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Zhang Y, Qu W, Yan R, Liu H, Zhang C, Li Z, Dong G. A reliable and quick method for screening alternative splicing variants for low-abundance genes. PLoS One 2024; 19:e0305201. [PMID: 38935635 PMCID: PMC11210779 DOI: 10.1371/journal.pone.0305201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
Alternative splicing (AS) is a universal phenomenon in eukaryotes, and it is still challenging to identify AS events. Several methods have been developed to identify AS events, such as expressed sequence tags (EST), microarrays and RNA-seq. However, EST has limitations in identifying low-abundance genes, while microarray and RNA-seq are high-throughput technologies, and PCR-based technology is needed for validation. To overcome the limitations of EST and shortcomings of high-throughput technologies, we established a method to identify AS events, especially for low-abundance genes, by reverse transcription (RT) PCR with gene-specific primers (GSPs) followed by nested PCR. This process includes two major steps: 1) the use of GSPs to amplify as long as the specific gene segment and 2) multiple rounds of nested PCR to screen the AS and confirm the unknown splicing variants. With this method, we successfully identified three new splicing variants, namely, GenBank Accession No. HM623886 for the bdnf gene (GenBank GeneID: 12064), GenBank Accession No. JF417977 for the trkc gene (GenBank GeneID: 18213) and GenBank Accession No. HM623888 for the glb-18 gene (GenBank GeneID: 172485). In addition to its reliability and simplicity, the method is also cost-effective and labor-intensive. In conclusion, we developed an RT-nested PCR method using gene-specific primers to efficiently identify known and novel AS variants. This approach overcomes the limitations of existing methods for detecting rare transcripts. By enabling the discovery of new isoforms, especially for low-abundance genes, this technique can aid research into aberrant splicing in disease. Future studies can apply this method to uncover AS variants involved in cancer, neurodegeneration, and other splicing-related disorders.
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Affiliation(s)
- Yanchun Zhang
- Department of Blood Transfusion Medicine, The Seventh Medical Center of PLA General Hospital, Beijing, China
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Wubin Qu
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Ruifen Yan
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
- College of Life Science, Northwest Agriculture and Forest University, Yangling, China
| | - Huqi Liu
- College of Life Science, Northwest Agriculture and Forest University, Yangling, China
| | - Chenggang Zhang
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Zhihui Li
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Guofu Dong
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
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2
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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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3
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Ning Y, Zhang Y, Tian T, Chen Y, Wang J, Lei K, Cui Z. Reclassifying BRCA1 c.4358-2A > G and BRCA2 c.475 + 5G > C variants from "Uncertain Significance" to "Pathogenic" based on minigene assays and clinical evidence. J Cancer Res Clin Oncol 2024; 150:62. [PMID: 38300310 PMCID: PMC10834553 DOI: 10.1007/s00432-023-05597-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND Pathogenic variants in BRCA genes play a crucial role in the pathogenesis of ovarian cancer. Intronic variants of uncertain significance (VUS) may contribute to pathogenicity by affecting splicing. Currently, the significance of many intronic variants in BRCA has not been clarified, impacting patient treatment strategies and the management of familial cases. METHOD A retrospective study was conducted to analyze BRCA intronic VUS in a cohort of 707 unrelated ovarian cancer patients at a single institution from 2018 to 2023. Three splicing predictors were employed to analyze detected intronic VUS. Variants predicted to have splicing alterations were selected for further validation through minigene assays. Patient and familial investigations were conducted to comprehend cancer incidence within pedigrees and the application of poly (ADP-ribose) polymerase inhibitors (PARPi) by the patients. In accordance with the guidelines of the American College of Medical Genetics and Genomics (ACMG), the intronic VUS were reclassified based on minigene assay results and clinical evidence. RESULT Approximately 9.8% (69/707) of patients were identified as carriers of 67 different VUS in BRCA1/2, with four intronic variants accounting for 6% (4/67) of all VUS. Splicing predictors indicated potential splicing alterations in splicing for BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C variants. Minigene assays utilizing the pSPL3 exon trapping vector revealed that these variants induced changes in splicing sites and frameshift, resulting in premature termination of translation (p. Ala1453Glyfs and p. Pro143Glyfs). According to ACMG guidelines, BRCA1 c.4358-2A>G and BRCA2 c.475+5G>C were reclassified as pathogenic variants. Pedigree investigations were conducted on patients with BRCA1 c.4358-2A>G variant, and the detailed utilization of PARPi provided valuable insights into research on PARPi resistance. CONCLUSION Two intronic VUS were reclassified as pathogenic variants. A precise classification of variants is crucial for the effective treatment and management of both patients and healthy carriers.
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Affiliation(s)
- Ying Ning
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Yu Zhang
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Tian Tian
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Yu Chen
- Department of Clinical Medicine, Qingdao University, Qingdao, 266003, China
| | - Jia Wang
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China
| | - Ke Lei
- Center of Tumor Immunology and Cytotherapy, Medical Research Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, No. 59 Haier Road, Laoshan District, Qingdao, 266000, China.
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4
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clin Chem 2024; 70:319-338. [PMID: 37725924 DOI: 10.1093/clinchem/hvad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Disrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast cancer susceptibility gene CHEK2 by splicing reporter minigenes. METHODS A total of 128 CHEK2 splice-site variants identified in the Breast Cancer After Diagnostic Gene Sequencing (BRIDGES) project (https://cordis.europa.eu/project/id/634935) were analyzed with MaxEntScan and subsetted to 52 variants predicted to impact splicing. Three CHEK2 minigenes, which span all 15 exons, were constructed and validated. The 52 selected variants were then genetically engineered into the minigenes and assayed in MCF-7 (human breast adenocarcinoma) cells. RESULTS Of 52 variants, 46 (88.5%) impaired splicing. Some of them led to complex splicing patterns with up to 11 different transcripts. Thirty-four variants induced splicing anomalies without any trace or negligible amounts of the full-length transcript. A total of 89 different transcripts were annotated, which derived from different events: single- or multi-exon skipping, alternative site-usage, mutually exclusive exon inclusion, intron retention or combinations of the abovementioned events. Fifty-nine transcripts were predicted to introduce premature termination codons, 7 kept the original open-reading frame, 5 removed the translation start codon, 6 affected the 5'UTR (Untranslated Region), and 2 included missense variations. Analysis of variant c.684-2A > G revealed the activation of a non-canonical TG-acceptor site and exon 6 sequences critical for its recognition. CONCLUSIONS Incorporation of minigene read-outs into an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme allowed us to classify 32 CHEK2 variants (27 pathogenic/likely pathogenic and 5 likely benign). However, 20 variants (38%) remained of uncertain significance, reflecting in part the complex splicing patterns of this gene.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, 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 Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 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-Universidad de Valladolid (CSIC-UVa), 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-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
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, Cambridge, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - 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 Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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5
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Sahu S, Sullivan TL, Mitrophanov AY, Galloux M, Nousome D, Southon E, Caylor D, Mishra AP, Evans CN, Clapp ME, Burkett S, Malys T, Chari R, Biswas K, Sharan SK. Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. PLoS Genet 2023; 19:e1010940. [PMID: 37713444 PMCID: PMC10529611 DOI: 10.1371/journal.pgen.1010940] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/27/2023] [Accepted: 08/28/2023] [Indexed: 09/17/2023] Open
Abstract
The unknown pathogenicity of a significant number of variants found in cancer-related genes is attributed to limited epidemiological data, resulting in their classification as variant of uncertain significance (VUS). To date, Breast Cancer gene-2 (BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determine their functional significance. Here we report the use of a humanized-mouse embryonic stem cell (mESC) line expressing a single copy of the human BRCA2 for a CRISPR-Cas9-based high-throughput functional assay. As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. Specifically, we used a pool of 180-mer single-stranded donor DNA to generate all possible combination of variants. Using a high throughput sequencing-based approach, we show a significant drop in the frequency of non-functional variants, whereas functional variants are enriched in the pool of the cells. We further demonstrate the response of these variants to the DNA-damaging agents, cisplatin and olaparib, allowing us to use cellular survival and drug response as parameters for variant classification. Using this approach, we have categorized 599 BRCA2 variants including 93-single nucleotide variants (SNVs) across the 11 codons, of which 28 are reported in ClinVar. We also functionally categorized 252 SNVs from exon 13 into 188 functional and 60 non-functional variants, demonstrating that saturation genome editing (SGE) coupled with drug sensitivity assays can enhance functional annotation of BRCA2 VUS.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Teresa L. Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | | | - Darryl Nousome
- CCR Bioinformatics Resource, Leidos Biomedical Sciences, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Dylan Caylor
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michelle E. Clapp
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
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6
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Thomassen M, Mesman RLS, Hansen TVO, Menendez M, Rossing M, Esteban‐Sánchez A, Tudini E, Törngren T, Parsons MT, Pedersen IS, Teo SH, Kruse TA, Møller P, Borg Å, Jensen UB, Christensen LL, Singer CF, Muhr D, Santamarina M, Brandao R, Andresen BS, Feng B, Canson D, Richardson ME, Karam R, Pesaran T, LaDuca H, Conner BR, Abualkheir N, Hoang L, Calléja FMGR, Andrews L, James PA, Bunyan D, Hamblett A, Radice P, Goldgar DE, Walker LC, Engel C, Claes KBM, Macháčková E, Baralle D, Viel A, Wappenschmidt B, Lazaro C, Vega A, Vreeswijk MPG, de la Hoya M, Spurdle AB. Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants: Application of a points-based ACMG/AMP approach. Hum Mutat 2022; 43:1921-1944. [PMID: 35979650 PMCID: PMC10946542 DOI: 10.1002/humu.24449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.
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Affiliation(s)
- Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Romy L. S. Mesman
- Department of Human GeneticsLeiden University Medical CenterLeidenthe Netherlands
| | - Thomas V. O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Mireia Menendez
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Maria Rossing
- Center for Genomic Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Therese Törngren
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Inge S. Pedersen
- Molecular Diagnostics, Aalborg University HospitalAalborgDenmark
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
- Department of Clinical MedicineAalborg UniversityAalborgDenmark
| | - Soo H. Teo
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
- Department of Surgery, Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Pål Møller
- Department of Tumour BiologyThe Norwegian Radium Hospital, Oslo University HospitalOsloNorway
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Uffe B. Jensen
- Department of Clinical GeneticsAarhus University HospitalAarhus NDenmark
| | | | - Christian F. Singer
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Daniela Muhr
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Marta Santamarina
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - Rita Brandao
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Bing‐Jian Feng
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Daffodil Canson
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | | | | | | | | | | | | | | | - Lesley Andrews
- Hereditary Cancer Clinic, Nelune Comprehensive Cancer Care CentreSydneyNew South WalesAustralia
| | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Dave Bunyan
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Amanda Hamblett
- Middlesex Health Shoreline Cancer CenterWestbrookConnecticutUSA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of ResearchFondazione IRCCS Istituto Nazionale dei Tumori (INT)MilanItaly
| | - David E. Goldgar
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | | | - Eva Macháčková
- Department of Cancer Epidemiology and GeneticsMasaryk Memorial Cancer InstituteBrnoCzech Republic
| | - Diana Baralle
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Alessandra Viel
- Division of Functional Onco‐genomics and GeneticsCentro di Riferimento Oncologico di Aviano (CRO), IRCCSAvianoItaly
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Conxi Lazaro
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Ana Vega
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - ENIGMA Consortium
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
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7
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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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8
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Minigene Splicing Assays Identify 20 Spliceogenic Variants of the Breast/Ovarian Cancer Susceptibility Gene RAD51C. Cancers (Basel) 2022; 14:cancers14122960. [PMID: 35740625 PMCID: PMC9221245 DOI: 10.3390/cancers14122960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
RAD51C loss-of-function variants are associated with an increased risk of breast and ovarian cancers. Likewise, splicing disruptions are a frequent mechanism of gene inactivation. Taking advantage of a previous splicing-reporter minigene with exons 2-8 (mgR51C_ex2-8), we proceeded to check its impact on the splicing of candidate ClinVar variants. A total of 141 RAD51C variants at the intron/exon boundaries were analyzed with MaxEntScan. Twenty variants were selected and genetically engineered into the wild-type minigene. All the variants disrupted splicing, and 18 induced major splicing anomalies without any trace or minimal amounts (<2.4%) of the minigene full-length (FL) transcript. Twenty-seven transcripts (including the wild-type and r.904A FL transcripts) were identified by fluorescent fragment electrophoresis; of these, 14 were predicted to truncate the RAD51C protein, 3 kept the reading frame, and 8 minor isoforms (1.1−4.7% of the overall expression) could not be characterized. Finally, we performed a tentative interpretation of the variants according to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, classifying 16 variants as likely pathogenic. Minigene assays have been proven as valuable tools for the initial characterization of potential spliceogenic variants. Hence, minigene mgR51C_ex2-8 provided useful splicing data for 40 RAD51C variants.
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9
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Discovery of BRCA1/BRCA2 Founder Variants by Haplotype Analysis. Cancer Genet 2022; 266-267:19-27. [DOI: 10.1016/j.cancergen.2022.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 11/20/2022]
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10
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Kaissarian NM, Meyer D, Kimchi-Sarfaty C. Synonymous Variants: Necessary Nuance in our Understanding of Cancer Drivers and Treatment Outcomes. J Natl Cancer Inst 2022; 114:1072-1094. [PMID: 35477782 PMCID: PMC9360466 DOI: 10.1093/jnci/djac090] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/24/2022] [Accepted: 04/18/2022] [Indexed: 11/13/2022] Open
Abstract
Once called "silent mutations" and assumed to have no effect on protein structure and function, synonymous variants are now recognized to be drivers for some cancers. There have been significant advances in our understanding of the numerous mechanisms by which synonymous single nucleotide variants (sSNVs) can affect protein structure and function by affecting pre-mRNA splicing, mRNA expression, stability, folding, miRNA binding, translation kinetics, and co-translational folding. This review highlights the need for considering sSNVs in cancer biology to gain a better understanding of the genetic determinants of human cancers and to improve their diagnosis and treatment. We surveyed the literature for reports of sSNVs in cancer and found numerous studies on the consequences of sSNVs on gene function with supporting in vitro evidence. We also found reports of sSNVs that have statistically significant associations with specific cancer types but for which in vitro studies are lacking to support the reported associations. Additionally, we found reports of germline and somatic sSNVs that were observed in numerous clinical studies and for which in silico analysis predicts possible effects on gene function. We provide a review of these investigations and discuss necessary future studies to elucidate the mechanisms by which sSNVs disrupt protein function and are play a role in tumorigeneses, cancer progression, and treatment efficacy. As splicing dysregulation is one of the most well recognized mechanisms by which sSNVs impact protein function, we also include our own in silico analysis for predicting which sSNVs may disrupt pre-mRNA splicing.
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Affiliation(s)
- Nayiri M Kaissarian
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US Food and Drug Administration, Silver Spring, MD, USA
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11
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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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12
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Li J, Wang P, Zhang C, Han S, Xiao H, Liu Z, Wang X, Liu W, Wei B, Ma J, Li H, Guo Y. Characterization of Synonymous BRCA1:c.132C>T as a Pathogenic Variant. Front Oncol 2022; 11:812656. [PMID: 35087763 PMCID: PMC8789006 DOI: 10.3389/fonc.2021.812656] [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: 11/10/2021] [Accepted: 12/08/2021] [Indexed: 11/26/2022] Open
Abstract
Breast cancer gene 1 (BRCA1) and BRCA2 are tumor suppressors involved in DNA damage response and repair. Carriers of germline pathogenic or likely pathogenic variants in BRCA1 or BRCA2 have significantly increased lifetime risks of breast cancer, ovarian cancer, and other cancer types; this phenomenon is known as hereditary breast and ovarian cancer (HBOC) syndrome. Accurate interpretation of BRCA1 and BRCA2 variants is important not only for disease management in patients, but also for determining preventative measures for their families. BRCA1:c.132C>T (p.Cys44=) is a synonymous variant recorded in the ClinVar database with “conflicting interpretations of its pathogenicity”. Here, we report our clinical tests in which we identified this variant in two unrelated patients, both of whom developed breast cancer at an early age with ovarian presentation a few years later and had a family history of relevant cancers. Minigene assay showed that this change caused a four-nucleotide loss at the end of exon 3, resulting in a truncated p.Cys44Tyrfs*5 protein. Reverse transcription-polymerase chain reaction identified two fragments (123 and 119 bp) using RNA isolated from patient blood samples, in consistency with the results of the minigene assay. Collectively, we classified BRCA1:c.132C>T (p.Cys44=) as a pathogenic variant, as evidenced by functional studies, RNA analysis, and the patients’ family histories. By analyzing variants recorded in the BRCA Exchange database, we found synonymous changes at the ends of exons could potentially influence splicing; meanwhile, current in silico tools could not predict splicing changes efficiently if the variants were in the middle of an exon, or in the deep intron region. Future studies should attempt to identify variants that influence gene expression and post-transcription modifications to improve our understanding of BRCA1 and BRCA2, as well as their related cancers.
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Affiliation(s)
- Jun Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Ping Wang
- Department of Pathophysiology, School of Basic Medical Science, Zhengzhou University, Zhengzhou, China
| | - Cuiyun Zhang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Sile Han
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Han Xiao
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiyuan Liu
- Amoy Diagnostics Co., Ltd. (AmoyDx), Xiamen, China
| | - Xiaoyan Wang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Weiling Liu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzou, China
| | - Bing Wei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
| | - Hongle Li
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Key Laboratory of Molecular Pathology, Zhengzhou, China.,Henan International Joint Laboratory of Cancer Genetics, Zhengzhou, China
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13
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Liu Q, Zhang H, Yang X, Liu X, Yin F, Guo P, Yin Y, Zheng K, Yang Z, Han Y. Systemic characterization of alternative splicing related to prognosis, immune infiltration, and drug sensitivity analysis in ovarian cancer. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:126. [PMID: 35282039 PMCID: PMC8848412 DOI: 10.21037/atm-21-6422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Background Alternative splicing (AS) plays an essential role in tumorigenesis and progression. This study intended to construct an innovative prognostic model based on AS events to gain more precise survival prediction and search for potential therapeutic targets in ovarian cancer. Methods Seven types of AS events in ovarian serous cystadenocarcinoma (OV) patients with RNA-seq were obtained using The Cancer Genome Atlas (TCGA) SpliceSeq tool and database. Cox and Kaplan-Meier curve analyses were employed to establish the prognostic models. Relying on drug sensitivity data from the CellMiner database, Genomics of Drug Sensitivity (GDS) was adopted to estimate the platinum-sensitive analysis. Furthermore, a prognostic splicing factor (SF)-AS network was constructed using Cytoscape. Finally, in order to explore the influence of the tumor microenvironment on the prognosis of OV patients, we first combined a similar network fusion and consensus clustering (SNF-CC) algorithm to identify three OV subtypes based on survival-related AS events and then utilized single-sample Gene Set Enrichment Analysis (ssGSEA) method to perform immune cell infiltration analysis. Results A total of 48,049 AS events and 21,841 related genes were selected from 318 OV samples, and 2,206 AS events associated with disease-free survival (DFS) were identified. Multivariate Cox and Kaplan-Meier curve analyses were then employed to establish the prognostic models. Receiver operating characteristic (ROC) analysis from 0.59 to 0.75 showed that these models were highly efficient in distinguishing patient survival. GDS was adopted with the CellMiner database to provide some insights for platinum-sensitive analysis of OV. Furthermore, a prognostic SF-AS network, which discovered a significant connection between SFs and prognostic AS genes, was constructed using Cytoscape. The combined SNF-CC algorithm revealed three distinct OV subtypes based on the prognostic AS events, and the associations between this novel molecular classification and immune cell infiltration were further explored. Conclusions We developed a powerful prognostic AS signature for OV and provided a deeper understanding of SF-AS network regulatory mechanisms, as well as platinum-sensitive and cancer immune microenvironments. These results revealed various candidate biomarkers and potential targets for OV treatment strategies.
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Affiliation(s)
- Qingyang Liu
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Hao Zhang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xiaocheng Yang
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Xuesong Liu
- School of Health Professions, Yingkou Vocational and Technical College, Yingkou, China
| | - Fanxing Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Panpan Guo
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Yuhan Yin
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Kaijiang Zheng
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
| | - Zhuo Yang
- Department of Gynecology, Cancer Hospital of Dalian University of Technology (Liaoning Cancer Hospital & Institute), Shenyang, China
| | - Yanshuo Han
- School of Life and Pharmaceutical Science, Dalian University of Technology, Dalian, China
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14
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Zhang D, Zou D, Deng Y, Yang L. Systematic analysis of the relationship between ovarian cancer prognosis and alternative splicing. J Ovarian Res 2021; 14:120. [PMID: 34526089 PMCID: PMC8442315 DOI: 10.1186/s13048-021-00866-1] [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: 05/02/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ovarian cancer(OC) is the gynecological tumor with the highest mortality rate, effective biomarkers are of great significance in improving its prognosis. In recent years, there have been many studies on alternative splicing (AS) events, and the role of AS events in tumor has become a focus of attention. Methods Data were downloaded from the TCGA database and Univariate Cox regression analysis was performed to determine AS events associated with OC prognosis.Eight prognostic models of OC were constructed in R package, and the accuracy of the models were evaluated by the time-dependent receiver operating characteristic (ROC) curves.Eight types of survival curves were drawn to evaluate the differences between the high and low risk groups.Independent prognostic factors of OC were analyzed by single factor independent analysis and multi-factor independent prognostic analysis.Again, Univariate Cox regression analysis was used to analyze the relationship between splicing factors(SF) and AS events, and Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis were performed on OS-related SFs to understand the pathways. Results Univariate Cox regression analysis showed that among the 15,278 genes, there were 31,286 overall survival (OS) related AS events, among which 1524 AS events were significantly correlated with OS. The area under the time-dependent receiver operating characteristic curve (AUC) of AT and ME were the largest and the RI was the smallest,which were 0.757 and 0.68 respectively. The constructed models have good value for the prognosis assessment of OC patients. Among the eight survival curves, AP was the most significant difference between the high and low risk groups, with a P value of 1.61e − 1.The results of single factor independent analysis and multi-factor independent prognostic analysis showed that risk score calculated by the model and age could be used as independent risk factors.According to univariate COX regression analysis,109 SFs were correlated with AS events and adjusted in two ways: positive and negative. Conclusions SFs and AS events can directly or indirectly affect the prognosis of OC patients. It is very important to find effective prognostic markers to improve the survival rate of OC. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00866-1.
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Affiliation(s)
- Di Zhang
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Dan Zou
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yue Deng
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lihua Yang
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
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15
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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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16
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Jimenez-Sainz J, Jensen RB. Imprecise Medicine: BRCA2 Variants of Uncertain Significance (VUS), the Challenges and Benefits to Integrate a Functional Assay Workflow with Clinical Decision Rules. Genes (Basel) 2021; 12:genes12050780. [PMID: 34065235 PMCID: PMC8161351 DOI: 10.3390/genes12050780] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022] Open
Abstract
Pathological mutations in homology-directed repair (HDR) genes impact both future cancer risk and therapeutic options for patients. HDR is a high-fidelity DNA repair pathway for resolving DNA double-strand breaks throughout the genome. BRCA2 is an essential protein that mediates the loading of RAD51 onto resected DNA breaks, a key step in HDR. Germline mutations in BRCA2 are associated with an increased risk for breast, ovarian, prostate, and pancreatic cancer. Clinical findings of germline or somatic BRCA2 mutations in tumors suggest treatment with platinum agents or PARP inhibitors. However, when genetic analysis reveals a variant of uncertain significance (VUS) in the BRCA2 gene, precision medicine-based decisions become complex. VUS are genetic changes with unknown pathological impact. Current statistics indicate that between 10–20% of BRCA sequencing results are VUS, and of these, more than 50% are missense mutations. Functional assays to determine the pathological outcome of VUS are urgently needed to provide clinical guidance regarding cancer risk and treatment options. In this review, we provide a brief overview of BRCA2 functions in HDR, describe how BRCA2 VUS are currently assessed in the clinic, and how genetic and biochemical functional assays could be integrated into the clinical decision process. We suggest a multi-step workflow composed of robust and accurate functional assays to correctly evaluate the potential pathogenic or benign nature of BRCA2 VUS. Success in this precision medicine endeavor will offer actionable information to patients and their physicians.
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Affiliation(s)
- Judit Jimenez-Sainz
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
| | - Ryan B. Jensen
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Correspondence: (J.J.-S.); (R.B.J.); Tel.:+1-203-737-6456 (R.B.J.)
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17
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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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18
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Nix P, Mundt E, Manley S, Coffee B, Roa B. Functional RNA Studies Are a Useful Tool in Variant Classification but Must Be Used With Caution: A Case Study of One BRCA2 Variant. JCO Precis Oncol 2020; 4:730-735. [PMID: 35050751 DOI: 10.1200/po.20.00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Paola Nix
- Myriad Genetic Laboratories, Salt Lake City, UT
| | - Erin Mundt
- Myriad Genetic Laboratories, Salt Lake City, UT
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19
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Lin X, Nagl S. A microfluidic chip for rapid analysis of DNA melting curves for BRCA2 mutation screening. LAB ON A CHIP 2020; 20:3824-3831. [PMID: 32926049 DOI: 10.1039/d0lc00624f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A microfluidic chip integrated with a microheater and a luminescent temperature sensor for rapid, spatial melting curve analysis was developed and applied for the screening of a breast cancer gene fragment. The method could detect genetic differences in around 3 minutes total for the whole procedure, which is much faster than established procedures. A microfabrication technique was developed to allow for bonding of a temperature sensing thin film and a Pt microheater with PDMS and the chips could be employed to generate and measure thermal gradients and the fluorescence intensity of stained DNA through multispectral optical imaging. The sensing layer consisting of poly(styrene-co-acrylonitrile) and a tris(1,10-phenanthroline)ruthenium(ii) temperature probe was generated by blade coating on a glass substrate with an attached Pt microheater. Calibration of the temperature between 20 and 90 °C yielded an overall resolution of around 0.13 K. The chip was employed for the screening of the BRCA 2 breast cancer gene; BRCA2 exon 5 was differentiated by its mutant rs80359463 by a 1.1 K difference in melting temperature and two fragments of BRCA2 exon 11 were differentiated by their mutants rs276174826 and rs876660311 by 0.7 K and 2.0 K, respectively. The standard deviations were between 0.1 and 0.5 K. Capable of detecting fluorescence in the DNA and temperature simultaneously and being imaged in a customized assembly, this microchip can be used to screen for mutations in a variety of DNA samples in disease diagnosis and prognosis.
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Affiliation(s)
- Xuyan Lin
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
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20
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Pellarin I, Belletti B, Baldassarre G. RNA splicing alteration in the response to platinum chemotherapy in ovarian cancer: A possible biomarker and therapeutic target. Med Res Rev 2020; 41:586-615. [PMID: 33058230 DOI: 10.1002/med.21741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/09/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022]
Abstract
Since its discovery, alternative splicing has been recognized as a powerful way for a cell to amplify the genetic information and for a living organism to adapt, evolve, and survive. We now know that a very high number of genes are regulated by alternative splicing and that alterations of splicing have been observed in different types of human diseases, including cancer. Here, we review the accumulating knowledge that links the regulation of alternative splicing to the response to chemotherapy, focusing our attention on ovarian cancer and platinum-based treatments. Moreover, we discuss how expanding information could be exploited to identify new possible biomarkers of platinum response, to better select patients, and/or to design new therapies able to overcome platinum resistance.
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Affiliation(s)
- Ilenia Pellarin
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
| | - Barbara Belletti
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
| | - Gustavo Baldassarre
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
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21
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Ryu JS, Lee HY, Cho EH, Yoon KA, Kim MK, Joo J, Lee ES, Kang HS, Lee S, Lee DO, Lim MC, Kong SY. Exon splicing analysis of intronic variants in multigene cancer panel testing for hereditary breast/ovarian cancer. Cancer Sci 2020; 111:3912-3925. [PMID: 32761968 PMCID: PMC7540976 DOI: 10.1111/cas.14600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022] Open
Abstract
The use of multigene panel testing for patients with a predisposition to breast/ovarian cancer is increasing as the identification of variants is useful for diagnosis and disease management. We identified pathogenic and likely pathogenic (P/LP) variants of high-and moderate-risk genes using a 23-gene germline cancer panel in 518 patients with hereditary breast and ovarian cancers (HBOC). The frequency of P/LP variants was 12.4% (64/518) for high- and moderate-penetrant genes, namely, BRCA2 (5.6%), BRCA1 (3.3%), CHEK2 (1.2%), MUTYH (0.8%), PALB2 (0.8%), MLH1 (0.4%), ATM (0.4%), BRIP1 (0.4%), TP53 (0.2%), and PMS2 (0.2%). Five patients possessed two P/LP variants in BRCA1/2 and other genes. We also compared the results from in silico splicing predictive tools and exon splicing patterns from patient samples by analyzing RT-PCR product sequences in six P/LP intronic variants and two intronic variants of unknown significance (VUS). Altered transcriptional fragments were detected for P/LP intronic variants in BRCA1, BRIP1, CHEK2, PARB2, and PMS2. Notably, we identified an in-frame deletion of the BRCA1 C-terminal (BRCT) domain by exon skipping in BRCA1 c.5152+6T>C-as known VUS-indicating a risk for HBOC. Thus, exon splicing analysis can improve the identification of veiled intronic variants that would aid decision making and determination of hereditary cancer risk.
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Affiliation(s)
- Jin-Sun Ryu
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea
| | - Hye-Young Lee
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea
| | - Eun Hae Cho
- Genomic research center, Green Cross Genome, Yongin, Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Min-Kyeong Kim
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea
| | - Jungnam Joo
- Division of Cancer Epidemiology and Management, Research Institute, National Cancer Center, Goyang, Korea
| | - Eun-Sook Lee
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Han-Sung Kang
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Seeyoun Lee
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Dong Ock Lee
- Center for Gynecologic Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Myong Cheol Lim
- Center for Gynecologic Cancer, Hospital, National Cancer Center, Goyang, Korea.,Division of Tumor Immunology and Center for Clinical Trial, Research Institute, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea.,Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
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22
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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23
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Canson D, Glubb D, Spurdle AB. Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 2020; 41:1705-1721. [PMID: 32623769 DOI: 10.1002/humu.24074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre-existing large-scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation.
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Affiliation(s)
- Daffodil Canson
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Dylan Glubb
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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24
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Tubeuf H, Caputo SM, Sullivan T, Rondeaux J, Krieger S, Caux-Moncoutier V, Hauchard J, Castelain G, Fiévet A, Meulemans L, Révillion F, Léoné M, Boutry-Kryza N, Delnatte C, Guillaud-Bataille M, Cleveland L, Reid S, Southon E, Soukarieh O, Drouet A, Di Giacomo D, Vezain M, Bonnet-Dorion F, Bourdon V, Larbre H, Muller D, Pujol P, Vaz F, Audebert-Bellanger S, Colas C, Venat-Bouvet L, Solano AR, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Gaildrat P, Sharan SK, Martins A. Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System. Cancer Res 2020; 80:3593-3605. [PMID: 32641407 DOI: 10.1158/0008-5472.can-20-0895] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
BRCA2 is a clinically actionable gene implicated in breast and ovarian cancer predisposition that has become a high priority target for improving the classification of variants of unknown significance (VUS). Among all BRCA2 VUS, those causing partial/leaky splicing defects are the most challenging to classify because the minimal level of full-length (FL) transcripts required for normal function remains to be established. Here, we explored BRCA2 exon 3 (BRCA2e3) as a model for calibrating variant-induced spliceogenicity and estimating thresholds for BRCA2 haploinsufficiency. In silico predictions, minigene splicing assays, patients' RNA analyses, a mouse embryonic stem cell (mESC) complementation assay and retrieval of patient-related information were combined to determine the minimal requirement of FL BRCA2 transcripts. Of 100 BRCA2e3 variants tested in the minigene assay, 64 were found to be spliceogenic, causing mild to severe RNA defects. Splicing defects were also confirmed in patients' RNA when available. Analysis of a neutral leaky variant (c.231T>G) showed that a reduction of approximately 60% of FL BRCA2 transcripts from a mutant allele does not cause any increase in cancer risk. Moreover, data obtained from mESCs suggest that variants causing a decline in FL BRCA2 with approximately 30% of wild-type are not pathogenic, given that mESCs are fully viable and resistant to DNA-damaging agents in those conditions. In contrast, mESCs producing lower relative amounts of FL BRCA2 exhibited either null or hypomorphic phenotypes. Overall, our findings are likely to have broader implications on the interpretation of BRCA2 variants affecting the splicing pattern of other essential exons. SIGNIFICANCE: These findings demonstrate that BRCA2 tumor suppressor function tolerates substantial reduction in full-length transcripts, helping to determine the pathogenicity of BRCA2 leaky splicing variants, some of which may not increase cancer risk.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Julie Rondeaux
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Sophie Krieger
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France - Normandie University, UNICAEN, Caen, France
| | | | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Gaia Castelain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alice Fiévet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France.,Service Génétique des Tumeurs, Gustave Roussy, Villejuif, France
| | - Laëtitia Meulemans
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | | | | | | | | | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Daniela Di Giacomo
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Myriam Vezain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Hélène Larbre
- Laboratoire d'Oncogénétique Moléculaire, Institut Godinot, Reims, France
| | - Danièle Muller
- Unité d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Fátima Vaz
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | | | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | | | - Angela R Solano
- Genotipificacion y Cancer Hereditario, Departmento de Analisis Clinicos, Centro de Educacion Medica e Investigaciones Clinicas (CEMIC), Ciudad Autonoma de Buenos Aires, Argentina
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
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25
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Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB. A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity. Bioinformatics 2020; 35:2315-2317. [PMID: 30475984 PMCID: PMC6596880 DOI: 10.1093/bioinformatics/bty960] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 10/29/2018] [Accepted: 11/22/2018] [Indexed: 02/02/2023] Open
Abstract
Summary Assessing the pathogenicity of genetic variants can be a complex and challenging task. Spliceogenic variants, which alter mRNA splicing, may yield mature transcripts that encode non-functional protein products, an important predictor of Mendelian disease risk. However, most variant annotation tools do not adequately assess spliceogenicity outside the native splice site and thus the disease-causing potential of variants in other intronic and exonic regions is often overlooked. Here, we present a plugin for the Ensembl Variant Effect Predictor that packages MaxEntScan and extends its functionality to provide splice site predictions using a maximum entropy model. The plugin incorporates a sliding window algorithm to predict splice site loss or gain for any variant that overlaps a transcript feature. We also demonstrate the utility of the plugin by comparing our predictions to two mRNA splicing datasets containing several cancer-susceptibility genes. Availability and implementation Source code is freely available under the Apache License, Version 2.0: https://github.com/Ensembl/VEP_plugins. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jannah Shamsani
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Stephen H Kazakoff
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Will McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Bryony A Thompson
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne VIC, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane QLD, Australia
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26
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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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27
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Li L, Cao Y, Zhao F, Mao B, Ren X, Wang Y, Guan Y, You Y, Li S, Yang T, Zhao X. Validation and Classification of Atypical Splicing Variants Associated With Osteogenesis Imperfecta. Front Genet 2019; 10:979. [PMID: 31737030 PMCID: PMC6832110 DOI: 10.3389/fgene.2019.00979] [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: 06/06/2019] [Accepted: 09/13/2019] [Indexed: 01/17/2023] Open
Abstract
Osteogenesis Imperfecta (OI) is a rare inherited bone dysplasia, which is mainly caused by mutations in genes encoding type I collagen including COL1A1 and COL1A2. It has been well established to identify the classical variants as well as consensus splicing-site-variants in these genes in our previous studies. However, how atypical variants affect splicing in OI patients remains unclear. From a cohort of 867 OI patients, we collected blood samples from 34 probands which contain 29 variants that are located close to splice donor/acceptor sites in either COL1A1 or COL1A2. By conducting minigene assay and sequencing analysis, we found that 17 out of 29 variants led to aberrant splicing effects, while no remarkable aberrant splicing effect was observed in the remaining 12 variants. Among the 17 variants that affect splicing, 14 variants led to single splicing influence: 9 led to exon skipping, 2 resulted in truncated exon, and 3 caused intron retention. There were three complicated cases showing more than one mutant transcript caused by recognition of several different splice sites. This functional study expands our knowledge of atypical splicing variants, and emphasizes the importance of clarifying the splicing effect for variants near exon/intron boundaries in OI.
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Affiliation(s)
- Lulu Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yixuan Cao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Feiyue Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Bin Mao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiuzhi Ren
- Department of Orthopaedics, The People's Hospital of Wuqing District, Tianjin, China
| | - Yanzhou Wang
- Department of Pediatric Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Yun Guan
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Yi You
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shan Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Tao Yang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
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28
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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29
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Sanz DJ, Harrison PT. Minigene assay to Evaluate CRISPR/Cas9-based excision of Intronic mutations that Cause Aberrant Splicing in Human Cells. Bio Protoc 2019; 9:e3251. [PMID: 33654776 DOI: 10.21769/bioprotoc.3251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 04/15/2019] [Accepted: 05/24/2019] [Indexed: 11/02/2022] Open
Abstract
The construction of Hybrid minigenes provides a robust and simple strategy to study the effects of disease-causing mutations on mRNA splicing when biological material from patient cells is not available. Hybrid minigenes can be used as splicing reporter plasmids allow RNA expression and heterologous splicing reactions between synthetic splicing signals in the vector and endogenous splicing signals in a cloned genomic DNA fragment that contains one or more introns and exons. Minigene-based assay has been used extensively to test the effect of mutations in the splicing of a target sequence. They can also be used to test the ability of CRISPR/Cas9 and one or more associated gRNAs to target specific sequences in the minigene, and determine the effect of these editing events on splicing. As an example, it is shown that CRISPR/Cas9-based, targeted excision of short intronic sequences containing mutations which create cryptic splice signals, can restore normal splicing in a CFTR Hybrid minigene.
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Affiliation(s)
- David J Sanz
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Patrick T Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
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30
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Wangensteen T, Felde CN, Ahmed D, Mæhle L, Ariansen SL. Diagnostic mRNA splicing assay for variants in BRCA1 and BRCA2 identified two novel pathogenic splicing aberrations. Hered Cancer Clin Pract 2019; 17:14. [PMID: 31143303 PMCID: PMC6532242 DOI: 10.1186/s13053-019-0113-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background Pathogenic variants in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Screening of these genes has become easily accessible in diagnostic laboratories. Sequencing and copy number analyses are used to detect pathogenic variants, but also lead to identification of variants of unknown clinical significance (VUS). If the effect of a VUS can be clarified, it has direct consequence for the clinical management of the patient and family members. A splicing assay is one of several tools that might help in the classification of VUS. We therefore established mRNA analyses for BRCA1 and BRCA2 in the diagnostic laboratory in 2015. We hereby report the results of mRNA analysis variants in BRCA1 and BRCA2 after three years. Methods Variants predicted to alter splicing and variants within the canonical splice sites were selected for splicing analyses. Splicing assays were performed by reverse transcription-PCR of patient RNA. A biallalic expression analysis was carried out whenever possible. Results Twenty-five variants in BRCA1 and BRCA2 were analyzed by splicing assays; nine showed altered transcripts and 16 showed normal splicing patterns. The two novel pathogenic variants in BRCA1 c.4484 + 3 A > C and c.5407–10G > A were characterized. Conclusions We conclude that mRNA analyses are useful in characterization of variants that may affect splicing. The results can guide classification of variants from unknown clinical significance to pathogenic or benign in a diagnostic laboratory, and thus be of direct clinical importance.
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Affiliation(s)
| | | | - Deeqa Ahmed
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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31
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Goina E, Acedo A, Buratti E, Velasco EA. Mis-splicing in breast cancer: identification of pathogenic BRCA2 variants by systematic minigene assays. J Pathol 2019; 248:409-420. [PMID: 30883759 DOI: 10.1002/path.5268] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/21/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022]
Abstract
Splicing disruption is a common mechanism of gene inactivation associated with germline variants of susceptibility genes. To study the role of BRCA2 mis-splicing in hereditary breast/ovarian cancer (HBOC), we performed a comprehensive analysis of variants from BRCA2 exons 2-9, as well as the initial characterization of the regulatory mechanisms of such exons. A pSAD-based minigene with exons 2-9 was constructed and validated in MCF-7 cells, producing the expected transcript (1016-nt/V1-BRCA2_exons_2-9-V2). DNA variants from mutational databases were analyzed by NNSplice and Human Splicing Finder softwares. To refine ESE-variant prediction, we mapped the regulatory regions through a functional strategy whereby 26 exonic microdeletions were introduced into the minigene and tested in MCF-7 cells. Thus, we identified nine spliceogenic ESE-rich intervals where ESE-variants may be located. Combining bioinformatics and microdeletion assays, 83 variants were selected and genetically engineered in the minigene. Fifty-three changes impaired splicing: 28 variants disrupted the canonical sites, four created new ones, 10 abrogated enhancers, eight created silencers and three caused a double-effect. Notably, nine spliceogenic-ESE variants were located within ESE-containing intervals. Capillary electrophoresis and sequencing revealed more than 23 aberrant transcripts, where exon skipping was the most common event. Interestingly, variant c.67G>A triggered the usage of a noncanonical GC-donor 4-nt upstream. Thirty-six variants that induced severe anomalies (>60% aberrant transcripts) were analyzed according to the ACMG guidelines. Thus, 28 variants were classified as pathogenic, five as likely pathogenic and three as variants of uncertain significance. Interestingly, 13 VUS were reclassified as pathogenic or likely pathogenic variants. In conclusion, a large fraction of BRCA2 variants (∼64%) provoked splicing anomalies lending further support to the high prevalence of this disease-mechanism. The low accuracy of ESE-prediction algorithms may be circumvented by functional ESE-mapping that represents an optimal strategy to identify spliceogenic ESE-variants. Finally, systematic functional assays by minigenes depict a valuable tool for the initial characterization of splicing anomalies and the clinical interpretation of variants. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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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
| | - Elisa Goina
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Emanuele Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
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Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel) 2019; 11:cancers11030295. [PMID: 30832263 PMCID: PMC6468917 DOI: 10.3390/cancers11030295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Highly penetrant variants of BRCA1/2 genes are involved in hereditary predisposition to breast and ovarian cancer. The detection of pathogenic BRCA variants has a considerable clinical impact, allowing appropriate cancer-risk management. However, a major drawback is represented by the identification of variants of uncertain significance (VUS). Many VUS potentially affect mRNA splicing, making transcript analysis an essential step for the definition of their pathogenicity. Here, we characterize the impact on splicing of ten BRCA1/2 variants. Aberrant splicing patterns were demonstrated for eight variants whose alternative transcripts were fully characterized. Different events were observed, including exon skipping, intron retention, and usage of de novo and cryptic splice sites. Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. Partial/complete splicing effect and quantitative contribution of different isoforms were assessed, leading to variant classification according to Evidence-based Network for the Interpretation of Mutant Alleles (ENIGMA) consortium guidelines. Two variants could be classified as pathogenic and two as likely benign, while due to a partial splicing effect, six variants remained of uncertain significance. The association with an undefined tumor risk justifies caution in recommending aggressive risk-reduction treatments, but prevents the possibility of receiving personalized therapies with potential beneficial effect. This indicates the need for applying additional approaches for the analysis of variants resistant to classification by gene transcript analyses.
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Investigating of variations in BRCA1 gene in Iranian families with breast cancer. Med J Islam Repub Iran 2018; 32:87. [PMID: 30788324 PMCID: PMC6376998 DOI: 10.14196/mjiri.32.87] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 01/14/2023] Open
Abstract
Background: Breast cancer is one of the most common cancers among Iranian women whose relationship with mutation status in BRCA1 is previously approved. Therefore, screening of the most mutated exons in BRCA1 in hereditary breast cancer patients provides beneficial information about the main disease-causing reason. Methods: A total of 14 Iranian hereditary breast cancer patients participated in this case series study. DNA was extracted from patients' blood samples for PCR assay. The quality of PCR products was determined using horizontal electrophoresis. Then, sequencing and analysis of the sequencing results were performed to investigate variation status in the sequences. Results: Five variants in 4 patients were found, including 1 pathogenic variant in exon 16 (H1686Q, NM_007294.3:c.5058T>A) and 4 novel intronic variants of uncertain significance (NC_000017.11:41228314G>T, NC_000017.11:41228309C>T, NC_000017.11:41228317G>T, and NC_000017.11:41203042G>A) in BRCA1. This study was the first to report 1 rare pathogenic variant in BRCA1 (H1686Q, NM_007294.3: c.5058T>A) in an Iranian family as the main disease-causing reason. Another interesting finding was non-existence of variations in almost all globally-reported and mutated exons in BRCA1. Conclusion: Investigation of these exons in BRCA1 showed the uniqueness of mutation pattern in Iranian breast cancer patients compared to other world regions. Due to the existence of other BRCA1 exons and also other predisposing genes in breast cancer, the main cause of cancer development in other participants might have been put in those exons and genes. We concluded that the most mutated exons in BRCA1 in Iranian population may not be the same as those found in other parts of the world.
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Vendrell JA, Vilquin P, Larrieux M, Van Goethem C, Solassol J. Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection. J Mol Diagn 2018; 20:754-764. [PMID: 30055349 DOI: 10.1016/j.jmoldx.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 11/16/2022] Open
Abstract
The recent deployment of next-generation sequencing approaches in routine laboratory analysis has considerably modified the landscape of BRCA1 and BRCA2 germline alteration detection in patients with a high risk of developing breast and/or ovarian cancer. Several commercial multiplex amplicon-based panels and bioinformatics solutions are currently available. In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single-nucleotide variants, insertion/deletion variants, and copy number variations (CNVs). Four assays (BRCA Tumor, BRCA HC, Ion AmpliSeq BRCA, and Access Array BRCA) and two commercial bioinformatics solutions (SeqNext software version 4.3.1 and Sophia DDM version 5.0.13) were tested on a set of 28 previously genotyped samples. All solutions exhibited accurate detection of single-nucleotide variants and insertion/deletion variants, except for Ion AmpliSeq BRCA, which exhibited a decrease in coverage. Of interest, for CNV analysis, the best accuracy was observed with the Sophia DDM platform regardless of the BRCA kit used. Finally, the performance of the most relevant combination (BRCA Tumor and Sophia DDM) was blindly validated on an independent set of 152 samples. Altogether, our results emphasize the need to accurately compare and control both molecular next-generation sequencing approaches and bioinformatics pipelines to limit the number of discrepant alterations and to provide a powerful tool for reliable detection of genetic alterations in BRCA1 and BRCA2, notably CNVs.
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Affiliation(s)
- Julie A Vendrell
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Paul Vilquin
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Marion Larrieux
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Charles Van Goethem
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Jérôme Solassol
- Solid Tumor Laboratory, Department of Pathology and Oncobiology, CHU Montpellier, University of Montpellier, Montpellier, France; The Institute of Cancer Research of Montpellier, INSERM U1194, University of Montpellier, Montpellier, France.
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Acedo A, Velasco EA. Identification of Eight Spliceogenic Variants in BRCA2 Exon 16 by Minigene Assays. Front Genet 2018; 9:188. [PMID: 29881398 PMCID: PMC5977032 DOI: 10.3389/fgene.2018.00188] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/08/2018] [Indexed: 11/17/2022] Open
Abstract
Genetic testing of BRCA1 and BRCA2 identifies a large number of variants of uncertain clinical significance whose functional and clinical interpretations pose a challenge for genetic counseling. Interestingly, a relevant fraction of DNA variants can disrupt the splicing process in cancer susceptibility genes. We have tested more than 200 variants throughout 19 BRCA2 exons mostly by minigene assays, 54% of which displayed aberrant splicing, thus confirming the utility of this assay to check genetic variants in the absence of patient RNA. Our goal was to investigate BRCA2 exon 16 with a view to characterizing spliceogenic variants recorded at the mutational databases. Seventy-two different BIC and UMD variants were analyzed with NNSplice and Human Splicing Finder, 12 of which were selected because they were predicted to disrupt essential splice motifs: canonical splice sites (ss; eight variants) and exonic/intronic splicing enhancers (four variants). These 12 candidate variants were introduced into the BRCA2 minigene with seven exons (14–20) by site-directed mutagenesis and then transfected into MCF-7 cells. Seven variants (six intronic and one missense) induced complete abnormal splicing patterns: c.7618-2A>T, c.7618-2A>G, c.7618-1G>C, c.7618-1G>A, c.7805G>C, c.7805+1G>A, and c.7805+3A>C, as well as a partial anomalous outcome by c.7802A>G. They generated at least 10 different transcripts: Δ16p44 (alternative 3’ss 44-nt downstream; acceptor variants), Δ16 (exon 16-skipping; donor variants), Δ16p55 (alternative 3’ss 55-nt downstream), Δ16q4 (alternative 5’ss 4-nt upstream), Δ16q100 (alternative 5’ss 4-nt upstream), ▾16q20 (alternative 5’ss 20-nt downstream), as well as minor (Δ16p93 and Δ16,17p69) and uncharacterized transcripts of 893 and 954 nucleotides. Isoforms Δ16p44, Δ16, Δ16p55, Δ16q4, Δ16q100, and ▾16q20 introduced premature termination codons which presumably inactivate BRCA2. According to the guidelines the American College of Medical Genetics and Genomics these eight variants could be classified as pathogenic or likely pathogenic whereas the Evidence-based Network for the Interpretation of Germline Mutant Alleles rules suggested seven class 4 and one class 3 variants. In conclusion, our study highlights the relevance of splicing functional assays by hybrid minigenes for the clinical classification of genetic variations. Hence, we provide new data about spliceogenic variants of BRCA2 exon 16 that are directly correlated with breast cancer susceptibility.
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Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain.,Biome Makers Inc., San Francisco, CA, United States
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
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36
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Infante M, Durán M, Marcos G, Lastra E, Gómez-Barrero S, Velasco EA. Genetic dissection of the BRCA2 promoter and transcriptional impact of DNA variants. Breast Cancer Res Treat 2018; 171:53-63. [PMID: 29766361 DOI: 10.1007/s10549-018-4826-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
PURPOSE Promoter mutations may affect transcription and can be associated with human diseases. However, the promoters of the breast cancer (BC) genes are not regularly screened. Our goal was to investigate the BRCA2 promoter in order to study a possible correlation between impaired transcription and disease. METHODS The proximal and core promoter of the BRCA2 gene was sequenced in 95 high-risk BC patients. A BRCA2-promoter insert [- 938 to + 312 from the transcription start site (TSS)] was generated and cloned into the firefly luciferase vector pGL4.10. Promoter variants and deletions were introduced by site-directed mutagenesis and quantified by Dual-Luciferase assays and semi-quantitative RT-PCR. RESULTS Three different variants were detected in high-risk BC patients: rs3092989, rs206118, and rs563971900. Functional mapping of 13 overlapping deletions revealed four down-regulating segments (TSS positions): -59_-10del/µdel3 (16% of activity of the wild-type construct), -104_-55del/µdel4 (62%), -239_-190del/µdel7 (39%), -464_-415/µdel12 (78%), suggesting the presence therein of putative transcriptional activator motifs. Additionally, six microdeletions rendered luciferase overexpression: +32_+81del/µdel1 (356%), -14_+36del/µdel2 (180%), -194_-145del/µdel6 (154%), -284_-235del/µdel8 (168%), -329_-280del/µdel9 (111%), and -509_-460del/µdel13 (139%), which is indicative of repressor elements. Functional assays of 15 promoter variants (including those detected in patients) showed that ten of them significantly altered expression with seven up-regulating (113-163%) and three down-regulating (rs551887850_G, rs570548398_T, rs55880202_T; 72-83%) SNPs. Eight of them were located in an ENCODE-DNase Hypersensitive Cluster (TSS - 185 to + 105) where most active transcriptional motifs are known to be placed. CONCLUSIONS BRCA2 expression is highly sensitive to promoter variations as most of them induced relevant changes. Moreover, we mapped critical regions of the BRCA2 promoter that may constitute potential targets for regulatory variants. Three SNPs moderately decreased luciferase activity, but confirmation of its potential pathogenicity requires further analysis. These data reinforce the need to screen the promoter regions of breast cancer genes with a view to discovering novel deleterious mutations.
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Affiliation(s)
- Eugenia Fraile-Bethencourt
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Beatriz Díez-Gómez
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Germán Marcos
- Servicio de Oncología, Hospital Río Hortega, Valladolid, Spain
| | - Enrique Lastra
- Servicio de Oncología, Hospital Universitario de Burgos, Burgos, Spain
| | | | - Eladio A Velasco
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain.
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37
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Lattimore VL, Pearson JF, Currie MJ, Spurdle AB, Robinson BA, Walker LC. Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants. Front Oncol 2018; 8:140. [PMID: 29774201 PMCID: PMC5943536 DOI: 10.3389/fonc.2018.00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 BRCA1 and 28 BRCA2 oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates (n > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across BRCA1 and BRCA2 can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of BRCA1 and BRCA2 mRNA aberrations associated with sequence variants of uncertain clinical significance.
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Affiliation(s)
- Vanessa L Lattimore
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand.,Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Bridget A Robinson
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Canterbury Regional Cancer and Haematology Service, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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38
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Colombo M, Lòpez‐Perolio I, Meeks HD, Caleca L, Parsons MT, Li H, De Vecchi G, Tudini E, Foglia C, Mondini P, Manoukian S, Behar R, Garcia EBG, Meindl A, Montagna M, Niederacher D, Schmidt AY, Varesco L, Wappenschmidt B, Bolla MK, Dennis J, Michailidou K, Wang Q, Aittomäki K, Andrulis IL, Anton‐Culver H, Arndt V, Beckmann MW, Beeghly‐Fadel A, Benitez J, Boeckx B, Bogdanova NV, Bojesen SE, Bonanni B, Brauch H, Brenner H, Burwinkel B, Chang‐Claude J, Conroy DM, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk T, Eriksson M, Fasching PA, Figueroa J, Fletcher O, Flyger H, Gabrielson M, García‐Closas M, Giles GG, González‐Neira A, Guénel P, Haiman CA, Hall P, Hamann U, Hartman M, Hauke J, Hollestelle A, Hopper JL, Jakubowska A, Jung A, Kosma V, Lambrechts D, Le Marchand L, Lindblom A, Lubinski J, Mannermaa A, Margolin S, Miao H, Milne RL, Neuhausen SL, Nevanlinna H, Olson JE, Peterlongo P, Peto J, Pylkäs K, Sawyer EJ, Schmidt MK, Schmutzler RK, Schneeweiss A, Schoemaker MJ, See MH, Southey MC, Swerdlow A, Teo SH, Toland AE, Tomlinson I, Truong T, van Asperen CJ, van den Ouweland AM, van der Kolk LE, Winqvist R, Yannoukakos D, Zheng W, Dunning AM, Easton DF, Henderson A, Hogervorst FB, Izatt L, Offitt K, Side LE, van Rensburg EJ, EMBRACE S, HEBON S, McGuffog L, Antoniou AC, Chenevix‐Trench G, Spurdle AB, Goldgar DE, de la Hoya M, Radice P. The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity. Hum Mutat 2018; 39:729-741. [PMID: 29460995 PMCID: PMC5947288 DOI: 10.1002/humu.23411] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 12/12/2022]
Abstract
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10-115 . There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
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Affiliation(s)
- Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Irene Lòpez‐Perolio
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Huong D. Meeks
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Laura Caleca
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Hongyan Li
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Patrizia Mondini
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Siranoush Manoukian
- Unit of Medical GeneticsDepartment of Medical Oncology and HematologyFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Raquel Behar
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Encarna B. Gómez Garcia
- Department of Clinical Genetics and GROWSchool for Oncology and Developmental BiologyMUMCMaastrichtThe Netherlands
| | - Alfons Meindl
- Department of Obstetrics and GynecologyUniversity HospitalLMU MunichGermany
| | - Marco Montagna
- Immunology and Molecular Oncology UnitVeneto Institute of Oncology IOV ‐ IRCCSPaduaItaly
| | - Dieter Niederacher
- Department of Gynaecology and ObstetricsUniversity Hospital DüsseldorfHeinrich‐Heine UniversityDuesseldorfGermany
| | - Ane Y. Schmidt
- Center for Genomic MedicineRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | | | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
| | - Manjeet K. Bolla
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Joe Dennis
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Department of Electron Microscopy/Molecular PathologyThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Qin Wang
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kristiina Aittomäki
- Department of Clinical GeneticsHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Irene L. Andrulis
- Fred A. Litwin Center for Cancer GeneticsLunenfeld‐Tanenbaum Research Institute of Mount Sinai HospitalTorontoOntario
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Hoda Anton‐Culver
- Department of EpidemiologyUniversity of California IrvineIrvineCalifornia
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Matthias W. Beckmann
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
| | - Alicia Beeghly‐Fadel
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | - Javier Benitez
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)ValenciaSpain
| | - Bram Boeckx
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Natalia V. Bogdanova
- Department of Radiation OncologyHannover Medical SchoolHannoverGermany
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
- N.N. Alexandrov Research Institute of Oncology and Medical RadiologyMinskBelarus
| | - Stig E. Bojesen
- Copenhagen General Population StudyHerlevand Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Department of Clinical BiochemistryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and GeneticsIstituto Europeo di OncologiaMilanItaly
| | - Hiltrud Brauch
- Dr. Margarete Fischer‐Bosch‐Institute of Clinical PharmacologyStuttgartGermany
- University of TübingenTübingenGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Division of Preventive OncologyGerman Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)HeidelbergGermany
| | - Barbara Burwinkel
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- Molecular Epidemiology GroupC080German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Jenny Chang‐Claude
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Research Group Genetic Cancer EpidemiologyUniversity Cancer Center Hamburg (UCCH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Don M. Conroy
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Fergus J. Couch
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterNew York
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA)Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Simon S. Cross
- Academic Unit of PathologyDepartment of NeuroscienceUniversity of SheffieldSheffieldUK
| | - Kamila Czene
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter Devilee
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Thilo Dörk
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
| | - Mikael Eriksson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter A. Fasching
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
- David Geffen School of MedicineDepartment of Medicine Division of Hematology and OncologyUniversity of California at Los AngelesLos AngelesCalifornia
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and InformaticsThe University of Edinburgh Medical SchoolEdinburghUK
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMaryland
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Henrik Flyger
- Department of Breast SurgeryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | | | - Graham G. Giles
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna González‐Neira
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
| | - Pascal Guénel
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | - Christopher A. Haiman
- Department of Preventive MedicineKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Per Hall
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Ute Hamann
- Molecular Genetics of Breast CancerDeutsches Krebsforschungszentrum (DKFZ)HeidelbergGermany
| | - Mikael Hartman
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
- Department of SurgeryNational University Health SystemSingaporeSingapore
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Antoinette Hollestelle
- Department of Medical OncologyFamily Cancer ClinicErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - John L. Hopper
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna Jakubowska
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Audrey Jung
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Veli‐Matti Kosma
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Diether Lambrechts
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Loid Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHawaii
| | - Annika Lindblom
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Jan Lubinski
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Arto Mannermaa
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Sara Margolin
- Department of Clinical Science and Education SödersjukhusetKarolinska InstitutetStockholmSweden
| | - Hui Miao
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
| | - Roger L. Milne
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Susan L. Neuhausen
- Department of Population SciencesBeckman Research Institute of City of HopeDuarteCalifornia
| | - Heli Nevanlinna
- Department of Obstetrics and GynecologyHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Janet E. Olson
- Department of Health Sciences ResearchMayo ClinicRochesterNew York
| | - Paolo Peterlongo
- IFOMThe FIRC (Italian Foundation for Cancer Research) Institute of Molecular OncologyMilanItaly
| | - Julian Peto
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | | | - Marjanka K. Schmidt
- Division of Molecular PathologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek HospitalAmsterdamThe Netherlands
- Division of Psychosocial Research and EpidemiologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Rita K. Schmutzler
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Andreas Schneeweiss
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- National Center for Tumor DiseasesUniversity of HeidelbergHeidelbergGermany
| | | | - Mee Hoong See
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
| | | | - Anthony Swerdlow
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
- Division of Breast Cancer ResearchThe Institute of Cancer ResearchLondonUK
| | - Soo H. Teo
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
- Cancer Research MalaysiaSubang JayaSelangorMalaysia
| | - Amanda E. Toland
- Department of Molecular VirologyImmunology and Medical GeneticsComprehensive Cancer CenterThe Ohio State UniversityColumbusOhio
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Thérèse Truong
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | | | | | - Lizet E. van der Kolk
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | - Drakoulis Yannoukakos
- Molecular Diagnostics LaboratoryINRASTESNational Centre for Scientific Research “Demokritos”AthensGreece
| | - Wei Zheng
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | | | - Alison M. Dunning
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Douglas F. Easton
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Alex Henderson
- Institute of Genetic MedicineCentre for LifeNewcastle Upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Frans B.L. Hogervorst
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Louise Izatt
- Clinical GeneticsGuy's and St. Thomas’ NHS Foundation TrustLondonUK
| | - Kenneth Offitt
- Clinical Genetics Research LaboratoryDept. of MedicineCancer Biology and GeneticsMemorial Sloan‐Kettering Cancer CenterNew YorkNew York
| | - Lucy E. Side
- Wessex Clinical Genetics ServiceMailpoint 627, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA
| | | | - Study EMBRACE
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeStrangeways Research LaboratoryWorts CausewayCambridgeUK
| | - Study HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON)Coordinating center: Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lesley McGuffog
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Georgia Chenevix‐Trench
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
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Dutil J, Godoy L, Rivera-Lugo R, Arroyo N, Albino E, Negrón L, Monteiro AN, Matta JL, Echenique M. No Evidence for the Pathogenicity of the BRCA2 c.6937 + 594T>G Deep Intronic Variant: A Case-Control Analysis. Genet Test Mol Biomarkers 2018; 22:85-89. [PMID: 29356578 DOI: 10.1089/gtmb.2017.0187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The role of deep intronic variants in hereditary cancer susceptibility has been largely understudied. Previously, the BRCA2 c.6937 + 594T>G variant has been shown to preferentially promote the inclusion of a 95 nucleotide cryptic exon and to introduce a premature termination codon. Our objective was to further assess the pathogenicity of the BRCA2 c.6937 + 594T>G deep intronic variant. PATIENTS AND METHODS We examined the association between BRCA2 c.6937 + 594T>G and breast cancer (BC) risk in 464 BC cases and 497 noncancer controls from Puerto Rico. RESULTS The overall frequency of the G allele was 2.1% in this population. There was no association between the TG/GG genotypes and BC risk in the uncorrected model and after correcting for confounders. There was only one carrier of the GG genotype. This individual did not have personal or family history of cancer and did not meet the National Comprehensive Cancer Network criteria for hereditary cancer genetic testing. CONCLUSIONS Although previous work has demonstrated that the BRCA2 c.6937 + 594T>G variant affects splicing, this association study does not support a pathogenic role for the BRCA2 c.6937 + 594T>G intronic variant in breast and ovarian cancer syndrome susceptibility. Furthermore, it emphasizes the need to take into account multiple diverse populations in association studies for the assessment of variant pathogenicity.
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Affiliation(s)
- Julie Dutil
- 1 Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University , Ponce, Puerto Rico
| | - Lenin Godoy
- 1 Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University , Ponce, Puerto Rico
| | - Rafael Rivera-Lugo
- 2 Department of Biology, University of Puerto Rico in Ponce , Ponce, Puerto Rico
| | - Nelly Arroyo
- 1 Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University , Ponce, Puerto Rico
| | - Elinette Albino
- 1 Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University , Ponce, Puerto Rico
| | - Luis Negrón
- 3 Hematology-Oncology Program, VA Caribbean Healthcare System , San Juan, Puerto Rico
| | - Alvaro N Monteiro
- 4 Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute , Tampa, Florida
| | - Jaime L Matta
- 1 Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University , Ponce, Puerto Rico
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Møller P, Hovig E. The BRCA2 variant c.68-7 T>A is associated with breast cancer. Hered Cancer Clin Pract 2017; 15:20. [PMID: 29158857 PMCID: PMC5683587 DOI: 10.1186/s13053-017-0080-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/31/2017] [Indexed: 01/01/2023] Open
Abstract
Background BRCA2 c.68-7T>A has been demonstrated to cause aberrant splicing and is possibly pathogenic. The population prevalence of the variant is 0.2%, which higher than usual for pathogenic BRCA2 variants. The pathogenicity of the variant is discussed. Methods The outpatient genetic clinic at The Norwegian Radium Hospital, part of Oslo University Hospital, has invited breast cancer kindreds for genetic examinations and prospective follow-up of high risk patients since 1988. We have complete files of all activities and results, and we examined the files for association between BRCA2 c.68-7T>A and breast cancer. Results Seventeen out of 714 (2.4%) breast cancer kindreds sequenced for BRCA2 carried the variant BRCA2 c.68-7T>A (p < 0.0001 compared to population controls). Segregation analysis was inconclusive (likelihood ratio 0.36) for pathogenicity. Two breast cancers were prospectively observed during 134 observation years (annual incidence rate 1.5% (95% CI 0.15% to 5.4%) and one additional breast cancer was diagnosed at first (prevalence) round. Conclusion BRCA2 c.68-7T>A is associated with breast cancer. In the families selected due to aggregation of breast cancer, carriers of the BRCA2 c.68-7T>A variant have increased risk for breast cancer. It is, however, possible that the variant has lower penetrance than the average pathogenic BRCA2 variants, and that in the families selected for having known aggregation of breast cancer other (modifying) factors contributed to the observed results.
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Affiliation(s)
- Pål Møller
- Research Group Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Hereditary Tumors, HELIOS-Klinikum Wuppertal, University of Witten-Herdecke, Wuppertal, Germany
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
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Jarhelle E, Riise Stensland HMF, Mæhle L, Van Ghelue M. Characterization of BRCA1 and BRCA2 variants found in a Norwegian breast or ovarian cancer cohort. Fam Cancer 2017; 16:1-16. [PMID: 27495310 DOI: 10.1007/s10689-016-9916-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Molecular screening of these two genes in patients with a family history of breast or ovarian cancer has revealed pathogenic variants as well as genetic variants of unknown significance (VUS). These VUS may cause a challenge in the genetic counseling process regarding clinical management of the patient and the family. We investigated 32 variants previously detected in 33 samples from patients with a family history of breast or ovarian cancer. cDNA was analyzed for alternative transcripts and selected missense variants located in the BRCT domains of BRCA1 were assessed for their trans-activation ability. Although an extensive cDNA analysis was done, only three of the 32 variants appeared to affect the splice-process (BRCA1 c.213-5T>A, BRCA1 c.5434C>G and BRCA2 c.68-7T>A). In addition, two variants located in the BRCT domains of BRCA1 (c.5075A>C p.Asp1692Ala and c.5513T>G p.Val1838Gly) were shown to abolish the BRCT domain trans-activation ability, whereas BRCA1 c.5125G>A p.Gly1709Arg exhibited equal trans-activation capability as the WT domain. These functional studies may offer further insights into the pathogenicity of certain identified variants; however, this assay is only applicable for a subset of missense variants.
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Affiliation(s)
- Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Hilde Monica Frostad Riise Stensland
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway.
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Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 13:40-48. [PMID: 29021971 PMCID: PMC5634819 DOI: 10.1016/j.bdq.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/22/2017] [Accepted: 09/02/2017] [Indexed: 11/21/2022]
Abstract
INTRODUCTION For the relative quantification of isoform expression, RT-qPCR has been the gold standard for over a decade. More recently, digital PCR is becoming widely implemented, as it is promised to be more accurate, sensitive and less affected by inhibitors, without the need for standard curves. In this study we evaluated RT-qPCR versus RT-droplet digital PCR (ddPCR) for the relative quantification of isoforms in controls and carriers of the splice site mutation BRCA1 c.212+3A>G, associated with increased expression of several isoforms. MATERIALS AND METHODS RNA was extracted from EBV cell lines of controls and heterozygous BRCA1 c.212+3A>G carriers. Transcript-specific plasmids were available to determine the efficiency, precision, reproducibility and accuracy of each method. RESULTS Both ddPCR and RT-qPCR were able to accurately quantify all targets and showed the same LOB, LOD and LOQ; also precision and reproducibility were similar. Both techniques have the same dynamic range and linearity at biologically relevant template concentrations. However, a significantly higher cost and workload was required for ddPCR experiments. CONCLUSIONS Our study recognizes the potential and validity of digital PCR but shows the value of a highly optimized qPCR for the relative quantification of isoforms. Cost efficiency and simplicity turned out to be better for RT-qPCR.
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Sanz DJ, Hollywood JA, Scallan MF, Harrison PT. Cas9/gRNA targeted excision of cystic fibrosis-causing deep-intronic splicing mutations restores normal splicing of CFTR mRNA. PLoS One 2017; 12:e0184009. [PMID: 28863137 PMCID: PMC5581164 DOI: 10.1371/journal.pone.0184009] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/16/2017] [Indexed: 12/27/2022] Open
Abstract
Cystic Fibrosis is an autosomal recessive disorder caused by mutations in the CFTR gene. CRISPR mediated, template-dependent homology-directed gene editing has been used to correct the most common mutation, c.1521_1523delCTT / p.Phe508del (F508del) which affects ~70% of individuals, but the efficiency was relatively low. Here, we describe a high efficiency strategy for editing of three different rare CFTR mutations which together account for about 3% of individuals with Cystic Fibrosis. The mutations cause aberrant splicing of CFTR mRNA due to the creation of cryptic splice signals that result in the formation of pseudoexons containing premature stop codons c.1679+1634A>G (1811+1.6kbA>G) and c.3718-2477C>T (3849+10kbC>T), or an out-of-frame 5' extension to an existing exon c.3140-26A>G (3272-26A>G). We designed pairs of Cas9 guide RNAs to create targeted double-stranded breaks in CFTR either side of each mutation which resulted in high efficiency excision of the target genomic regions via non-homologous end-joining repair. When evaluated in a mini-gene splicing assay, we showed that targeted excision restored normal splicing for all three mutations. This approach could be used to correct aberrant splicing signals or remove disruptive transcription regulatory motifs caused by deep-intronic mutations in a range of other genetic disorders.
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Affiliation(s)
- David J. Sanz
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Jennifer A. Hollywood
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Patrick T. Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
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Xiping Z, Qingshan W, Shuai Z, Hongjian Y, Xiaowen D. A summary of relationships between alternative splicing and breast cancer. Oncotarget 2017; 8:51986-51993. [PMID: 28881705 PMCID: PMC5584306 DOI: 10.18632/oncotarget.17727] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/05/2017] [Indexed: 12/13/2022] Open
Abstract
Alternative splicing (AS) is the process of combinatorial rearrangement of parts of exons, and/or parts of introns into mature RNA to result in a multitude of transcripts. AS is a biological process through which organisms produce as many protein variants as possible by a limited genetic resource. It plays an important role in growth and development of the organisms. Over the past few years, alternative splicing has been discovered to be critical for genesis and development of malignant tumors, including breast cancer. If the relationships between AS and breast cancer can be discussed more deeply, it will be helpful for better diagnosis, judging prognosis and intervening with breast cancer. In this paper, the relationships between AS and breast cancer are elaborated from different angles, in hope that this summary is beneficial for readers to understand the roles of AS and breast cancer.
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Affiliation(s)
- Zhang Xiping
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Wei Qingshan
- Cataloging Department, Library of Xi'an Jiaotong University, Xi'an 710049, Shaanxi Province, China
| | - Zhao Shuai
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Yang Hongjian
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
| | - Ding Xiaowen
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, Zhejiang Province, China
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45
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Molecular characterization and clinical interpretation of BRCA1/BRCA2 variants in families from Murcia (south-eastern Spain) with hereditary breast and ovarian cancer: clinical–pathological features in BRCA carriers and non-carriers. Fam Cancer 2017; 16:477-489. [DOI: 10.1007/s10689-017-9985-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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46
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Byrjalsen A, Steffensen AY, Hansen TVO, Wadt K, Gerdes AM. Classification of the spliceogenic BRCA1 c.4096+3A>G variant as likely benign based on cosegregation data and identification of a healthy homozygous carrier. Clin Case Rep 2017; 5:876-879. [PMID: 28588830 PMCID: PMC5458035 DOI: 10.1002/ccr3.944] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 12/16/2022] Open
Abstract
BRCA1, c.4096+3A>G was identified in a consanguineous Danish family with several cases of breast/ovarian cancer. In silico analysis and splicing assays indicated that the variant caused aberrant splicing. However, based on segregation data and the finding of a healthy homozygous carrier, we classify the BRCA1 c.4096+3A>G variant as likely benign.
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Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
| | - Ane Y Steffensen
- Center for Genomic Medicine Copenhagen University Hospital Copenhagen Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine Copenhagen University Hospital Copenhagen Denmark
| | - Karin Wadt
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
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Kozlovski I, Siegfried Z, Amar-Schwartz A, Karni R. The role of RNA alternative splicing in regulating cancer metabolism. Hum Genet 2017; 136:1113-1127. [PMID: 28429085 DOI: 10.1007/s00439-017-1803-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
Abstract
Tumor cells alter their metabolism by a wide array of mechanisms to promote growth and proliferation. Dysregulated expression and/or somatic mutations of key components of the glycolytic pathway/TCA cycle as well as other metabolic pathways allow tumor cells to improve their ability to survive harsh conditions such as hypoxia and the presence of reactive oxygen species, as well as the ability to obtain nutrients to increase lipids, protein, and nucleic acids biogenesis. Approximately 95% of the human protein encoding genes undergo alternative splicing (AS), a regulated process of gene expression that greatly diversifies the proteome by creating multiple proteins from a single gene. In recent years, a growing body of evidence suggests that unbalanced AS, the formation of certain pro-tumorigenic isoforms and the reduction of anti-tumorigenic isoforms, is implicated in a variety of cancers. It is becoming increasingly clear that cancer-associated AS contributes to increased growth and proliferation, partially due to effects on metabolic reprogramming. Here, we summarize the known roles of AS in regulating cancer metabolism. We present evidence supporting the idea that AS, in many types of cancer, acts as a molecular switch that alters metabolism to drive tumorigenesis. We propose that the elucidation of misregulated AS and its downstream effects on cancer metabolism emphasizes the need for new therapeutic approaches aiming to modulate the splicing machinery to selectively target cancer cells.
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Affiliation(s)
- Itamar Kozlovski
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, IMRIC, Hebrew University-Hadassah Medical School, Ein Karem, 91120, Jerusalem, Israel.
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Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18. PLoS Genet 2017; 13:e1006691. [PMID: 28339459 PMCID: PMC5384790 DOI: 10.1371/journal.pgen.1006691] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 04/07/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022] Open
Abstract
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants. A splicing reporter minigene with BRCA2 exons 14 to-20 (MGBR2_ex14-20) was constructed in the pSAD vector. Fifty-two candidate variants were selected with splicing prediction programs, introduced in MGBR2_ex14-20 by site-directed mutagenesis and assayed in triplicate in MCF-7 cells. Wild type MGBR2_ex14-20 produced a stable transcript of the expected size (1,806 nucleotides) and structure (V1-[BRCA2_exons_14–20]–V2). Functional mapping by microdeletions revealed essential sequences for exon recognition on the 3’ end of exon 17 (c.7944-7973) and the 5’ end of exon 18 (c.7979-7988, c.7999-8013). Thirty out of the 52 selected variants induced anomalous splicing in minigene assays with >16 different aberrant transcripts, where exon skipping was the most common event. A wide range of splicing motifs were affected including the canonical splice sites (15 variants), novel alternative sites (3 variants), the polypyrimidine tract (3 variants) and enhancers/silencers (9 variants). According to the guidelines of the American College of Medical Genetics and Genomics (ACMG), 20 variants could be classified as pathogenic (c.7806-2A>G, c.7806-1G>A, c.7806-1G>T, c.7806-1_7806-2dup, c.7976+1G>A, c.7977-3_7978del, c.7977-2A>T, c.7977-1G>T, c.7977-1G>C, c.8009C>A, c.8331+1G>T and c.8331+2T>C) or likely pathogenic (c.7806-9T>G, c.7976G>C, c.7976G>A, c.7977-7C>G, c.7985C>G, c.8023A>G, c.8035G>T and c.8331G>A), accounting for 30.8% of all pathogenic/likely pathogenic variants of exons 17–18 at the BRCA Share database. The remaining 8 variants (c.7975A>G, c.7977-6T>G, c.7988A>T, c.7992T>A, c.8007A>G, c.8009C>T, c.8009C>G, and c.8072C>T) induced partial splicing anomalies with important ratios of the full-length transcript (≥70%), so that they remained classified as VUS. Aberrant splicing is therefore especially prevalent in BRCA2 exons 17 and 18 due to the presence of active ESEs involved in exon recognition. Splicing functional assays with minigenes are a valuable strategy for the initial characterization of the splicing outcomes and the subsequent clinical interpretation of variants of any disease-gene, although these results should be checked, whenever possible, against patient RNA. A significant proportion of disease-causing mutations of inherited disorders impair splicing. Massive sequencing projects of genetic diseases generate thousands of sequence variations that require functional and clinical interpretations. We have shown that splicing reporter minigenes of the breast cancer genes BRCA1 and BRCA2 are useful tools to functionally test DNA variants. In this work, we have constructed a 7-exon BRCA2 minigene (exons 14 to 20) where we mapped critical splicing regulatory sequences and tested 52 selected variants of exons 17 and 18 detected in breast cancer patients. We finely located three DNA segments on both exons that presumably contain splicing enhancer sequences. We observed that a total of 30 variants of any type disrupted the splicing patterns and, given the severity of their outcomes, we classified 20 of them as pathogenic or likely pathogenic. We also showed that a wide range of splicing elements were affected including canonical and novel 5’ and 3’ splice sites, the polypyrimidine tract and enhancer and silencer sequences. We concluded that splicing aberrations are frequent in Hereditary Breast and Ovarian Cancer and that minigenes are valuable tools to functionally classify DNA variants of any human disease gene under the splicing viewpoint.
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Rodríguez-Balada M, Roig B, Martorell L, Melé M, Salvat M, Vilella E, Borràs J, Gumà J. In silico, in vitro and case-control analyses as an effective combination for analyzing BRCA1 and BRCA2 unclassified variants in a population-based sample. Cancer Genet 2016; 209:487-492. [PMID: 27886673 DOI: 10.1016/j.cancergen.2016.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/12/2016] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
Ascertaining the clinical consequences of BRCA1 and BRCA2 variants of uncertain significance (VUS) is currently indispensable for providing effective genetic counseling and preventive actions for families with hereditary breast and ovarian cancer (HBOC). To this end, we conducted a combination of in silico prediction and cDNA splicing analyses of 13 BRCA1 and 10 BRCA2 VUS identified in our cohort as well as a case-control analysis in a population-based sample of 10 recurrent VUS. We observed consistent results between the in silico predictions and sequencing analyses for all analyzed VUS. An abnormal cDNA pattern was observed for variants c.212+1G>A and c.5278-1G>A in BRCA1 and c.516+2T>A and c.8168A>G in BRCA2 according to in silico splicing prediction. A case-control study of VUS confirmed the polymorphisms of the c.67+62A>G, c.7008-62A>G and c.8851G>A BRCA2 variants previously published. c.4068G>A in the BRCA2 gene can also be considered a polymorphism due to its occurrence at a frequency greater than 1% in our population. Our study shows that employing population-based analysis and a combination of several in silico methods yields highly accurate information, resulting in a reliable tool for selecting variants for cDNA sequencing analysis in routine cancer genetic counseling units.
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Affiliation(s)
- Marta Rodríguez-Balada
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Bàrbara Roig
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, C/Sant Llorenç, Reus, Spain
| | - Mireia Melé
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Mònica Salvat
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, C/Sant Llorenç, Reus, Spain
| | - Joan Borràs
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain
| | - Josep Gumà
- Cancer Genetic Counseling Unit (Oncology Research Group), Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus, IISPV, Universitat Rovira i Virgili, Av. Del Dr. Josep Laporte, Reus, Spain.
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50
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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