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Schwenk V, Leal Silva RM, Scharf F, Knaust K, Wendlandt M, Häusser T, Pickl JMA, Steinke-Lange V, Laner A, Morak M, Holinski-Feder E, Wolf DA. Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC/Lynch syndrome. J Med Genet 2023; 60:747-759. [PMID: 36593122 PMCID: PMC10423559 DOI: 10.1136/jmg-2022-108931] [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: 09/08/2022] [Accepted: 12/10/2022] [Indexed: 01/03/2023]
Abstract
PURPOSE Whereas most human genes encode multiple mRNA isoforms with distinct function, clinical workflows for assessing this heterogeneity are not readily available. This is a substantial shortcoming, considering that up to 25% of disease-causing gene variants are suspected of disrupting mRNA splicing or mRNA abundance. Long-read sequencing can readily portray mRNA isoform diversity, but its sensitivity is relatively low due to insufficient transcriptome penetration. METHODS We developed and applied capture-based target enrichment from patient RNA samples combined with Oxford Nanopore long-read sequencing for the analysis of 123 hereditary cancer transcripts (capture and ultradeep long-read RNA sequencing (CAPLRseq)). RESULTS Validating CAPLRseq, we confirmed 17 cases of hereditary non-polyposis colorectal cancer/Lynch syndrome based on the demonstration of splicing defects and loss of allele expression of mismatch repair genes MLH1, PMS2, MSH2 and MSH6. Using CAPLRseq, we reclassified two variants of uncertain significance in MSH6 and PMS2 as either likely pathogenic or benign. CONCLUSION Our data show that CAPLRseq is an automatable and adaptable workflow for effective transcriptome-based identification of disease variants in a clinical diagnostic setting.
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Affiliation(s)
| | | | | | | | | | - Tanja Häusser
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
| | - Julia M A Pickl
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Klinikum der Universität München, Munich, Germany
| | | | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
| | - Monika Morak
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Klinikum der Universität München, Munich, Germany
| | - Elke Holinski-Feder
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Dieter A Wolf
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Department of Medicine II, Technical University Munich, Munich, Germany
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2
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Morak M, Pineda M, Martins A, Gaildrat P, Tubeuf H, Drouet A, Gómez C, Dámaso E, Schaefer K, Steinke-Lange V, Koehler U, Laner A, Hauchard J, Chauris K, Holinski-Feder E, Capellá G. Splicing analyses for variants in MMR genes: best practice recommendations from the European Mismatch Repair Working Group. Eur J Hum Genet 2022; 30:1051-1059. [PMID: 35676339 PMCID: PMC9437034 DOI: 10.1038/s41431-022-01106-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Over 20% of the DNA mismatch repair (MMR) germline variants in suspected Lynch syndrome patients are classified as variants of uncertain significance (VUS). Well-established functional assays are pivotal for assessing the biological impact of these variants and provide relevant evidence for clinical classification. In our collaborative European Mismatch Repair Working Group (EMMR-WG) we compared three different experimental approaches for evaluating the effect of seven variants on mRNA splicing in MMR genes: (i) RT-PCR of full-length transcripts (FLT), (ii) RT-PCR of targeted transcript sections (TTS), both from patient biological samples and (iii) minigene splicing assays. An overall good concordance was observed between splicing patterns in TTS, FLT and minigene analyses for all variants. The FLT analysis depicted a higher number of different isoforms and mitigated PCR-bias towards shorter isoforms. TTS analyses may miss aberrant isoforms and minigene assays may under/overestimate the severity of certain splicing defects. The interpretation of the experimental findings must be cautious to adequately discriminate abnormal events from physiological complex alternative splicing patterns. A consensus strategy for investigating the impact of MMR variants on splicing was defined. First, RNA should be obtained from patient's cell cultures (such as fresh lymphocyte cultures) incubated with/without a nonsense-mediated decay inhibitor. Second, FLT RT-PCR analysis is recommended to oversee all generated isoforms. Third, TTS analysis and minigene assays are useful independent approaches for verifying and clarifying FLT results. The use of several methodologies is likely to increase the strength of the experimental evidence which contributes to improve variant interpretation.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | | | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Karine Chauris
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany. .,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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3
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Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 2019; 23:270-281.e3. [PMID: 29617666 PMCID: PMC6055527 DOI: 10.1016/j.celrep.2018.03.052] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/21/2018] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.
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Affiliation(s)
- Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Qingsong Gao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Héctor Climente-González
- Institut Curie, 75248 Paris Cedex, France; MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 77300 Fontainebleau, France; INSERM U900, 75248 Paris Cedex, France
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajees Varghese
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mo Huang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Sohini Sengupta
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zhi Li
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Jeffrey H Miner
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew J Walter
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Benjamin Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eduardo Eyras
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Computational RNA Biology Group, Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
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4
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Chau C, van Doorn R, van Poppelen NM, van der Stoep N, Mensenkamp AR, Sijmons RH, van Paassen BW, van den Ouweland AMW, Naus NC, van der Hout AH, Potjer TP, Bleeker FE, Wevers MR, van Hest LP, Jongmans MCJ, Marinkovic M, Bleeker JC, Jager MJ, Luyten GPM, Nielsen M. Families with BAP1-Tumor Predisposition Syndrome in The Netherlands: Path to Identification and a Proposal for Genetic Screening Guidelines. Cancers (Basel) 2019; 11:cancers11081114. [PMID: 31382694 PMCID: PMC6721807 DOI: 10.3390/cancers11081114] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 12/26/2022] Open
Abstract
Germline pathogenic variants in the BRCA1-associated protein-1 (BAP1) gene cause the BAP1-tumor predisposition syndrome (BAP1-TPDS, OMIM 614327). BAP1-TPDS is associated with an increased risk of developing uveal melanoma (UM), cutaneous melanoma (CM), malignant mesothelioma (MMe), renal cell carcinoma (RCC), meningioma, cholangiocarcinoma, multiple non-melanoma skin cancers, and BAP1-inactivated nevi. Because of this increased risk, it is important to identify patients with BAP1-TPDS. The associated tumors are treated by different medical disciplines, emphasizing the need for generally applicable guidelines for initiating genetic analysis. In this study, we describe the path to identification of BAP1-TPDS in 21 probands found in the Netherlands and the family history at the time of presentation. We report two cases of de novo BAP1 germline mutations (2/21, 9.5%). Findings of this study combined with previously published literature, led to a proposal of guidelines for genetic referral. We recommend genetic analysis in patients with ≥2 BAP1-TPDS-associated tumors in their medical history and/or family history. We also propose to test germline BAP1 in patients diagnosed with UM <40 years, CM <18 years, MMe <50 years, or RCC <46 years. Furthermore, other candidate susceptibility genes for tumor types associated with BAP1-TPDS are discussed, which can be included in gene panels when testing patients.
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Affiliation(s)
- Cindy Chau
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Natasha M van Poppelen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Nienke van der Stoep
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arjen R Mensenkamp
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Barbara W van Paassen
- Department of Clinical Genetics, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Nicole C Naus
- Department of Ophthalmology, Erasmus Medical Center, 3015 GD Rotterdam, The Netherlands
| | | | - Thomas P Potjer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Fonnet E Bleeker
- Department of Clinical Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marijke R Wevers
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, Amsterdam University Medical Centers, 1081 HV Amsterdam, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Clinical Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Clinical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Marina Marinkovic
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jaco C Bleeker
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gregorius P M Luyten
- Department of Ophthalmology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands.
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5
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Morak M, Schaefer K, Steinke-Lange V, Koehler U, Keinath S, Massdorf T, Mauracher B, Rahner N, Bailey J, Kling C, Haeusser T, Laner A, Holinski-Feder E. Full-length transcript amplification and sequencing as universal method to test mRNA integrity and biallelic expression in mismatch repair genes. Eur J Hum Genet 2019; 27:1808-1820. [PMID: 31332305 DOI: 10.1038/s41431-019-0472-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/13/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
In pathogenicity assessment, RNA-based analyses are important for the correct classification of variants, and require gene-specific cut-offs for allelic representation and alternative/aberrant splicing. Beside this, the diagnostic yield of RNA-based techniques capable to detect aberrant splicing or allelic loss due to intronic/regulatory variants has to be elaborated. We established a cDNA analysis for full-length transcripts (FLT) of the four DNA mismatch repair (MMR) genes to investigate the splicing pattern and transcript integrity with active/inhibited nonsense-mediated mRNA-decay (NMD). Validation was based on results from normal controls, samples with premature termination codons (PTC), samples with splice-site defects (SSD), and samples with pathogenic putative missense variants. The method was applied to patients with variants of uncertain significance (VUS) or unexplained immunohistochemical MMR deficiency. We categorized the allelic representation into biallelic (50 ± 10%) or allelic loss (≤10%), and >10% and <40% as unclear. We defined isoforms up to 10% and exon-specific exceptions as alternative splicing, set the cut-off for SSD in cDNA + P to 30-50%, and regard >10% and <30% as unclear. FLT cDNA analyses designated 16% of all putative missense variants and 12% of VUS as SSD, detected MMR-defects in 19% of the unsolved patients, and re-classified >30% of VUS. Our method allows a standardized, systematic cDNA analysis of the MMR FLTs to assess the pathogenicity mechanism of VUS on RNA level, which will gain relevance for precision medicine and gene therapy. Diagnostic accuracy will be enhanced by detecting MMR defects in hitherto unsolved patients. The data generated will help to calibrate a high-throughput NGS-based mRNA-analysis and optimize prediction programs.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany. .,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany.
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany.,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Udo Koehler
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Susanne Keinath
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Trisari Massdorf
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany.,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Brigitte Mauracher
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany
| | - Nils Rahner
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Jessica Bailey
- Clinical Genetics, St. George's University Hospital NHS Foundation Trust, London, UK
| | | | - Tanja Haeusser
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Andreas Laner
- MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, 80336, Munich, Germany. .,MGZ - Medical Genetics Center, Bayerstr. 3-5, 80335, Munich, Germany.
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6
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Chen S, Ni W, Yin XZ, Liu HQ, Lu C, Zheng QJ, Zhao GX, Xu YF, Wu L, Zhang L, Wang N, Li HF, Wu ZY. Clinical features and mutation spectrum in Chinese patients with CADASIL: A multicenter retrospective study. CNS Neurosci Ther 2017; 23:707-716. [PMID: 28710804 DOI: 10.1111/cns.12719] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 06/13/2017] [Accepted: 06/23/2017] [Indexed: 12/16/2022] Open
Abstract
AIM To characterize clinical features and mutation spectrum in Chinese patients with CADASIL. METHODS We collected 261 clinically suspected Chinese CADASIL patients from three hospitals located in different regions of China. Sanger sequencing is performed to screen the exons 2 to 24 of NOTCH3 gene. Clinical and genetic data were retrospectively studied. Haplotype analyses were performed in patients carrying p.Arg544Cys and p.Arg607Cys, respectively. RESULTS A total of 214 patients were finally genetically diagnosed as CADASIL, with 45 known NOTCH3 mutations and a novel c.1817G>T mutation. We found that patients carrying p.Arg607Cys or p.Arg544Cys mutation located in exon 11 occupied nearly 35% in our mutation spectrum. In retrospectively study of clinical data, we found a higher number of patients having cognitive impairment and a lower number of patients having migraine with aura. Furthermore, we identified that patients carrying mutations in exon 11 seemed to experience a later disease onset (p=6.8×10-5 ). Additionally, a common haplotype was found in patients from eastern China carrying p.Arg607Cys, and the patients from Fujian carrying p.Arg544Cys shared the same haplotype with patients from Taiwan carrying p.Arg544Cys. CONCLUSIONS These findings broaden the mutational and clinical spectrum of CADASIL and provide additional evidences for the existence of founder effect in CADASIL patients.
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Affiliation(s)
- Sheng Chen
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China.,Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Xin-Zhen Yin
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Han-Qiu Liu
- Department of Radiology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cong Lu
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qiao-Juan Zheng
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Gui-Xian Zhao
- Department of Neurology and Institute of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong-Feng Xu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Liang Zhang
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hong-Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China.,Joint Institute for Genetics and Genome Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
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7
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Malone AF, Funk SD, Alhamad T, Miner JH. Functional assessment of a novel COL4A5 splice region variant and immunostaining of plucked hair follicles as an alternative method of diagnosis in X-linked Alport syndrome. Pediatr Nephrol 2017; 32:997-1003. [PMID: 28013382 PMCID: PMC5400701 DOI: 10.1007/s00467-016-3565-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Many COL4A5 splice region variants have been described in patients with X-linked Alport syndrome, but few have been confirmed by functional analysis to actually cause defective splicing. We sought to demonstrate that a novel COL4A5 splice region variant in a family with Alport syndrome is pathogenic using functional studies. We also describe an alternative method of diagnosis. METHODS Targeted next-generation sequencing results of an individual with Alport syndrome were analyzed and the results confirmed by Sanger sequencing in family members. A splicing reporter minigene assay was used to examine the variant's effect on splicing in transfected cells. Plucked hair follicles from patients and controls were examined for collagen IV proteins using immunofluorescence microscopy. RESULTS A novel splice region mutation in COL4A5, c.1780-6T>G, was identified and segregated with disease in this family. This variant caused frequent skipping of exon 25, resulting in a frameshift and truncation of collagen α5(IV) protein. We also developed and validated a new approach to characterize the expression of collagen α5(IV) protein in the basement membranes of plucked hair follicles. Using this approach we demonstrated reduced collagen α5(IV) protein in affected male and female individuals in this family, supporting frequent failure of normal splicing. CONCLUSIONS Differing normal to abnormal transcript ratios in affected individuals carrying splice region variants may contribute to variable disease severity observed in Alport families. Examination of plucked hair follicles in suspected X-linked Alport syndrome patients may offer a less invasive alternative method of diagnosis and serve as a pathogenicity test for COL4A5 variants of uncertain significance.
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8
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Analysis of CCM1 expression uncovers novel minor-form exons and variable splicing patterns. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0435-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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van der Klift HM, Mensenkamp AR, Drost M, Bik EC, Vos YJ, Gille HJJP, Redeker BEJW, Tiersma Y, Zonneveld JBM, García EG, Letteboer TGW, Olderode-Berends MJW, van Hest LP, van Os TA, Verhoef S, Wagner A, van Asperen CJ, Ten Broeke SW, Hes FJ, de Wind N, Nielsen M, Devilee P, Ligtenberg MJL, Wijnen JT, Tops CMJ. Comprehensive Mutation Analysis of PMS2 in a Large Cohort of Probands Suspected of Lynch Syndrome or Constitutional Mismatch Repair Deficiency Syndrome. Hum Mutat 2016; 37:1162-1179. [PMID: 27435373 DOI: 10.1002/humu.23052] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 01/01/2023]
Abstract
Monoallelic PMS2 germline mutations cause 5%-15% of Lynch syndrome, a midlife cancer predisposition, whereas biallelic PMS2 mutations cause approximately 60% of constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer syndrome. Recently improved DNA- and RNA-based strategies are applied to overcome problematic PMS2 mutation analysis due to the presence of pseudogenes and frequent gene conversion events. Here, we determined PMS2 mutation detection yield and mutation spectrum in a nationwide cohort of 396 probands. Furthermore, we studied concordance between tumor IHC/MSI (immunohistochemistry/microsatellite instability) profile and mutation carrier state. Overall, we found 52 different pathogenic PMS2 variants explaining 121 Lynch syndrome and nine CMMRD patients. In vitro mismatch repair assays suggested pathogenicity for three missense variants. Ninety-one PMS2 mutation carriers (70%) showed isolated loss of PMS2 in their tumors, for 31 (24%) no or inconclusive IHC was available, and eight carriers (6%) showed discordant IHC (presence of PMS2 or loss of both MLH1 and PMS2). Ten cases with isolated PMS2 loss (10%; 10/97) harbored MLH1 mutations. We confirmed that recently improved mutation analysis provides a high yield of PMS2 mutations in patients with isolated loss of PMS2 expression. Application of universal tumor prescreening methods will however miss some PMS2 germline mutation carriers.
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Affiliation(s)
- Heleen M van der Klift
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands. .,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
| | - Arjen R Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mark Drost
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Yvonne J Vos
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hans J J P Gille
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Bert E J W Redeker
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Yvonne Tiersma
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - José B M Zonneveld
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Encarna Gómez García
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Tom G W Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maran J W Olderode-Berends
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liselotte P van Hest
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Theo A van Os
- Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Senno Verhoef
- Netherlands Cancer Institute, Amsterdam, The Netherlands.,Clinical Genetics Service, Saint Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Juul T Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
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10
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van der Klift HM, Jansen AML, van der Steenstraten N, Bik EC, Tops CMJ, Devilee P, Wijnen JT. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med 2015; 3:327-45. [PMID: 26247049 PMCID: PMC4521968 DOI: 10.1002/mgg3.145] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants.
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Affiliation(s)
- Heleen M van der Klift
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Anne M L Jansen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands
| | | | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Pathology, Leiden University Medical Center Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
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11
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Sun Z, Yu X, Wang H, Zhang S, Zhao Z, Xu R. Clinical significance of mismatch repair gene expression in sporadic colorectal cancer. Exp Ther Med 2014; 8:1416-1422. [PMID: 25289032 PMCID: PMC4186363 DOI: 10.3892/etm.2014.1927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/25/2014] [Indexed: 01/20/2023] Open
Abstract
Mismatch repair (MMR) genes play an important role in the occurrence and development of sporadic colorectal cancer; however, the effect of MMR genes on clinicopathological features and prognosis remains unclear. The aim of the present study was to observe the clinical significance of MMR gene expression in sporadic colorectal cancer. Clinicopathological data and postoperative samples from 404 patients with sporadic colorectal cancer were obtained from the Affiliated Tumor Hospital of Xinjiang Medical University. The immunohistochemistry PV-9000 two-step method was performed to measure the protein expression of human mutL homolog 1 (hMLH1), human mutS homolog (hMSH) 2, human postmeiotic segregation increased 2 (hPSM2) and hMSH6. Differences in clinicopathological features, family history and survival time subsequent to surgery between groups with normal and aberrant MMR protein (MMRP) expression were compared. A total of 27.23% of all patients showed aberrant nuclear staining of MMRP. Among the patients with aberrant MMRP expression, a higher proportion of patients showed aberrant expression of more than one type of MMRP than aberrant expression of only one type of MMRP. Aberrant expression of hMLH1/hPSM2 was most commonly observed (29/404). In addition, aberrant MMRP expression in colorectal cancer was indicated predominantly in the right hemicolon. Histological type primarily showed mucinous adenocarcinoma. In addition, with increasing body mass index (BMI), the MMRP deficiency rate was also shown to increase gradually. There was a close association between MMRP expression deficiency and family history of cancer (P<0.05). For TNM stage III patients, the Kaplan-Meier survival curve showed that the aberrant MMRP expression group had a three-year disease-free survival (DFS) rate of 66.67%, which was longer than the DFS rate of the normal group (55.41%), with no statistical difference (P>0.05). In conclusion, the immunohistochemistry PV-9000 two-step method can be used to measure MMRP expression in colorectal cancer. Aberrant MMRP expression is closely correlated with tumor location, histological type, BMI and tumor family history in sporadic colorectal cancer. Aberrant MMRP expression may have an effect on the prognosis of stage III patients.
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Affiliation(s)
- Zhenqiang Sun
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China ; Research Laboratory of Disease Genomics, Cancer Research Institute, Central South University, Changsha, Hunan 4170078, P.R. China
| | - Xianbo Yu
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Haijiang Wang
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Shuo Zhang
- Department of Pathology, The Second Affiliated Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Zeliang Zhao
- Department of Gastrointestinal Surgery, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
| | - Ruiwei Xu
- Infection & Statistical Office, Affiliated Tumor Hospital, Xinjiang Medical University, Urumqi, Xinjiang 830011, P.R. China
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Walker LC, Whiley PJ, Houdayer C, Hansen TVO, Vega A, Santamarina M, Blanco A, Fachal L, Southey MC, Lafferty A, Colombo M, De Vecchi G, Radice P, Spurdle AB. Evaluation of a 5-Tier Scheme Proposed for Classification of Sequence Variants Using Bioinformatic and Splicing Assay Data: Inter-Reviewer Variability and Promotion of Minimum Reporting Guidelines. Hum Mutat 2013; 34:1424-31. [DOI: 10.1002/humu.22388] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 07/12/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Logan C. Walker
- Department of Pathology; University of Otago; Christchurch; New Zealand
| | | | - Claude Houdayer
- Service de Génétique, INSERM U830, Institut Curie et Université Paris Descartes; Sorbonne Paris Cité; Paris; France
| | - Thomas V. O. Hansen
- Center for Genomic Medicine; Copenhagen University Hospital; Rigshospitalet; Copenhagen; Denmark
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Marta Santamarina
- Grupo de Medicina Xenómica -USC, University of Santiago de Compostela; CIBERER; IDIS; Santiago de Compostela; Spain
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Melissa C. Southey
- Epidemiology Laboratory, Department of Pathology; The University of Melbourne; Melbourne; Victoria; Australia
| | | | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Biology Division; Queensland Institute of Medical Research; Herston; Queensland; Australia
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