1
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Chumakova OS, Baulina NM. Advanced searching for hypertrophic cardiomyopathy heritability in real practice tomorrow. Front Cardiovasc Med 2023; 10:1236539. [PMID: 37583586 PMCID: PMC10425241 DOI: 10.3389/fcvm.2023.1236539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease associated with morbidity and mortality at any age. As studies in recent decades have shown, the genetic architecture of HCM is quite complex both in the entire population and in each patient. In the rapidly advancing era of gene therapy, we have to provide a detailed molecular diagnosis to our patients to give them the chance for better and more personalized treatment. In addition to emphasizing the importance of genetic testing in routine practice, this review aims to discuss the possibility to go a step further and create an expanded genetic panel that contains not only variants in core genes but also new candidate genes, including those located in deep intron regions, as well as structural variations. It also highlights the benefits of calculating polygenic risk scores based on a combination of rare and common genetic variants for each patient and of using non-genetic HCM markers, such as microRNAs that can enhance stratification of risk for HCM in unselected populations alongside rare genetic variants and clinical factors. While this review is focusing on HCM, the discussed issues are relevant to other cardiomyopathies.
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Affiliation(s)
- Olga S. Chumakova
- Laboratory of Functional Genomics of Cardiovascular Diseases, National Medical Research Centre of Cardiology Named After E.I. Chazov, Moscow, Russia
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2
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Genotype-Phenotype Correlations in Neurofibromatosis Type 1: Identification of Novel and Recurrent NF1 Gene Variants and Correlations with Neurocognitive Phenotype. Genes (Basel) 2022; 13:genes13071130. [PMID: 35885913 PMCID: PMC9316015 DOI: 10.3390/genes13071130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 02/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is one of the most common genetic tumor predisposition syndrome, caused by mutations in the NF1. To date, few genotype-phenotype correlations have been discerned in NF1, due to a highly variable clinical presentation. We aimed to study the molecular spectrum of NF1 and genotype-phenotype correlations in a monocentric study cohort of 85 NF1 patients (20 relatives, 65 sporadic cases). Clinical data were collected at the time of the mutation analysis and reviewed for accuracy in this investigation. An internal phenotypic categorization was applied. The 94% of the patients enrolled showed a severe phenotype with at least one systemic complication and a wide range of associated malignancies. Spine deformities were the most common complications in this cohort. We also reported 66 different NF1 mutations, of which 7 are novel mutations. Correlation analysis identified a slight significant inverse correlation between age at diagnosis and delayed acquisition of psychomotor skills with residual multi-domain cognitive impairment. Odds ratio with 95% confidence interval showed a higher prevalence of learning disabilities in patients carrying frameshift mutations. Overall, our results aim to offer an interesting contribution to studies on the genotype–phenotype of NF1 and in genetic management and counselling.
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3
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Aguilar M, Zhang H, Zhang M, Cantarell B, Sahoo SS, Li HD, Cuevas IC, Lea J, Miller DS, Chen H, Zheng W, Gagan J, Lucas E, Castrillon DH. Serial genomic analysis of endometrium supports the existence of histologically indistinct endometrial cancer precursors. J Pathol 2021; 254:20-30. [PMID: 33506979 PMCID: PMC8252414 DOI: 10.1002/path.5628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 11/18/2022]
Abstract
The endometrium is unique as an accessible anatomic location that can be repeatedly biopsied and where diagnostic biopsies do not extirpate neoplastic lesions. We exploited these features to retrospectively characterize serial genomic alterations along the precancer/cancer continuum in individual women. Cases were selected based on (1) endometrial cancer diagnosis/hysterectomy and (2) preceding serial endometrial biopsies including for some patients an early biopsy before a precancer histologic diagnosis. A comprehensive panel was designed for endometrial cancer genes. Formalin‐fixed, paraffin‐embedded specimens for each cancer, preceding biopsies, and matched germline samples were subjected to barcoded high‐throughput sequencing to identify mutations and track their origin and allelic frequency progression. In total, 92 samples from 21 patients were analyzed, providing an opportunity for new insights into early endometrial cancer progression. Definitive invasive endometrial cancers exhibited expected mutational spectra, and canonical driver mutations were detectable in preceding biopsies. Notably, ≥1 cancer mutations were detected prior to the histopathologic diagnosis of an endometrial precancer in the majority of patients. In 18/21 cases, ≥1 mutations were confirmed by abnormal protein levels or subcellular localization by immunohistochemistry, confirming genomic data and providing unique views of histologic correlates. In 19 control endometria, mutation counts were lower, with a lack of canonical endometrial cancer hotspot mutations. Our study documents the existence of endometrial lesions that are histologically indistinct but are bona fide endometrial cancer precursors. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Mitzi Aguilar
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Musi Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Brandi Cantarell
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Subhransu S Sahoo
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hao-Dong Li
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ileana C Cuevas
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jayanthi Lea
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David S Miller
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hao Chen
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wenxin Zheng
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elena Lucas
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Diego H Castrillon
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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4
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Morbidoni V, Baschiera E, Forzan M, Fumini V, Ali DS, Giorgi G, Buson L, Desbats MA, Cassina M, Clementi M, Salviati L, Trevisson E. Hybrid Minigene Assay: An Efficient Tool to Characterize mRNA Splicing Profiles of NF1 Variants. Cancers (Basel) 2021; 13:cancers13050999. [PMID: 33673681 PMCID: PMC7957615 DOI: 10.3390/cancers13050999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is caused by heterozygous loss of function mutations in the NF1 gene. Although patients are diagnosed according to clinical criteria and few genotype-phenotype correlations are known, molecular analysis remains important. NF1 displays allelic heterogeneity, with a high proportion of variants affecting splicing, including deep intronic alleles and changes outside the canonical splice sites, making validation problematic. Next Generation Sequencing (NGS) technologies integrated with multiplex ligation-dependent probe amplification (MLPA) have largely overcome RNA-based techniques but do not detect splicing defects. A rapid minigene-based system was set up to test the effects of NF1 variants on splicing. We investigated 29 intronic and exonic NF1 variants identified in patients during the diagnostic process. The minigene assay showed the coexistence of multiple mechanisms of splicing alterations for seven variants. A leaky effect on splicing was documented in one de novo substitution detected in a sporadic patient with a specific phenotype without neurofibromas. Our splicing assay proved to be a reliable and fast method to validate novel NF1 variants potentially affecting splicing and to detect hypomorphic effects that might have phenotypic consequences, avoiding the requirement of patient's RNA.
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Affiliation(s)
- Valeria Morbidoni
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Elisa Baschiera
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Monica Forzan
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Valentina Fumini
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Dario Seif Ali
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Gianpietro Giorgi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Lisa Buson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Maria Andrea Desbats
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
| | - Leonardo Salviati
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women’s and Children’s Health, University of Padova, 35128 Padova, Italy; (V.M.); (E.B.); (M.F.); (V.F.); (D.S.A.); (G.G.); (L.B.); (M.A.D.); (M.C.); (M.C.); (L.S.)
- Istituto di Ricerca Pediatrica—IRP, Fondazione Città della Speranza, 35127 Padova, Italy
- Correspondence: ; Tel.: + 39-(04)-9821-1402
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5
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Schmidt B, Hildebrandt A. Deep learning in next-generation sequencing. Drug Discov Today 2021; 26:173-180. [PMID: 33059075 PMCID: PMC7550123 DOI: 10.1016/j.drudis.2020.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/16/2020] [Accepted: 10/07/2020] [Indexed: 12/22/2022]
Abstract
Next-generation sequencing (NGS) methods lie at the heart of large parts of biological and medical research. Their fundamental importance has created a continuously increasing demand for processing and analysis methods of the data sets produced, addressing questions such as variant calling, metagenomic classification and quantification, genomic feature detection, or downstream analysis in larger biological or medical contexts. In addition to classical algorithmic approaches, machine-learning (ML) techniques are often used for such tasks. In particular, deep learning (DL) methods that use multilayered artificial neural networks (ANNs) for supervised, semisupervised, and unsupervised learning have gained significant traction for such applications. Here, we highlight important network architectures, application areas, and DL frameworks in a NGS context.
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Affiliation(s)
- Bertil Schmidt
- Institut für Informatik, Johannes Gutenberg University Mainz, Germany.
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6
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Vanden Bempt I, Vander Borght S, Sciot R, Spans L, Claerhout S, Brems H, Lehnert S, Dehaspe L, Fransis S, Neuville B, Topal B, Schöffski P, Legius E, Debiec-Rychter M. Comprehensive targeted next-generation sequencing approach in the molecular diagnosis of gastrointestinal stromal tumor. Genes Chromosomes Cancer 2020; 60:239-249. [PMID: 33258138 DOI: 10.1002/gcc.22923] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 12/26/2022] Open
Abstract
Mutational analysis guides therapeutic decision making in patients with advanced-stage gastrointestinal stromal tumors (GISTs). We evaluated three targeted next-generation sequencing (NGS) assays, consecutively used over 4 years in our laboratory for mutational analysis of 162 primary GISTs: Agilent GIST MASTR, Illumina TruSight 26 and an in-house developed 96 gene panels. In addition, we investigated the feasibility of a more comprehensive approach by adding targeted RNA sequencing (Archer FusionPlex, 11 genes) in an attempt to reduce the number of Wild Type GISTs. We found KIT or PDGFRA mutations in 149 out of 162 GISTs (92.0%). Challenging KIT exon 11 alterations were initially missed by different assays in seven GISTs and typically represented deletions at the KIT intron 10-exon 11 boundary or large insertions/deletions (>24 base pairs). Comprehensive analysis led to the additional identification of driver alterations in 8/162 GISTs (4.9%): apart from BRAF and SDHA mutations (one case each), we found five GISTs harboring somatic neurofibromatosis type 1 (NF1) alterations (3.1%) and one case with an in-frame TRIM4-BRAF fusion not reported in GIST before. Eventually, no driver alteration was found in two out of 162 GISTs (1.2%) and three samples (1.9%) failed analysis. Our study shows that a comprehensive targeted NGS approach is feasible for routine mutational analysis of GIST, thereby substantially reducing the number of Wild Type GISTs, and highlights the need to optimize assays for challenging KIT exon 11 alterations.
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Affiliation(s)
- Isabelle Vanden Bempt
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.,Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Raf Sciot
- Department of Pathology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Lien Spans
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Sofie Claerhout
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Hilde Brems
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Stefan Lehnert
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Luc Dehaspe
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Sabine Fransis
- Department of Pathology, Ziekenhuis Oost Limburg, Genk, Belgium
| | - Bart Neuville
- Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, Genk, Belgium
| | - Baki Topal
- Department of Abdominal Surgery, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, and Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium.,Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium
| | - Eric Legius
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Maria Debiec-Rychter
- Department for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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7
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Malekkou A, Sevastou I, Mavrikiou G, Georgiou T, Vilageliu L, Moraitou M, Michelakakis H, Prokopiou C, Drousiotou A. A novel mutation deep within intron 7 of the GBA gene causes Gaucher disease. Mol Genet Genomic Med 2020; 8:e1090. [PMID: 31943857 PMCID: PMC7057115 DOI: 10.1002/mgg3.1090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Mutations in the GBA gene that encodes the lysosomal enzyme acid β-glucocerebrosidase cause Gaucher disease (GD), the most common lysosomal storage disorder. Most of the mutations are missense/nonsense, however, a few splicing mutations within or close to conserved consensus donor or acceptor splice sites have also been described. The aim of the study was to identify the mutation(s) in a Cypriot patient with type I GD. METHODS The genomic DNA of the proband was screened for nine common mutations using Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. All exons and exon-intron boundaries, and the 5'UTR and 3'UTR regions of the GBA gene, were investigated by Sanger sequencing. RNA analysis was performed using standard procedures, and the abnormal transcript was further cloned into pGEM-T-Easy plasmid vector and sequenced. The relevant intronic region was further sequenced by the Sanger method to identify the genetic variant. RESULTS A novel point mutation, g.12599C > A (c.999 + 242C > A), was detected deep in intron 7 of the GBA gene. This type of mutation has been previously described for other diseases but this is the first time, as far as we know, that it is described for GD. This mutation creates a new donor splice site leading to aberrant splicing and resulting in the insertion of the first 239nt of intron 7 as a pseudoexon in the mRNA, creating a premature stop codon. CONCLUSION This study expands the mutation spectrum of GD and highlights the importance of RNA sequencing for the molecular diagnosis of patients bearing mutations in nonexonic regions.
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Affiliation(s)
- Anna Malekkou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Ioanna Sevastou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Gavriella Mavrikiou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Theodoros Georgiou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Lluisa Vilageliu
- Department of Genetics, Faculty of Biology, Universitat de Barcelona, IBUB, CIBERER, Barcelona, Spain
| | - Marina Moraitou
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - Helen Michelakakis
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | | | - Anthi Drousiotou
- Department of Biochemical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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8
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Understanding human DNA variants affecting pre-mRNA splicing in the NGS era. ADVANCES IN GENETICS 2019; 103:39-90. [PMID: 30904096 DOI: 10.1016/bs.adgen.2018.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Pre-mRNA splicing, an essential step in eukaryotic gene expression, relies on recognition of short sequences on the primary transcript intron ends and takes place along transcription by RNA polymerase II. Exonic and intronic auxiliary elements may modify the strength of exon definition and intron recognition. Splicing DNA variants (SV) have been associated with human genetic diseases at canonical intron sites, as well as exonic substitutions putatively classified as nonsense, missense or synonymous variants. Their effects on mRNA may be modulated by cryptic splice sites associated to the SV allele, comprehending exon skipping or shortening, and partial or complete intron retention. As splicing mRNA outputs result from combinatorial effects of both intrinsic and extrinsic factors, in vitro functional assays supported by computational analyses are recommended to assist SV pathogenicity assessment for human Mendelian inheritance diseases. The increasing use of next-generating sequencing (NGS) targeting full genomic gene sequence has raised awareness of the relevance of deep intronic SV in genetic diseases and inclusion of pseudo-exons into mRNA. Finally, we take advantage of recent advances in sequencing and computational technologies to analyze alternative splicing in cancer. We explore the Catalog of Somatic Mutations in Cancer (COSMIC) to describe the proportion of splice-site mutations in cis and trans regulatory elements. Genomic data from large cohorts of different cancer types are increasingly available, in addition to repositories of normal and somatic genetic variations. These are likely to bring new insights to understanding the genetic control of alternative splicing by mapping splicing quantitative trait loci in tumors.
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9
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Wu-Chou YH, Hung TC, Lin YT, Cheng HW, Lin JL, Lin CH, Yu CC, Chen KT, Yeh TH, Chen YR. Genetic diagnosis of neurofibromatosis type 1: targeted next- generation sequencing with Multiple Ligation-Dependent Probe Amplification analysis. J Biomed Sci 2018; 25:72. [PMID: 30290804 PMCID: PMC6172719 DOI: 10.1186/s12929-018-0474-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a dominantly inherited tumor predisposition syndrome that targets the peripheral nervous system. It is caused by mutations of the NF1 gene which serve as a negative regulator of the cellular Ras/MAPK (mitogen-activated protein kinases) signaling pathway. Owing to the complexity in some parts of clinical diagnoses and the need for better understanding of its molecular relationships, a genetic characterization of this disorder will be helpful in the clinical setting. METHODS In this study, we present a customized targeted gene panel of NF1/KRAS/BRAF/p53 and SPRED1 genes combined with Multiple Ligation-Dependent Probe Amplification analysis for the NF1 mutation screening in a cohort of patients clinically suspected as NF1. RESULTS In this study, we identified 73 NF1 mutations and two BRAF novel variants from 100 NF1 patients who were suspected as having NF1. These genetic alterations are heterogeneous and distribute in a complicated way without clustering in either cysteine-serine-rich domain or within the GAP-related domain. We also detected fifteen multi-exon deletions within the NF1 gene by MLPA Analysis. CONCLUSIONS Our results suggested that a genetic screening using a NGS panel with high coverage of Ras-signaling components combined with Multiple Ligation-Dependent Probe Amplification analysis will enable differential diagnosis of patients with overlapping clinical features.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan.
| | - Tzu-Chao Hung
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Yin-Ting Lin
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Hsing-Wen Cheng
- Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Ju-Li Lin
- Division of Genetics and Endocrinology, Department of Pediatrics, Chang Gung University College of Medicine and Chang Gung Children's and Memorial Hospital, No.5, Fushing Street, Kweishan, Taoyuan, Taiwan
| | - Chih-Hung Lin
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Chung-Chih Yu
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Kuo-Ting Chen
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Tu-Hsueh Yeh
- Neuroscience Research Center, Department of Neurology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Ray Chen
- Department of Plastic & Reconstructive Surgery, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan.
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10
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Mao B, Chen S, Chen X, Yu X, Zhai X, Yang T, Li L, Wang Z, Zhao X, Zhang X. Clinical characteristics and spectrum of NF1 mutations in 12 unrelated Chinese families with neurofibromatosis type 1. BMC MEDICAL GENETICS 2018; 19:101. [PMID: 29914388 PMCID: PMC6006597 DOI: 10.1186/s12881-018-0615-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/23/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder caused by a heterozygous germline mutation in the tumor suppressor gene NF1. Because of the existence of highly homologous pseudogenes, the large size of the gene, and the heterogeneity of mutation types and positions, the detection of variations in NF1 is more difficult than that for an ordinary gene. METHODS In this study, we collected samples from 23 patients among 46 study participants from 12 unrelated Chinese families with NF1. We used a combination of Sanger sequencing, targeted next-generation sequencing, and multiplex ligation-dependent probe amplification to identify potential mutations of different types. RESULTS Seven recurrent mutations and four novel mutations were identified with the aforementioned methods, which were subsequently confirmed by either restriction fragment length polymorphism analysis or Sanger sequencing. Truncating mutations accounted for 73% (8/11) of all mutations identified. We also exhaustively investigated the clinical manifestations of NF1 in patients via acquired pathography, photographs and follow-up. However, no clear genotype-phenotype correlation has been found to date. CONCLUSION In conclusion, the novel mutations identified broaden the spectrum of NF1 mutations in Chinese; however, obvious correlations between genotype and phenotype were not observed in this study.
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Affiliation(s)
- Bin Mao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Siyu Chen
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Xin Chen
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Xiumei Yu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Hebei North University, Zhangjiakou, 075061, China
| | - Xiaojia Zhai
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Tao Yang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Lulu Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zheng Wang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
| | - Xue Zhang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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11
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Koczkowska M, Chen Y, Callens T, Gomes A, Sharp A, Johnson S, Hsiao MC, Chen Z, Balasubramanian M, Barnett CP, Becker TA, Ben-Shachar S, Bertola DR, Blakeley JO, Burkitt-Wright EMM, Callaway A, Crenshaw M, Cunha KS, Cunningham M, D'Agostino MD, Dahan K, De Luca A, Destrée A, Dhamija R, Eoli M, Evans DGR, Galvin-Parton P, George-Abraham JK, Gripp KW, Guevara-Campos J, Hanchard NA, Hernández-Chico C, Immken L, Janssens S, Jones KJ, Keena BA, Kochhar A, Liebelt J, Martir-Negron A, Mahoney MJ, Maystadt I, McDougall C, McEntagart M, Mendelsohn N, Miller DT, Mortier G, Morton J, Pappas J, Plotkin SR, Pond D, Rosenbaum K, Rubin K, Russell L, Rutledge LS, Saletti V, Schonberg R, Schreiber A, Seidel M, Siqveland E, Stockton DW, Trevisson E, Ullrich NJ, Upadhyaya M, van Minkelen R, Verhelst H, Wallace MR, Yap YS, Zackai E, Zonana J, Zurcher V, Claes K, Martin Y, Korf BR, Legius E, Messiaen LM. Genotype-Phenotype Correlation in NF1: Evidence for a More Severe Phenotype Associated with Missense Mutations Affecting NF1 Codons 844-848. Am J Hum Genet 2018; 102:69-87. [PMID: 29290338 PMCID: PMC5777934 DOI: 10.1016/j.ajhg.2017.12.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
Neurofibromatosis type 1 (NF1), a common genetic disorder with a birth incidence of 1:2,000-3,000, is characterized by a highly variable clinical presentation. To date, only two clinically relevant intragenic genotype-phenotype correlations have been reported for NF1 missense mutations affecting p.Arg1809 and a single amino acid deletion p.Met922del. Both variants predispose to a distinct mild NF1 phenotype with neither externally visible cutaneous/plexiform neurofibromas nor other tumors. Here, we report 162 individuals (129 unrelated probands and 33 affected relatives) heterozygous for a constitutional missense mutation affecting one of five neighboring NF1 codons-Leu844, Cys845, Ala846, Leu847, and Gly848-located in the cysteine-serine-rich domain (CSRD). Collectively, these recurrent missense mutations affect ∼0.8% of unrelated NF1 mutation-positive probands in the University of Alabama at Birmingham (UAB) cohort. Major superficial plexiform neurofibromas and symptomatic spinal neurofibromas were more prevalent in these individuals compared with classic NF1-affected cohorts (both p < 0.0001). Nearly half of the individuals had symptomatic or asymptomatic optic pathway gliomas and/or skeletal abnormalities. Additionally, variants in this region seem to confer a high predisposition to develop malignancies compared with the general NF1-affected population (p = 0.0061). Our results demonstrate that these NF1 missense mutations, although located outside the GAP-related domain, may be an important risk factor for a severe presentation. A genotype-phenotype correlation at the NF1 region 844-848 exists and will be valuable in the management and genetic counseling of a significant number of individuals.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela Sharp
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sherrell Johnson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meng-Chang Hsiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zhenbin Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK
| | | | - Troy A Becker
- Medical Genetics, John Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Shay Ben-Shachar
- The Genetic Institute, Tel-Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel-Aviv 6997801, Israel
| | - Debora R Bertola
- Department of Pediatrics, University of São Paulo, São Paulo 05403-000, Brazil
| | - Jaishri O Blakeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Emma M M Burkitt-Wright
- Genomic Medicine, Division of Evolution and Genomic Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury SP2 8BJ, UK
| | - Melissa Crenshaw
- Medical Genetics, John Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Karin S Cunha
- Department of Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24220-900, Brazil
| | - Mitch Cunningham
- Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit Medical Center, Detroit, MI 48201, USA
| | - Maria D D'Agostino
- Department of Medical Genetics, McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Karin Dahan
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Alessandro De Luca
- Molecular Genetics Unit, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo 71013, Italy
| | - Anne Destrée
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Radhika Dhamija
- Department of Clinical Genomics and Neurology, Mayo Clinic, Phoenix, AZ 85259, USA
| | - Marica Eoli
- Unit of Molecular Neuro-Oncology, IRCCS Foundation, Carlo Besta Neurological Institute, Milan 20133, Italy
| | - D Gareth R Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | | | | | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Jose Guevara-Campos
- Pediatrics Service, Felipe Guevara Rojas Hospital, University of Oriente, El Tigre-Anzoátegui, Venezuela 6034, Spain
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Concepcion Hernández-Chico
- Department of Genetics, Hospital Universitario Ramón y Cayal, Institute of Health Research (IRYCIS), Madrid 28034, Spain and Center for Biomedical Research-Network of Rare Diseases (CIBERER)
| | - LaDonna Immken
- Dell Children's Medical Center of Central Texas, Austin, TX 78723, USA
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - Kristi J Jones
- Department of Clinical Genetics, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Beth A Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Aaina Kochhar
- Department of Genetics, Valley Children's Healthcare, Madera, CA 93636, USA
| | - Jan Liebelt
- Women's and Children's Hospital/SA Pathology, North Adelaide, SA 5006, Australia
| | - Arelis Martir-Negron
- Division of Clinical Genetics, Center for Genomic Medicine, Miami Cancer Institute, Miami, FL 33176, USA
| | | | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Meriel McEntagart
- St George's University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Nancy Mendelsohn
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - David T Miller
- Multidisciplinary Neurofibromatosis Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp 2650, Belgium
| | - Jenny Morton
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - John Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, NY 10016, USA
| | - Scott R Plotkin
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dinel Pond
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - Kenneth Rosenbaum
- Division of Genetics and Metabolism, Children's National Health System, Washington, DC 20010, USA
| | - Karol Rubin
- University of Minnesota Health, Minneapolis, MN 55404, USA
| | - Laura Russell
- Department of Medical Genetics, McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Lane S Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan 20133, Italy
| | - Rhonda Schonberg
- Division of Genetics and Metabolism, Children's National Health System, Washington, DC 20010, USA
| | - Allison Schreiber
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Meredith Seidel
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elizabeth Siqveland
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - David W Stockton
- Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit Medical Center, Detroit, MI 48201, USA
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy and Italy Istituto di Ricerca Pediatria, IRP, Città della Speranza, Padova 35128, Italy
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Cardiff University, Cardiff CF14 4XN, UK
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GE, the Netherlands
| | - Helene Verhelst
- Department of Paediatrics, Division of Paediatric Neurology, Ghent University Hospital, Ghent 9000, Belgium
| | - Margaret R Wallace
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore; Faculty of Health Sciences, School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Zonana
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Vickie Zurcher
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y Cayal, Institute of Health Research (IRYCIS), Madrid 28034, Spain and Center for Biomedical Research-Network of Rare Diseases (CIBERER)
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Eric Legius
- Department of Human Genetics, KU Leuven - University of Leuven, Leuven 3000, Belgium
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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12
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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