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Wang Y, Zuo J, Duan C, Peng H, Huang J, Zhao L, Zhang L, Dong Z. Large language models assisted multi-effect variants mining on cerebral cavernous malformation familial whole genome sequencing. Comput Struct Biotechnol J 2024; 23:843-858. [PMID: 38352937 PMCID: PMC10861960 DOI: 10.1016/j.csbj.2024.01.014] [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: 10/16/2023] [Revised: 01/04/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024] Open
Abstract
Cerebral cavernous malformation (CCM) is a polygenic disease with intricate genetic interactions contributing to quantitative pathogenesis across multiple factors. The principal pathogenic genes of CCM, specifically KRIT1, CCM2, and PDCD10, have been reported, accompanied by a growing wealth of genetic data related to mutations. Furthermore, numerous other molecules associated with CCM have been unearthed. However, tackling such massive volumes of unstructured data remains challenging until the advent of advanced large language models. In this study, we developed an automated analytical pipeline specialized in single nucleotide variants (SNVs) related biomedical text analysis called BRLM. To facilitate this, BioBERT was employed to vectorize the rich information of SNVs, while a deep residue network was used to discriminate the classes of the SNVs. BRLM was initially constructed on mutations from 12 different types of TCGA cancers, achieving an accuracy exceeding 99%. It was further examined for CCM mutations in familial sequencing data analysis, highlighting an upstream master regulator gene fibroblast growth factor 1 (FGF1). With multi-omics characterization and validation in biological function, FGF1 demonstrated to play a significant role in the development of CCMs, which proved the effectiveness of our model. The BRLM web server is available at http://1.117.230.196.
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Affiliation(s)
- Yiqi Wang
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jinmei Zuo
- Physical Examination Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Chao Duan
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Hao Peng
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Jia Huang
- The Second Clinical Medical College, Lanzhou University, No. 222, South Tianshui Road, Lanzhou 730030, Gansu, China
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, No. 32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Li Zhang
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
- Department of Neurosurgery, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
| | - Zhiqiang Dong
- College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Wuhan 430070, Hubei, China
- Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, No.32, Renmin South Road, Shiyan 442000, Hubei, China
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Chaussenot A, Ayrignac X, Chatron N, Granchon-Riolzir T, Labauge P, Tournier-Lasserve E, Riant F. Loss of heterozygosity in CCM2 cDNA revealing a structural variant causing multiple cerebral cavernous malformations. Eur J Hum Genet 2024; 32:876-878. [PMID: 38755314 PMCID: PMC11219781 DOI: 10.1038/s41431-024-01626-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/29/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024] Open
Abstract
Loss-of-function variants in CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10 genes are identified in the vast majority of familial cases with multiple cerebral cavernous malformations. However, genomic DNA sequencing combined with large rearrangement screening fails to detect a pathogenic variant in 5% of the patients. We report a family with two affected members harboring multiple CCM lesions, one with severe hemorrhages and one asymptomatic. No causative variant was detected using DNA sequencing of the three CCM genes, CNV detection analysis, and RNA sequencing. However, a loss of heterozygosity in CCM2 was observed on cDNA sequences in one of the two affected members, which strongly suggested that this locus might be involved. Whole genome sequencing (WGS) identified a balanced structural variant on chromosome 7 with a breakpoint interrupting the CCM2 gene, preventing normal mRNA synthesis. These data underline the importance of WGS in undiagnosed patients with typical multiple CCM.
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Affiliation(s)
- Annabelle Chaussenot
- Department of Medical Genetics, Hôpital de l'Archet 2, CHU de Nice, Nice, France
| | - Xavier Ayrignac
- Department of Neurology, Gui de Chauliac Montpellier University Hospital, Montpellier University, Montpellier, France
| | - Nicolas Chatron
- Department of Medical Genetics, Hospices Civils de Lyon, Groupe Hospitalier Est, Bron, France
- Laboratoire AURAGEN (Plan France Médecine Génomique 2025), Lyon, France
| | - Terry Granchon-Riolzir
- Department of Neurovascular Molecular Genetics AP-HP, Saint-Louis Hospital, Paris, France
- Reference Center for Rare Vascular Diseases of the Central Nervous System and the Retina (CERVCO), APHP Lariboisiere Hospital, Paris, France
| | - Pierre Labauge
- Department of Neurology, Gui de Chauliac Montpellier University Hospital, Montpellier University, Montpellier, France
| | - Elisabeth Tournier-Lasserve
- Department of Neurovascular Molecular Genetics AP-HP, Saint-Louis Hospital, Paris, France
- Reference Center for Rare Vascular Diseases of the Central Nervous System and the Retina (CERVCO), APHP Lariboisiere Hospital, Paris, France
| | - Florence Riant
- Laboratoire AURAGEN (Plan France Médecine Génomique 2025), Lyon, France.
- Department of Neurovascular Molecular Genetics AP-HP, Saint-Louis Hospital, Paris, France.
- Reference Center for Rare Vascular Diseases of the Central Nervous System and the Retina (CERVCO), APHP Lariboisiere Hospital, Paris, France.
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3
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Genetics of brain arteriovenous malformations and cerebral cavernous malformations. J Hum Genet 2023; 68:157-167. [PMID: 35831630 DOI: 10.1038/s10038-022-01063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/13/2022] [Accepted: 06/26/2022] [Indexed: 11/08/2022]
Abstract
Cerebrovascular malformations comprise abnormal development of cerebral vasculature. They can result in hemorrhagic stroke due to rupture of lesions as well as seizures and neurological defects. The most common forms of cerebrovascular malformations are brain arteriovenous malformations (bAVMs) and cerebral cavernous malformations (CCMs). They occur in both sporadic and inherited forms. Rapidly evolving molecular genetic methodologies have helped to identify causative or associated genes involved in genesis of bAVMs and CCMs. In this review, we highlight the current knowledge regarding the genetic basis of these malformations.
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Skowronek D, Pilz RA, Bonde L, Schamuhn OJ, Feldmann JL, Hoffjan S, Much CD, Felbor U, Rath M. Cas9-Mediated Nanopore Sequencing Enables Precise Characterization of Structural Variants in CCM Genes. Int J Mol Sci 2022; 23:ijms232415639. [PMID: 36555281 PMCID: PMC9779250 DOI: 10.3390/ijms232415639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Deletions in the CCM1, CCM2, and CCM3 genes are a common cause of familial cerebral cavernous malformations (CCMs). In current molecular genetic laboratories, targeted next-generation sequencing or multiplex ligation-dependent probe amplification are mostly used to identify copy number variants (CNVs). However, both techniques are limited in their ability to specify the breakpoints of CNVs and identify complex structural variants (SVs). To overcome these constraints, we established a targeted Cas9-mediated nanopore sequencing approach for CNV detection with single nucleotide resolution. Using a MinION device, we achieved complete coverage for the CCM genes and determined the exact size of CNVs in positive controls. Long-read sequencing for a CCM1 and CCM2 CNV revealed that the adjacent ANKIB1 and NACAD genes were also partially or completely deleted. In addition, an interchromosomal insertion and an inversion in CCM2 were reliably re-identified by long-read sequencing. The refinement of CNV breakpoints by long-read sequencing enabled fast and inexpensive PCR-based variant confirmation, which is highly desirable to reduce costs in subsequent family analyses. In conclusion, Cas9-mediated nanopore sequencing is a cost-effective and flexible tool for molecular genetic diagnostics which can be easily adapted to various target regions.
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Affiliation(s)
- Dariush Skowronek
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Robin A. Pilz
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Loisa Bonde
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Ole J. Schamuhn
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Janne L. Feldmann
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University, 44801 Bochum, Germany
| | - Christiane D. Much
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
| | - Matthias Rath
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, 17475 Greifswald, Germany
- Department of Human Medicine and Institute for Molecular Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
- Correspondence:
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Pluta N, Hoffjan S, Zimmer F, Köhler C, Lücke T, Mohr J, Vorgerd M, Nguyen HHP, Atlan D, Wolf B, Zaum AK, Rost S. Homozygous Inversion on Chromosome 13 Involving SGCG Detected by Short Read Whole Genome Sequencing in a Patient Suffering from Limb-Girdle Muscular Dystrophy. Genes (Basel) 2022; 13:genes13101752. [PMID: 36292638 PMCID: PMC9601614 DOI: 10.3390/genes13101752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
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Affiliation(s)
- Natalie Pluta
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University Bochum, 44801 Bochum, Germany
- Correspondence:
| | - Frederic Zimmer
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Cornelia Köhler
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Thomas Lücke
- Department of Neuropaediatrics, University Children’s Hospital, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Jennifer Mohr
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr-University Bochum, 44789 Bochum, Germany
| | | | - David Atlan
- Phenosystems SA, 1440 Braine le Chateau, Belgium
| | - Beat Wolf
- iCoSys, University of Applied Sciences Western Switzerland, 1700 Fribourg, Switzerland
| | - Ann-Kathrin Zaum
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Medical Genetics Center (MGZ), 80335 Munich, Germany
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Pilz RA, Skowronek D, Hamed M, Weise A, Mangold E, Radbruch A, Pietsch T, Felbor U, Rath M. Using CRISPR/Cas9 genome editing in human iPSCs for deciphering the pathogenicity of a novel CCM1 transcription start site deletion. Front Mol Biosci 2022; 9:953048. [PMID: 36090026 PMCID: PMC9453596 DOI: 10.3389/fmolb.2022.953048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Cerebral cavernous malformations are clusters of aberrant vessels that can lead to severe neurological complications. Pathogenic loss-of-function variants in the CCM1, CCM2, or CCM3 gene are associated with the autosomal dominant form of the disease. While interpretation of variants in protein-coding regions of the genes is relatively straightforward, functional analyses are often required to evaluate the impact of non-coding variants. Because of multiple alternatively spliced transcripts and different transcription start points, interpretation of variants in the 5′ untranslated and upstream regions of CCM1 is particularly challenging. Here, we identified a novel deletion of the non-coding exon 1 of CCM1 in a proband with multiple CCMs which was initially classified as a variant of unknown clinical significance. Using CRISPR/Cas9 genome editing in human iPSCs, we show that the deletion leads to loss of CCM1 protein and deregulation of KLF2, THBS1, NOS3, and HEY2 expression in iPSC-derived endothelial cells. Based on these results, the variant could be reclassified as likely pathogenic. Taken together, variants in regulatory regions need to be considered in genetic CCM analyses. Our study also demonstrates that modeling variants of unknown clinical significance in an iPSC-based system can help to come to a final diagnosis.
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Affiliation(s)
- Robin A. Pilz
- Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Dariush Skowronek
- Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Motaz Hamed
- Department of Neurosurgery, University Hospital Bonn, Bonn, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, Medical Faculty and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Torsten Pietsch
- Institute of Neuropathology, DGNN Brain Tumor Reference Center, University of Bonn, Bonn, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Matthias Rath
- Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- *Correspondence: Matthias Rath,
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7
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Padarti A, Belkin O, Abou-Fadel J, Zhang J. In-silico analysis of nonsynonymous genomic variants within CCM2 gene reaffirm the existence of dual cores within typical PTB domain. Biochem Biophys Rep 2022; 29:101218. [PMID: 35128084 PMCID: PMC8808078 DOI: 10.1016/j.bbrep.2022.101218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/11/2022] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose The objective of this study is to validate the existence of dual cores within the typical phosphotyrosine binding (PTB) domain and to identify potentially damaging and pathogenic nonsynonymous coding single nuclear polymorphisms (nsSNPs) in the canonical PTB domain of the CCM2 gene that causes cerebral cavernous malformations (CCMs). Methods The nsSNPs within the coding sequence for PTB domain of human CCM2 gene, retrieved from exclusive database searches, were analyzed for their functional and structural impact using a series of bioinformatic tools. The effects of mutations on the tertiary structure of the PTB domain in human CCM2 protein were predicted to examine the effect of nsSNPs on the tertiary structure of PTB Cores. Results Our mutation analysis, through alignment of protein structures between wildtype CCM2 and mutant, predicted that the structural impacts of pathogenic nsSNPs is biophysically limited to only the spatially adjacent substituted amino acid site with minimal structural influence on the adjacent core of the PTB domain, suggesting both cores are independently functional and essential for proper CCM2 PTB function. Conclusion Utilizing a combination of protein conservation and structure-based analysis, we analyzed the structural effects of inherited pathogenic mutations within the CCM2 PTB domain. Our results predicted that the pathogenic amino acid substitutions lead to only subtle changes locally, confined to the surrounding tertiary structure of the PTB core within which it resides, while no structural disturbance to the neighboring PTB core was observed, reaffirming the presence of independently functional dual cores in the CCM2 typical PTB domain. The pathogenic amino acid mutants lead to subtle structural changes in the PTB core. No structural disturbance to the neighboring PTB core was observed. Data reaffirm the presence of dual functional cores in the CCM2 PTB domain. More new genetic variants leading to CCM pathogenesis were suggested.
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Damián A, Ionescu RO, Rodríguez de Alba M, Tamayo A, Trujillo-Tiebas MJ, Cotarelo-Pérez MC, Pérez Rodríguez O, Villaverde C, de la Fuente L, Romero R, Núñez-Moreno G, Mínguez P, Ayuso C, Cortón M. Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts. Int J Mol Sci 2021; 22:ijms222312713. [PMID: 34884523 PMCID: PMC8657747 DOI: 10.3390/ijms222312713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.
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Affiliation(s)
- Alejandra Damián
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Raluca Oancea Ionescu
- Department of Medical Genetics, University Hospital Clínico San Carlos, 28040 Madrid, Spain; (R.O.I.); (M.C.C.P.)
| | - Marta Rodríguez de Alba
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Alejandra Tamayo
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - María Carmen Cotarelo-Pérez
- Department of Medical Genetics, University Hospital Clínico San Carlos, 28040 Madrid, Spain; (R.O.I.); (M.C.C.P.)
| | - Olga Pérez Rodríguez
- Department of Pediatrics, University Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Raquel Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Gonzalo Núñez-Moreno
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (A.D.); (M.R.d.A.); (A.T.); (M.J.T.-T); (C.V.); (L.d.l.F.); (R.R.); (G.N.-M); (P.M.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 28290 Madrid, Spain
- Correspondence:
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9
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First interchromosomal insertion in a patient with cerebral and spinal cavernous malformations. Sci Rep 2020; 10:6306. [PMID: 32286434 PMCID: PMC7156631 DOI: 10.1038/s41598-020-63337-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 01/06/2023] Open
Abstract
Autosomal dominant cerebral cavernous malformations (CCM) are leaky vascular lesions that can cause epileptic seizures and stroke-like symptoms. Germline mutations in either CCM1, CCM2 or CCM3 are found in the majority of patients with multiple CCMs or a positive family history. Recently, the first copy number neutral inversion in CCM2 has been identified by whole genome sequencing in an apparently mutation-negative CCM family. We here asked the question whether further structural genomic rearrangements can be detected within NGS gene panel data of unsolved CCM cases. Hybrid capture NGS data of eight index patients without a pathogenic single nucleotide, indel or copy number variant were analyzed using two bioinformatics pipelines. In a 58-year-old male with multiple CCMs in his brain and spinal cord, we identified a 294 kb insertion within the coding sequence of CCM2. Fine mapping of the breakpoints, molecular cytogenetic studies, and multiplex ligation-dependent probe amplification verified that the structural variation was an inverted unbalanced insertion that originated from 1p12-p11.2. As this rearrangement disrupts exon 6 of CCM2 on 7p13, it was classified as pathogenic. Our study demonstrates that efforts to detect structural variations in known disease genes increase the diagnostic sensitivity of genetic analyses for well-defined Mendelian disorders.
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10
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Zafar A, Quadri SA, Farooqui M, Ikram A, Robinson M, Hart BL, Mabray MC, Vigil C, Tang AT, Kahn ML, Yonas H, Lawton MT, Kim H, Morrison L. Familial Cerebral Cavernous Malformations. Stroke 2020; 50:1294-1301. [PMID: 30909834 DOI: 10.1161/strokeaha.118.022314] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Atif Zafar
- From the Departments of Neurology (A.Z., M.F., A.I., M.R., L.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Syed A Quadri
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston (S.A.Q.)
| | - Mudassir Farooqui
- From the Departments of Neurology (A.Z., M.F., A.I., M.R., L.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Asad Ikram
- From the Departments of Neurology (A.Z., M.F., A.I., M.R., L.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Myranda Robinson
- From the Departments of Neurology (A.Z., M.F., A.I., M.R., L.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Blaine L Hart
- Radiology (B.L.H., M.C.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Marc C Mabray
- Radiology (B.L.H., M.C.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | | | - Alan T Tang
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia (A.T.T., M.L.K.)
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia (A.T.T., M.L.K.)
| | - Howard Yonas
- Neurosurgery (H.Y.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
| | - Michael T Lawton
- Department of Neurosurgery, Barrow Neurological Institute, Phoenix, AZ (M.T.L.)
| | - Helen Kim
- Department of Anesthesia and Perioperative Care and Department of Epidemiology and Biostatistics, University of California San Francisco (H.K.)
| | - Leslie Morrison
- From the Departments of Neurology (A.Z., M.F., A.I., M.R., L.M.), University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque
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11
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Much CD, Schwefel K, Skowronek D, Shoubash L, von Podewils F, Elbracht M, Spiegler S, Kurth I, Flöel A, Schroeder HWS, Felbor U, Rath M. Novel Pathogenic Variants in a Cassette Exon of CCM2 in Patients With Cerebral Cavernous Malformations. Front Neurol 2019; 10:1219. [PMID: 31824402 PMCID: PMC6879547 DOI: 10.3389/fneur.2019.01219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/01/2019] [Indexed: 01/11/2023] Open
Abstract
Autosomal dominant cerebral cavernous malformation (CCM) represents a genetic disorder with a high mutation detection rate given that stringent inclusion criteria are used and copy number variation analyses are part of the diagnostic workflow. Pathogenic variants in either CCM1 (KRIT1), CCM2 or CCM3 (PDCD10) can be identified in 87–98% of CCM families with at least two affected individuals. However, the interpretation of novel sequence variants in the 5′-region of CCM2 remains challenging as there are various alternatively spliced transcripts and different transcription start sites. Comprehensive genetic and clinical data of CCM2 patients with variants in cassette exons that are either skipped or included into alternative CCM2 transcripts in the splicing process can significantly facilitate clinical variant interpretation. We here report novel pathogenic CCM2 variants in exon 3 and the adjacent donor splice site, describe the natural history of CCM disease in mutation carriers and provide further evidence for the classification of the amino acids encoded by the nucleotides of this cassette exon as a critical region within CCM2. Finally, we illustrate the advantage of a combined single nucleotide and copy number variation detection approach in NGS-based CCM1/CCM2/CCM3 gene panel analyses which can significantly reduce diagnostic turnaround time.
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Affiliation(s)
- Christiane D Much
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Konrad Schwefel
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Dariush Skowronek
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Loay Shoubash
- Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany
| | - Felix von Podewils
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Stefanie Spiegler
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Agnes Flöel
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany
| | - Henry W S Schroeder
- Department of Neurosurgery, University Medicine Greifswald, Greifswald, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Matthias Rath
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
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12
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Abstract
PURPOSE OF REVIEW Vascular malformations (VaMs) are a consequence of disrupted morphogenesis that may involve arterial, capillary, venous, or lymphatic endothelium alone or in a combination. VaMs can have serious health impacts, leading to life-threatening conditions sometimes. Genetic mutations affecting proliferation, migration, adhesion, differentiation, and survival of endothelial cells, as well as integrity of extracellular matrix are believed to be the pathogenesis of these disorders. Here, we present an updated review of genetic mutations and potential therapeutic targets for VaMs. RECENT FINDINGS Increased number of genetic mutations have been discovered in vascular anomalies via targeted deep sequencing. When a genetic defect is identified, it often presents in only a small percentage of cells within the malformation. In addition, mutations within the same gene may result in different clinical phenotypes. Management of VaMs can be challenging depending on the severity and functional impairment associated. There are no standard treatment algorithms available to date for VaMs, therefore the disorder has significant unmet clinical needs. Currently, the focus of therapeutic development is to target constitutively activated intracellular signaling pathways resulted from genetic mutations. SUMMARY Knowledge about the genetic mutations and altered signaling pathways related to VaMs have improved our understanding about the pathogenesis of vascular anomalies and provided insights to the development of new targeted therapies.
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13
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Karschnia P, Nishimura S, Louvi A. Cerebrovascular disorders associated with genetic lesions. Cell Mol Life Sci 2019; 76:283-300. [PMID: 30327838 PMCID: PMC6450555 DOI: 10.1007/s00018-018-2934-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 01/15/2023]
Abstract
Cerebrovascular disorders are underlain by perturbations in cerebral blood flow and abnormalities in blood vessel structure. Here, we provide an overview of the current knowledge of select cerebrovascular disorders that are associated with genetic lesions and connect genomic findings with analyses aiming to elucidate the cellular and molecular mechanisms of disease pathogenesis. We argue that a mechanistic understanding of genetic (familial) forms of cerebrovascular disease is a prerequisite for the development of rational therapeutic approaches, and has wider implications for treatment of sporadic (non-familial) forms, which are usually more common.
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Affiliation(s)
- Philipp Karschnia
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA
| | - Sayoko Nishimura
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA
| | - Angeliki Louvi
- Departments of Neurosurgery and Neuroscience, Program on Neurogenetics, Yale School of Medicine, P.O. Box 208082, New Haven, CT, 06520-8082, USA.
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14
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Nardella G, Visci G, Guarnieri V, Castellana S, Biagini T, Bisceglia L, Palumbo O, Trivisano M, Vaira C, Scerrati M, Debrasi D, D'Angelo V, Carella M, Merla G, Mazza T, Castori M, D'Agruma L, Fusco C. A single-center study on 140 patients with cerebral cavernous malformations: 28 new pathogenic variants and functional characterization of a PDCD10 large deletion. Hum Mutat 2018; 39:1885-1900. [PMID: 30161288 DOI: 10.1002/humu.23629] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/12/2018] [Accepted: 07/22/2018] [Indexed: 12/12/2022]
Abstract
Cerebral cavernous malformation (CCM) is a capillary malformation arising in the central nervous system. CCM may occur sporadically or cluster in families with autosomal dominant transmission, incomplete penetrance, and variable expressivity. Three genes are associated with CCM KRIT1, CCM2, and PDCD10. This work is a retrospective single-center molecular study on samples from multiple Italian clinical providers. From a pool of 317 CCM index patients, we found germline variants in either of the three genes in 80 (25.2%) probands, for a total of 55 different variants. In available families, extended molecular analysis found segregation in 60 additional subjects, for a total of 140 mutated individuals. From the 55 variants, 39 occurred in KRIT1 (20 novel), 8 in CCM2 (4 novel), and 8 in PDCD10 (4 novel). Effects of the three novel KRIT1 missense variants were characterized in silico. We also investigated a novel PDCD10 deletion spanning exon 4-10, on patient's fibroblasts, which showed significant reduction of interactions between KRIT1 and CCM2 encoded proteins and impaired autophagy process. This is the largest study in Italian CCM patients and expands the known mutational spectrum of KRIT1, CCM2, and PDCD10. Our approach highlights the relevance of seeking supporting information to pathogenicity of new variants for the improvement of management of CCM.
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Affiliation(s)
- Grazia Nardella
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy.,Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Grazia Visci
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vito Guarnieri
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Luigi Bisceglia
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marina Trivisano
- Department of Neuroscience, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Carmela Vaira
- Department of Neurosurgery, Università Politecnica delle Marche, Ancona, Italy
| | - Massimo Scerrati
- Department of Neurosurgery, Università Politecnica delle Marche, Ancona, Italy
| | - Davide Debrasi
- Department of Pediatrics, Università Federico II, Naples, Italy
| | | | - Massimo Carella
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Leonardo D'Agruma
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Carmela Fusco
- Division of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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15
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Spiegler S, Rath M, Paperlein C, Felbor U. Cerebral Cavernous Malformations: An Update on Prevalence, Molecular Genetic Analyses, and Genetic Counselling. Mol Syndromol 2018; 9:60-69. [PMID: 29593473 PMCID: PMC5836221 DOI: 10.1159/000486292] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2017] [Indexed: 11/19/2022] Open
Abstract
Based on the latest gnomAD dataset, the prevalence of symptomatic hereditary cerebral cavernous malformations (CCMs) prone to cause epileptic seizures and stroke-like symptoms was re-evaluated in this review and calculated to be 1:5,400-1:6,200. Furthermore, state-of-the-art molecular genetic analyses of the known CCM loci are described which reach an almost 100% mutation detection rate for familial CCMs if whole genome sequencing is performed for seemingly mutation-negative families. An update on the spectrum of CCM1, CCM2, and CCM3 mutations demonstrates that deep-intronic mutations and submicroscopic copy-number neutral genomic rearrangements are rare. Finally, this review points to current guidelines on genetic counselling, neuroimaging, medical as well as neurosurgical treatment and highlights the formation of active patient organizations in various countries.
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Affiliation(s)
- Stefanie Spiegler
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald
| | - Matthias Rath
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald
| | - Christin Paperlein
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Ute Felbor
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald
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