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Fanale D, Pivetti A, Cancelliere D, Spera A, Bono M, Fiorino A, Pedone E, Barraco N, Brando C, Perez A, Guarneri MF, Russo TDB, Vieni S, Guarneri G, Russo A, Bazan V. BRCA1/2 variants of unknown significance in hereditary breast and ovarian cancer (HBOC) syndrome: looking for the hidden meaning. Crit Rev Oncol Hematol 2022; 172:103626. [PMID: 35150867 DOI: 10.1016/j.critrevonc.2022.103626] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 01/04/2023] Open
Abstract
Hereditary breast and ovarian cancer syndrome is caused by germline mutations in BRCA1/2 genes. These genes are very large and their mutations are heterogeneous and scattered throughout the coding sequence. In addition to the above-mentioned mutations, variants of uncertain/unknown significance (VUSs) have been identified in BRCA genes, which make more difficult the clinical management of the patient and risk assessment. In the last decades, several laboratories have developed different databases that contain more than 2000 variants for the two genes and integrated strategies which include multifactorial prediction models based on direct and indirect genetic evidence, to classify the VUS and attribute them a clinical significance associated with a deleterious, high-low or neutral risk. This review provides a comprehensive overview of literature studies concerning the VUSs, in order to assess their impact on the population and provide new insight for the appropriate patient management in clinical practice.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Pivetti
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Daniela Cancelliere
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Spera
- Department of Radiotherapy, San Giovanni di Dio Hospital, ASP of Agrigento, Agrigento, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | | | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Salvatore Vieni
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Italy
| | - Girolamo Guarneri
- Gynecology Section, Mother - Child Department, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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2
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Billaud A, Chevalier LM, Augereau P, Frenel JS, Passot C, Campone M, Morel A. Functional pre-therapeutic evaluation by genome editing of variants of uncertain significance of essential tumor suppressor genes. Genome Med 2021; 13:174. [PMID: 34749799 PMCID: PMC8576946 DOI: 10.1186/s13073-021-00976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Targeted therapies in oncology are promising but variants of uncertain significance (VUS) limit their use for clinical management and necessitate functional testing in vitro. Using BRCA1 and BRCA2 variants, which have consequences on PARP inhibitor sensitivity, and POLE variants, potential biomarkers of immunotherapy response, we developed a rapid functional assay based on CRISPR-Cas9 genome editing to determine the functional consequences of these variants having potentially direct implications on patients' access to targeted therapies. METHODS We first evaluated the functional impact of 26 BRCA1 and 7 BRCA2 variants by editing and comparing NGS results between the variant of interest and a silent control variant. Ten of these variants had already been classified as benign or pathogenic and were used as controls. Finally, we extended this method to the characterization of POLE VUS. RESULTS For the 23 variants that were unclassified or for which conflicting interpretations had been reported, 15 were classified as functionally normal and 6 as functionally abnormal. Another two variants were found to have intermediate consequences, both with potential impacts on splicing. We then compared these scores to the patients' responses to PARP inhibitors when possible. Finally, to prove the application of our method to the classification of variants from other tumor suppressor genes, we exemplified with three POLE VUS. Among them, two were classified with an intermediate functional impact and one was functionally abnormal. Eventually, four POLE variants previously classified in databases were also evaluated. However, we found evidence of a discordance with the classification, variant p.Leu424Val being found here functionally normal. CONCLUSIONS Our new rapid functional assay can be used to characterize the functional implication of BRCA1 and BRCA2 variants, giving patients whose variants were evaluated as functionally abnormal access to PARP inhibitor treatment. Retrospective analysis of patients' responses to PARP inhibitors, where accessible, was consistent with our functional score evaluation and confirmed the accuracy of our protocol. This method could potentially be extended to the classification of VUS from all essential tumor suppressor genes and can be performed within a timeframe compatible with clinical applications, thereby having a direct theranostic impact.
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Affiliation(s)
- Amandine Billaud
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Louise-Marie Chevalier
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Paule Augereau
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Jean-Sebastien Frenel
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
| | - Christophe Passot
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
| | - Mario Campone
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France
- Université de Nantes, Inserm, CRCINA, F-44000, Nantes, France
| | - Alain Morel
- Université d'Angers, Inserm, CRCINA, SFR ICAT, F-49000, Angers, France.
- Institut de Cancérologie de l'Ouest Nantes-Angers, F-49000, Angers, France.
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3
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Yang Y, Chen J, Qin H, Jin Y, Zhang L, Yang S, Wang H, Fu L, Hong E, Yu Y, Lu J, Chang Y, Ni X, Xu M, Shi T, Guo Y. A Novel Germline Compound Heterozygous Mutation of BRCA2 Gene Associated With Familial Peripheral Neuroblastic Tumors in Two Siblings. Front Genet 2021; 12:652718. [PMID: 34367235 PMCID: PMC8343186 DOI: 10.3389/fgene.2021.652718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives To investigate the genetic variants that are responsible for peripheral neuroblastic tumors (PNTs) oncogenesis in one family case. Materials and Methods One family was recruited, including the healthy parents, sister affected by neuroblastoma (NB), and brother who suffered from ganglioneuroma (GN). Whole-genome sequencing (WGS) of germline DNA from all the family members and RNA-seq of tumor RNA from the siblings were performed. Mutants were validated by Sanger sequencing and co-IP was performed to assess the impact of the mutant on chemosensitivity in the SH-SY5Y cell line. Results A novel compound heterozygous mutation of BRCA2 was locked as the cause of carcinogenesis. One allele was BRCA2-S871X (stop-gain) from the siblings’ mother, the other was BRCA2-N372H (missense) from their father. This novel compound heterozygous mutations of the BRCA2 gene associated with PNTs by disordering DNA damage and response (DDR) signal pathway. Moreover, chemosensitivity was reduced in the NB cell line due to the BRCA2-N372H mutant. Conclusion In summary, these results revealed a novel germline compound heterozygous mutation of the BRCA2 gene associated with familial PNTs.
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Affiliation(s)
- Yeran Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Jiwei Chen
- Center for Bioinformatics and Computational Biology, School of Life Sciences, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Hong Qin
- Department of Surgical Oncology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Li Zhang
- Center for Bioinformatics and Computational Biology, School of Life Sciences, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Shen Yang
- Department of Surgical Oncology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Huanmin Wang
- Department of Surgical Oncology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Libing Fu
- Department of Pathology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Enyu Hong
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China
| | - Yongbo Yu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Yan Chang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Xin Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
| | - Min Xu
- Department of Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, School of Life Sciences, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Biobank for Clinical Data and Samples in Pediatric, National Center for Children's Health, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, Beijing, China.,Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Capital Medical University, Beijing, China
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4
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Shestak AG, Bukaeva AA, Saber S, Zaklyazminskaya EV. Allelic Dropout Is a Common Phenomenon That Reduces the Diagnostic Yield of PCR-Based Sequencing of Targeted Gene Panels. Front Genet 2021; 12:620337. [PMID: 33633783 PMCID: PMC7901947 DOI: 10.3389/fgene.2021.620337] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023] Open
Abstract
Primary cardiomyopathies (CMPs) are monogenic but multi-allelic disorders with dozens of genes involved in pathogenesis. The implementation of next-generation sequencing (NGS) approaches has resulted in more time- and cost-efficient DNA diagnostics of cardiomyopathies. However, the diagnostic yield of genetic testing for each subtype of CMP fails to exceed 60%. The aim of this study was to demonstrate that allelic dropout (ADO) is a common phenomenon that reduces the diagnostic yield in primary cardiomyopathy genetic testing based on targeted gene panels assayed on the Ion Torrent platform. We performed mutational screening with three custom targeted gene panels based on sets of oligoprimers designed automatically using AmpliSeq Designer® containing 1049 primer pairs for 37 genes with a total length of 153 kb. DNA samples from 232 patients were screened with at least one of these targeted gene panels. We detected six ADO events in both IonTorrent PGM (three cases) and capillary Sanger sequencing (three cases) data, identifying ADO-causing variants in all cases. All ADO events occurred due to common or rare single nucleotide variants (SNVs) in the oligoprimer binding sites and were detected because of the presence of “marker” SNVs in the target DNA fragment. We ultimately identified that PCR-based NGS involves a risk of ADO that necessitates the use of Sanger sequencing to validate NGS results. We assume that oligoprimer design without ADO data affects the amplification efficiency of up to 0.77% of amplicons.
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Affiliation(s)
- Anna G Shestak
- Medical Genetics Laboratory, Petrovsky National Research Center of Surgery, Moscow, Russia
| | - Anna A Bukaeva
- Medical Genetics Laboratory, Petrovsky National Research Center of Surgery, Moscow, Russia
| | - Siamak Saber
- Cardiac Electrophysiology Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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5
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Haque MM, Kowtal P, Sarin R. Identification and characterization of TP53 gene Allele Dropout in Li-Fraumeni syndrome and Oral cancer cohorts. Sci Rep 2018; 8:11705. [PMID: 30076369 PMCID: PMC6076284 DOI: 10.1038/s41598-018-30238-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/21/2018] [Indexed: 12/20/2022] Open
Abstract
Allele Drop out (ADO) arising from non-amplification of one allele may produce false negative result and impact clinical management. In cancer, germline and somatic genetic analysis is being increasingly used but the prevalence, nature and implications of ADO has not been studied in any cohort. In a cohort of 290 Li Fraumeni/Li Fraumeni Like Syndrome cases undergoing TP53 genetic testing, of the 69 pathogenic mutations identified so far, 5 were initially missed and 4 were misgenotyped as homozygous mutation due to germline ADO. Of the 9 germline ADOs, 8 were sequence dependent, arising from a polymorphism (rs12951053) in the primer annealing region of exon 7. Of 35 somatic TP53 variants identified by exome sequencing in 50 oral cancer tissues registered under International Cancer Genome Consortium (ICGC), as a result of ADO, 4 were not detectable and 6 were not called as variant on Sanger Sequencing due to low peak height. High prevalence of germline and somatic ADO in the most frequently mutated cancer gene TP53, highlights the need for systematic evaluation of ADO prevalence and causes in clinically important cancer genes. False negative result for high penetrance germline mutations or actionable somatic mutations in oncogenes could have major clinical implications.
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Affiliation(s)
- Mohammed Moquitul Haque
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Pradnya Kowtal
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Rajiv Sarin
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India. .,Cancer Genetics Clinic, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, Maharashtra, India.
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6
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Dos Santos ES, Caputo SM, Castera L, Gendrot M, Briaux A, Breault M, Krieger S, Rogan PK, Mucaki EJ, Burke LJ, Bièche I, Houdayer C, Vaur D, Stoppa-Lyonnet D, Brown MA, Lallemand F, Rouleau E. Assessment of the functional impact of germline BRCA1/2 variants located in non-coding regions in families with breast and/or ovarian cancer predisposition. Breast Cancer Res Treat 2017; 168:311-325. [PMID: 29236234 DOI: 10.1007/s10549-017-4602-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE The molecular mechanism of breast and/or ovarian cancer susceptibility remains unclear in the majority of patients. While germline mutations in the regulatory non-coding regions of BRCA1 and BRCA2 genes have been described, screening has generally been limited to coding regions. The aim of this study was to evaluate the contribution of BRCA1/2 non-coding variants. METHODS Four BRCA1/2 non-coding regions were screened using high-resolution melting analysis/Sanger sequencing or next-generation sequencing on DNA extracted from index cases with breast and ovarian cancer predisposition (3926 for BRCA1 and 3910 for BRCA2). The impact of a set of variants on BRCA1/2 gene regulation was evaluated by site-directed mutagenesis, transfection, followed by Luciferase gene reporter assay. RESULTS We identified a total of 117 variants and tested twelve BRCA1 and 8 BRCA2 variants mapping to promoter and intronic regions. We highlighted two neighboring BRCA1 promoter variants (c.-130del; c.-125C > T) and one BRCA2 promoter variants (c.-296C > T) inhibiting significantly the promoter activity. In the functional assays, a regulating region within the intron 12 was found with the same enhancing impact as within the intron 2. Furthermore, the variants c.81-3980A > G and c.4186-2022C > T suppress the positive effect of the introns 2 and 12, respectively, on the BRCA1 promoter activity. We also found some variants inducing the promoter activities. CONCLUSION In this study, we highlighted some variants among many, modulating negatively the promoter activity of BRCA1 or 2 and thus having a potential impact on the risk of developing cancer. This selection makes it possible to conduct future validation studies on a limited number of variants.
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Affiliation(s)
- E Santana Dos Santos
- Department of Oncology, Center for Translational Oncology, Cancer Institute of the State of São Paulo - ICESP, São Paulo, Brazil
- Service de Génétique, Institut Curie, Paris, France
- A.C.Camargo Cancer Center, São Paulo, Brazil
| | - S M Caputo
- Service de Génétique, Institut Curie, Paris, France
| | - L Castera
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - M Gendrot
- Service de Génétique, Institut Curie, Paris, France
| | - A Briaux
- Service de Génétique, Institut Curie, Paris, France
| | - M Breault
- Service de Génétique, Institut Curie, Paris, France
| | - S Krieger
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - P K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - E J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Canada
| | - L J Burke
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - I Bièche
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - C Houdayer
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - D Vaur
- Laboratoire de Biologie et de Génétique du Cancer, CLCC François Baclesse, INSERM 1079 Centre Normand de Génomique et de MédecinePersonnalisée, Caen, France
| | - D Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Paris, France
| | - M A Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - F Lallemand
- Service de Génétique, Institut Curie, Paris, France.
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7
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Tessereau C, Léoné M, Buisson M, Duret L, Sinilnikova OM, Mazoyer S. Occurrence of a non deleterious gene conversion event in the BRCA1 gene. Genes Chromosomes Cancer 2015; 54:646-52. [PMID: 26171949 DOI: 10.1002/gcc.22278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 12/12/2022] Open
Abstract
The duplication in the primate lineage of a portion of the breast and ovarian cancer susceptibility gene BRCA1 has created a BRCA1 pseudogene 45 kb away. Non-allelic homologous recombination (NAHR) between BRCA1 and BRCA1P1 has generated recurrent deleterious germ-line 37-kb deletions encompassing the first two exons of BRCA1, accounting for several breast and ovarian cancer families in various populations. In principle, NAHR intermediates resolution could also lead through a non-crossover configuration to interlocus gene conversion (IGC), but none had been described as yet. Here, we report for the first time an IGC event identified in a breast and ovarian cancer family involving exactly the same segment as that involved in the 37-kb deletions. Close examination of the consequences of this IGC event showed that it does not impact BRCA1 expression. Detailed analysis of the regions of homology between BRCA1 and its pseudogene revealed the specificity of the segment where recombination systematically occurs.
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Affiliation(s)
- Chloé Tessereau
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Mélanie Léoné
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Monique Buisson
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR5558, Université Lyon 1, Lyon, France
| | - Olga M Sinilnikova
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France.,Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Sylvie Mazoyer
- "Genetics of Breast Cancer" Team, Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
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8
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Trujillano D, Weiss MER, Schneider J, Köster J, Papachristos EB, Saviouk V, Zakharkina T, Nahavandi N, Kovacevic L, Rolfs A. Next-generation sequencing of the BRCA1 and BRCA2 genes for the genetic diagnostics of hereditary breast and/or ovarian cancer. J Mol Diagn 2014; 17:162-70. [PMID: 25556971 DOI: 10.1016/j.jmoldx.2014.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 01/01/2023] Open
Abstract
Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1 and BRCA2 genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1 and BRCA2 genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1 and BRCA2 mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1 and BRCA2 panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1 and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1 and BRCA2 variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1 and BRCA2 genes and provides a greater opportunity for more comprehensive testing of at-risk patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Arndt Rolfs
- Centogene AG, Rostock, Germany; Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
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9
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Coulet F, Fajac A, Colas C, Eyries M, Dion-Minière A, Rouzier R, Uzan S, Lefranc JP, Carbonnel M, Cornelis F, Cortez A, Soubrier F. GermlineRAD51Cmutations in ovarian cancer susceptibility. Clin Genet 2013; 83:332-6. [DOI: 10.1111/j.1399-0004.2012.01917.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/25/2012] [Accepted: 06/15/2012] [Indexed: 12/17/2022]
Affiliation(s)
- F Coulet
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Département de Génétique; Paris; F-75651; France
| | - A Fajac
- Hôpital Tenon; Assistance Publique-Hopitaux de Paris, Laboratoire d'Histologie Biologie Tumorale; Paris; F-75651; France
| | - C Colas
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Département de Génétique; Paris; F-75651; France
| | - M Eyries
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Département de Génétique; Paris; F-75651; France
| | - A Dion-Minière
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Département de Génétique; Paris; F-75651; France
| | - R Rouzier
- Hôpital Tenon; Assistance Publique-Hopitaux de Paris, Service de Chirurgie Gynecologique; Paris; F-75651; France
| | - S Uzan
- Hôpital Tenon; Assistance Publique-Hopitaux de Paris, Service de Chirurgie Gynecologique; Paris; F-75651; France
| | - J-P Lefranc
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Service de Chirurgie Gynecologique; Paris; F-75651; France
| | - M Carbonnel
- Hôpital Jean Verdier; Assistance Publique-Hopitaux de Paris, Service de Chirurgie Gynecologique; Bondy; F-93143; France
| | - F Cornelis
- Hôpital Jean Verdier; Assistance Publique-Hopitaux de Paris, Service d'Anatomo-pathologie; Bondy; F-93143; France
| | - A Cortez
- Hôpital Tenon; Assistance Publique-Hopitaux de Paris, Service d'Anatomo-pathologie; Paris; F-75651; France
| | - F Soubrier
- Groupe hospitalier Pitié-Salpêtrière; Assistance Publique-Hopitaux de Paris, Université Pierre et Marie Curie, Département de Génétique; Paris; F-75651; France
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10
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Anczuków O, Buisson M, Léoné M, Coutanson C, Lasset C, Calender A, Sinilnikova OM, Mazoyer S. BRCA2 Deep Intronic Mutation Causing Activation of a Cryptic Exon: Opening toward a New Preventive Therapeutic Strategy. Clin Cancer Res 2012; 18:4903-9. [DOI: 10.1158/1078-0432.ccr-12-1100] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Rare germline large rearrangements in the BRCA1/2 genes and eight candidate genes in 472 patients with breast cancer predisposition. Breast Cancer Res Treat 2012; 133:1179-90. [DOI: 10.1007/s10549-012-2009-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/26/2012] [Indexed: 01/12/2023]
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12
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Hernan I, Borràs E, de Sousa Dias M, Gamundi MJ, Mañé B, Llort G, Agúndez JAG, Blanca M, Carballo M. Detection of genomic variations in BRCA1 and BRCA2 genes by long-range PCR and next-generation sequencing. J Mol Diagn 2012; 14:286-93. [PMID: 22426013 DOI: 10.1016/j.jmoldx.2012.01.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 01/10/2012] [Accepted: 01/24/2012] [Indexed: 02/09/2023] Open
Abstract
Advances in sequencing technologies, such as next-generation sequencing (NGS), represent an opportunity to perform genetic testing in a clinical scenario. In this study, we developed and tested a method for the detection of mutations in the large BRCA1 and BRCA2 tumor suppressor genes, using long-range PCR (LR-PCR) and NGS, in samples from individuals with a personal and/or family history of breast and/or ovarian cancer. Eleven LR-PCR fragments, between 3000 and 15,300 bp, containing all coding exons and flanking splice junctions of BRCA1 and BRCA2, were obtained from DNA samples of five individuals carrying mutations in either BRCA1 or BRCA2. Libraries for NGS were prepared using an enzymatic (Nextera technology) method. We analyzed five individual samples in parallel by NGS and obtained complete coverage of all LR-PCR fragments, with an average coding sequence depth for each nucleotide of >30 reads, running from ×7 (in exon 22 of BRCA1) to >×150. We detected and confirmed 100% of the mutations that predispose to the risk of cancer, together with other genomic variations in BRCA1 and BRCA2. Our approach demonstrates that genomic LR-PCR, together with NGS, using the GS Junior 454 System platform, is an effective method for patient sample analysis of BRCA1 and BRCA2 genes. In addition, this method could be performed in regular molecular genetics laboratories.
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Affiliation(s)
- Imma Hernan
- Molecular Genetics Unit, Hospital of Terrassa, Terrassa, Spain
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13
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Obul J, Itoga S, Abliz M, Sato K, Ishige T, Utsuno E, Matsushita K, Matsubara H, Nomura F. High-resolution melting analyses for gene scanning of APC, MLH1, MSH2, and MSH6 associated with hereditary colorectal cancer. Genet Test Mol Biomarkers 2012; 16:406-11. [PMID: 22283331 DOI: 10.1089/gtmb.2011.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Hereditary colorectal cancer accounts for approximately 4-5% of all colorectal cancers. The causative genes for familial adenomatous polyposis and hereditary nonpolyposis colorectal cancer are large, making comprehensive analyses difficult. Therefore, high-throughput and practical methods are required to make an early diagnosis of hereditary colorectal cancers and identify high-risk individuals. For this purpose, we developed a novel gene scanning method by high-resolution melting (HRM) analysis. METHODS High-resolution melting (HRM) analysis is a promising prescreening method for nucleic acid sequence variants because of its high sensitivity and high-throughput capability. We evaluated HRM for screening APC, MLH1, MSH2, and MSH6 genes for point mutations, small deletions, and insertions. Simultaneously, we evaluated quantitative polymerase chain reaction-HRM (qPCR-HRM) for screening the MSH2 gene for large rearrangements. RESULTS All 28 point mutations and 1 large rearrangement were successfully detected by qPCR-HRM analysis. CONCLUSIONS A fast and reliable mutation detection strategy with HRM and qPCR-HRM was used to diagnose hereditary colorectal cancers. Because this method is simple and economical, it may be useful in diagnostic laboratories.
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Affiliation(s)
- Jurat Obul
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan.
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14
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Hondow HL, Fox SB, Mitchell G, Scott RJ, Beshay V, Wong SQ, Dobrovic A. A high-throughput protocol for mutation scanning of the BRCA1 and BRCA2 genes. BMC Cancer 2011; 11:265. [PMID: 21702907 PMCID: PMC3146935 DOI: 10.1186/1471-2407-11-265] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/24/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Detection of mutations by DNA sequencing can be facilitated by scanning methods to identify amplicons which may have mutations. Current scanning methods used for the detection of germline sequence variants are laborious as they require post-PCR manipulation. High resolution melting (HRM) is a cost-effective rapid screening strategy, which readily detects heterozygous variants by melting curve analysis of PCR products. It is well suited to screening genes such as BRCA1 and BRCA2 as germline pathogenic mutations in these genes are always heterozygous. METHODS Assays for the analysis of all coding regions and intron-exon boundaries of BRCA1 and BRCA2 were designed, and optimised. A final set of 94 assays which ran under identical amplification conditions were chosen for BRCA1 (36) and BRCA2 (58). Significant attention was placed on primer design to enable reproducible detection of mutations within the amplicon while minimising unnecessary detection of polymorphisms. Deoxyinosine residues were incorporated into primers that overlay intronic polymorphisms. Multiple 384 well plates were used to facilitate high throughput. RESULTS 169 BRCA1 and 239 BRCA2 known sequence variants were used to test the amplicons. We also performed an extensive blinded validation of the protocol with 384 separate patient DNAs. All heterozygous variants were detected with the optimised assays. CONCLUSIONS This is the first HRM approach to screen the entire coding region of the BRCA1 and BRCA2 genes using one set of reaction conditions in a multi plate 384 well format using specifically designed primers. The parallel screening of a relatively large number of samples enables better detection of sequence variants. HRM has the advantages of decreasing the necessary sequencing by more than 90%. This markedly reduced cost of sequencing will result in BRCA1 and BRCA2 mutation testing becoming accessible to individuals who currently do not undergo mutation testing because of the significant costs involved.
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Affiliation(s)
- Heather L Hondow
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Stephen B Fox
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gillian Mitchell
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Rodney J Scott
- School of Biomedical Sciences, University of Newcastle, New South Wales, 2308, Australia
| | - Victoria Beshay
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | - Stephen Q Wong
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
| | | | - Alexander Dobrovic
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett St, Melbourne, Victoria, 8006, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
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15
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Caux-Moncoutier V, Castéra L, Tirapo C, Michaux D, Rémon MA, Laugé A, Rouleau E, De Pauw A, Buecher B, Gauthier-Villars M, Viovy JL, Stoppa-Lyonnet D, Houdayer C. EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Hum Mutat 2011; 32:325-34. [PMID: 21120943 DOI: 10.1002/humu.21414] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Accepted: 11/08/2010] [Indexed: 11/07/2022]
Abstract
The detection of unknown mutations remains a serious challenge and, despite the expected benefits for the patient's health, a large number of genes are not screened on a routine basis. We present the diagnostic application of EMMA (Enhanced Mismatch Mutation Analysis(®) , Fluigent, Paris, France), a novel method based on heteroduplex analysis by capillary electrophoresis using innovative matrices. BRCA1 and BRCA2 were screened for point mutations and large rearrangements in 1,525 unrelated patients (372 for the validation step and 1,153 in routine diagnosis) using a single analytical condition. Seven working days were needed for complete BRCA1/2 screening in 30 patients by one technician (excluding DNA extraction and sequencing). A total of 137 mutations were found, including a BRCA2 duplication of exons 19 and 20, previously missed by Comprehensive BRACAnalysis(®) . The mutation detection rate was 11.9%, which is consistent with patient inclusions. This study therefore suggests that EMMA represents a valuable short-term and midterm option for many diagnostic laboratories looking for an easy, reliable, and affordable strategy, enabling fast and sensitive analysis for a large number of genes.
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16
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de Juan Jiménez I, Cardeñosa EE, Suela SP, González EB, Trejo DS, Lluch OF, Gilabert PB. Advantage of high-resolution melting curve analysis over conformation-sensitive gel electrophoresis for mutational screening of BRCA1 and BRCA2 genes. Clin Chim Acta 2010; 412:578-82. [PMID: 21147080 DOI: 10.1016/j.cca.2010.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/03/2010] [Accepted: 12/04/2010] [Indexed: 01/06/2023]
Abstract
BACKGROUND Mutation screening of BRCA1 and BRCA2 (BRCAs) genes is a time-consuming and costly procedure that demands faster and cheaper alternative methods for routine diagnostics. The present study is aimed at comparing the results obtained with screening mutations methods, conformation sensitive gel electrophoresis (CSGE) and high-resolution melting analysis (HRMA), for BRCAs attending to their specificity, sensitivity, reliability and cost-efficiency. METHODS We included 52 DNA samples of index patients from high-risk families. The mutational screening was performed by CSGE according to the Ganguly (1993) method and HRMA according to a modified De Leeneer (2008) method. The assays were performed in 384 well plates in the LightCycler 480 (Roche). All PCR products showing altered patterns were confirmed by sequencing. RESULTS The results obtained with the mutational study of BRCAs genes showed that HRMA exhibited higher sensitivity than CSGE as it was able to detect a wide mutational spectra of genetic variants in a larger number of samples. Aditionally, the combination of HRMA with hybiridization probes in a second step of the assay allows the specific confirmation of mutations. Furthermore, HRMA use less time, allowing the reduction of analysis time. CONCLUSIONS HRMA offers clear advantages over CSGE for the mutation screening of BRCAs genes as it has greater sensitivity and higher efficiency and it is less time-consuming.
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Affiliation(s)
- Inmaculada de Juan Jiménez
- Laboratory of Molecular Biology, Clinical Analysis Service, Hospital Universitario La Fe, Valencia, Spain
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