA2 is essential for appropriate genetic counselling of individuals carrying these variants. We previously showed that variant BRCA1 c.5096G>A p.Arg1699Gln in the BRCA1 transcriptional transactivation domain demonstrated equivocal results from a series of functional assays, and proposed that this variant may confer low to moderate risk of cancer. METHODS Measures of genetic risk (report of family history, segregation) were assessed for 68 BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) families recruited through family cancer clinics, comparing results with 34 families carrying the previously classified pathogenic BRCA1 c.5095C>T p.Arg1699Trp (R1699W) mutation at the same residue, and to 243 breast cancer families with no BRCA1 pathogenic mutation (BRCA-X). RESULTS Comparison of BRCA1 carrier prediction scores of probands using the BOADICEA risk prediction tool revealed that BRCA1 c.5096G>A p.Arg1699Gln variant carriers had family histories that were less 'BRCA1-like' than BRCA1 c.5095C>T p.Arg1699Trp mutation carriers (p<0.00001), but more 'BRCA1-like' than BRCA-X families (p=0.0004). Further, modified segregation analysis of the subset of 30 families with additional genotyping showed that BRCA1 c.5096G >A p.Arg1699Gln had reduced penetrance compared with the average truncating BRCA1 mutation penetrance (p=0.0002), with estimated cumulative risks to age 70 of breast or ovarian cancer of 24%. CONCLUSIONS Our results provide substantial evidence that the BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) variant, demonstrating ambiguous functional deficiency across multiple assays, is associated with intermediate risk of breast and ovarian cancer, highlighting challenges for risk modelling and clinical management of patients of this and other potential moderate-risk variants.
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Affiliation(s)
- Amanda B Spurdle
- Division of Genetics and Population Health, Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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Support of the 'fallopian tube hypothesis' in a prospective series of risk-reducing salpingo-oophorectomy specimens. Eur J Cancer 2012; 49:132-41. [PMID: 22921157 DOI: 10.1016/j.ejca.2012.07.021] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/07/2012] [Accepted: 07/26/2012] [Indexed: 01/13/2023]
Abstract
OBJECTIVE To determine the prevalence, localisation and type of occult (non)invasive cancer in risk-reducing salpingo-oophorectomy (RRSO) specimens in BRCA-mutation carriers and high-risk women from BRCA-negative families. METHODS A consecutive series of RRSO specimens of asymptomatic, screen-negative high-risk women were prospectively collected in our tertiary multidisciplinary cancer clinic from January 2000 until March 2012. All high-risk women in this study underwent genetic testing on BRCA-mutations. The surgico-pathological protocol comprised complete resection of ovaries and fallopian tubes, transverse sectioning at 2-3 mm (sectioning and extensively examining the fimbrial end [SEE-FIM] protocol from 2006) and double independent pathology review of morphologically deviant sections. RESULTS Three hundred and sixty RRSOs were performed in 188 BRCA1-carriers, 115 BRCA2-carriers and 57 BRCA-negative women at a median age of 44.0 years. Four occult invasive cancers were detected in BRCA-carriers (1.3%, 95%-confidence interval (CI) 0.03-2.61), all in BRCA1-carriers >40 years of age. All cancers, of which two tubal and two ovarian cancers, were FIGO-stage I/II. Three non-invasive serous intraepithelial carcinomas (STICs) were detected in BRCA-carriers (1.0%, 95%-CI 0.00-2.10). In BRCA-negative women one STIC was found (1.8%, 95%-CI 0.00-5.16), however she carried an unclassified variant in BRCA2. Total follow-up after RRSO was 1691 woman-years, in which one BRCA1-carrier developed peritoneal cancer (0.3%, 95%-CI 0.00-0.82). CONCLUSIONS A low prevalence of occult invasive cancer (1.1%) was found in young asymptomatic, screen-negative women at increased ovarian cancer risk undergoing RRSO. This study adds to the advice to perform RRSO in BRCA1-carriers before the age of 40. Our findings support the hypothesis of the fallopian tube as the primary site of origin of pelvic high-grade serous cancer.
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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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Acedo A, Sanz DJ, Durán M, Infante M, Pérez-Cabornero L, Miner C, Velasco EA. Comprehensive splicing functional analysis of DNA variants of the BRCA2 gene by hybrid minigenes. Breast Cancer Res 2012; 14:R87. [PMID: 22632462 PMCID: PMC3446350 DOI: 10.1186/bcr3202] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 05/15/2012] [Accepted: 05/25/2012] [Indexed: 11/10/2022] Open
Abstract
Introduction The underlying pathogenic mechanism of a large fraction of DNA variants of disease-causing genes is the disruption of the splicing process. We aimed to investigate the effect on splicing of the BRCA2 variants c.8488-1G > A (exon 20) and c.9026_9030del (exon 23), as well as 41 BRCA2 variants reported in the Breast Cancer Information Core (BIC) mutation database. Methods DNA variants were analyzed with the splicing prediction programs NNSPLICE and Human Splicing Finder. Functional analyses of candidate variants were performed by lymphocyte RT-PCR and/or hybrid minigene assays. Forty-one BIC variants of exons 19, 20, 23 and 24 were bioinformatically selected and generated by PCR-mutagenesis of the wild type minigenes. Results Lymphocyte RT-PCR of c.8488-1G > A showed intron 19 retention and a 12-nucleotide deletion in exon 20, whereas c.9026_9030del did not show any splicing anomaly. Minigene analysis of c.8488-1G > A displayed the aforementioned aberrant isoforms but also exon 20 skipping. We further evaluated the splicing outcomes of 41 variants of four BRCA2 exons by minigene analysis. Eighteen variants presented splicing aberrations. Most variants (78.9%) disrupted the natural splice sites, whereas four altered putative enhancers/silencers and had a weak effect. Fluorescent RT-PCR of minigenes accurately detected 14 RNA isoforms generated by cryptic site usage, exon skipping and intron retention events. Fourteen variants showed total splicing disruptions and were predicted to truncate or eliminate essential domains of BRCA2. Conclusions A relevant proportion of BRCA2 variants are correlated with splicing disruptions, indicating that RNA analysis is a valuable tool to assess the pathogenicity of a particular DNA change. The minigene system is a straightforward and robust approach to detect variants with an impact on splicing and contributes to a better knowledge of this gene expression step.
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Affiliation(s)
- Alberto Acedo
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Valladolid, Sanz y Forés 3, Valladolid 47003, Spain
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Follow-up of carriers of BRCA1 and BRCA2 variants of unknown significance: variant reclassification and surgical decisions. Genet Med 2012; 13:998-1005. [PMID: 21811163 DOI: 10.1097/gim.0b013e318226fc15] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE : Approximately 5-10% of patients who undergo genetic testing of BRCA1 and BRCA2 receive a variant of unknown significance (VUS) result. The ambiguous nature of a VUS may increase difficulty in patient understanding and decision making regarding risk reduction and surveillance options, including cancer risk-reducing surgeries. VUS reclassification to benign or deleterious may occur in time; however, clinical decisions may need to be made expeditiously, and some patients may pursue irreversible treatments before VUS reclassification. METHODS : We reviewed the surgical decisions of 107 women postdisclosure of a BRCA VUS result counseled at our institute between 1998 and 2009. CONCLUSION : Among women receiving a BRCA VUS result at our center, 11 of 107 (10.3%) pursued cancer risk-reducing mastectomy and 22 of 107 (20.6%) pursued cancer risk-reducing bilateral salpingo-oophorectomy. Reclassification of VUS occurred up to 9 years after testing, and 5 of 22 (22.7%) women followed up for 8 or more years continue to have a VUS result. We discuss considerations for providers of genetic services to discuss with patients who receive a VUS result.
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25
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De Bock GH, Hesselink JW, Roorda C, De Vries J, Hollema H, Jaspers JP, Kok T, Werker PM, Oosterwijk JC, Mourits MJ. Model of care for women at increased risk of breast and ovarian cancer. Maturitas 2012; 71:3-5. [DOI: 10.1016/j.maturitas.2011.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/17/2011] [Indexed: 01/26/2023]
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26
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Lindor NM, Guidugli L, Wang X, Vallée MP, Monteiro ANA, Tavtigian S, Goldgar DE, Couch FJ. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum Mutat 2011; 33:8-21. [PMID: 21990134 DOI: 10.1002/humu.21627] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 09/26/2011] [Indexed: 01/23/2023]
Abstract
Clinical mutation screening of the BRCA1 and BRCA2 genes for the presence of germline inactivating mutations is used to identify individuals at elevated risk of breast and ovarian cancer. Variants identified during screening are usually classified as pathogenic (increased risk of cancer) or not pathogenic (no increased risk of cancer). However, a significant proportion of genetic tests yields variants of uncertain significance (VUS) that have undefined risk of cancer. Individuals carrying these VUS cannot benefit from individualized cancer risk assessment. Recently, a quantitative "posterior probability model" for assessing the clinical relevance of VUS in BRCA1 or BRCA2, which integrates multiple forms of genetic evidence has been developed. Here, we provide a detailed review of this model. We describe the components of the model and explain how these can be combined to calculate a posterior probability of pathogenicity for each VUS. We explain how the model can be applied to public data and provide tables that list the VUS that have been classified as not pathogenic or pathogenic using this method. While we use BRCA1 and BRCA2 VUS as examples, the method can be used as a framework for classification of the pathogenicity of VUS in other cancer genes.
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Affiliation(s)
- Noralane M Lindor
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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27
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Spurdle AB, Healey S, Devereau A, Hogervorst FBL, Monteiro ANA, Nathanson KL, Radice P, Stoppa-Lyonnet D, Tavtigian S, Wappenschmidt B, Couch FJ, Goldgar DE. ENIGMA--evidence-based network for the interpretation of germline mutant alleles: an international initiative to evaluate risk and clinical significance associated with sequence variation in BRCA1 and BRCA2 genes. Hum Mutat 2011; 33:2-7. [PMID: 21990146 DOI: 10.1002/humu.21628] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 09/26/2011] [Indexed: 12/27/2022]
Abstract
As genetic testing for predisposition to human diseases has become an increasingly common practice in medicine, the need for clear interpretation of the test results is apparent. However, for many disease genes, including the breast cancer susceptibility genes BRCA1 and BRCA2, a significant fraction of tests results in the detection of a genetic variant for which disease association is not known. The finding of an "unclassified" variant (UV)/variant of uncertain significance (VUS) complicates genetic test reporting and counseling. As these variants are individually rare, a large collaboration of researchers and clinicians will facilitate studies to assess their association with cancer predisposition. It was with this in mind that the ENIGMA consortium (www.enigmaconsortium.org) was initiated in 2009. The membership is both international and interdisciplinary, and currently includes more than 100 research scientists and clinicians from 19 countries. Within ENIGMA, there are presently six working groups focused on the following topics: analysis, clinical, database, functional, tumor histopathology, and mRNA splicing. ENIGMA provides a mechanism to pool resources, exchange methods and data, and coordinately develop and apply algorithms for classification of variants in BRCA1 and BRCA2. It is envisaged that the research and clinical application of models developed by ENIGMA will be relevant to the interpretation of sequence variants in other disease genes.
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28
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Miller-Samuel S, MacDonald DJ, McDonald DJ, Weitzel JN, Santiago F, Martino MA, Namey T, Augustyn A, Mueller R, Forman A, Bradbury AR, Morris GJ. Variants of uncertain significance in breast cancer-related genes: real-world implications for a clinical conundrum. Part one: clinical genetics recommendations. Semin Oncol 2011; 38:469-80. [PMID: 21810505 DOI: 10.1053/j.seminoncol.2011.04.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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29
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Chang S, Wang RH, Akagi K, Kim KA, Martin BK, Cavallone L, Haines DC, Basik M, Mai P, Poggi E, Isaacs C, Looi LM, Mun KS, Greene MH, Byers SW, Teo SH, Deng CX, Sharan SK. Tumor suppressor BRCA1 epigenetically controls oncogenic microRNA-155. Nat Med 2011; 17:1275-82. [PMID: 21946536 DOI: 10.1038/nm.2459] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 08/03/2011] [Indexed: 12/13/2022]
Abstract
BRCA1, a well-known tumor suppressor with multiple interacting partners, is predicted to have diverse biological functions. However, so far its only well-established role is in the repair of damaged DNA and cell cycle regulation. In this regard, the etiopathological study of low-penetrant variants of BRCA1 provides an opportunity to uncover its other physiologically important functions. Using this rationale, we studied the R1699Q variant of BRCA1, a potentially moderate-risk variant, and found that it does not impair DNA damage repair but abrogates the repression of microRNA-155 (miR-155), a bona fide oncomir. Mechanistically, we found that BRCA1 epigenetically represses miR-155 expression via its association with HDAC2, which deacetylates histones H2A and H3 on the miR-155 promoter. We show that overexpression of miR-155 accelerates but the knockdown of miR-155 attenuates the growth of tumor cell lines in vivo. Our findings demonstrate a new mode of tumor suppression by BRCA1 and suggest that miR-155 is a potential therapeutic target for BRCA1-deficient tumors.
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Affiliation(s)
- Suhwan Chang
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
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Vargas AC, Reis-Filho JS, Lakhani SR. Phenotype-genotype correlation in familial breast cancer. J Mammary Gland Biol Neoplasia 2011; 16:27-40. [PMID: 21400086 DOI: 10.1007/s10911-011-9204-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 03/01/2011] [Indexed: 12/25/2022] Open
Abstract
Familial breast cancer accounts for a small but significant proportion of breast cancer cases worldwide. Identification of the candidate genes is always challenging specifically in patients with little or no family history. Therefore, a multidisciplinary team is required for the proper detection and further management of these patients. Pathologists have played a pivotal role in the cataloguing of genotypic-phenotypic correlations in families with hereditary cancer syndromes. These efforts have led to the identification of histological and phenotypic characteristics that can help predict the presence or absence of germline mutations of specific cancer predisposition genes. However, the panoply of cancer phenotypes associated with mutations of genes other than in BRCA1 is yet to be fully characterised; in fact, many cancer syndromes, germline mutations and gene sequence variants are under investigation for their possible morphological associations. Here we review the current understanding of phenotype-genotype correlation in familial breast cancer.
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Affiliation(s)
- Ana Cristina Vargas
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, Australia
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31
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Vargas AC, Da Silva L, Lakhani SR. The contribution of breast cancer pathology to statistical models to predict mutation risk in BRCA carriers. Fam Cancer 2011; 9:545-53. [PMID: 20577821 DOI: 10.1007/s10689-010-9362-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BRCA1 and BRCA2 associated breast cancer comprises a small but important group of hereditary breast cancer. Testing for BRCA1 and BRCA2 has significant clinical and personal implications for the patients in terms of therapy and follow-up of individual family members. The sequencing of the genes is expensive and since the information derived may have a profound effect on the individual and family members, it is important that testing is done only when the risk of carrying a mutation is thought to be high. Over the last decade, researchers have developed a number of statistical models for predicting risk for harboring mutations in these genes and the risk of subsequently developing breast and ovarian cancer. These models usually take into account the type of tumor and age at occurrence as well as family history. Data from pathological analysis show that although breast tumours are heterogeneous, there are histological characteristics that are seen more frequently in carriers of BRCA1 germ line mutations compared to BRCA2 and sporadic breast cancers. A number of authors have suggested that the addition of pathological data to risk algorithms may improve the predictive power of these models and provide a more accurate way of identifying individuals who may benefit from testing. Here we review the pathology of familial breast cancer and assess the evidence to justify the use of pathology in refining risk assessment models.
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Affiliation(s)
- Ana Cristina Vargas
- Molecular and Cellular Pathology, The University of Queensland Centre for Clinical Research, The Royal Brisbane and Women's Hospital, Building 71/918, Brisbane, QLD 4029, Australia
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32
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Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R, Penland CM, Cutting GR. Evaluation of the disease liability of CFTR variants. Methods Mol Biol 2011; 742:355-372. [PMID: 21547743 DOI: 10.1007/978-1-61779-120-8_21] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Over 1600 novel sequence variants in the CFTR gene have been reported to the CF Mutation Database (http://www.genet.sickkids.on.ca/cftr/Home.html). While about 25 mutations are well characterized by clinical studies and functional assays, the disease liability of most of the remaining mutations is either unclear or unknown. This gap in knowledge has implications for diagnosis, therapy selection, and counseling for patients and families carrying an uncharacterized CFTR mutation. This chapter will describe a critical approach to assessing the disease implications of CFTR mutations utilizing clinical data, literature review, functional testing, and bioinformatic in silico methods.
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Affiliation(s)
- Patrick R Sosnay
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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33
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Steffensen AY, Jønson L, Ejlertsen B, Gerdes AM, Nielsen FC, Hansen TVO. Identification of a Danish breast/ovarian cancer family double heterozygote for BRCA1 and BRCA2 mutations. Fam Cancer 2010; 9:283-7. [PMID: 20455026 PMCID: PMC2921502 DOI: 10.1007/s10689-010-9345-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mutations in the two breast cancer susceptibility genes BRCA1 and BRCA2 are associated with increased risk of breast and ovarian cancer. Patients with mutations in both genes are rarely reported and often involve Ashkenazi founder mutations. Here we report the first identification of a Danish breast and ovarian cancer family heterozygote for mutations in the BRCA1 and BRCA2 genes. The BRCA1 nucleotide 5215G > A/c.5096G > A mutation results in the missense mutation Arg1699Gln, while the BRCA2 nucleotide 859 + 4A > G/c.631 + 4A > G is novel. Exon trapping experiments and reverse transcriptase (RT)–PCR analysis revealed that the BRCA2 mutation results in skipping of exon 7, thereby introducing a frameshift and a premature stop codon. We therefore classify the mutation as disease causing. Since the BRCA1 Arg1699Gln mutation is also suggested to be disease-causing, we consider this family double heterozygote for BRCA1 and BRCA2 mutations.
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Affiliation(s)
- Ane Y Steffensen
- Department of Clinical Biochemistry 4111, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen, Denmark
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34
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Rouleau E, Lefol C, Moncoutier V, Castera L, Houdayer C, Caputo S, Bièche I, Buisson M, Mazoyer S, Stoppa-Lyonnet D, Noguès C, Lidereau R. A missense variant within BRCA1 exon 23 causing exon skipping. ACTA ACUST UNITED AC 2010; 202:144-6. [PMID: 20875879 DOI: 10.1016/j.cancergencyto.2010.07.122] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 06/16/2010] [Accepted: 07/08/2010] [Indexed: 12/12/2022]
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35
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Walker LC, Whiley PJ, Couch FJ, Farrugia DJ, Healey S, Eccles DM, Lin F, Butler SA, Goff SA, Thompson BA, Lakhani SR, Da Silva LM, Tavtigian SV, Goldgar DE, Brown MA, Spurdle AB. Detection of splicing aberrations caused by BRCA1 and BRCA2 sequence variants encoding missense substitutions: implications for prediction of pathogenicity. Hum Mutat 2010; 31:E1484-505. [PMID: 20513136 DOI: 10.1002/humu.21267] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Missense substitutions in high-risk cancer susceptibility genes create clinical uncertainty in the genetic counseling process. Multifactorial likelihood classification approaches and in vitro assays are useful for the classification of exonic sequence variants in BRCA1 and BRCA2, but these currently rely on the assumption that changes in protein function are the major biological mechanism of pathogenicity. This study investigates the potentially pathogenic role of aberrant splicing for exonic variants predicted to encode missense substitutions using patient-derived RNA. No splicing aberrations were identified for BRCA1c.5054C>T and BRCA2c.7336A>G, c.8839G>A, and c.9154C>T. However, RT-PCR analysis identified a major splicing aberration for BRCA1c.4868C>G(p.Ala1623Gly), a variant encoding a missense substitution considered likely to be neutral. Splicing aberrations were also observed for BRCA2c.7988A>T(p.Glu2663Val) and c.8168A>G(p.Asp2723Gly), but both variant and wildtype alleles were shown to be present in full-length mRNA transcripts, suggesting that variant protein may be translated. BRCA2 protein function assays indicated that BRCA2p.Glu2663Val, p.Asp2723Gly and p.Arg3052Trp missense proteins have abrogated function consistent with pathogenicity. Multifactorial likelihood analysis provided evidence for pathogenicity for BRCA1 c.5054C>T(p.Thr1685Ile) and BRCA2c.7988A>T(p.Glu2663Val), c.8168A>G(p.Asp2723Gly) and c.9154C>T(p.Arg3052Trp), supporting experimentally derived evidence. These findings highlight the need for improved bioinformatic prediction of splicing aberrations and to refine multifactorial likelihood models used to assess clinical significance.
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Affiliation(s)
- Logan C Walker
- Queensland Institute of Medical Research, Brisbane, Australia
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van Harssel JJT, van Roozendaal CEP, Detisch Y, Brandão RD, Paulussen ADC, Zeegers M, Blok MJ, Gómez García EB. Efficiency of BRCAPRO and Myriad II mutation probability thresholds versus cancer history criteria alone for BRCA1/2 mutation detection. Fam Cancer 2010; 9:193-201. [PMID: 19949876 PMCID: PMC2871096 DOI: 10.1007/s10689-009-9305-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Considerable differences exist amongst countries in the mutation probability methods and thresholds used to select patients for BRCA1/2 genetic screening. In order to assess the added value of mutation probability methods, we have retrospectively calculated the BRCAPRO and Myriad II probabilities in 306 probands who had previously been selected for DNA-analysis according to criteria based on familial history of cancer. DNA-analysis identified 52 mutations (16.9%) and 11 unclassified variants (UVs, 3.6%). Compared to cancer history, a threshold ≥10% with BRCAPRO or with Myriad II excluded about 40% of the patients from analysis, including four with a mutation and probabilities <10% with both programs. All four probands had a BRCA2 mutation. BRCAPRO and Myriad II showed similar specificity at 10% threshold, overall BRCAPRO was more sensitive than Myriad II for the detection of mutations. Only two of the probands with an UV had probabilities >20% with BRCAPRO and Myriad II. In summary, BRCAPRO and Myriad II are more efficient than cancer history alone to exclude patients without a mutation. BRCAPRO performs better for the detection of BRCA1 mutations than of BRCA2 mutations. The Myriad II scores provided no additional information than the BRCAPRO scores alone for the detection of patients with a mutation. The use of thresholds excluded from analysis the majority of patients carrying an UV.
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Affiliation(s)
- J. J. T. van Harssel
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
- Present Address: Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - C. E. P. van Roozendaal
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Y. Detisch
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - R. D. Brandão
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
- Research Institute Growth & Development (GROW), University of Maastricht, Maastricht, The Netherlands
| | - A. D. C. Paulussen
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - M. Zeegers
- Department of Complex Genetics, Nutrition and Toxicology Research Institute, Maastricht University, Maastricht, The Netherlands
- Unit of Genetic Epidemiology, Department of Public Health, Epidemiology and Biostatistics, School of Medicine, University of Birmingham, Birmingham, UK
| | - M. J. Blok
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
| | - E. B. Gómez García
- Department of Clinical Genetics, University Medical Centre Maastricht, P.O. Box 5800, 6202 AZ Maastricht, The Netherlands
- Research Institute Growth & Development (GROW), University of Maastricht, Maastricht, The Netherlands
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Iyevleva AG, Suspitsin EN, Kroeze K, Gorodnova TV, Sokolenko AP, Buslov KG, Voskresenskiy DA, Togo AV, Kovalenko SP, Stoep NVD, Devilee P, Imyanitov EN. Non-founder BRCA1 mutations in Russian breast cancer patients. Cancer Lett 2010; 298:258-63. [PMID: 20727672 DOI: 10.1016/j.canlet.2010.07.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/11/2010] [Accepted: 07/13/2010] [Indexed: 11/27/2022]
Abstract
A few founder BRCA1 mutations (5382insC, 4154delA, 185delAG) account for up to 15% of high-risk (young-onset or familial or bilateral) breast cancer (BC) cases in Russia. The impact of non-founder BRCA1 mutations in this country is less studied; in particular, there are no reports analyzing gross rearrangements of this gene in the Russian patient series. We selected for the study 95 founder mutation negative high-risk BC cases. Combination of high-resolution melting (HRM) and sequencing revealed six presumably BC-associated alleles (2080delA, 4808C>G, 5214C>T, 5236G>A, 5460G>T, 5622C>T) and one variant of an unknown significance (4885G>A). The pathogenic role of the 5236G>A mutation leading to G1706E substitution was further confirmed by the loss of heterozygosity analysis of the corresponding tumor tissue. Multiplex ligation-dependent probe amplification (MLPA) revealed two additional BRCA1 heterozygotes, which carried BRCA1 deletions involving exons 1-2 and 3-7, respectively. Based on the results of this investigation and the review of prior Russian studies, three BRCA1 mutations (2080delA, 3819del5, 3875del4) were considered with respect to their possible founder effect and tested in the additional series of 210 high-risk BC patients; two BRCA heterozygotes (2080delA and 3819del5) were revealed. We conclude that the non-founder mutations constitute the minority of BRCA1 defects in Russia.
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Abstract
In the past few years, ovarian cancer research has focused increasingly on disease prevention; but an increasing number of women refer to gynecology and clinical genetics clinics with a family history of ovarian cancer and inherited familial mutations. The interest on the issue has increased also due to the identification of BReast CAncer1 (BRCA1) and BRCA2 genes mutations. The importance of recognizing the characteristics of hereditary ovarian cancer (HOC) and manage women at risk appropriately will provide more accurate care of the high-risk population. Women at risk can be identified by pedigree analysis and may receive counseling from interdisciplinary cancer genetics clinics, while those at high risk need to receive genetic testing. Risk calculation programs define risks and assist in decision-making in clinical options and genetic testing; they provide information on the risks of the disease, mutation status, and the use of genetic testing in the management of high-risk families. Furthermore, while a large number of surrogate preliminary markers have been identified, there are still limited studies on ovarian cancer genomics. Different options for risk management of HOC are available: surveillance, chemoprevention and prophylactic surgery. Surveillance in HOC high-risk patients is still not accurate. Chemoprevention is currently a controversial topic, because a number of major issues still need to be addressed in developing and testing agents for ovarian cancer chemoprevention. Prophylactic surgery has been shown to effectively decrease cancer risk, and it has the possibility to substantially reduce ovarian cancer mortality.
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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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Li L, Biswas K, Habib LA, Kuznetsov SG, Hamel N, Kirchhoff T, Wong N, Armel S, Chong G, Narod SA, Claes K, Offit K, Robson ME, Stauffer S, Sharan SK, Foulkes WD. Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant. Hum Mutat 2009; 30:1543-50. [PMID: 19795481 PMCID: PMC3501199 DOI: 10.1002/humu.21101] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Variants of unknown significance (VUS) in BRCA1 and BRCA2 are common, and present significant challenges for genetic counseling. We observed that BRCA2: c.6853A>G (p.I2285V) (Breast Cancer Information Core [BIC] name: 7081A>G; http://research.nhgri.nih.gov/bic/) co-occurs in trans with the founder mutation c.5946delT (p.S1982RfsX22) (BIC name: 6174delT), supporting the published classification of p.I2285V as a neutral variant. However, we also noted that when compared with wild-type BRCA2, p.I2285V resulted in increased exclusion of exon 12. Functional assay using allelic complementation in Brca2-null mouse embryonic stem cells revealed that p.I2285V, an allele with exon 12 deleted and wild-type BRCA2 were all phenotypically indistinguishable, as measured by sensitivity to DNA-damaging agents, effect on irradiation-induced Rad51 foci formation, homologous recombination, and overall genomic integrity. An allele frequency study showed the p.I2285V variant was identified in 15 out of 722 (2.1%) Ashkenazi Jewish cases and 10 out of 475 (2.1%) ethnically-matched controls (odds ratio, 0.99; 95% confidence interval: 0.44-2.21; P=0.97). Thus the p.I2285V variant is not associated with an increased risk for breast cancer. Taken together, our clinical and functional studies strongly suggest that exon 12 is functionally redundant and therefore missense variants in this exon are likely to be neutral. Such comprehensive functional studies will be important adjuncts to genetic studies of variants.
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Affiliation(s)
- Lili Li
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada
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Mohammadi L, Vreeswijk MP, Oldenburg R, van den Ouweland A, Oosterwijk JC, van der Hout AH, Hoogerbrugge N, Ligtenberg M, Ausems MG, van der Luijt RB, Dommering CJ, Gille JJ, Verhoef S, Hogervorst FB, van Os TA, Gómez García E, Blok MJ, Wijnen JT, Helmer Q, Devilee P, van Asperen CJ, van Houwelingen HC. A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; BRCA1 and BRCA2 as an example. BMC Cancer 2009; 9:211. [PMID: 19563646 PMCID: PMC2714556 DOI: 10.1186/1471-2407-9-211] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Accepted: 06/29/2009] [Indexed: 01/12/2023] Open
Abstract
Background Assessment of the clinical significance of unclassified variants (UVs) identified in BRCA1 and BRCA2 is very important for genetic counselling. The analysis of co-segregation of the variant with the disease in families is a powerful tool for the classification of these variants. Statistical methods have been described in literature but these methods are not always easy to apply in a diagnostic setting. Methods We have developed an easy to use method which calculates the likelihood ratio (LR) of an UV being deleterious, with penetrance as a function of age of onset, thereby avoiding the use of liability classes. The application of this algorithm is publicly available http://www.msbi.nl/cosegregation. It can easily be used in a diagnostic setting since it requires only information on gender, genotype, present age and/or age of onset for breast and/or ovarian cancer. Results We have used the algorithm to calculate the likelihood ratio in favour of causality for 3 UVs in BRCA1 (p.M18T, p.S1655F and p.R1699Q) and 5 in BRCA2 (p.E462G p.Y2660D, p.R2784Q, p.R3052W and p.R3052Q). Likelihood ratios varied from 0.097 (BRCA2, p.E462G) to 230.69 (BRCA2, p.Y2660D). Typing distantly related individuals with extreme phenotypes (i.e. very early onset cancer or old healthy individuals) are most informative and give the strongest likelihood ratios for or against causality. Conclusion Although co-segregation analysis on itself is in most cases insufficient to prove pathogenicity of an UV, this method simplifies the use of co-segregation as one of the key features in a multifactorial approach considerably.
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Affiliation(s)
- Leila Mohammadi
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.
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Sweet K, Senter L, Pilarski R, Wei L, Toland AE. Characterization of BRCA1 ring finger variants of uncertain significance. Breast Cancer Res Treat 2009; 119:737-43. [PMID: 19543972 DOI: 10.1007/s10549-009-0438-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/03/2009] [Indexed: 11/28/2022]
Abstract
The majority of pathogenic mutations in BRCA1 result in a truncated protein. Although most missense changes in BRCA1 are of unknown functional significance, a handful of deleterious missense mutations have been identified. The majority of these occur in splice sites or highly conserved protein domains. Previously, we developed a predictive model, VUS Predict, to classify BRCA variants of uncertain significance as neutral or deleterious. It uses evolutionary prediction algorithms together with clinical information from cancer pathology reports and BRCA genetic testing results. Because of the higher probability that missense changes occurring in conserved BRCA1 domains are of pathogenic significance, we identified all individuals in our cohort who had been tested for BRCA1 and BRCA2 mutations who had missense changes in the BRCA1 ring finger domain and sought to classify those changes. We applied VUS Predict to three previously uncharacterized variants and four missense changes known to be deleterious. Two variants, L22S and T37K, were predicted to be deleterious and one variant, K45Q, was predicted to be neutral by VUS Predict. The mutations C39R, C44Y, C44S, and C61G were confirmed as deleterious.
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Affiliation(s)
- Kevin Sweet
- Clinical Cancer Genetics Program, Columbus, OH, USA
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