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Khan MA, Varma AK. In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2. J Biomol Struct Dyn 2023; 41:9879-9889. [PMID: 36404616 DOI: 10.1080/07391102.2022.2148127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as 'Variants of Uncertain Significance' (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mudassar Ali Khan
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Ashok K Varma
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
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2
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De Paolis E, Paris I, Tilocca B, Roncada P, Foca L, Tiberi G, D’Angelo T, Pavese F, Muratore M, Carbognin L, Garganese G, Masetti R, Di Leone A, Fabi A, Scambia G, Urbani A, Generali D, Minucci A, Santonocito C. Assessing the pathogenicity of BRCA1/2 variants of unknown significance: Relevance and challenges for breast cancer precision medicine. Front Oncol 2023; 12:1053035. [PMID: 36741700 PMCID: PMC9891372 DOI: 10.3389/fonc.2022.1053035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Breast cancer (BC) is the leading cause of cancer-related death in women worldwide. Pathogenic variants in BRCA1 and BRCA2 genes account for approximately 50% of all hereditary BC, with 60-80% of patients characterized by Triple Negative Breast Cancer (TNBC) at an early stage phenotype. The identification of a pathogenic BRCA1/2 variant has important and expanding roles in risk-reducing surgeries, treatment planning, and familial surveillance. Otherwise, finding unclassified Variants of Unknown Significance (VUS) limits the clinical utility of the molecular test, leading to an "imprecise medicine". Methods We reported the explanatory example of the BRCA1 c.5057A>C, p.(His1686Pro) VUS identified in a patient with TNBC. We integrated data from family history and clinic-pathological evaluations, genetic analyses, and bioinformatics in silico investigations to evaluate the VUS classification. Results Our evaluation posed evidences for the pathogenicity significance of the investigated VUS: 1) association of the BRCA1 variant to cancer-affected members of the family; 2) absence of another high-risk mutation; 3) multiple indirect evidences derived from gene and protein structural analysis. Discussion In line with the ongoing efforts to uncertain variants classification, we speculated about the relevance of an in-depth assessment of pathogenicity of BRCA1/2 VUS for a personalized management of patients with BC. We underlined that the efficient integration of clinical data with the widest number of supporting molecular evidences should be adopted for the proper management of patients, with the final aim of effectively guide the best prognostic and therapeutic paths.
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Affiliation(s)
- Elisa De Paolis
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Ida Paris
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,*Correspondence: Ida Paris,
| | - Bruno Tilocca
- Department of Health Science, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Catanzaro, Italy
| | - Laura Foca
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giordana Tiberi
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Tatiana D’Angelo
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Francesco Pavese
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Margherita Muratore
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Luisa Carbognin
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giorgia Garganese
- Gynaecology and Breast Care Center, Mater Olbia Hospital, Olbia, Italy,Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Ginecologia ed Ostetricia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Masetti
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alba Di Leone
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessandra Fabi
- Unit of Precision Medicine in Breast Cancer, Scientific Directorate, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Giovanni Scambia
- Division of Oncological Gynecology, Department of Women’s and Children’s Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Urbani
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Concetta Santonocito
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
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DİRİCAN E, KARABULUT UZUNÇAKMAK S, ÖZCAN H. Şizofreni hastalarında CYB mtDNA mutasyonları ve PI3K/AKT/mTOR sinyal yolağındaki genlerin ekspresyon durumu. CUKUROVA MEDICAL JOURNAL 2022. [DOI: 10.17826/cumj.1186118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Amaç: Bu çalışma, şizofreni hastalarında sitokrom b (CYB) mitokondriyal DNA (mtDNA) mutasyonlarını taramayı ve PI3K/AKT/mTOR sinyal yolağındaki genlerin mRNA ifadelerini analiz etmeyi amaçlamıştır.
Gereç ve Yöntem: Bu çalışmada 44 şizofreni hastasından ve 41 sağlıklı bireyden DNA (hasta) ve RNA (hasta ve kontrol) izolasyonu için tam kan alındı. CYB mtDNA mutasyonları için örnekler PCR ile amplifiye edildi ve Sanger DNA dizi analiziyle tanımlandı. PIK3CA, AKT1 ve mTOR genlerinin mRNA ekspresyonu için RT-PCR ve 2-∆∆Ct metodu kullanıldı.
Bulgular: Şizofreni hastalarında m.15326 A>G (43/44), m.15452 C>A (5/44), m.15078 A>G (3/44), m.14872 C>T (3/44) ve m.14798 T>C (3/44) en sık rastalanan CYB mtDNA mutasyonlarıydı. İn silico analizler, mutasyonların bir kısmının zararlı, hastalık yapıcı veya benign karakterle ilişkili olduğunu gösterdi. Şizofreni hastalarında PIK3CA, AKT1 ve mTOR genlerinin mRNA ekspresyonu sağlıklı bireylere göre anlamlı derecede yüksekti. PIK3CA ve AKT1 genleri arasında anlamlı orta şiddette pozitif bir korelasyon tespit edildi. Ayrıca ROC analizi ile PIK3CA, AKT1 ve mTOR genlerinin hasta grubunda iyi tanısal güce sahip olduğu belirlendi. ROC analizleri, özellikle PIK3CA'nın şizofreni hastaları için % 80 duyarlılık ve % 63,4 seçicilik ile önemli bir tanı değerine sahip olduğunu gösterdi.
Sonuç: Şizofreni hastalarında hem CYB mtDNA mutasyon sıklığı hem de PIK3CA, AKT1 ve mTOR mRNA ekspresyon düzeyi sağlıklı bireylere göre daha yüksekti. Bu mekanizmaları daha geniş şizofreni popülasyonunda çalışmanın hastalığın tanı, tedavi veya prognozunda değerli olabileceğine inanıyoruz.
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Affiliation(s)
- Ebubekir DİRİCAN
- BAYBURT ÜNİVERSİTESİ, BAYBURT SAĞLIK HİZMETLERİ MESLEK YÜKSEKOKULU
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4
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2022. [DOI: 10.1016/j.jncc.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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5
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Khan MA, Siddiqui MQ, Kuligina E, Varma AK. Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. Int J Biol Macromol 2022; 209:716-724. [PMID: 35413318 DOI: 10.1016/j.ijbiomac.2022.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair mechanism of DNA double-strand breaks and interstrand cross-links by Homologous recombination. Germline mutations identified in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer. Missense mutations are identified all over the gene, including the DNA binding region of BRCA2 that interacts with FANCD2. However, the majority of these missense mutations are classified as 'Variants of Uncertain Significance' due to a lack of structural, functional and clinical correlations. Therefore, multi-disciplinary in-silico, in-vitro and biophysical approaches have been explored to characterize an unclassified missense mutation, BRCA2 Arg2502Cys, identified from a case-control study. Circular-dichroism and Fluorescence spectroscopy show that the Arg2502Cys mutation in hBRCA2 (residues 2350-2545) decreases the α-helical/β-sheet propensity of the wild-type protein and perturb the tertiary structure conformation. Molecular dynamics simulations revealed alteration in the intramolecular H-bonds, overall compactness and stability of the hydrophobic core were observed in the mutant protein. Principle component analysis indicated that Arg2502Cys mutant exhibited comparatively large conformational transitions and periodic fluctuation. Therefore, to our conclusion, BRCA2 Arg2502Cys mutant perturbed the structural integrity and conformational dynamics of BRCA2.
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Affiliation(s)
- Mudassar Ali Khan
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Present address: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Ekaterina Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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6
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Li J, Zhao B, Huang T, Qin Z, Wang SM. Human BRCA pathogenic variants were originated during recent human history. Life Sci Alliance 2022; 5:5/5/e202101263. [PMID: 35165121 PMCID: PMC8860097 DOI: 10.26508/lsa.202101263] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/05/2023] Open
Abstract
BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.
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Affiliation(s)
- Jiaheng Li
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Bojin Zhao
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Teng Huang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - Zixin Qin
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
| | - San Ming Wang
- MoE Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau, China
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7
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Abu-Helalah M, Azab B, Mubaidin R, Ali D, Jafar H, Alshraideh H, Drou N, Awidi A. BRCA1 and BRCA2 genes mutations among high risk breast cancer patients in Jordan. Sci Rep 2020; 10:17573. [PMID: 33067490 PMCID: PMC7568559 DOI: 10.1038/s41598-020-74250-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Familial breast cancer is estimated to account for 15-20% of all cases of breast cancer. Surveillance for familial breast cancer is well-established world-wide. However, this service does not exist in Jordan, due to the scarcity of information with regard to the genetic profiling of these patients, and therefore lack of recommendations for policy-makers. As such, patients with very strong family history of breast or ovarian cancers are not screened routinely; leading to preventable delay in diagnosis. Whole coding sequencing for BCRA1/BCRA2 using next-generation sequencing (NGS)/Ion PGM System was performed. Sanger sequencing were then used to confirm the pathogenic variants detected by NGS. In this study, 192 breast cancer patients (and 8 ovarian cancer cases) were included. The prevalence of recurrent pathogenic mutations was 14.5%, while the prevalence of newly detected mutations was 3.5%. Two novel pathogenic mutations were identified in BRCA2 genes. The common mutations in the Ashkenazi population used for screening may not apply in the Jordanian population, as previously reported mutations were not prevalent, and other new mutations were identified. These data will aid to establish a specific screening test for BRCA 1/BRCA2 in the Jordanian population.
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Affiliation(s)
- Munir Abu-Helalah
- Department of Public Health, Faculty of Medicine, Mutah University, Karak, Jordan.,Faculty of Medicine, Al-Faisal University, Riyadh, Kingdom of Saudi Arabia
| | - Belal Azab
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan.,Department of Pathology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Rasmi Mubaidin
- Radiation Therapy Department, Al-Bashir Hospital, Ministry of Health, Amman, Jordan
| | - Dema Ali
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan
| | - Hanan Jafar
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan.,Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman, Jordan
| | - Hussam Alshraideh
- Industrial Engineering Department, University of Science and Technology, Irbid, Jordan.,Industrial Engineering Department, American University of Sharjah, Sharjah, UAE
| | - Nizar Drou
- NYU Abu Dhabi Center for Genomics and System Biology, Abu Dhabi, UAE
| | - Abdalla Awidi
- Cell Therapy Center, The University of Jordan, Amman, 11942, Jordan. .,Department of Medicine, School of Medicine, The University of Jordan, Amman, Jordan.
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Tavtigian SV, Harrison SM, Boucher KM, Biesecker LG. Fitting a naturally scaled point system to the ACMG/AMP variant classification guidelines. Hum Mutat 2020; 41:1734-1737. [PMID: 32720330 PMCID: PMC8011844 DOI: 10.1002/humu.24088] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 12/29/2022]
Abstract
Recently, we demonstrated that the qualitative American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) guidelines for evaluation of Mendelian disease gene variants are fundamentally compatible with a quantitative Bayesian formulation. Here, we show that the underlying ACMG/AMP "strength of evidence categories" can be abstracted into a point system. These points are proportional to Log(odds), are additive, and produce a system that recapitulates the Bayesian formulation of the ACMG/AMP guidelines. The strengths of this system are its simplicity and that the connection between point values and odds of pathogenicity allows empirical calibration of the strength of evidence for individual data types. Weaknesses include that a narrow range of prior probabilities is locked in and that the Bayesian nature of the system is inapparent. We conclude that a points-based system has the practical attribute of user-friendliness and can be useful so long as the underlying Bayesian principles are acknowledged.
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Affiliation(s)
- Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, USA.,Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA
| | | | - Kenneth M. Boucher
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT, USA.,Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Leslie G. Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
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9
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Curated multiple sequence alignment for the Adenomatous Polyposis Coli (APC) gene and accuracy of in silico pathogenicity predictions. PLoS One 2020; 15:e0233673. [PMID: 32750050 PMCID: PMC7402488 DOI: 10.1371/journal.pone.0233673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/05/2020] [Indexed: 11/19/2022] Open
Abstract
Computational algorithms are often used to assess pathogenicity of Variants of Uncertain Significance (VUS) that are found in disease-associated genes. Most computational methods include analysis of protein multiple sequence alignments (PMSA), assessing interspecies variation. Careful validation of PMSA-based methods has been done for relatively few genes, partially because creation of curated PMSAs is labor-intensive. We assessed how PMSA-based computational tools predict the effects of the missense changes in the APC gene, in which pathogenic variants cause Familial Adenomatous Polyposis. Most Pathogenic or Likely Pathogenic APC variants are protein-truncating changes. However, public databases now contain thousands of variants reported as missense. We created a curated APC PMSA that contained >3 substitutions/site, which is large enough for statistically robust in silico analysis. The creation of the PMSA was not easily automated, requiring significant querying and computational analysis of protein and genome sequences. Of 1924 missense APC variants in the NCBI ClinVar database, 1800 (93.5%) are reported as VUS. All but two missense variants listed as P/LP occur at canonical splice or Exonic Splice Enhancer sites. Pathogenicity predictions by five computational tools (Align-GVGD, SIFT, PolyPhen2, MAPP, REVEL) differed widely in their predictions of Pathogenic/Likely Pathogenic (range 17.5–75.0%) and Benign/Likely Benign (range 25.0–82.5%) for APC missense variants in ClinVar. When applied to 21 missense variants reported in ClinVar and securely classified as Benign, the five methods ranged in accuracy from 76.2–100%. Computational PMSA-based methods can be an excellent classifier for variants of some hereditary cancer genes. However, there may be characteristics of the APC gene and protein that confound the results of in silico algorithms. A systematic study of these features could greatly improve the automation of alignment-based techniques and the use of predictive algorithms in hereditary cancer genes.
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Hosseini S, Schmidt EDL, Bakker FT. Leucine-rich repeat receptor-like kinase II phylogenetics reveals five main clades throughout the plant kingdom. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:547-560. [PMID: 32175641 PMCID: PMC7496461 DOI: 10.1111/tpj.14749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 01/17/2020] [Accepted: 02/27/2020] [Indexed: 05/22/2023]
Abstract
Receptor-like kinases (RLKs) represent the largest group of cell surface receptors in plants. The monophyletic leucine-rich repeat (LRR)-RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERKs) and NSP-interacting kinases known to be involved in developmental processes and cellular immunity in plants. There are only a few published studies on the phylogenetics of LRR-RLKII; unfortunately these suffer from poor taxon/gene sampling. Hence, it is not clear how many and what main clades this family contains, let alone what structure-function relationships exist. We used 1342 protein sequences annotated as 'SERK' and 'SERK-like' plus related sequences in order to estimate phylogeny within the LRR-RLKII clade, using the nematode protein kinase Pelle as an outgroup. We reconstruct five main clades (LRR-RLKII 1-5), in each of which the main pattern of land plant relationships re-occurs, confirming previous hypotheses that duplication events happened in this gene subfamily prior to divergence among land plant lineages. We show that domain structures and intron-exon boundaries within the five clades are well conserved in evolution. Furthermore, phylogenetic patterns based on the separate LRR and kinase parts of LRR-RLKs are incongruent: whereas the LRR part supports a LRR-RLKII 2/3 sister group relationship, the kinase part supports clades 1/2. We infer that the kinase part includes few 'radical' amino acid changes compared with the LRR part. Finally, our results confirm that amino acids involved in each LRR-RLKII-receptor complex interaction are located at N-capping residues, and that the short amino acid motifs of this interaction domain are highly conserved throughout evolution within the five LRR-RLKII clades.
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Affiliation(s)
- Samin Hosseini
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
| | - Ed D. L. Schmidt
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
| | - Freek T. Bakker
- Biosystematics GroupWageningen UniversityRadix Building 107, Droevendaalsesteeg 16708 PB WageningenThe Netherlands
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11
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McVeigh ÚM, McVeigh TP, Curran C, Miller N, Morris DW, Kerin MJ. Diagnostic yield of a custom-designed multi-gene cancer panel in Irish patients with breast cancer. Ir J Med Sci 2020; 189:849-864. [PMID: 32008151 DOI: 10.1007/s11845-020-02174-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/20/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Breast cancer is genetically heterogeneous, and parellel multi-gene sequencing is the most cost- and time-efficient manner to investigate breast cancer predisposition. Numerous multi-gene panels (MGPs) are commercially available, but many include genes with weak/unproven associaton with breast cancer, or with predisposition to cancer of other types. This study investigates the utility of a custom-designed multi-gene panel in an Irish cohort with breast cancer. METHODS A custom panel comprising 83 genes offered by 19 clinical "breast cancer predisposition" MGPs was designed and applied to germline DNA from 91 patients with breast cancer and 77 unaffected ethnicially matched controls. Variants were identified and classified using a custom pipeline. RESULTS Nineteen loss-of-function (LOF) and 334 missense variants were identified. After removing common and/or benign variants, 15 LOF and 30 missense variants were analysed. Variants in known breast cancer susceptibility genes were identified, including in BRCA1 and ATM in cases, and in NF1 and CHEK2 in controls. Most variants identified were in genes associated with predisposition to cancers other than breast cancer (BRIP1, RAD50, MUTYH, and mismatch repair genes), or in genes with unknown or unproven association with cancer. CONCLUSION Using multi-gene panels enables rapid, cost-effective identification of individuals with high-risk cancer predisposition syndromes. However, this approach also leads to an increased amount of uncertain results. Clinical management of individuals with particular genetic variants in the absence of a matching phenotype/family history is challenging. Further population and functional evidence is required to fully elucidate the clinical relevance of variants in genes of uncertain significance.
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Affiliation(s)
- Úna M McVeigh
- Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.
| | - Terri P McVeigh
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Catherine Curran
- Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland
| | - Nicola Miller
- Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Micheal J Kerin
- Discipline of Surgery, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland
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12
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Cifuentes-C L, Rivera-Herrera AL, Barreto G. BRCA1 and BRCA2 mutations in a sample of breast and ovarian cancer families from the Colombian pacific. Colomb Med (Cali) 2019; 50:163-175. [PMID: 32284662 PMCID: PMC7141151 DOI: 10.25100/cm.v50i3.2385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Introduction: Breast cancer is the most common neoplasia of women from all over the world especially women from Colombia. 5%10% of all cases are caused by hereditary factors, 25% of those cases have mutations in the BRCA1/BRCA2 genes. Objective: The purpose of this study was to identify the mutations associated with the risk of familial breast and/or ovarian cancer in a population of Colombian pacific. Methods: 58 high-risk breast and/or ovarian cancer families and 20 controls were screened for germline mutations in BRCA1 and BRCA2, by Single Strand Conformation Polymorphism (SSCP) and sequencing. Results: Four families (6.9%) were found to carry BRCA1 mutations and eight families (13.8%) had mutations in BRCA2. In BRCA1, we found three Variants of Uncertain Significance (VUS), of which we concluded, using in silico tools, that c.8112C>G and c.3119G>A (p.Ser1040Asn) are probably deleterious, and c.3083G>A (p.Arg1028His) is probably neutral. In BRCA2, we found three variants of uncertain significance: two were previously described and one novel mutation. Using in silico analysis, we concluded that c.865A>G (p.Asn289Asp) and c.6427T>C (p.Ser2143Pro) are probably deleterious and c.125A>G (p.Tyr42Cys) is probably neutral. Only one of them has previously been reported in Colombia. We also identified 13 polymorphisms (4 in BRCA1 and 9 in BRCA2), two of them are associated with a moderate increase in breast cancer risk (BRCA2 c.1114A>C and c.875566T>C). Conclusion: According to our results, the Colombian pacific population presents diverse mutational spectrum for BRCA genes that differs from the findings in other regions in the country.
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Affiliation(s)
- Laura Cifuentes-C
- Universidad del Valle, Departamento de Biología, Human Molecular Genetics Lab, Cali, Colombia
| | | | - Guillermo Barreto
- Universidad del Valle, Departamento de Biología, Human Molecular Genetics Lab, Cali, Colombia
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13
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Unclassified Variants of BRCA1 and BRCA2 in Korean Patients With Ovarian Cancer. Int J Gynecol Cancer 2019; 28:308-315. [PMID: 29240602 DOI: 10.1097/igc.0000000000001161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE The aim of the present study was to investigate unclassified variants (UVs) in BRCA1 and 2 of Korean patients with ovarian cancer. METHODS We retrospectively analyzed 138 patients diagnosed with ovarian/fallopian tubal/peritoneal cancer between January 2013 and January 2016, whose BRCA genetic test results and clinical characteristics were available for review. Patient peripheral blood lymphocyte specimens were assessed for BRCA mutations and variations by direct sequencing. Identified UVs were classified according to several algorithms. RESULTS The results of genetic testing revealed 31 (22.5%, 31/138) pathogenic BRCA mutations (24 BRCA1, 7 BRCA2 mutations). The BRCA1 c.390C>A mutation was observed in 4 patients (12.9%, 4/31). Thirty-four (24.6%, 34/138) BRCA UVs were identified in 33 patients. Of these, the BRCA1 c.4883T>C and BRCA2 c.8187G>T variants were each detected in 4 patients (4/34, 11.8%). According to the used algorithms and cosegregation test, the BRCA1 c.5339T>C and BRCA2 c.8437_8439delGGA variants were both predicted to be likely pathogenic. CONCLUSIONS The 2 identified likely pathogenic UVs require further verification with clinical evidence. Clarifying the clinical significance of UVs is an increasingly important step for cancer treatment in the current era of precision medicine.
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14
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Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M, Burn J, Chanock S, Rätsch G, Spurdle AB. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet 2018; 14:e1007752. [PMID: 30586411 PMCID: PMC6324924 DOI: 10.1371/journal.pgen.1007752] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2. The goal of this study and paper has been to develop an international resource to generate an informed and current understanding of the impact of genetic variation on cancer risk across the cancer predisposition genes, BRCA1 and BRCA2. Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org, to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype.
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Affiliation(s)
- Melissa S. Cline
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Rachel G. Liao
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Michael T. Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Faisal Alquaddoomi
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Biocybernetics Laboratory, Computer Science Department, University of California, Los Angeles, California, United States of America
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Samantha Baxter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Larry Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, Arizona, United States of America
| | - Amy Coffin
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Brian Craft
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Robert Currie
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Chloe C. Dlott
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Lena Dolman
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie O. M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Susan M. Domchek
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Zachary Fischmann
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - William D. Foulkes
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Judy Garber
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary J. Goldman
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Peter Goodhand
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Steven Harrison
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Haussler
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kazuto Kato
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Human Genetics, McGill University, Montreal, Québec, Canada
| | - Charles Markello
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Biomolecular Science & Engineering, University of California, Santa Cruz, California, United States of America
| | - Robert Nussbaum
- Invitae, San Francisco, California, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Sharon E. Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jem Rashbass
- National Disease Registration, National Cancer Registration and Analysis Service, Public Health England, London, United Kingdom
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, United States of America
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Wendy S. Rubinstein
- CancerLinQ at American Society of Clinical Oncology (ASCO), Alexandria, Virginia, United States of America
| | | | - Sean Tavtigian
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, United States of America
| | - Adrian Thorogood
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Can Zhang
- Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Marc Zimmermann
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
| | | | - John Burn
- Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
- * E-mail: (GR); (ABS)
| | - Amanda B. Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
- * E-mail: (GR); (ABS)
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15
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Tavtigian SV, Greenblatt MS, Harrison SM, Nussbaum RL, Prabhu SA, Boucher KM, Biesecker LG. Modeling the ACMG/AMP variant classification guidelines as a Bayesian classification framework. Genet Med 2018; 20:1054-1060. [PMID: 29300386 PMCID: PMC6336098 DOI: 10.1038/gim.2017.210] [Citation(s) in RCA: 292] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/13/2017] [Indexed: 02/05/2023] Open
Abstract
PURPOSE We evaluated the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines for internal consistency and compatibility with Bayesian statistical reasoning. METHODS The ACMG/AMP criteria were translated into a naive Bayesian classifier, assuming four levels of evidence and exponentially scaled odds of pathogenicity. We tested this framework with a range of prior probabilities and odds of pathogenicity. RESULTS We modeled the ACMG/AMP guidelines using biologically plausible assumptions. Most ACMG/AMP combining criteria were compatible. One ACMG/AMP likely pathogenic combination was mathematically equivalent to pathogenic and one ACMG/AMP pathogenic combination was actually likely pathogenic. We modeled combinations that include evidence for and against pathogenicity, showing that our approach scored some combinations as pathogenic or likely pathogenic that ACMG/AMP would designate as variant of uncertain significance (VUS). CONCLUSION By transforming the ACMG/AMP guidelines into a Bayesian framework, we provide a mathematical foundation for what was a qualitative heuristic. Only 2 of the 18 existing ACMG/AMP evidence combinations were mathematically inconsistent with the overall framework. Mixed combinations of pathogenic and benign evidence could yield a likely pathogenic, likely benign, or VUS result. This quantitative framework validates the approach adopted by the ACMG/AMP, provides opportunities to further refine evidence categories and combining rules, and supports efforts to automate components of variant pathogenicity assessments.
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Affiliation(s)
- Sean V Tavtigian
- Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Marc S Greenblatt
- Department of Medicine and University of Vermont Cancer Center, University of Vermont Robert Larner, MD, College of Medicine, Burlington, Vermont, USA
| | - Steven M Harrison
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Snehit A Prabhu
- Department of Genetics and Department of Biomedical Data Science, Stanford University, Palo Alto, California, USA
| | - Kenneth M Boucher
- Division of Epidemiology and Huntsman Cancer Institute, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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16
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Watanabe G, Chiba N, Nomizu T, Furuta A, Sato K, Miyashita M, Tada H, Suzuki A, Ohuchi N, Ishida T. Increased centrosome number in BRCA-related breast cancer specimens determined by immunofluorescence analysis. Cancer Sci 2018; 109:2027-2035. [PMID: 29601120 PMCID: PMC5989840 DOI: 10.1111/cas.13595] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/04/2018] [Accepted: 03/21/2018] [Indexed: 01/25/2023] Open
Abstract
BRCA‐related breast carcinoma can be prevented through prophylactic surgery and an intensive follow‐up regimen. However, BRCA genetic tests cannot be routinely performed, and some BRCA mutations could not be defined as deleterious mutations or normal variants. Therefore, an easy functional assay of BRCA will be useful to evaluate BRCA status. As it has been reported that BRCA functions in the regulation of centrosome number, we focused on centrosome number in cancer tissues. Here, 70 breast cancer specimens with known BRCA status were analyzed using immunofluorescence of γ‐tubulin (a marker of centrosome) foci. The number of foci per cell was higher in cases with BRCA mutation compared to wild‐type cases, that is, 1.9 (95% confidence interval [CI], 1.5‐2.3) vs 0.5 (95% CI, 0.2‐0.8) (P < .001). Specifically, foci numbers per cell in BRCA1 and BRCA2 mutation cases were 1.2 (95% CI, 0.6‐1.8) and 2.2 (95% CI, 1.7‐2.6), respectively, both higher than those in wild‐type cases (P = .042 and P < .0001, respectively). The predictive value of γ‐tubulin foci as determined by area under the curve (AUC = 0.86) for BRCA status was superior to BRCAPRO (AUC = 0.69), Myriad Table (AUC = 0.61), and KOHBRA BRCA risk calculator (AUC = 0.65) pretest values. The use of γ‐tubulin foci to predict BRCA status had sensitivity = 83% (19/23), specificity = 89% (42/47), and positive predictive value = 77% (20/26). Thus, γ‐tubulin immunofluorescence, a functional assessment of BRCA, can be used as a new prospective test of BRCA status.
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Affiliation(s)
- Gou Watanabe
- Division of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Natsuko Chiba
- Department of Cancer Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tadashi Nomizu
- Department of Surgery, Hoshi General Hospital, Fukushima, Japan
| | - Akihiko Furuta
- Department of Breast Surgery, Ishinomaki Red Cross Hospital, Ishinomaki, Japan
| | - Kaolu Sato
- Department of Breast Surgery, Ishinomaki Red Cross Hospital, Ishinomaki, Japan
| | - Minoru Miyashita
- Division of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Tada
- Division of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akihiko Suzuki
- Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Noriaki Ohuchi
- Division of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takanori Ishida
- Division of Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Japan
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17
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Emerling CA, Widjaja AD, Nguyen NN, Springer MS. Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci. J Med Genet 2017; 54:787-794. [PMID: 28814606 DOI: 10.1136/jmedgenet-2017-104837] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 07/07/2017] [Accepted: 07/10/2017] [Indexed: 12/20/2022]
Abstract
Throughout Earth's history, evolution's numerous natural 'experiments' have resulted in a diverse range of phenotypes. Though de novo phenotypes receive widespread attention, degeneration of traits inherited from an ancestor is a very common, yet frequently neglected, evolutionary path. The latter phenomenon, known as regressive evolution, often results in vertebrates with phenotypes that mimic inherited disease states in humans. Regressive evolution of anatomical and/or physiological traits is typically accompanied by inactivating mutations underlying these traits, which frequently occur at loci identical to those implicated in human diseases. Here we discuss the potential utility of examining the genomes of vertebrates that have experienced regressive evolution to inform human medical genetics. This approach is low cost and high throughput, giving it the potential to rapidly improve knowledge of disease genetics. We discuss two well-described examples, rod monochromacy (congenital achromatopsia) and amelogenesis imperfecta, to demonstrate the utility of this approach, and then suggest methods to equip non-experts with the ability to corroborate candidate genes and uncover new disease loci.
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Affiliation(s)
- Christopher A Emerling
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
- Department of Biology, University of California, Riverside, California, USA
| | - Andrew D Widjaja
- Department of Biochemistry, University of California, Riverside, California, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Nancy N Nguyen
- Department of Bioengineering, University of California, Riverside, California, USA
- Department of Bioengineering, University of California, Los Angeles, California, USA
| | - Mark S Springer
- Department of Biology, University of California, Riverside, California, USA
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18
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Han Y, Lin Y, Sun Q, Wang S, Gao Y, Shao L. Mutation spectrum of Chinese patients with Bartter syndrome. Oncotarget 2017; 8:101614-101622. [PMID: 29254190 PMCID: PMC5731900 DOI: 10.18632/oncotarget.21355] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Bartter syndrome (BS) has been rarely reported in Chinese population except for a few case reports. This investigation was aimed to analyze the mutations of the causal genes in sixteen Chinese patients with BS, and review their followup and treatment. METHODS Identify mutations by the next generation sequencing and the multiplex ligation-dependent probe amplification (MLPA). Clinical characteristics and biochemical findings at the first presentation as well as follow-up were reviewed. RESULTS 15 different CLCNKB gene mutations were identified in fourteen patients with BS, including 11 novel ones. A novel missense mutation and a novel small deletion were found from SLC12A1 gene. A novel gross deletion was found in CLCNKA gene. A recurrent missense mutation was identified from BSND gene. We found that the whole gene deletion mutation of CLCNKB gene was the most frequent mutation (32%), and the rate of gross deletion was up to 50 percent in this group of Chinese patients. CONCLUSION The present study has found 19 mutations, including 14 novel ones, which would enrich the human gene mutation database (HGMD) and provide valuable references to the genetic counseling and diagnosis of the Chinese population.
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Affiliation(s)
- Yue Han
- Central Laboratory, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
- Department of Nephrology, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
| | - Yi Lin
- Pediatrics, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
| | - Qing Sun
- Department of Nephrology, Qingdao Women and Children's Hospital, Qingdao University, Qingdao 266011, P.R. China
| | - Shujuan Wang
- Department of Nephrology, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
| | - Yanxia Gao
- Department of Nephrology, Qingdao Branch of Qilu Hospital of Shandong University, Qingdao, Shandong 266000, P.R. China
| | - Leping Shao
- Central Laboratory, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
- Department of Nephrology, Affiliated Hospital, Qingdao University, Qingdao 266003, P.R. China
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19
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Hamameh SL, Renbaum P, Kamal L, Dweik D, Salahat M, Jaraysa T, Rayyan AA, Casadei S, Mandell JB, Gulsuner S, Lee MK, Walsh T, King MC, Levy-Lahad E, Kanaan M. Genomic analysis of inherited breast cancer among Palestinian women: Genetic heterogeneity and a founder mutation in TP53. Int J Cancer 2017; 141:750-756. [PMID: 28486781 PMCID: PMC5526459 DOI: 10.1002/ijc.30771] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/24/2017] [Accepted: 04/25/2017] [Indexed: 02/01/2023]
Abstract
Breast cancer among Palestinian women has lower incidence than in Europe or North America, yet is very frequently familial. We studied genetic causes of this familial clustering in a consecutive hospital-based series of 875 Palestinian patients with invasive breast cancer, including 453 women with diagnosis by age 40, or with breast or ovarian cancer in a mother, sister, grandmother or aunt ("discovery series"); and 422 women diagnosed after age 40 and with negative family history ("older-onset sporadic patient series"). Genomic DNA from women in the discovery series was sequenced for all known breast cancer genes, revealing a pathogenic mutation in 13% (61/453) of patients. These mutations were screened in all patients and in 300 Palestinian female controls, revealing 1.0% (4/422) carriers among older, nonfamilial patients and two carriers among controls. The mutational spectrum was highly heterogeneous, including pathogenic mutations in 11 different genes: BRCA1, BRCA2, TP53, ATM, CHEK2, BARD1, BRIP1, PALB2, MRE11A, PTEN and XRCC2. BRCA1 carriers were significantly more likely than other patients to have triple negative tumors (p = 0.03). The single most frequent mutation was TP53 p.R181C, which was significantly enriched in the discovery series compared to controls (p = 0.01) and was responsible for 15% of breast cancers among young onset or familial patients. TP53 p.R181C predisposed specifically to breast cancer with incomplete penetrance, and not to other Li-Fraumeni cancers. Palestinian women with young onset or familial breast cancer and their families would benefit from genetic analysis and counseling.
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Affiliation(s)
- Suhair Lolas Hamameh
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Paul Renbaum
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Lara Kamal
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Dima Dweik
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Mohammad Salahat
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Tamara Jaraysa
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Amal Abu Rayyan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
| | - Silvia Casadei
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Jessica B. Mandell
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Suleyman Gulsuner
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Ming K. Lee
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Tom Walsh
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Mary-Claire King
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle WA, USA
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Share Zedek Medical Center, and Faculty of Medicine, Hebrew University, Jerusalem, ISRAEL
| | - Moein Kanaan
- Hereditary Research Laboratory and Department of Life Sciences, Bethlehem University, Bethlehem, PALESTINE
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Sadowski CE, Kohlstedt D, Meisel C, Keller K, Becker K, Mackenroth L, Rump A, Schröck E, Wimberger P, Kast K. BRCA1/2 missense mutations and the value of in-silico analyses. Eur J Med Genet 2017; 60:572-577. [PMID: 28807866 DOI: 10.1016/j.ejmg.2017.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 01/12/2023]
Abstract
INTRODUCTION The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants. METHODS We conducted mutation analysis of BRCA1/2 in 523 index patients with suspected hereditary breast and ovarian cancer (HBOC). Classification of the genetic variants was performed according to the German Consortium (GC)-HBOC database. Additionally, all missense variants were classified by the following three in-silico prediction tools: SIFT, Mutation Taster (MT2) and PolyPhen2 (PPH2). RESULTS Overall 201 different variants, 68 of which constituted missense variants were ranked as pathogenic, neutral, or unknown. The classification of missense variants by in-silico tools resulted in a higher amount of pathogenic mutations (25% vs. 13.2%) compared to the GC-HBOC-classification. Altogether, more than fifty percent (38/68, 55.9%) of missense variants were ranked differently. Sensitivity of in-silico-tools for mutation prediction was 88.9% (PPH2), 100% (SIFT) and 100% (MT2). CONCLUSION We found a relevant discrepancy in variant classification by using in-silico prediction tools, resulting in potential overestimation and/or underestimation of cancer risk. More reliable, notably gene-specific, prediction tools and functional tests are needed to improve clinical counseling.
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Affiliation(s)
- Carolin E Sadowski
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Kohlstedt
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cornelia Meisel
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katja Keller
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kerstin Becker
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Luisa Mackenroth
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Andreas Rump
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Evelin Schröck
- National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Clinical Genetics, Technische Universität Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Karin Kast
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Germany; National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany; German Cancer Consortium (DKTK), Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones. Sci Rep 2016; 6:33652. [PMID: 27644547 PMCID: PMC5028881 DOI: 10.1038/srep33652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/30/2016] [Indexed: 12/02/2022] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333* was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333* and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals.
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22
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Young EL, Feng BJ, Stark AW, Damiola F, Durand G, Forey N, Francy TC, Gammon A, Kohlmann WK, Kaphingst KA, McKay-Chopin S, Nguyen-Dumont T, Oliver J, Paquette AM, Pertesi M, Robinot N, Rosenthal JS, Vallee M, Voegele C, Hopper JL, Southey MC, Andrulis IL, John EM, Hashibe M, Gertz J, Le Calvez-Kelm F, Lesueur F, Goldgar DE, Tavtigian SV. Multigene testing of moderate-risk genes: be mindful of the missense. J Med Genet 2016; 53:366-76. [PMID: 26787654 PMCID: PMC4893078 DOI: 10.1136/jmedgenet-2015-103398] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/18/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Moderate-risk genes have not been extensively studied, and missense substitutions in them are generally returned to patients as variants of uncertain significance lacking clearly defined risk estimates. The fraction of early-onset breast cancer cases carrying moderate-risk genotypes and quantitative methods for flagging variants for further analysis have not been established. METHODS We evaluated rare missense substitutions identified from a mutation screen of ATM, CHEK2, MRE11A, RAD50, NBN, RAD51, RINT1, XRCC2 and BARD1 in 1297 cases of early-onset breast cancer and 1121 controls via scores from Align-Grantham Variation Grantham Deviation (GVGD), combined annotation dependent depletion (CADD), multivariate analysis of protein polymorphism (MAPP) and PolyPhen-2. We also evaluated subjects by polygenotype from 18 breast cancer risk SNPs. From these analyses, we estimated the fraction of cases and controls that reach a breast cancer OR≥2.5 threshold. RESULTS Analysis of mutation screening data from the nine genes revealed that 7.5% of cases and 2.4% of controls were carriers of at least one rare variant with an average OR≥2.5. 2.1% of cases and 1.2% of controls had a polygenotype with an average OR≥2.5. CONCLUSIONS Among early-onset breast cancer cases, 9.6% had a genotype associated with an increased risk sufficient to affect clinical management recommendations. Over two-thirds of variants conferring this level of risk were rare missense substitutions in moderate-risk genes. Placement in the estimated OR≥2.5 group by at least two of these missense analysis programs should be used to prioritise variants for further study. Panel testing often creates more heat than light; quantitative approaches to variant prioritisation and classification may facilitate more efficient clinical classification of variants.
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Affiliation(s)
- E L Young
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - B J Feng
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A W Stark
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Damiola
- Breast Cancer Genetics Group, Cancer Research Centre of Lyon, Centre Léon Bérard, Lyon, France
| | - G Durand
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Forey
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T C Francy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - A Gammon
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - W K Kohlmann
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - K A Kaphingst
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - S McKay-Chopin
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - T Nguyen-Dumont
- Genetic Epidemiology Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - J Oliver
- Instituto de Ciencias Básicas y Medicina Experimental del Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - A M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Pertesi
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - N Robinot
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J S Rosenthal
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - M Vallee
- Cancer Genomics Laboratory, CHUQ Research Center, Quebec City, Canada
| | - C Voegele
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - J L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia Department of Epidemiology (Genome Epidemiology Lab), Seoul National University School of Public Health, Seoul, Korea
| | - M C Southey
- Department of Communication and Huntsman Cancer Institute, University of Utah
| | - I L Andrulis
- Department of Molecular Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - E M John
- Cancer Prevention Institute of California, Fremont, California, USA Department of Health Research and Policy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California, USA
| | - M Hashibe
- Department of Family and Preventive Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - J Gertz
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - F Le Calvez-Kelm
- Genetic Cancer Susceptibility group, International Agency for Research on Cancer, Lyon, France
| | - F Lesueur
- Genetic Epidemiology of Cancer Team, Inserm, U900, Institut Curie, Paris, France
| | - D E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - S V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
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Incidence of BRCA1 somatic mutations and response to neoadjuvant chemotherapy in Chinese women with triple-negative breast cancer. Gene 2016; 584:26-30. [PMID: 26956035 DOI: 10.1016/j.gene.2016.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/25/2016] [Accepted: 03/02/2016] [Indexed: 01/27/2023]
Abstract
BACKGROUND The prevalence of BRCA1 somatic mutations status in triple-negative breast cancer (TNBC) has not been well documented. The aims of this study were to determine the frequency of BRCA1 somatic mutations and to investigate the association between BRCA1 deleterious somatic mutation status and response to neoadjuvant chemotherapy in women with TNBC. METHODS Two hundred and five TNBC patients without BRCA1 germline mutations were enrolled in this study. Fresh tumor tissues were available for this cohort of 205 patients, including 112 patients with fresh core needle biopsy tumor tissues before treatment and 93 patients with fresh tumor tissues procured after surgery. BRCA1 somatic mutations were determined in the tumor samples using PCR-direct sequencing assay. Among the 112 patients with core needle biopsy samples, 97 patients received neoadjuvant chemotherapy. RESULTS Eight patients (3.9%) carried a BRCA1 pathogenic somatic mutation in this cohort of 205 TNBC patients. These eight BRCA1 deleterious somatic mutations included five frameshift or nonsense mutations (c.191_212del22, c.1664delA, c.4674_4675+17del, c.3671_3672insTTCC, c.1162A>T), one splicing site mutation (c.134+2T>G) and two missense mutations (c.5511G>C and c.286G>A). No significant differences in tumor characteristics between BRCA1 deleterious somatic mutation carriers and non-carriers were observed. The pCR (pathologic complete response) rate was 32.0% in the 97 patients who received neoadjuvant chemotherapy. BRCA1 deleterious somatic mutation carriers (n=5) had a higher pCR rate than did non-carriers (n=92) (BRCA1 carriers vs non-carriers, 60.0% vs 30.4%, P=0.32), although it did not reach a significance due to a small sample size. CONCLUSIONS A small subset of TNBC patients carried a BRCA1 deleterious somatic mutation; BRCA1 somatic mutation carriers are likely to respond to neoadjuvant chemotherapy.
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Functional assays provide a robust tool for the clinical annotation of genetic variants of uncertain significance. NPJ Genom Med 2016; 1. [PMID: 28781887 PMCID: PMC5539989 DOI: 10.1038/npjgenmed.2016.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variants of Uncertain Significance (VUS) are genetic variants whose association with a disease phenotype has not been established. They are a common finding in sequencing-based genetic tests and pose a significant clinical challenge. The objective of this study was to assess the use of functional data to classify variants according to pathogenicity. We conduct functional analysis of a large set of BRCA1 VUS combining a validated functional assay with VarCall, a Bayesian hierarchical model to estimate the likelihood of pathogenicity given the functional data. The results from the functional assays were incorporated into a joint analysis of 214 BRCA1 VUS to predict their likelihood of pathogenicity (breast cancer). We show that applying the VarCall model (1.0 sensitivity; lower bound of 95% confidence interval (CI)=0.75 and 1.0 specificity; lower bound of 95% CI=0.83) to the current set of BRCA1 variants, use of the functional data would significantly reduce the number of VUS associated with the C-terminal region of the BRCA1 protein by ~87%. We extend this work developing yeast-based functional assays for two other genes coding for BRCT domain containing proteins, MCPH1 and MDC1. Analysis of missense variants in MCPH1 and MDC1 shows that structural inference based on the BRCA1 data set can aid in prioritising variants for further analysis. Taken together our results indicate that systematic functional assays can provide a robust tool to aid in clinical annotation of VUS. We propose that well-validated functional assays could be used for clinical annotation even in the absence of additional sources of evidence.
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25
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Computational approaches to study the effects of small genomic variations. J Mol Model 2015; 21:251. [PMID: 26350246 DOI: 10.1007/s00894-015-2794-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/23/2015] [Indexed: 10/23/2022]
Abstract
Advances in DNA sequencing technologies have led to an avalanche-like increase in the number of gene sequences deposited in public databases over the last decade as well as the detection of an enormous number of previously unseen nucleotide variants therein. Given the size and complex nature of the genome-wide sequence variation data, as well as the rate of data generation, experimental characterization of the disease association of each of these variations or their effects on protein structure/function would be costly, laborious, time-consuming, and essentially impossible. Thus, in silico methods to predict the functional effects of sequence variations are constantly being developed. In this review, we summarize the major computational approaches and tools that are aimed at the prediction of the functional effect of mutations, and describe the state-of-the-art databases that can be used to obtain information about mutation significance. We also discuss future directions in this highly competitive field.
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26
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Kluska A, Balabas A, Paziewska A, Kulecka M, Nowakowska D, Mikula M, Ostrowski J. New recurrent BRCA1/2 mutations in Polish patients with familial breast/ovarian cancer detected by next generation sequencing. BMC Med Genomics 2015; 8:19. [PMID: 25948282 PMCID: PMC4429836 DOI: 10.1186/s12920-015-0092-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/23/2015] [Indexed: 12/19/2022] Open
Abstract
Background Targeted PCR-based genetic testing for BRCA1 and BRCA2 can be performed at a lower cost than full gene testing; however, it may overlook mutations responsible for familial breast and/or ovarian cancers. In the present study, we report the utility of next generation sequencing (NGS) to identify new pathogenic variants of BRCA1/2. Methods BRCA1 and BRCA2 exons were amplified using the Ion AmpliSeq BRCA1/2 Panel and sequenced on the Ion Torrent PGM sequencer in 512 women with familial and/or only early onset breast and/or ovarian cancers who were negative for selected BRCA1/2 mutations. Results 146 single nucleotide variants (SNVs) and 32 indels were identified. Of them, 14 SNVs and 17 indels were considered as pathogenic or likely pathogenic. One and 18 pathogenic mutations had been detected previously in the Polish and other populations, respectively, and 12 deleterious mutations were previously unknown. Eight mutations were recurrent; Q563X (BRCA1), N3124I (BRCA2) and c.4516delG (BRCA1) were found in eight, six and four patients, respectively, and two other mutations (c.9118-2A > G and c.7249delCA in BRCA2) were detected in three patients each. Altogether, BRCA1/2 pathogenic mutations were identified in 52 out of 512 (10%) patients. Conclusions NGS substantially improved the detection rates of a wide spectrum of mutations in Polish patients with familial breast and/or ovarian cancer. Although targeted screening for specific BRCA1 mutations can be offered to all Polish breast or ovarian cancer patients, NGS-based testing is justified in patients with breast or ovarian cancer likely related to BRCA1/2 who test negative for the selected BRCA1/2 pathogenic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0092-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Maria Kulecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
| | - Dorota Nowakowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland.
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781, Warsaw, Poland. .,Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813, Warsaw, Poland.
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Protein stability versus function: effects of destabilizing missense mutations on BRCA1 DNA repair activity. Biochem J 2015; 466:613-24. [DOI: 10.1042/bj20141077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The majority of the unstable BRCA1 BRCT domain missense mutations we studied disrupted DNA repair in vivo, but reduced cellular function only weakly correlated with reduced structural stability. The findings have an impact on assessing cancer susceptibility in patients with BRCA1 mutations.
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Ahlborn LB, Dandanell M, Steffensen AY, Jønson L, Nielsen FC, Hansen TVO. Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic. Breast Cancer Res Treat 2015; 150:289-98. [PMID: 25724305 PMCID: PMC4368840 DOI: 10.1007/s10549-015-3313-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/15/2015] [Indexed: 01/23/2023]
Abstract
Pathogenic germline mutations in the BRCA1 gene predispose carriers to early onset breast and ovarian cancer. Clinical genetic screening of BRCA1 often reveals variants with uncertain clinical significance, complicating patient and family management. Therefore, functional examinations are urgently needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala), whereas five BRCA1 variants had no effect on splicing (c.4985T>C/p.Phe1662Ser, c.5072C>A/p.Thr1691Lys, c.5153G>C/p.Trp1718Ser, c.5154G>T/p.Trp1718Cys, and c.5333A>G/p.Asp1778Gly). Eight of the variants having an effect on splicing (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala) were previously determined to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification of BRCA1 missense variants located close to exon/intron boundaries.
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Affiliation(s)
- Lise B. Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Mette Dandanell
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ane Y. Steffensen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas v. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
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Tavtigian SV, Chenevix-Trench G. Growing recognition of the role for rare missense substitutions in breast cancer susceptibility. Biomark Med 2014; 8:589-603. [PMID: 24796624 DOI: 10.2217/bmm.13.143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Most cancer susceptibility genes function as tumor suppressors; accordingly, the focus of mutation screening in breast cancer families has been to identify protein-truncating mutations. However, it is now clear that, for some breast cancer susceptibility genes, a significant proportion of the burden of disease comes from rare missense substitutions. Among genes that have been extensively evaluated, BRCA1, BRCA2, PALB2 and BRIP1 stand as examples where the majority of mutations lead to protein truncation;TP53 provides a counter example, where the majority of pathogenic variants are missense substitutions. In ATM and CHEK2, missense substitutions are probably equally or more important in terms of their frequency and attributable risk. Therefore, ongoing efforts to identify new susceptibility genes should not ignore missense variation.
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Affiliation(s)
- Sean V Tavtigian
- Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. Breast Cancer Res Treat 2014; 147:119-32. [PMID: 25085752 DOI: 10.1007/s10549-014-3065-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/15/2014] [Indexed: 02/06/2023]
Abstract
BRCA1 and BRCA2 sequencing analysis detects variants of uncertain clinical significance in approximately 2 % of patients undergoing clinical diagnostic testing in our laboratory. The reclassification of these variants into either a pathogenic or benign clinical interpretation is critical for improved patient management. We developed a statistical variant reclassification tool based on the premise that probands with disease-causing mutations are expected to have more severe personal and family histories than those having benign variants. The algorithm was validated using simulated variants based on approximately 145,000 probands, as well as 286 BRCA1 and 303 BRCA2 true variants. Positive and negative predictive values of ≥99 % were obtained for each gene. Although the history weighting algorithm was not designed to detect alleles of lower penetrance, analysis of the hypomorphic mutations c.5096G>A (p.Arg1699Gln; BRCA1) and c.7878G>C (p.Trp2626Cys; BRCA2) indicated that the history weighting algorithm is able to identify some lower penetrance alleles. The history weighting algorithm is a powerful tool that accurately assigns actionable clinical classifications to variants of uncertain clinical significance. While being developed for reclassification of BRCA1 and BRCA2 variants, the history weighting algorithm is expected to be applicable to other cancer- and non-cancer-related genes.
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Chen BYH, Huang CH, Lin YH, Huang CC, Deng CX, Hsu LC. The K898E germline variant in the PP1-binding motif of BRCA1 causes defects in DNA Repair. Sci Rep 2014; 4:5812. [PMID: 25056273 PMCID: PMC4108927 DOI: 10.1038/srep05812] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/04/2014] [Indexed: 01/26/2023] Open
Abstract
BRCA1 is a phosphoprotein involved in many biological processes, including transcription, ubiquitination, checkpoint control, homologous recombination, and DNA repair. We have demonstrated that protein phosphatase 1α (PP1α) interacts with BRCA1 via a PP1-binding motif 898KVTF901, and can dephosphorylate multiple serine residues phosphorylated by checkpoint kinases. A K898E germline missense variant in the PP1-binding motif of BRCA1 has been found in an Ashkenazi patient and a non-Ashkenazi Argentinean patient with breast and ovarian cancer, but its clinical significance is still unknown. Here we report that the lysine residue in the PP1-binding motif of BRCA1 is highly conserved across many mammalian species. The K898E mutation interferes with the interaction between BRCA1 and PP1α. Moreover, while the expression of wild-type BRCA1 in Brca1-deficient cells improved cell survival after DNA damage induced by ionizing radiation (IR), expression of BRCA1 K898E proved unable to enhance cell survival. DNA damage repair mechanisms remained defective in these BRCA1 K898E-reconstituted cells, as revealed by the comet assay and IR-induced Rad51 foci formation assay. These results reflect the significance of the interaction between BRCA1 and PP1, and indicate that the K898E variant may render carriers susceptible to DNA damage and malignant transformation.
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Affiliation(s)
- Bert Yu-Hung Chen
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 10050, Taiwan, ROC
| | - Cheng-Hsiang Huang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 10050, Taiwan, ROC
| | - Ying-Hsi Lin
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 10050, Taiwan, ROC
| | - Ching-Chun Huang
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 10050, Taiwan, ROC
| | - Chu-Xia Deng
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lih-Ching Hsu
- School of Pharmacy, College of Medicine, National Taiwan University, Taipei 10050, Taiwan, ROC
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Prendergast D, Woad KJ, Chamley LW, Holland OJ, Shelling AN. SPACA3gene variants in a New Zealand cohort of infertile and fertile couples. HUM FERTIL 2014; 17:106-13. [DOI: 10.3109/14647273.2014.907506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Carvalho RS, Abreu RBV, Velkova A, Marsillac S, Rodarte RS, Suarez-Kurtz G, Iversen ES, Monteiro ANA, Carvalho MA. Probing structure-function relationships in missense variants in the carboxy-terminal region of BRCA1. PLoS One 2014; 9:e97766. [PMID: 24845084 PMCID: PMC4028255 DOI: 10.1371/journal.pone.0097766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/23/2014] [Indexed: 11/25/2022] Open
Abstract
Germline inactivating variants in BRCA1 lead to a significantly increased risk of breast and ovarian cancers in carriers. While the functional effect of many variants can be inferred from the DNA sequence, determining the effect of missense variants present a significant challenge. A series of biochemical and cell biological assays have been successfully used to explore the impact of these variants on the function of BRCA1, which contribute to assessing their likelihood of pathogenicity. It has been determined that variants that co-localize with structural or functional motifs are more likely to disrupt the stability and function of BRCA1. Here we assess the functional impact of 37 variants chosen to probe the functional impact of variants in phosphorylation sites and in the BRCT domains. In addition, we perform a meta-analysis of 170 unique variants tested by the transcription activation assays in the carboxy-terminal domain of BRCA1 using a recently developed computation model to provide assessment for functional impact and their likelihood of pathogenicity.
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Affiliation(s)
- Renato S Carvalho
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America; Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Renata B V Abreu
- Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Sylvia Marsillac
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | | | | | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, United States of America
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Marcelo A Carvalho
- Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil; Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE. Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. PLoS One 2014; 9:e94554. [PMID: 24728327 PMCID: PMC3984285 DOI: 10.1371/journal.pone.0094554] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/17/2014] [Indexed: 01/05/2023] Open
Abstract
Technological advances coupled with decreasing costs are bringing whole genome and whole exome sequencing closer to routine clinical use. One of the hurdles to clinical implementation is the high number of variants of unknown significance. For cancer-susceptibility genes, the difficulty in interpreting the clinical relevance of the genomic variants is compounded by the fact that most of what is known about these variants comes from the study of highly selected populations, such as cancer patients or individuals with a family history of cancer. The genetic variation in known cancer-susceptibility genes in the general population has not been well characterized to date. To address this gap, we profiled the nonsynonymous genomic variation in 158 genes causally implicated in carcinogenesis using high-quality whole genome sequences from an ancestrally diverse cohort of 681 healthy individuals. We found that all individuals carry multiple variants that may impact cancer susceptibility, with an average of 68 variants per individual. Of the 2,688 allelic variants identified within the cohort, most are very rare, with 75% found in only 1 or 2 individuals in our population. Allele frequencies vary between ancestral groups, and there are 21 variants for which the minor allele in one population is the major allele in another. Detailed analysis of a selected subset of 5 clinically important cancer genes, BRCA1, BRCA2, KRAS, TP53, and PTEN, highlights differences between germline variants and reported somatic mutations. The dataset can serve a resource of genetic variation in cancer-susceptibility genes in 6 ancestry groups, an important foundation for the interpretation of cancer risk from personal genome sequences.
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Affiliation(s)
- Dale L. Bodian
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Justine N. McCutcheon
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Prachi Kothiyal
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Kathi C. Huddleston
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Ramaswamy K. Iyer
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
| | - Joseph G. Vockley
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
- * E-mail:
| | - John E. Niederhuber
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Virginia, United States of America
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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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Dowty JG, Lee E, McKean-Cowdin R, Henderson BE, Bernstein L, Ursin G, Hopper JL. Estimating risks for variants of unknown significance according to their predicted pathogenicity classes with application to BRCA1. Breast Cancer Res Treat 2014; 144:171-7. [PMID: 24481681 DOI: 10.1007/s10549-014-2845-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/17/2014] [Indexed: 11/29/2022]
Abstract
Sequence-based testing of disease-susceptibility genes has identified many variants of unknown significance (VUSs) whose pathogenicity is unknown at the time of their measurement. Female breast cancer cases aged 20-49 years at diagnosis and who have VUSs in BRCA1 and no mutations in BRCA2 have previously been identified through the population-based Los Angeles County Cancer Surveillance Program. These nominal BRCA1 VUSs have been classified as "low," "medium," and "high" risk by four classification methods: Align-GVGD, Polyphen, Grantham matrix scores, and sequence conservation in mammalian species. Average hazard ratios (HRs) for classes of variants, i.e., the age-specific incidences of cancer for carriers of such variants divided by the population incidences, were estimated from the cancer family histories of first- and second-degree relatives of the index cases using modified segregation analysis. The study sample comprised 270 index cases and 4,543 of their relatives. There was weak evidence that the risk of breast cancer increases with the degree of sequence conservation (P = 0.03) and that missense variants at highly conserved sites are associated with a 5.6-fold (95 % confidence interval 1.4-22.2; P = 0.05) increased incidence of breast cancer. An upper bound of 2.3 is given for the average breast cancer HRs corresponding to variants classified as "low risk" by any of the four VUS classification methods. In summary, we have given a method to estimate cancer risks for groups of VUSs by combining existing classification methods with traditional penetrance analyses. This analysis suggests that classification methods for BRCA1 variants based on sequence conservation might be useful in a clinical setting. We have shown in principle that our method can be used to classify VUSs into clinically useful risk categories, but our specific findings should not be put into clinical practice unless confirmed by larger studies.
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Affiliation(s)
- J G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Level 3/207 Bouverie St., Carlton, VIC, 3053, Australia
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Eggington JM, Bowles KR, Moyes K, Manley S, Esterling L, Sizemore S, Rosenthal E, Theisen A, Saam J, Arnell C, Pruss D, Bennett J, Burbidge LA, Roa B, Wenstrup RJ. A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes. Clin Genet 2013; 86:229-37. [PMID: 24304220 DOI: 10.1111/cge.12315] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/18/2013] [Accepted: 11/05/2013] [Indexed: 11/30/2022]
Abstract
Genetic testing has the potential to guide the prevention and treatment of disease in a variety of settings, and recent technical advances have greatly increased our ability to acquire large amounts of genetic data. The interpretation of this data remains challenging, as the clinical significance of genetic variation detected in the laboratory is not always clear. Although regulatory agencies and professional societies provide some guidance regarding the classification, reporting, and long-term follow-up of variants, few protocols for the implementation of these guidelines have been described. Because the primary aim of clinical testing is to provide results to inform medical management, a variant classification program that offers timely, accurate, confident and cost-effective interpretation of variants should be an integral component of the laboratory process. Here we describe the components of our laboratory's current variant classification program (VCP), based on 20 years of experience and over one million samples tested, using the BRCA1/2 genes as a model. Our VCP has lowered the percentage of tests in which one or more BRCA1/2 variants of uncertain significance (VUSs) are detected to 2.1% in the absence of a pathogenic mutation, demonstrating how the coordinated application of resources toward classification and reclassification significantly impacts the clinical utility of testing.
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Affiliation(s)
- J M Eggington
- Myriad Genetic Laboratories, Inc., Salt Lake City, UT, USA
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Tram E, Savas S, Ozcelik H. Missense variants of uncertain significance (VUS) altering the phosphorylation patterns of BRCA1 and BRCA2. PLoS One 2013; 8:e62468. [PMID: 23704879 PMCID: PMC3660339 DOI: 10.1371/journal.pone.0062468] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/21/2013] [Indexed: 12/20/2022] Open
Abstract
Mutations in BRCA1 and BRCA2 are responsible for a large proportion of breast-ovarian cancer families. Protein-truncating mutations have been effectively used in the clinical management of familial breast cancer due to their deleterious impact on protein function. However, the majority of missense variants identified throughout the genes continue to pose an obstacle for predictive informative testing due to low frequency and lack of information on how they affect BRCA1/2 function. Phosphorylation of BRCA1 and BRCA2 play an important role in their function as regulators of DNA repair, transcription and cell cycle in response to DNA damage but whether missense variants of uncertain significance (VUS) are able to disrupt this important process is not known. Here we employed a novel approach using NetworKIN which predicts in vivo kinase-substrate relationship, and evolutionary conservation algorithms SIFT, PolyPhen and Align-GVGD. We evaluated whether 191 BRCA1 and 43 BRCA2 VUS from the Breast Cancer Information Core (BIC) database can functionally alter the consensus phosphorylation motifs and abolish kinase recognition and binding to sites known to be phosphorylated in vivo. Our results show that 13.09% (25/191) BRCA1 and 13.95% (6/43) BRCA2 VUS altered the phosphorylation of BRCA1 and BRCA2. We highlight six BRCA1 (K309T, S632N, S1143F, Q1144H, Q1281P, S1542C) and three BRCA2 (S196I, T207A, P3292L) VUS as potentially clinically significant. These occurred rarely (n<2 in BIC), mutated evolutionarily conserved residues and abolished kinase binding to motifs established in the literature involved in DNA repair, cell cycle regulation, transcription or response to DNA damage. Additionally in vivo phosphorylation sites identified via through-put methods are also affected by VUS and are attractive targets for studying their biological and functional significance. We propose that rare VUS affecting phosphorylation may be a novel and important mechanism for which BRCA1 and BRCA2 functions are disrupted in breast cancer.
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Affiliation(s)
- Eric Tram
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hilmi Ozcelik
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Blay P, Santamaría I, Pitiot AS, Luque M, Alvarado MG, Lastra A, Fernández Y, Paredes A, Freije JMP, Balbín M. Mutational analysis of BRCA1 and BRCA2 in hereditary breast and ovarian cancer families from Asturias (Northern Spain). BMC Cancer 2013; 13:243. [PMID: 23683081 PMCID: PMC3662577 DOI: 10.1186/1471-2407-13-243] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 05/14/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The prevalence of BRCA1 and BRCA2 mutations in Spain is heterogeneous and varies according to geographical origin of studied families. The contribution of these mutations to hereditary breast and ovarian cancer has not been previously investigated in Asturian populations (Northern Spain). METHODS In the present work, 256 unrelated high-risk probands with breast and/or ovarian cancer from families living in Asturias were analyzed for the presence of a BRCA1 or BRCA2 gene mutation from October 2007 to May 2012. The entire coding sequences and each intron/exon boundaries of BRCA1/2 genes were screened both by direct sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). RESULTS A total of 59 families (23%) were found to carry a pathogenic germ line mutation, 39 in BRCA1 and 20 in BRCA2. Twenty nine additional families (12%) carried an unknown significance variant. We detected 28 distinct pathogenic mutations (16 in BRCA1 and 12 in BRCA2), of which 3 mutations in BRCA1 (c.1674delA, c.1965C>A and c.2900_2901dupCT) and 5 in BRCA2 (c.262_263delCT, c.2095C>T, c.3263dupC, c.4030_4035delinsC, c.8042_8043delCA) had not been previously described.The novel mutations c.2900_2901dupCT in BRCA1 and c.4030_4035delinsC in BRCA2 occurred in 8 and 6 families respectively and clustered in two separated small geographically isolated areas suggesting a founder effect. These 2 mutations, together with the Galician BRCA1 mutation c.211A>G (9 families), and the common BRCA1 mutation c.3331_3334delCAAG (6 families), account for approximately 50% of all affected families. By contrast, very frequent mutations in other Spanish series such as the BRCA1 Ashkenazi founder mutation c.68_69delAG, was found in only one family. CONCLUSIONS In this study we report the BRCA1 and BRCA2 spectrum of mutations and their geographical distribution in Asturias, which largely differ from other areas of Spain. Our findings may help design a first step recurrent mutation panel for screening high-risk breast and/or ovarian cancer families from this specific area.
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Affiliation(s)
- Pilar Blay
- Unidad de Cáncer Familiar, Servicio de Oncología Médica, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Calle de Celestino Villamil, Oviedo 33006, Spain.
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Serbian high-risk families: extensive results on BRCA mutation spectra and frequency. J Hum Genet 2013; 58:501-7. [DOI: 10.1038/jhg.2013.30] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/18/2013] [Accepted: 04/03/2013] [Indexed: 01/01/2023]
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Lindor NM, Goldgar DE, Tavtigian SV, Plon SE, Couch FJ. BRCA1/2 sequence variants of uncertain significance: a primer for providers to assist in discussions and in medical management. Oncologist 2013; 18:518-24. [PMID: 23615697 DOI: 10.1634/theoncologist.2012-0452] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION DNA variants of uncertain significance (VUS) are common outcomes of clinical genetic testing for susceptibility to cancer. A statistically rigorous model that provides a pathogenicity score for each variant has been developed to aid in the clinical management of patients undergoing genetic testing. METHODS The information in this article is derived from multiple publications on VUS in BRCA genes, distilled for communicating with clinicians who may encounter VUS in their practice. RESULTS The posterior probability scores for BRCA1 or BRCA2 VUS, calculated from a multifactorial likelihood model, are explained, and links for looking up specific VUS are provided. The International Agency on Cancer Research (IARC) of the World Health Organization has proposed a simple five-tier system for clinical management that is not widely known to clinicians. Classes 1 and 2 in this system are managed as neutral variants, classes 4 and 5 are managed as pathogenic variants, and class 3 variants still have insufficient evidence to move to either end of this scale and, thus, cannot be used in medical management. CONCLUSIONS Development of models that integrate multiple independent lines of evidence has allowed classification of a growing number of VUS in the BRCA1 and BRCA2 genes. The pathogenicity score that is generated by this model maps to the IARC system for clinical management, which will assist clinicians in the medical management of those patients who obtain a VUS result upon testing.
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Affiliation(s)
- Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, Arizona 85259, USA.
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42
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Towler WI, Zhang J, Ransburgh DJR, Toland AE, Ishioka C, Chiba N, Parvin JD. Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing. Hum Mutat 2012; 34:439-45. [PMID: 23161852 DOI: 10.1002/humu.22251] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 01/13/2023]
Abstract
Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study. All 29 variants were also analyzed for function in double-strand break repair by the single-strand annealing (SSA) pathway. We found that among the pathogenic mutations in BRCA1, all were defective for DNA repair by either pathway. The HDR assay was accurate because all pathogenic mutants were defective for HDR, and all nonpathogenic variants were fully functional for HDR. Repair by SSA accurately identified pathogenic mutants, but several nonpathogenic variants were scored as defective or partially defective. These results indicated that specific amino acid residues of the BRCA1 protein have different effects in the two related DNA repair pathways, and these results validate the HDR assay as highly correlative with BRCA1-associated breast cancer.
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Affiliation(s)
- William I Towler
- Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
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43
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Keshavarzi F, Javadi GR, Zeinali S. BRCA1 and BRCA2 germline mutations in 85 Iranian breast cancer patients. Fam Cancer 2012; 11:57-67. [PMID: 21918854 DOI: 10.1007/s10689-011-9477-3] [Citation(s) in RCA: 14] [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
Breast cancer is the most common cancer in Iranian women (Mousavi et al in Asian Pac J Cancer Prev 9(2):275-278, 2008). Genetic predisposition accounts for 15% of all breast cancers and germline mutations in breast cancer susceptibility genes, BRCA1 and BRCA2 are responsible for a substantial proportion of high-risk breast and breast/ovarian cancer families (Collaborative Group on Hormonal Factors in Breast Cancer in Lancet 350:1047-1059, 1997; Lee et al in Int Nurs Rev 55:355-359, 2008; Hulka and Stark in Lancet 346:883-887, 1995; Kelsey in Epidemiol Rev 15:256-263, 1993; Tischer et al in J Biol Chem 266:11947-11954, 1991; Newman et al in: Proc Natl Acad Sci USA 85:3044-3048, 1988). Therefore, the aim of this study was to investigate mutations of BRCA1/2 in high risk Iranian families. We screened 85 patients who met our minimal criteria. The entire coding sequences and each intron/exon boundaries of BRCA1/2 genes were screened by direct sequencing. In the present study, we could detect the novel following mutations: p.Glu1735 p.Gly1140Ser, p.Ile26Val, p.Leu1418X, p.Glu23Gln, p.Leu3X, p.Asn1403His, p.Lys581X, p.Pro938Arg, p.Thr77Arg, p.Arg7Cys, p.Ser177Thr, IVS7+83(TT), IVS8-70(-CATT), IVS2+9(-GC), IVS1-20(-GA), IVS1-8(-AG), IVS2+24(AG), IVS5-8 (A-G), IVS2(35-39)TTcctatGAT in BRCA1 and p.Glu1391Gly, 1994_1995 (Ins A), IVS6-70-T>G in BRCA2. In agreement with findings in other populations, we found that family history is a good predictor of being a mutation carrier. Five pathogenic BRCA1 mutations and one pathogenic BRCA2 mutation were detected in 85 index cases.
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Affiliation(s)
- Fatemeh Keshavarzi
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.
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BRCA1/BRCA2 gene mutations/SNPs and BRCA1 haplotypes in early-onset breast cancer patients of Indian ethnicity. Med Oncol 2012; 29:3272-81. [PMID: 22752604 DOI: 10.1007/s12032-012-0294-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
Abstract
We examined BRCA1/2 mutations and single nucleotide polymorphisms (SNPs) for identification of BRCA1 haplotypes, in early-onset breast cancer patients and their relatives, sporadic breast cancer patients, and unrelated normal healthy females, of Indian ethnicity. Peripheral blood DNA was amplified by polymerase chain reaction, at BRCA1/2 coding exons and subject to nucleotide sequencing using ABI 3100 Genetic Analyzer. We observed BRCA1/BRCA2 mutations in 52 % early-onset breast cancer patients and in 57 % relatives. Deleterious mutations detected in early-onset patients and relatives were 187delAG, 632insT, 1052delT, Q759X, Q780X, R1203X, 5154delC, IVS14 + 1G > A, IVS17 + 1G > T, and 632insT in BRCA1 gene; and 4075delGT, 5076delAA, 6079delAGTT, and W3127X in BRCA2 gene. A high degree of penetrance of BRCA1/2 gene mutations was observed in the relatives. BRCA1/2 SNPs were identified in the Indian population, and association of BRCA1 haplotypes with breast cancer was investigated. A significantly increased frequency of the SNPs 203G/A, 3624A/G and 7470A/G SNPs in BRCA2 gene was observed in normal controls indicative of a protective effect of the SNPs. BRCA1 haplotype 2 was most frequently observed in our population. Our study indicates a high incidence of BRCA1/BRCA2 gene mutations in the Indian patients. The BRCA1/2 mutations and SNPs are detailed on our website http://relibrca.rellife.com .
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Becker AA, Graeser MK, Landwehr C, Hilger T, Baus W, Wappenschmidt B, Meindl A, Weber RG, Schmutzler RK. A 24-color metaphase-based radiation assay discriminates heterozygous BRCA2 mutation carriers from controls by chromosomal radiosensitivity. Breast Cancer Res Treat 2012; 135:167-75. [PMID: 22729890 DOI: 10.1007/s10549-012-2119-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/26/2012] [Indexed: 11/30/2022]
Abstract
Numerous allelic variants identified in the familial breast cancer and DNA repair genes BRCA1 and BRCA2 are of unknown impact on protein function or clinical relevance, referred to as unclassified variants (UCV). Lymphocytes from pathogenic BRCA1/2 mutation carriers exhibit an increased level of chromosomal damage after irradiation. We established a radiation assay for the discrimination of pathogenic BRCA2 variants versus controls based on the level of chromosomal damage upon irradiation (p < 0.001). As a consequence, lymphocytes from UCV carriers could be separated into two distinct groups with normal or diminished DNA double strand break repair capacity. Our results suggested that all five UCV tested were benign and that one family carried a putative mutation in an as yet undetected DNA-repair gene. Thus, our test may serve as a valuable tool that aids the classification of BRCA2 UCV, but very likely also of BRCA1 UCV or aberrations in other genes involved in the DNA-repair system.
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Affiliation(s)
- Alexandra A Becker
- Centre for Hereditary Breast and Ovarian Cancer, University Hospital Cologne, Kerpener Str. 62, 50931 Cologne, Germany
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Ghani-Kakhki M, Robinson PN, Morlot S, Mitter D, Trimborn M, Albrecht B, Varon R, Sperling K, Neitzel H. Two Missense Mutations in the Primary Autosomal Recessive Microcephaly Gene MCPH1 Disrupt the Function of the Highly Conserved N-Terminal BRCT Domain of Microcephalin. Mol Syndromol 2012; 3:6-13. [PMID: 22855649 DOI: 10.1159/000338975] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2012] [Indexed: 12/23/2022] Open
Abstract
Primary microcephaly MCPH1 is an extremely rare autosomal recessive disorder associated with congenital microcephaly, mental retardation and a distinctive cellular phenotype of misregulated chromosome condensation. The MCPH1 gene encodes an 835-amino acid protein, microcephalin, which contains 1 N-terminal and 2 C-terminal BRCT (BRCA1 C-terminus) domains. BRCT domains are predominantly found in proteins involved in cell cycle control and DNA repair. Here we describe 1 novel and 1 previously reported MCPH1 missense mutation, p.Trp75Arg and p.Ser72Leu, respectively, in the N-terminal BRCT domain of microcephalin associated with severe congenital microcephaly. Both residues are entirely conserved in the MCPH1 orthologs of all vertebrate species and Drosophila. Proliferating lymphocytes of the patients with p.Trp75Arg and p.Ser72Leu show the unique cellular MCPH1 phenotype of misregulated chromosome condensation, indicating that these missense alterations disrupt the function of the N-terminal BRCT domain of the protein. Interestingly, both residues are strictly conserved in BRCT domains of BRCA1. ClustalW alignments show that the residue p.Ser72 of microcephalin corresponds to p.Ser1715 of the N-terminal BRCT domain of BRCA1, while the microcephalin residue p.Trp75 is analogous to p.Trp1718 in the N-terminal BRCT and to p.Trp1837 in C-terminal BRCT domains of BRCA1. Missense alterations for all 3 corresponding BRCA1 residues were described and are predicted to be deleterious resulting in the destabilization of the BRCA1 protein. Our data on the 2 MCPH1 missense alterations provide further evidence for the functional significance of these residues in BRCT domains.
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Affiliation(s)
- M Ghani-Kakhki
- Institute of Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
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Kloss-Brandstätter A, Erhart G, Lamina C, Meister B, Haun M, Coassin S, Seifert M, Klein-Franke A, Paulweber B, Kedenko L, Kollerits B, Swinkels DW, Vermeulen SH, Galesloot TE, Kronenberg F, Weiss G. Candidate gene sequencing of SLC11A2 and TMPRSS6 in a family with severe anaemia: common SNPs, rare haplotypes, no causative mutation. PLoS One 2012; 7:e35015. [PMID: 22509377 PMCID: PMC3324414 DOI: 10.1371/journal.pone.0035015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 03/08/2012] [Indexed: 12/26/2022] Open
Abstract
Background Iron-refractory iron deficiency anaemia (IRIDA) is a rare disorder which was linked to mutations in two genes (SLC11A2 and TMPRSS6). Common polymorphisms within these genes were associated with serum iron levels. We identified a family of Serbian origin with asymptomatic non-consanguineous parents with three of four children presenting with IRIDA not responding to oral but to intravenous iron supplementation. After excluding all known causes responsible for iron deficiency anaemia we searched for mutations in SLC11A2 and TMPRSS6 that could explain the severe anaemia in these children. Methodology/Results We sequenced the exons and exon–intron boundaries of SLC11A2 and TMPRSS6 in all six family members. Thereby, we found seven known and fairly common SNPs, but no new mutation. We then genotyped these seven SNPs in the population-based SAPHIR study (n = 1,726) and performed genetic association analysis on iron and ferritin levels. Only two SNPs, which were top-hits from recent GWAS on iron and ferritin, exhibited an effect on iron and ferritin levels in SAPHIR. Six SAPHIR participants carrying the same TMPRSS6 genotypes and haplotype-pairs as one anaemic son showed lower ferritin and iron levels than the average. One individual exhibiting the joint SLC11A2/TMPRSS6 profile of the anaemic son had iron and ferritin levels lying below the 5th percentile of the population's iron and ferritin level distribution. We then checked the genotype constellations in the Nijmegen Biomedical Study (n = 1,832), but the profile of the anaemic son did not occur in this population. Conclusions We cannot exclude a gene-gene interaction between SLC11A2 and TMPRSS6, but we can also not confirm it. As in this case candidate gene sequencing did not reveal causative rare mutations, the samples will be subjected to whole exome sequencing.
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Affiliation(s)
- Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Gertraud Erhart
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Claudia Lamina
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Bernhard Meister
- Department of Paediatrics II, Innsbruck Medical University, Innsbruck, Austria
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Stefan Coassin
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Markus Seifert
- Department of Internal Medicine I, Clinical Immunology and Infectious Diseases, Innsbruck Medical University, Innsbruck, Austria
| | | | - Bernhard Paulweber
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Lyudmyla Kedenko
- First Department of Internal Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Barbara Kollerits
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
| | - Dorine W. Swinkels
- Department of Laboratory Medicine, Laboratory of Genetic, Endocrine and Metabolic Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Sita H. Vermeulen
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Tessel E. Galesloot
- Department of Epidemiology, Biostatistics and HTA, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
- * E-mail: (FK); (GW)
| | - Günter Weiss
- Department of Internal Medicine I, Clinical Immunology and Infectious Diseases, Innsbruck Medical University, Innsbruck, Austria
- * E-mail: (FK); (GW)
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Rath MG, Fathali-Zadeh F, Langheinz A, Tchatchou S, Voigtländer T, Heil J, Golatta M, Schott S, Drasseck T, Behnecke A, Burgemeister AL, Evers C, Bugert P, Junkermann H, Schneeweiss A, Bartram CR, Sohn C, Sutter C, Burwinkel B. Molecular and clinical characterization of an in frame deletion of uncertain clinical significance in the BRCA2 gene. Breast Cancer Res Treat 2012; 133:725-34. [PMID: 22228431 DOI: 10.1007/s10549-011-1917-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 01/07/2023]
Abstract
In this study, we analyzed a "variant of uncertain significance" (VUS) located in exon 23 of the BRCA2 gene exhibited by six members of five distinct families with hereditary breast cancer (BC). The variant was identified by DNA sequencing, and cDNA analysis revealed its co-expression with wild-type mRNA. We analyzed co-occurrence with other pathological mutations in BRCA1/2, performed a case-control study, looked for evolutionary data and used in-silico analyses to predict its potential clinical significance. Sequencing revealed an in frame deletion of 126 nucleotides in exon 23, leading to a deletion of 42 amino acids (c.9203_9328del126, p.Pro2992_Thr3033del). All of the VUS-carriers suffered from either BC or ovarian/pancreatic cancer. No other definite pathologic mutation of BRCA genes was found in the five families. The identified deletion could not be observed in a control cohort of 2,652 healthy individuals, but in 5 out of 916 (0.5%) tested BC families without a bona fide pathogenic BRCA1/2 mutation (P = 0.0011). According to these results, the in frame deletion c.9203_9328del126 is a rare mutation strongly associated with familial BC. In summary, our investigations indicate that this BRCA2 deletion is pathogenic.
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Affiliation(s)
- Michelle G Rath
- Division Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
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Vallée MP, Francy TC, Judkins MK, Babikyan D, Lesueur F, Gammon A, Goldgar DE, Couch FJ, Tavtigian SV. Classification of missense substitutions in the BRCA genes: a database dedicated to Ex-UVs. Hum Mutat 2012; 33:22-8. [PMID: 21990165 PMCID: PMC3478957 DOI: 10.1002/humu.21629] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 09/26/2011] [Indexed: 01/15/2023]
Abstract
Unclassified sequence variants (UVs) arising from clinical mutation screening of cancer susceptibility genes present a frustrating issue to clinical genetics services and the patients that they serve. We created an open-access database holding missense substitutions from the breast and ovarian cancer susceptibility genes BRCA1 and BRCA2. The main inclusion criterion is that each variant should have been assessed in a published work that used the Bayesian integrated evaluation of unclassified BRCA gene variants. Transfer of data on these substitutions from the original publications to our database afforded an opportunity to analyze the missense substitutions under a single model and to remove inconsistencies that arose during the evolution of the integrated evaluation over the last decade. This analysis also afforded the opportunity to reclassify these missense substitutions according to the recently published IARC 5-Class system. From an initial set of 248 missense substitutions, 31 were set aside due to nonnegligible probability to interfere with splicing. Of the remaining substitutions, 28 fell into one of the two pathogenic classes (IARC Class 4 or 5), 174 fell into one of the two nonpathogenic classes (IARC Class 1 or 2), and 15 remain in IARC Class 3, "Uncertain." The database is available at http://brca.iarc.fr/LOVD.
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Affiliation(s)
| | - Tiana C. Francy
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - Megan K. Judkins
- Graduate Program in Genetic Counseling, University of Utah School of Medicine, Salt Lake City, USA
| | - Davit Babikyan
- Laboratory of Cancer Genetics, Center of Medical Genetics and Primary Health Care, Yerevan, Armenia
| | | | - Amanda Gammon
- High Risk Cancer Clinics, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
| | - David E. Goldgar
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, USA
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, USA
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50
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Sequence Variants of BRCA1 and BRCA2 Genes in Four Iranian Families with Breast and Ovarian Cancer. IRANIAN JOURNAL OF PUBLIC HEALTH 2011; 40:57-66. [PMID: 23113073 PMCID: PMC3481774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 02/03/2011] [Indexed: 11/24/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 genes have been recognized to be responsible for 20-30% of hereditary breast cancers and approximately 50% of familial breast and ovarian cancers. Therefore, the demand for BRCA1 and BRCA2 mutation screening is rapidly increasing as their identification will affect medical management of people at increased risk. Because of high costs involved in analysis of BRCA1 and 2 genes, contribution of different mutation types in BRCA1 and 2 and not knowing who should be tested has hampered wide spread use of molecular testing of high -risk families. There is a need to identify the genes and types of mutations involved in breast or ovarian cancers at different age of onsets and polymorphism and polymorphic variations in our population. METHODS Twenty-seven patients with either early onset breast cancer (at age≤ 35 years) or a personal and/or family history of breast or ovarian cancer and 50 control subjects participated in this study. After collecting blood samples and extracting DNA, BRCA1 and BRCA2 genes were fully sequenced. RESULTS Thirteen missense substitutions in BRCA1 and BRCA2 (9 and 4, respectively) were revealed. Two nucleotide substitutions were novel (Gly1140Ser in BRCA1 and Glu1391Gly in BRCA2). The Glu1038Pro and Gly1140Ser were found in large series of breast and ovarian cancer and matched controls. CONCLUSION Some nucleotide substitutions were seen only in single families and other in several. In other cases, mutations were seen in both BRCA1 and BRCA2 genes. Clinical significance of these mutations was evaluated comparing with normal controls.
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