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Sanoguera-Miralles L, Llinares-Burguet I, Bueno-Martínez E, Ramadane-Morchadi L, Stuani C, Valenzuela-Palomo A, García-Álvarez A, Pérez-Segura P, Buratti E, de la Hoya M, Velasco-Sampedro EA. Comprehensive splicing analysis of the alternatively spliced CHEK2 exons 8 and 10 reveals three enhancer/silencer-rich regions and 38 spliceogenic variants. J Pathol 2024; 262:395-409. [PMID: 38332730 DOI: 10.1002/path.6243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/28/2023] [Indexed: 02/10/2024]
Abstract
Splicing is controlled by a large set of regulatory elements (SREs) including splicing enhancers and silencers, which are involved in exon recognition. Variants at these motifs may dysregulate splicing and trigger loss-of-function transcripts associated with disease. Our goal here was to study the alternatively spliced exons 8 and 10 of the breast cancer susceptibility gene CHEK2. For this purpose, we used a previously published minigene with exons 6-10 that produced the expected minigene full-length transcript and replicated the naturally occurring events of exon 8 [Δ(E8)] and exon 10 [Δ(E10)] skipping. We then introduced 12 internal microdeletions of exons 8 and 10 by mutagenesis in order to map SRE-rich intervals by splicing assays in MCF-7 cells. We identified three minimal (10-, 11-, 15-nt) regions essential for exon recognition: c.863_877del [ex8, Δ(E8): 75%] and c.1073_1083del and c.1083_1092del [ex10, Δ(E10): 97% and 62%, respectively]. Then 87 variants found within these intervals were introduced into the wild-type minigene and tested functionally. Thirty-eight of them (44%) impaired splicing, four of which (c.883G>A, c.883G>T, c.884A>T, and c.1080G>T) induced negligible amounts (<5%) of the minigene full-length transcript. Another six variants (c.886G>A, c.886G>T, c.1075G>A, c.1075G>T, c.1076A>T, and c.1078G>T) showed significantly strong impacts (20-50% of the minigene full-length transcript). Thirty-three of the 38 spliceogenic variants were annotated as missense, three as nonsense, and two as synonymous, underlying the fact that any exonic change is capable of disrupting splicing. Moreover, c.883G>A, c.883G>T, and c.884A>T were classified as pathogenic/likely pathogenic variants according to ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based criteria. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Lobna Ramadane-Morchadi
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Cristiana Stuani
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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2
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Kleiblová P, Černá M, Zemánková P, Matějková K, Nehasil P, Hojný J, Horáčková K, Janatová M, Soukupová J, Šťastná B, Kleibl Z. Parallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predisposition. Folia Biol (Praha) 2024; 70:62-73. [PMID: 38830124 DOI: 10.14712/fb2024070010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Germline DNA testing using the next-gene-ration sequencing (NGS) technology has become the analytical standard for the diagnostics of hereditary diseases, including cancer. Its increasing use places high demands on correct sample identification, independent confirmation of prioritized variants, and their functional and clinical interpretation. To streamline these processes, we introduced parallel DNA and RNA capture-based NGS using identical capture panel CZECANCA, which is routinely used for DNA analysis of hereditary cancer predisposition. Here, we present the analytical workflow for RNA sample processing and its analytical and diagnostic performance. Parallel DNA/RNA analysis allowed credible sample identification by calculating the kinship coefficient. The RNA capture-based approach enriched transcriptional targets for the majority of clinically relevant cancer predisposition genes to a degree that allowed analysis of the effect of identified DNA variants on mRNA processing. By comparing the panel and whole-exome RNA enrichment, we demonstrated that the tissue-specific gene expression pattern is independent of the capture panel. Moreover, technical replicates confirmed high reproducibility of the tested RNA analysis. We concluded that parallel DNA/RNA NGS using the identical gene panel is a robust and cost-effective diagnostic strategy. In our setting, it allows routine analysis of 48 DNA/RNA pairs using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) in a single run with sufficient coverage to analyse 226 cancer predisposition and candidate ge-nes. This approach can replace laborious Sanger confirmatory sequencing, increase testing turnaround, reduce analysis costs, and improve interpretation of the impact of variants by analysing their effect on mRNA processing.
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Affiliation(s)
- Petra Kleiblová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.
| | - Marta Černá
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemánková
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Matějková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petr Nehasil
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jan Hojný
- Institute of Pathology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Klára Horáčková
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Markéta Janatová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Jana Soukupová
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Barbora Šťastná
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdeněk Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
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3
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Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
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Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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4
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Walker LC, de la Hoya M, Wiggins GA, Lindy A, Vincent LM, Parsons M, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.24.23286431. [PMID: 36865205 PMCID: PMC9980257 DOI: 10.1101/2023.02.24.23286431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
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Zhang X, Cai M, Ma Y, Chen J, Huang S, Cai M, Ding Y, Ma D, Gao Q, Hu X, Zhu C, Yi L. Minigene Assay as an Effective Molecular Diagnostic Strategy in Determining the Pathogenicity of Noncanonical Splice-Site Variants in FLCN. J Mol Diagn 2023; 25:110-120. [PMID: 36410626 DOI: 10.1016/j.jmoldx.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Primary spontaneous pneumothorax (PSP) or pulmonary cyst is one of the manifestations of Birt-Hogg-Dubé syndrome, which is caused by pathogenic variants in FLCN gene. Genetic testing in patients with PSP identifies a certain number of missense or intronic variants. These variants are usually considered as variants of uncertain significance, whose functional interpretations pose a challenge in clinical genetics. To improve recognition of pathogenic splice-altering variants in FLCN gene, computational tools are used to prioritize potential splice-altering variants and then a hybrid minigene assay is performed to verify the RNA splicing pattern. Herein, variants in FLCN exon 11 and its flanking sequence are focused. Eight variants detected in 11 patients with PSP are evaluated, and six variants are prioritized by in silico tools as potential splice-altering variants of uncertain significance. Four variants (c.1177-5_1177-3delCTC, c.1292_1300+4del, c.1300+4C>T, and c.1300+5G>A) are demonstrated by minigene assay to alter RNA splicing of FLCN, and the last three of them are novel. RT-PCR of patient-derived RNA gives consistent results. Genotype-phenotype correlation analysis in patients with PSP with these variants demonstrates good concordance. Our results underline the importance of RNA analysis, which could provide molecular evidence for pathogenicity of a variant, and provide essential information for the clinical interpretation of variants. Combining the clinical information, a definitive diagnosis could be made.
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Affiliation(s)
- Xinxin Zhang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Minghui Cai
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Yuanchun Ma
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Jie Chen
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Shaoping Huang
- Department of Histology and Embryology, School of Medicine, Southeast University, Nanjing, China
| | - Mengru Cai
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Yibing Ding
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Dehua Ma
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Qian Gao
- Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengchu Zhu
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China.
| | - Long Yi
- Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China; Jiangsu Key Laboratory for Molecular Medicine, School of Medicine, Nanjing University, Nanjing, China.
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Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022; 14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [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: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
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Affiliation(s)
- Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Susana Gómez-Barrero
- Facultad de Ciencias de la Salud, Universidad Alfonso X “El Sabio”, Avda. de la Universidad 1, Villanueva de la Cañada, 28691 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Eladio A. Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
- Correspondence:
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7
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Bueno‐Martínez E, Sanoguera‐Miralles L, Valenzuela‐Palomo A, Esteban‐Sánchez A, Lorca V, Llinares‐Burguet I, Allen J, García‐Álvarez A, Pérez‐Segura P, Durán M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco‐Sampedro EA. Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants. J Pathol 2022; 258:83-101. [PMID: 35716007 PMCID: PMC9541484 DOI: 10.1002/path.5979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 12/29/2022]
Abstract
The ataxia telangiectasia-mutated (ATM) protein is a major coordinator of the DNA damage response pathway. ATM loss-of-function variants are associated with 2-fold increased breast cancer risk. We aimed at identifying and classifying spliceogenic ATM variants detected in subjects of the large-scale sequencing project BRIDGES. A total of 381 variants at the intron-exon boundaries were identified, 128 of which were predicted to be spliceogenic. After further filtering, we ended up selecting 56 variants for splicing analysis. Four functional minigenes (mgATM) spanning exons 4-9, 11-17, 25-29, and 49-52 were constructed in the splicing plasmid pSAD. Selected variants were genetically engineered into the four constructs and assayed in MCF-7/HeLa cells. Forty-eight variants (85.7%) impaired splicing, 32 of which did not show any trace of the full-length (FL) transcript. A total of 43 transcripts were identified where the most prevalent event was exon/multi-exon skipping. Twenty-seven transcripts were predicted to truncate the ATM protein. A tentative ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme that integrates mgATM data allowed us to classify 29 ATM variants as pathogenic/likely pathogenic and seven variants as likely benign. Interestingly, the likely pathogenic variant c.1898+2T>G generated 13% of the minigene FL-transcript due to the use of a noncanonical GG-5'-splice-site (0.014% of human donor sites). Circumstantial evidence in three ATM variants (leakiness uncovered by our mgATM analysis together with clinical data) provides some support for a dosage-sensitive expression model in which variants producing ≥30% of FL-transcripts would be predicted benign, while variants producing ≤13% of FL-transcripts might be pathogenic. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Inés Llinares‐Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética MolecularValladolidSpain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco‐Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
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8
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Lyon E, Temple-Smolkin RL, Hegde M, Gastier-Foster JM, Palomaki GE, Richards CS. An Educational Assessment of Evidence Used for Variant Classification: A Report of the Association for Molecular Pathology. J Mol Diagn 2022; 24:555-565. [PMID: 35429647 DOI: 10.1016/j.jmoldx.2021.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/12/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022] Open
Abstract
The Association for Molecular Pathology Variant Interpretation Testing Among Laboratories (VITAL) Working Group convened to evaluate the Standards and Guidelines for the Interpretation of Sequence Variants implementation into clinical practice, identify problematic classification rules, and define implementation challenges. Variants and associated clinical information were provided to volunteer respondents. Participant variant classifications were compared with intended consensus-derived classifications of the Working Group. The 24 variant challenges received 1379 responses; 1119 agreed with the intended response (81%; 95% CI, 79% to 83%). Agreement ranged from 44% to 100%, with 16 challenges (67%; 47% to 82%) reaching consensus (≥80% agreement). Participant classifications were also compared to a calculated interpretation of the ACMG Guidelines using the participant-reported criteria as input. The 24 variant challenges had 1368 responses with specific evidence provided and 1121 (82%; 80% to 84%) agreed with the calculated interpretation. Agreement for challenges ranged from 63% to 98%; 15 (63%; 43% to 79%) reaching consensus. Among 81 individual participants, 32 (40%; 30% to 50%) reached agreement with at least 80% of the intended classifications and 42 (52%; 41% to 62%) with the calculated classifications. This study demonstrated that although variant classification remains challenging, published guidelines are being utilized and adapted to improve variant calling consensus. This study identified situations where clarifications are warranted and provides a model for competency assessment.
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Affiliation(s)
- Elaine Lyon
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Madhuri Hegde
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Global Genetics Laboratory, PerkinElmer Genomics, Pittsburgh, Pennsylvania
| | - Julie M Gastier-Foster
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Departments of Pediatrics and Pathology/Immunology, Baylor College of Medicine, Houston, Texas; Pathology Department, Texas Children's Hospital, Houston, Texas; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | - Glenn E Palomaki
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Pathology and Laboratory Medicine, Women & Infants Hospital and the Alpert Medical School at Brown University, Providence, Rhode Island
| | - C Sue Richards
- The Variant Interpretation Testing Among Laboratories (VITAL) Working Group of the Clinical Practice Committee, Association for Molecular Pathology (AMP), Rockville, Maryland; Department of Molecular and Medical Genetics and Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon.
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9
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Ng PS, Boonen RA, Wijaya E, Chong CE, Sharma M, Knaup S, Mariapun S, Ho WK, Lim J, Yoon SY, Mohd Taib NA, See MH, Li J, Lim SH, Tan EY, Tan BKT, Tan SM, Tan VKM, van Dam RM, Rahmat K, Yip CH, Carvalho S, Luccarini C, Baynes C, Dunning AM, Antoniou A, van Attikum H, Easton DF, Hartman M, Teo SH. Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore. J Med Genet 2022; 59:481-491. [PMID: 33811135 PMCID: PMC9046754 DOI: 10.1136/jmedgenet-2020-107471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Rare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population. METHODS Mutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays. RESULTS PTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks. CONCLUSION Despite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations.
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Affiliation(s)
- Pei Sze Ng
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Rick Acm Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Chan Eng Chong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Milan Sharma
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Sabine Knaup
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Weang Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University of Nottingham - Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Joanna Lim
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Sook-Yee Yoon
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Mee Hoong See
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Swee Ho Lim
- Breast Department, KK Women's and Children's Hospital, Singapore
- Duke-NUS Breast Centre, Singhealth, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital Department of General Surgery, Singapore
| | - Veronique Kiat-Mien Tan
- Singhealth Duke-NUS Breast Centre, Singhealth, Singapore
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Rob Martinus van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Nutrition, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Kartini Rahmat
- Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care and Department of Oncology, University of Cambridge, Cambridge, UK
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- University Malaya Cancer Research Institute, University of Malaya Medical Centre, Kuala Lumpur, Wilayah Persekutuan, Malaysia
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10
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Valenzuela‐Palomo A, Bueno‐Martínez E, Sanoguera‐Miralles L, Lorca V, Fraile‐Bethencourt E, Esteban‐Sánchez A, Gómez‐Barrero S, Carvalho S, Allen J, García‐Álvarez A, Pérez‐Segura P, Dorling L, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Splicing predictions, minigene analyses, and ACMG-AMP clinical classification of 42 germline PALB2 splice-site variants. J Pathol 2022; 256:321-334. [PMID: 34846068 PMCID: PMC9306493 DOI: 10.1002/path.5839] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
PALB2 loss-of-function variants confer high risk of developing breast cancer. Here we present a systematic functional analysis of PALB2 splice-site variants detected in approximately 113,000 women in the large-scale sequencing project Breast Cancer After Diagnostic Gene Sequencing (BRIDGES; https://bridges-research.eu/). Eighty-two PALB2 variants at the intron-exon boundaries were analyzed with MaxEntScan. Forty-two variants were selected for the subsequent splicing functional assays. For this purpose, three splicing reporter minigenes comprising exons 1-12 were constructed. The 42 potential spliceogenic variants were introduced into the minigenes by site-directed mutagenesis and assayed in MCF-7/MDA-MB-231 cells. Splicing anomalies were observed in 35 variants, 23 of which showed no traces or minimal amounts of the expected full-length transcripts of each minigene. More than 30 different variant-induced transcripts were characterized, 23 of which were predicted to truncate the PALB2 protein. The pathogenicity of all variants was interpreted according to an in-house adaptation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) variant classification scheme. Up to 23 variants were classified as pathogenic/likely pathogenic. Remarkably, three ±1,2 variants (c.49-2A>T, c.108+2T>C, and c.211+1G>A) were classified as variants of unknown significance, as they produced significant amounts of either in-frame transcripts of unknown impact on the PALB2 protein function or the minigene full-length transcripts. In conclusion, we have significantly contributed to the ongoing effort of identifying spliceogenic variants in the clinically relevant PALB2 cancer susceptibility gene. Moreover, we suggest some approaches to classify the findings in accordance with the ACMG-AMP rationale. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alberto Valenzuela‐Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Elena Bueno‐Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Lara Sanoguera‐Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Víctor Lorca
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eugenia Fraile‐Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
- Knight Cancer Research BuildingPortlandORUSA
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | | | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Alicia García‐Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
| | - Pedro Pérez‐Segura
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Leila Dorling
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Peter Devilee
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maaike PG Vreeswijk
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética MolecularConsejo Superior de Investigaciones Científicas (CSIC‐UVa)ValladolidSpain
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11
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Bueno-Martínez E, Sanoguera-Miralles L, Valenzuela-Palomo A, Lorca V, Gómez-Sanz A, Carvalho S, Allen J, Infante M, Pérez-Segura P, Lázaro C, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants. Cancers (Basel) 2021; 13:2845. [PMID: 34200360 PMCID: PMC8201001 DOI: 10.3390/cancers13112845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
RAD51D loss-of-function variants increase lifetime risk of breast and ovarian cancer. Splicing disruption is a frequent pathogenic mechanism associated with variants in susceptibility genes. Herein, we have assessed the splicing and clinical impact of splice-site and exonic splicing enhancer (ESE) variants identified through the study of ~113,000 women of the BRIDGES cohort. A RAD51D minigene with exons 2-9 was constructed in splicing vector pSAD. Eleven BRIDGES splice-site variants (selected by MaxEntScan) were introduced into the minigene by site-directed mutagenesis and tested in MCF-7 cells. The 11 variants disrupted splicing, collectively generating 25 different aberrant transcripts. All variants but one produced negligible levels (<3.4%) of the full-length (FL) transcript. In addition, ESE elements of the alternative exon 3 were mapped by testing four overlapping exonic microdeletions (≥30-bp), revealing an ESE-rich interval (c.202_235del) with critical sequences for exon 3 recognition that might have been affected by germline variants. Next, 26 BRIDGES variants and 16 artificial exon 3 single-nucleotide substitutions were also assayed. Thirty variants impaired splicing with variable amounts (0-65.1%) of the FL transcript, although only c.202G>A demonstrated a complete aberrant splicing pattern without the FL transcript. On the other hand, c.214T>C increased efficiency of exon 3 recognition, so only the FL transcript was detected (100%). In conclusion, 41 RAD51D spliceogenic variants (28 of which were from the BRIDGES cohort) were identified by minigene assays. We show that minigene-based mapping of ESEs is a powerful approach for identifying ESE hotspots and ESE-disrupting variants. Finally, we have classified nine variants as likely pathogenic according to ACMG/AMP-based guidelines, highlighting the complex relationship between splicing alterations and variant interpretation.
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Affiliation(s)
- Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Alicia Gómez-Sanz
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Mar Infante
- Cancer Genetics, Unidad de Excelencia Instituto de Biología y Genética Molecular (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and CIBERONC, 08908 Hospitalet de Llobregat, Spain;
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Hospital Clinico San Carlos, 28040 Madrid, Spain; (V.L.); (A.G.-S.); (P.P.-S.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer Laboratory, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (E.B.-M.); (L.S.-M.); (A.V.-P.)
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12
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
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13
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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14
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Leman R, Harter V, Atkinson A, Davy G, Rousselin A, Muller E, Castéra L, Lemoine F, de la Grange P, Guillaud-Bataille M, Vaur D, Krieger S. SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data. Bioinformatics 2020; 36:1634-1636. [PMID: 31617569 DOI: 10.1093/bioinformatics/btz784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/06/2019] [Accepted: 10/14/2019] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Alternative splicing is an important biological process widely analyzed in molecular diagnostic settings. Indeed, a variant can be pathogenic by splicing alteration and a suspected pathogenic variant (e.g. truncating variant) can be rescued by splicing. In this context, detecting and quantifying alternative splicing is challenging. We developed SpliceLauncher, a fast and easy to use open source tool that aims at detecting, annotating and quantifying alternative splice junctions at high resolution. AVAILABILITY AND IMPLEMENTATION SpliceLauncher is available at https://github.com/raphaelleman/SpliceLauncher. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen 76031, France.,Normandie Univ, UNICAEN, Caen 14000, France
| | - Valentin Harter
- Centre de Traitement des Données du Cancéropôle Nord-Ouest, Plateforme de Recherche Clinique Ligue Contre le Cancer, Centre François Baclesse, 3 Avenue Général Harris, 14076 Caen, Cedex 5, France
| | - Alexandre Atkinson
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France
| | - Grégoire Davy
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen 76031, France.,Normandie Univ, UNICAEN, Caen 14000, France
| | - Antoine Rousselin
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France
| | - Etienne Muller
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France
| | - Laurent Castéra
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen 76031, France.,Normandie Univ, UNICAEN, Caen 14000, France
| | - Fréderic Lemoine
- Unité Bioinformatique Evolutive.,Hub Bioinformatique et Biostatistique, C3BI USR 3756, Institut Pasteur & CNRS, Paris, France
| | | | | | - Dominique Vaur
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen 76031, France.,Normandie Univ, UNICAEN, Caen 14000, France
| | - Sophie Krieger
- Laboratoire de biologie et de génétique du cancer, Centre François Baclesse, Caen 14076, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, Rouen 76031, France.,Normandie Univ, UNICAEN, Caen 14000, France
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15
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Boonen RACM, Vreeswijk MPG, van Attikum H. Functional Characterization of PALB2 Variants of Uncertain Significance: Toward Cancer Risk and Therapy Response Prediction. Front Mol Biosci 2020; 7:169. [PMID: 33195396 PMCID: PMC7525363 DOI: 10.3389/fmolb.2020.00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years it has become clear that pathogenic variants in PALB2 are associated with a high risk for breast, ovarian and pancreatic cancer. However, the clinical relevance of variants of uncertain significance (VUS) in PALB2, which are increasingly identified through clinical genetic testing, is unclear. Here we review recent advances in the functional characterization of VUS in PALB2. A combination of assays has been used to assess the impact of PALB2 VUS on its function in DNA repair by homologous recombination, cell cycle regulation and the control of cellular levels of reactive oxygen species (ROS). We discuss the outcome of this comprehensive analysis of PALB2 VUS, which showed that VUS in PALB2’s Coiled-Coil (CC) domain can impair the interaction with BRCA1, whereas VUS in its WD40 domain affect PALB2 protein stability. Accordingly, the CC and WD40 domains of PALB2 represent hotspots for variants that impair PALB2 protein function. We also provide a future perspective on the high-throughput analysis of VUS in PALB2, as well as the functional characterization of variants that affect PALB2 RNA splicing. Finally, we discuss how results from these functional assays can be valuable for predicting cancer risk and responsiveness to cancer therapy, such as treatment with PARP inhibitor- or platinum-based chemotherapy.
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Affiliation(s)
- Rick A C M Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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16
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Gailite L, Valenzuela-Palomo A, Sanoguera-Miralles L, Rots D, Kreile M, Velasco EA. UGT1A1 Variants c.864+5G>T and c.996+2_996+5del of a Crigler-Najjar Patient Induce Aberrant Splicing in Minigene Assays. Front Genet 2020; 11:169. [PMID: 32211025 PMCID: PMC7067894 DOI: 10.3389/fgene.2020.00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/12/2020] [Indexed: 11/13/2022] Open
Abstract
A large fraction of DNA variants impairs pre-mRNA splicing in human hereditary disorders. Crigler-Najjar syndrome (CNS) is characterized by a severe unconjugated hyperbilirubinemia caused by variants in the UGT1A1 gene. We previously reported one CNS-type II patient with two splice-site variants in trans (c.864+5G>T and c.996+2_996+5del). According to MaxEntScan, both disrupt their corresponding donor sites (c.864+5G>T: 6.99 → 2.28; c.996+2_996+5del: 5.96 → -11.02), so they were selected for subsequent functional tests. Given the unavailability of patient RNA, we constructed an UGT1A1 splicing-reporter minigene with exons 1-4 to characterize the underlying splicing anomaly. The variant c.996+2_996+5del generated two aberrant transcripts, Δ(E2) (exon 2 skipping/64%) and ▼(E2q135) (intron retention of 135-nt/36%), which lead to the loss of 18 conserved amino-acids and the gain of 45 new ones of a critical functional domain, respectively. The c.864+5G>T variant mainly produced the aberrant transcript Δ(E1q141) (141-nt deletion/70.4%) and the full-length isoform (29.6%). Δ(E1q141) would provoke the loss of 47 amino-acids of the N-terminal domain that encodes for substrate specificity. Thus, the three anomalous transcripts are likely to inactivate UGT1A1. Moreover, this patient is also homozygous for the promoter variant A(TA)7TAA that decreases UGT1A1 expression by 70%, so the full-length transcript produced by c.864+5G>T would be even more reduced (<9%), thus supporting the diagnosis of CNS-type II. Therefore, minigenes represent valuable tools for the functional and clinical classifications of genetic variants.
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Affiliation(s)
- Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Madara Kreile
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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17
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Walker LC, Lattimore VL, Kvist A, Kleiblova P, Zemankova P, de Jong L, Wiggins GAR, Hakkaart C, Cree SL, Behar R, Houdayer C, Investigators KC, Parsons MT, Kennedy MA, Spurdle AB, de la Hoya M. Comprehensive Assessment of BARD1 Messenger Ribonucleic Acid Splicing With Implications for Variant Classification. Front Genet 2019; 10:1139. [PMID: 31803232 PMCID: PMC6877745 DOI: 10.3389/fgene.2019.01139] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
Introduction: Case-control analyses have shown BARD1 variants to be associated with up to >2-fold increase in risk of breast cancer, and potentially greater risk of triple negative breast cancer. BARD1 is included in several gene sequencing panels currently marketed for the prediction of risk of cancer, however there are no gene-specific guidelines for the classification of BARD1 variants. We present the most comprehensive assessment of BARD1 messenger RNA splicing, and demonstrate the application of these data for the classification of truncating and splice site variants according to American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines. Methods: Nanopore sequencing, short-read RNA-seq (whole transcriptome and targeted), and capillary electrophoresis analysis were performed by four laboratories to investigate alternative BARD1 splicing in blood, breast, and fimbriae/ovary related specimens from non-cancer affected tissues. Splicing data were also collated from published studies of nine different tissues. The impact of the findings for PVS1 annotation was assessed for truncating and splice site variants. Results: We identified 62 naturally occurring alternative spliced BARD1 splicing events, including 19 novel events found by next generation sequencing and/or reverse transcription PCR analysis performed for this study. Quantitative analysis showed that naturally occurring splicing events causing loss of clinically relevant domains or nonsense mediated decay can constitute up to 11.9% of overlapping natural junctions, suggesting that aberrant splicing can be tolerated up to this level. Nanopore sequencing of whole BARD1 transcripts characterized 16 alternative isoforms from healthy controls, revealing that the most complex transcripts combined only two alternative splicing events. Bioinformatic analysis of ClinVar submitted variants at or near BARD1 splice sites suggest that all consensus splice site variants in BARD1 should be considered likely pathogenic, with the possible exception of variants at the donor site of exon 5. Conclusions: No BARD1 candidate rescue transcripts were identified in this study, indicating that all premature translation-termination codons variants can be annotated as PVS1. Furthermore, our analysis suggests that all donor and acceptor (IVS+/-1,2) variants can be considered PVS1 or PVS1_strong, with the exception of variants targeting the exon 5 donor site, that we recommend considering as PVS1_moderate.
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Affiliation(s)
- Logan C. Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Petra Kleiblova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czechia
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czechia
| | - Lucy de Jong
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - George A. R. Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Christopher Hakkaart
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L. Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Raquel Behar
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - kConFab Investigators
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Research Department, Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Michael T. Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Martin A. Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
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18
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Caloca MJ, Gómez-Barrero S, Velasco EA. Minigene Splicing Assays Identify 12 Spliceogenic Variants of BRCA2 Exons 14 and 15. Front Genet 2019; 10:503. [PMID: 31191615 PMCID: PMC6546720 DOI: 10.3389/fgene.2019.00503] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
A relevant fraction of BRCA2 variants is associated with splicing alterations and with an increased risk of hereditary breast and ovarian cancer (HBOC). In this work, we have carried out a thorough study of variants from BRCA2 exons 14 and 15 reported at mutation databases. A total of 294 variants from exons 14 and 15 and flanking intronic sequences were analyzed with the online splicing tools NNSplice and Human Splicing Finder. Fifty-three out of these 294 variants were selected as candidate splicing variants. All variants but one, were introduced into the minigene MGBR2_ex14-20 (with exons 14–20) by site-directed mutagenesis and assayed in MCF-7 cells. Twelve of the remaining 52 variants (23.1%) impaired splicing at different degrees, yielding from 5 to 100% of aberrant transcripts. Nine variants affected the natural acceptor or donor sites of both exons and three affected putative enhancers or silencers. Fluorescent capillary electrophoresis revealed at least 10 different anomalous transcripts: (E14q5), Δ (E14p10), Δ(E14p246), Δ(E14q256), Δ(E14), Δ(E15p12), Δ(E15p13), Δ(E15p83), Δ(E15) and a 942-nt fragment of unknown structure. All transcripts, except for Δ(E14q256) and Δ(E15p12), are expected to truncate the BRCA2 protein. Nine variants induced severe splicing aberrations with more than 90% of abnormal transcripts. Thus, according to the guidelines of the American College of Medical Genetics and Genomics, eight variants should be classified as pathogenic (c.7008-2A > T, c.7008-1G > A, c.7435+1G > C, c.7436-2A > T, c.7436-2A > G, c.7617+1G > A, c.7617+1G > T, and c.7617+2T > G), one as likely pathogenic (c.7008-3C > G) and three remain as variants of uncertain clinical significance or VUS (c.7177A > G, c.7447A > G and c.7501C > T). In conclusion, functional assays by minigenes constitute a valuable strategy to primarily check the splicing impact of DNA variants and their clinical interpretation. While bioinformatics predictions of splice site variants were accurate, those of enhancer or silencer variants were poor (only 3/23 spliceogenic variants) which showed weak impacts on splicing (∼5–16% of aberrant isoforms). So, the Exonic Splicing Enhancer and Silencer (ESE and ESS, respectively) prediction algorithms require further improvement.
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Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - María José Caloca
- Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | | | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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