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Cheng J, Çelik MH, Kundaje A, Gagneur J. MTSplice predicts effects of genetic variants on tissue-specific splicing. Genome Biol 2021; 22:94. [PMID: 33789710 PMCID: PMC8011109 DOI: 10.1186/s13059-021-02273-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 01/14/2021] [Indexed: 12/20/2022] Open
Abstract
We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models constitutive regulatory sequences, with a new neural network that models tissue-specific regulatory sequences. MTSplice outperforms MMSplice on predicting tissue-specific variations associated with genetic variants in most tissues of the GTEx dataset, with largest improvements on brain tissues. Furthermore, MTSplice predicts that autism-associated de novo mutations are enriched for variants affecting splicing specifically in the brain. We foresee that MTSplice will aid interpreting variants associated with tissue-specific disorders.
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Affiliation(s)
- Jun Cheng
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany.
| | - Muhammed Hasan Çelik
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Boltzmannstraße, Garching, 85748, Germany.
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.
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102
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de Bruijn SE, Fadaie Z, Cremers FPM, Kremer H, Roosing S. The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. Int J Mol Sci 2021; 22:2943. [PMID: 33799353 PMCID: PMC7998853 DOI: 10.3390/ijms22062943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
The identification of pathogenic variants in monogenic diseases has been of interest to researchers and clinicians for several decades. However, for inherited diseases with extremely high genetic heterogeneity, such as hearing loss and retinal dystrophies, establishing a molecular diagnosis requires an enormous effort. In this review, we use these two genetic conditions as examples to describe the initial molecular genetic identification approaches, as performed since the early 90s, and subsequent improvements and refinements introduced over the years. Next, the history of DNA sequencing from conventional Sanger sequencing to high-throughput massive parallel sequencing, a.k.a. next-generation sequencing, is outlined, including their advantages and limitations and their impact on identifying the remaining genetic defects. Moreover, the development of recent technologies, also coined "third-generation" sequencing, is reviewed, which holds the promise to overcome these limitations. Furthermore, we outline the importance and complexity of variant interpretation in clinical diagnostic settings concerning the massive number of different variants identified by these methods. Finally, we briefly mention the development of novel approaches such as optical mapping and multiomics, which can help to further identify genetic defects in the near future.
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Affiliation(s)
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Hannie Kremer
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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103
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Ing A, Wlodaver A, Kirschmann D, Toledo E, McCabe C, Kadri S, McIntyre MK, Salazar J, Firestein K, Charrow J, Sanders V, Laguna T, Yap KL. Transcript analysis for variant classification resolution in a child with primary ciliary dyskinesia. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005363. [PMID: 33608380 PMCID: PMC7903884 DOI: 10.1101/mcs.a005363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Transcriptional analysis can be utilized to reconcile variants of uncertain significance, particularly those predicted to impact splicing. Laboratory analysis of the predicted mRNA transcript may allow inference of the in vivo impact of the variant and aid prediction of its clinical significance. We present a patient with classical features of primary ciliary dyskinesia (PCD) who was identified to have compound heterozygous variants in the DNAH11 gene (c.10691 + 2T > C, c.13523_13543dup21) via trio whole-exome sequencing in 2013. These variants were originally classified as Mutation and Likely Mutation. However, these variants were downgraded to variants of uncertain significance (VUSs) during reanalysis in 2016 because of uncertainty that they caused a loss of function of the gene. c.10691 + 2T > C is predicted to abrogate the canonical splice site and lead to the skipping of exon 65, but the adjoining of exon 64 and exon 66 in the DNAH11 transcript preserves the reading frame of the resultant protein. c.13523_13543dup21 is located in the last exon of the DNAH11 coding sequence, upstream of the canonical stop codon, which suggests a reduced likelihood to trigger nonsense-mediated decay (NMD). Transcriptional analysis was performed to characterize the impact of the variants, resulting in reclassification of c.10691 + 2T > C to Likely Pathogenic by providing evidence that it results in a deleterious effect and subsequent downstream reclassification of c.13523_13543dup21 to Likely Pathogenic as well. Our case illustrates the potential impact of transcriptional analysis on variant resolution, supporting its usage on variants that exert an unpredictable effect on splicing.
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Affiliation(s)
- Alexander Ing
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Alissa Wlodaver
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Dawn Kirschmann
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Erica Toledo
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Christopher McCabe
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Sabah Kadri
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Mary Kate McIntyre
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Joanne Salazar
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Kristina Firestein
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Joel Charrow
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Victoria Sanders
- Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Division of Genetics, Birth Defects and Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Theresa Laguna
- Division of Pulmonary and Sleep Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Kai Lee Yap
- Center for Genomics, Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA.,Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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104
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Next-Generation Molecular Investigations in Lysosomal Diseases: Clinical Integration of a Comprehensive Targeted Panel. Diagnostics (Basel) 2021; 11:diagnostics11020294. [PMID: 33673364 PMCID: PMC7918778 DOI: 10.3390/diagnostics11020294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Diagnosis of lysosomal disorders (LDs) may be hampered by their clinical heterogeneity, phenotypic overlap, and variable age at onset. Conventional biological diagnostic procedures are based on a series of sequential investigations and require multiple sampling. Early diagnosis may allow for timely treatment and prevent clinical complications. In order to improve LDs diagnosis, we developed a capture-based next generation sequencing (NGS) panel allowing the detection of single nucleotide variants (SNVs), small insertions and deletions, and copy number variants (CNVs) in 51 genes related to LDs. The design of the LD panel covered at least coding regions, promoter region, and flanking intronic sequences for 51 genes. The validation of this panel consisted in testing 21 well-characterized samples and evaluating analytical and diagnostic performance metrics. Bioinformatics pipelines have been validated for SNVs, indels and CNVs. The clinical output of this panel was tested in five novel cases. This capture-based NGS panel provides an average coverage depth of 474× which allows the detection of SNVs and CNVs in one comprehensive assay. All the targeted regions were covered above the minimum required depth of 30×. To illustrate the clinical utility, five novel cases have been sequenced using this panel and the identified variants have been confirmed using Sanger sequencing or quantitative multiplex PCR of short fluorescent fragments (QMPSF). The application of NGS as first-line approach to analyze suspected LD cases may speed up the identification of alterations in LD-associated genes. NGS approaches combined with bioinformatics analyses, are a useful and cost-effective tool for identifying the causative variations in LDs.
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105
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Reeskamp LF, Balvers M, Peter J, van de Kerkhof L, Klaaijsen LN, Motazacker MM, Grefhorst A, van Riel NAW, Hovingh GK, Defesche JC, Zuurbier L. Intronic variant screening with targeted next-generation sequencing reveals first pseudoexon in LDLR in familial hypercholesterolemia. Atherosclerosis 2021; 321:14-20. [PMID: 33601267 DOI: 10.1016/j.atherosclerosis.2021.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 01/23/2023]
Abstract
BACKGROUND AND AIMS Familial hypercholesterolemia (FH) is caused by pathogenic variants in LDLR, APOB, or PCSK9 genes (designated FH+). However, a significant number of clinical FH patients do not carry these variants (designated FH-). Here, we investigated whether variants in intronic regions of LDLR attribute to FH by affecting pre-mRNA splicing. METHODS LDLR introns are partly covered in routine sequencing of clinical FH patients using next-generation sequencing. Deep intronic variants, >20 bp from intron-exon boundary, were considered of interest once (a) present in FH- patients (n = 909) with LDL-C >7 mmol/L (severe FH-) or after in silico analysis in patients with LDL-C >5 mmol/L (moderate FH-) and b) absent in FH + patients (control group). cDNA analysis and co-segregation analysis were performed to assess pathogenicity of the identified variants. RESULTS Three unique variants were present in the severe FH- group. One of these was the previously described likely pathogenic variant c.2140+103G>T. Three additional variants were selected based on in silico analyses in the moderate FH- group. One of these variants, c.2141-218G>A, was found to result in a pseudo-exon inclusion, producing a premature stop codon. This variant co-segregated with the hypercholesterolemic phenotype. CONCLUSIONS Through a screening approach, we identified a deep intronic variant causal for FH. This finding indicates that filtering intronic variants in FH- patients for the absence in FH + patients might enrich for true FH-causing variants and suggests that intronic regions of LDLR need to be considered for sequencing in FH- patients.
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Affiliation(s)
- Laurens F Reeskamp
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manon Balvers
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; HORAIZON Technology BV, Delft, the Netherlands
| | - Jorge Peter
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Laura van de Kerkhof
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Lisette N Klaaijsen
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mahdi M Motazacker
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Aldo Grefhorst
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Natal A W van Riel
- Department of Experimental Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Joep C Defesche
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Linda Zuurbier
- Department of Clinical Genetics, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
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106
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Demir S, Yalçıntepe S, Atlı Eİ, Sanrı A, Yıldırım R, Tütüncüler F, Çelik M, Atlı E, Özemri Sağ Ş, Eker D, Temel Ş, Gürkan H. Targeted High-Throughput Sequencing Analysis Results of Osteogenesis Imperfecta Patients from Different Regions of Turkey. Genet Test Mol Biomarkers 2021; 25:59-67. [PMID: 33470886 DOI: 10.1089/gtmb.2020.0169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Objective: Osteogenesis imperfecta (OI) includes a group of disorders characterized by susceptibility to bone fractures with different severities. The increasing number of genes that may underlie the disorder, along with the broad phenotypic spectrum that overlaps with other skeletal diseases, provided a compelling case for the use of high-throughput sequencing (HTS) technology as an aid to OI diagnoses. The aim of this analysis was to present the data from our 5-year targeted HTS results, that includes the reporting of 9 novel and 24 known mutations, found in OI patients, from 5 different regions of Turkey. Materials and Methods: We performed a retrospective cross-sectional study, reporting the HTS results of 43 patients (23 female and 20 male; mean age: 9.5 years), directed to our center with a suspicion of OI between February 2015 and May 2020. Genetic analyses were also performed for 24 asymptomatic parents to aid the segregation analyses. We utilized an HTS panel targeting the coding regions of 57 genes associated with a reduction, increase, or abnormal development of bone mineralization. In addition, we sequenced the entire coding region of the IFITM5 gene through HTS. Results: Thirty-nine patients had at least one pathogenic/likely pathogenic variation (90.69%) in the COL1A1 (56.41%), COL1A2 (20.51%), FKBP10 (7.7%), P3H1 (5.13%), IFITM5 (5.13%), CTRAP (2.56%), or TMEM38B (2.56%) genes. Nine of the determined pathogenic/likely pathogenic variations were novel. The recurrent pathogenic mutations were c.1081C>T (p.Arg361Ter) (3/43), c.1405C>T (p.Arg469Ter) (2/43), and c.3749del (p.Gly1250AlafsTer81) in COL1A1 gene, along with c.-14C>T variation in the 5'UTR of the IFITM5 gene (2/43) and the c.890_897dup variation in the FKBP10 gene (2/43). Three out of 43 patients were carrying at least one additional variant of unknown significance, highlighting the importance of a multigene panel approach and segregation analyses. Conclusion: We suggest that a targeted HTS panel is a feasible tool for genetic diagnosis of OI in patients.
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Affiliation(s)
- Selma Demir
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Sinem Yalçıntepe
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Emine İkbal Atlı
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Aslıhan Sanrı
- Department of Pediatrics, Samsun Ondokuz Mayıs Üniversitesi, Samsun, Turkey
| | - Ruken Yıldırım
- Department of Pediatric Endocrinology, Diyarbakır Hospital of Pediatric Diseases, Diyarbakır, Turkey
| | - Filiz Tütüncüler
- Department of Pediatric Endocrinology and Trakya University Faculty of Medicine, Edirne, Turkey
| | - Mehmet Çelik
- Department of Endocrinology, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Engin Atlı
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Şebnem Özemri Sağ
- Department of Medical Genetics, Faculty of Medicine, Uludağ University, Bursa, Turkey
| | - Damla Eker
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Şehime Temel
- Department of Medical Genetics, Faculty of Medicine, Uludağ University, Bursa, Turkey
| | - Hakan Gürkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
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107
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Di Scipio M, Tavares E, Deshmukh S, Audo I, Green-Sanderson K, Zubak Y, Zine-Eddine F, Pearson A, Vig A, Tang CY, Mollica A, Karas J, Tumber A, Yu CW, Billingsley G, Wilson MD, Zeitz C, Héon E, Vincent A. Phenotype Driven Analysis of Whole Genome Sequencing Identifies Deep Intronic Variants that Cause Retinal Dystrophies by Aberrant Exonization. Invest Ophthalmol Vis Sci 2021; 61:36. [PMID: 32881472 PMCID: PMC7443117 DOI: 10.1167/iovs.61.10.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose To demonstrate the effectiveness of combining retinal phenotyping and focused variant filtering from genome sequencing (GS) in identifying deep intronic disease causing variants in inherited retinal dystrophies. Methods Affected members from three pedigrees with classical enhanced S-cone syndrome (ESCS; Pedigree 1), congenital stationary night blindness (CSNB; Pedigree 2), and achromatopsia (ACHM; Pedigree 3), respectively, underwent detailed ophthalmologic evaluation, optical coherence tomography, and electroretinography. The probands underwent panel-based genetic testing followed by GS analysis. Minigene constructs (NR2E3, GPR179 and CNGB3) and patient-derived cDNA experiments (NR2E3 and GPR179) were performed to assess the functional effect of the deep intronic variants. Results The electrophysiological findings confirmed the clinical diagnosis of ESCS, CSNB, and ACHM in the respective pedigrees. Panel-based testing revealed heterozygous pathogenic variants in NR2E3 (NM_014249.3; c.119-2A>C; Pedigree 1) and CNGB3 (NM_019098.4; c.1148delC/p.Thr383Ilefs*13; Pedigree 3). The GS revealed heterozygous deep intronic variants in Pedigrees 1 (NR2E3; c.1100+1124G>A) and 3 (CNGB3; c.852+4751A>T), and a homozygous GPR179 variant in Pedigree 2 (NM_001004334.3; c.903+343G>A). The identified variants segregated with the phenotype in all pedigrees. All deep intronic variants were predicted to generate a splice acceptor gain causing aberrant exonization in NR2E3 [89 base pairs (bp)], GPR179 (197 bp), and CNGB3 (73 bp); splicing defects were validated through patient-derived cDNA experiments and/or minigene constructs and rescued by antisense oligonucleotide treatment. Conclusions Deep intronic mutations contribute to missing heritability in retinal dystrophies. Combining results from phenotype-directed gene panel testing, GS, and in silico splice prediction tools can help identify these difficult-to-detect pathogenic deep intronic variants.
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Affiliation(s)
- Matteo Di Scipio
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Erika Tavares
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Shriya Deshmukh
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, United Kingdom
| | - Kit Green-Sanderson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Yuliya Zubak
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Fayçal Zine-Eddine
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Alexander Pearson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anjali Vig
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Chen Yu Tang
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Antonio Mollica
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jonathan Karas
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
| | - Caberry W Yu
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Gail Billingsley
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michael D Wilson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Héon
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Ajoy Vincent
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
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108
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Louie W, Shen MW, Tahiry Z, Zhang S, Worstell D, Cassa CA, Sherwood RI, Gifford DK. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol 2021; 17:e1008605. [PMID: 33417623 PMCID: PMC7819613 DOI: 10.1371/journal.pcbi.1008605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/21/2021] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Restoring gene function by the induced skipping of deleterious exons has been shown to be effective for treating genetic disorders. However, many of the clinically successful therapies for exon skipping are transient oligonucleotide-based treatments that require frequent dosing. CRISPR-Cas9 based genome editing that causes exon skipping is a promising therapeutic modality that may offer permanent alleviation of genetic disease. We show that machine learning can select Cas9 guide RNAs that disrupt splice acceptors and cause the skipping of targeted exons. We experimentally measured the exon skipping frequencies of a diverse genome-integrated library of 791 splice sequences targeted by 1,063 guide RNAs in mouse embryonic stem cells. We found that our method, SkipGuide, is able to identify effective guide RNAs with a precision of 0.68 (50% threshold predicted exon skipping frequency) and 0.93 (70% threshold predicted exon skipping frequency). We anticipate that SkipGuide will be useful for selecting guide RNA candidates for evaluation of CRISPR-Cas9-mediated exon skipping therapy.
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Affiliation(s)
- Wilson Louie
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Max W. Shen
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Zakir Tahiry
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sophia Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel Worstell
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - David K. Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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109
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Tafazoli A, Wawrusiewicz-Kurylonek N, Posmyk R, Miltyk W. Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area. J Clin Med 2020; 10:jcm10010034. [PMID: 33374421 PMCID: PMC7796098 DOI: 10.3390/jcm10010034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
Pharmacogenomics (PGx) is the knowledge of diverse drug responses and effects in people, based on their genomic profiles. Such information is considered as one of the main directions to reach personalized medicine in future clinical practices. Since the start of applying next generation sequencing (NGS) methods in drug related clinical investigations, many common medicines found their genetic data for the related metabolizing/shipping proteins in the human body. Yet, the employing of technology is accompanied by big obtained data, which most of them have no clear guidelines for consideration in routine treatment decisions for patients. This review article talks about different types of NGS derived PGx variants in clinical studies and try to display the current and newly developed approaches to deal with pharmacogenetic data with/without clear guidelines for considering in clinical settings.
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Affiliation(s)
- Alireza Tafazoli
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Clinical Research Centre, Medical University of Białystok, 15-276 Bialystok, Poland
| | | | - Renata Posmyk
- Department of Clinical Genetics, Medical University of Białystok, 15-089 Białystok, Poland; (N.W.-K.); (R.P.)
| | - Wojciech Miltyk
- Department of Analysis and Bioanalysis of Medicines, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Białystok, 15-089 Białystok, Poland;
- Correspondence: ; Tel.: +48-857485845
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110
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Yang L, Zhang Q, Zhang S, Liu Y, Liu Y, Wang T. Generalized Hailey-Hailey disease: Novel splice-site mutations of ATP2C1 gene in Chinese population and a literature review. Mol Genet Genomic Med 2020; 9:e1580. [PMID: 33345454 PMCID: PMC8077163 DOI: 10.1002/mgg3.1580] [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: 06/21/2020] [Revised: 10/15/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hailey-Hailey disease (HHD; OMIM: 169600) is an autosomal dominate genodermatosis, characterized by recurrent blisters and erosions clinically and remarkable acantholysis pathologically. The underlying pathogenic factor is the mutation of ATP2C1 gene (OMIM: 604384), which encodes secretory pathway Ca2+ /Mn2+ -ATPase (SPCA1). Skin folds are the predilection site of HHD. Atypical cases with a generalized pattern have rarely been reported, making it prone to misdiagnosis. METHODS In this study, we presented three Chinese pedigrees of Hailey-Hailey disease with generalized skin lesions. ATP2C1 mutations were screened by DNA sequencing and their transcripts were further confirmed by minigene assay. We also performed a literature review of previously published generalized HHD over past two decades together with our cases. RESULTS Three splice-site mutations were identified: c.2487+1G>A, c.2126+1G>A, and c.1891-2A>G, which resulted in an exon 25-truncated transcript, two exon 22-truncated transcripts, and two exon 21-truncated transcripts, respectively. The c.2487+1G>A and the c.1891-2A>G mutations are novel mutations which have not been reported before. No clustered mutations of ATP2C1 gene were found in generalized HHD patients in literature along with our novel mutations. CONCLUSION We found no hot spot mutations in ATP2C1 correlated with the generalized pattern of HHD. Our study expanded the spectrum of ATP2C1 mutations, which would be useful for disease diagnosis and genetic counseling.
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Affiliation(s)
- Lu Yang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianli Zhang
- Department of Medical Genetics and National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shiyu Zhang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuehua Liu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaping Liu
- Department of Medical Genetics and National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Wang
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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111
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Bi-Allelic Pathogenic Variations in MERTK Including Deletions Are Associated with an Early Onset Progressive Form of Retinitis Pigmentosa. Genes (Basel) 2020; 11:genes11121517. [PMID: 33353011 PMCID: PMC7766129 DOI: 10.3390/genes11121517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
Bi-allelic pathogenic variants in MERTK cause retinitis pigmentosa (RP). Since deletions of more than one exon have been reported repeatedly for MERTK, CNV (copy number variation) analysis of next-generation sequencing (NGS) data has proven important in molecular genetic diagnostics of MERTK. CNV analysis was performed on NGS data of 677 individuals with inherited retinal diseases (IRD) and confirmed by quantitative RT-PCR analysis. Clinical evaluation was based on retrospective records. Clinical re-examination included visual field examination, dark adaption, scotopic and photopic full-field electroretinograms (ffERG), multifocal ERG (mfERG) and optic coherence tomography (OCT). Fourteen variants were detected in MERTK in six individuals, three of which were deletions of more than one exon. Clinical examinations of five out of six individuals revealed a severe phenotype with early-onset generalized retinal dystrophy with night blindness and progressive visual field loss; however, one individual had a milder phenotype. Three individuals had hearing impairments. We show that deletions represent a substantial part of the causative variants in MERTK and emphasize that CNV analysis should be included in the molecular genetic diagnostics of IRDs.
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112
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Tidwell T, Deshotel M, Palumbos J, Miller C, Bayrak-Toydemir P, Carey JC. Novel de novo ARCN1 intronic variant causes rhizomelic short stature with microretrognathia and developmental delay. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005728. [PMID: 33154040 PMCID: PMC7784487 DOI: 10.1101/mcs.a005728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/16/2020] [Indexed: 12/31/2022] Open
Abstract
The archain 1 (ARCN1) gene encodes the coatomer subunit delta protein and is a component of the COPI coatomer complex, which is involved in retrograde vesical trafficking from the Golgi complex to the endoplasmic reticulum. Variants in ARCN1 have recently been associated with rhizomelic short stature with microcephaly, microretrognathia, and developmental delay. Here we report a 3.5-yr-old boy with microcephaly, global developmental delay, and multiple congenital abnormalities and the ARCN1-related syndrome caused by a novel de novo intronic variant. Whole-exome sequencing of the proband and his parents was utilized to determine the genetic origin of the patient's disorder and identified a de novo variant, NM_001655.5:c.654-15A > G, in the ARCN1 gene. Follow-up functional characterization of mRNA from the patient demonstrated that this variant creates a splicing defect of the ARCN1 mRNA. ARCN1-related syndrome represents an emerging disorder of developmental delay, and this report represents the sixth described patient. Despite the few instances reported in literature, the phenotype is consistent between our patient and previously reported individuals.
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Affiliation(s)
| | | | - Janice Palumbos
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
| | - Chris Miller
- ARUP Laboratories, Salt Lake City, Utah 84108, USA
| | - Pinar Bayrak-Toydemir
- ARUP Laboratories, Salt Lake City, Utah 84108, USA.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84113, USA
| | - John C Carey
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
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Maia N, Soares AR, Fortuna AM, Marques I, Gonçalves A, Santos R, Melo Pires M, de Brouwer APM, Jorge P. Usher syndrome and Nebulin-associated myopathy in a single patient due to variants in MYO7A and NEB. Clin Case Rep 2020; 8:2476-2482. [PMID: 33363762 PMCID: PMC7752365 DOI: 10.1002/ccr3.3146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/08/2020] [Accepted: 06/14/2020] [Indexed: 12/02/2022] Open
Abstract
In a patient with Usher syndrome and atypical muscle complaints, we have identified two separate variants in MYO7A andNEB genes by exome sequencing. The homozygous variants in these two recessive genes could explain the full phenotype of our patient.
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Affiliation(s)
- Nuno Maia
- Unidade de Genética MolecularCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
| | - Ana Rita Soares
- Unidade de Genética MédicaCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
| | - Ana Maria Fortuna
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
- Unidade de Genética MédicaCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
| | - Isabel Marques
- Unidade de Genética MolecularCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
| | - Ana Gonçalves
- Unidade de Genética MolecularCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
| | - Rosário Santos
- Unidade de Genética MolecularCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
| | - Manuel Melo Pires
- Serviço de NeuropatologiaCentro Hospitalar e Universitário do Porto (CHUP)PortoPortugal
| | - Arjan P. M. de Brouwer
- Department of Human GeneticsDonders Institute for Brain, Cognition and BehaviourRadboud University NijmegenNijmegenThe Netherlands
| | - Paula Jorge
- Unidade de Genética MolecularCentro de Genética Médica Jacinto de Magalhães (CGM)Centro Hospitalar Universitário do Porto (CHUP)PortoPortugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB)Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do PortoPortoPortugal
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A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies. Hum Genet 2020; 140:593-607. [PMID: 33095315 PMCID: PMC7981318 DOI: 10.1007/s00439-020-02228-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/14/2020] [Indexed: 11/04/2022]
Abstract
Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can provide an accurate diagnosis, 24–60% of ciliopathy patients who undergo genetic testing do not receive a genetic diagnosis. This is partly because following current guidelines from the American College of Medical Genetics and the Association for Molecular Pathology, it is difficult to provide a confident clinical diagnosis of disease caused by missense or non-coding variants, which account for more than one-third of cases of disease. Mutations in PRPF31 are the second most common cause of the degenerative retinal ciliopathy autosomal dominant retinitis pigmentosa. Here, we present a high-throughput high-content imaging assay providing quantitative measure of effect of missense variants in PRPF31 which meets the recently published criteria for a baseline standard in vitro test for clinical variant interpretation. This assay utilizes a new PRPF31+/– human retinal cell line generated using CRISPR gene editing to provide a stable cell line with significantly fewer cilia in which novel missense variants are expressed and characterised. We show that high-content imaging of cells expressing missense variants in a ciliopathy gene on a null background can allow characterisation of variants according to the cilia phenotype. We hope that this will be a useful tool for clinical characterisation of PRPF31 variants of uncertain significance, and can be extended to variant classification in other ciliopathies.
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115
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Improving Genetic Testing in Hereditary Cancer by RNA Analysis: Tools to Prioritize Splicing Studies and Challenges in Applying American College of Medical Genetics and Genomics Guidelines. J Mol Diagn 2020; 22:1453-1468. [PMID: 33011440 DOI: 10.1016/j.jmoldx.2020.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 11/23/2022] Open
Abstract
RNA analyses are a potent tool to identify spliceogenic effects of DNA variants, although they are time-consuming and cannot always be performed. We present splicing assays of 20 variants that represent a variety of mutation types in 10 hereditary cancer genes and attempt to incorporate these results into American College of Medical Genetics and Genomics (ACMG) classification guidelines. Sixteen single-nucleotide variants, 3 exon duplications, and 1 single-exon deletion were selected and prioritized by in silico algorithms. RNA was extracted from short-term lymphocyte cultures to perform RT-PCR and Sanger sequencing, and allele-specific expression was assessed whenever possible. Aberrant transcripts were detected in 14 variants (70%). Variant interpretation was difficult, especially comparing old classification standards to generic ACMG guidelines and a proposal was devised to weigh functional analyses at RNA level. According to the ACMG guidelines, only 12 variants were reclassified as pathogenic/likely pathogenic because the other two variants did not gather enough evidence. This study highlights the importance of RNA studies to improve variant classification. However, it also indicates the challenge of incorporating these results into generic ACMG guidelines and the need to refine these criteria gene specifically. Nevertheless, 60% of variants were reclassified, thus improving genetic counseling and surveillance for carriers of these variants.
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116
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Maia N, Soares G, Silva C, Marques I, Rodrigues B, Santos R, Melo-Pires M, de Brouwer APM, Temudo T, Jorge P. Two Compound Heterozygous Variants in SNX14 Cause Stereotypies and Dystonia in Autosomal Recessive Spinocerebellar Ataxia 20. Front Genet 2020; 11:1038. [PMID: 33193593 PMCID: PMC7543990 DOI: 10.3389/fgene.2020.01038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/11/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nuno Maia
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Gabriela Soares
- Unidade de Genética Médica, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
| | - Cecília Silva
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Isabel Marques
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Bárbara Rodrigues
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Rosário Santos
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
| | - Arjan PM de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Teresa Temudo
- Serviço de Neurologia Pediátrica, Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
| | - Paula Jorge
- Unidade de Genética Molecular, Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUP), Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica (UMIB), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Porto, Portugal
- *Correspondence: Paula Jorge,
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Khan M, Arno G, Fakin A, Parfitt DA, Dhooge PPA, Albert S, Bax NM, Duijkers L, Niblock M, Hau KL, Bloch E, Schiff ER, Piccolo D, Hogden MC, Hoyng CB, Webster AR, Cremers FPM, Cheetham ME, Garanto A, Collin RWJ. Detailed Phenotyping and Therapeutic Strategies for Intronic ABCA4 Variants in Stargardt Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:412-427. [PMID: 32653833 PMCID: PMC7352060 DOI: 10.1016/j.omtn.2020.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/15/2020] [Accepted: 06/09/2020] [Indexed: 01/17/2023]
Abstract
Stargardt disease is a progressive retinal disorder caused by bi-allelic mutations in the ABCA4 gene that encodes the ATP-binding cassette, subfamily A, member 4 transporter protein. Over the past few years, we and others have identified several pathogenic variants that reside within the introns of ABCA4, including a recurrent variant in intron 36 (c.5196+1137G>A) of which the pathogenicity so far remained controversial. Detailed clinical characterization of this variant confirmed its pathogenic nature, and classified it as an allele of intermediate severity. Moreover, we discovered several additional ABCA4 variants clustering in intron 36. Several of these variants resulted in aberrant splicing of ABCA4, i.e., the inclusion of pseudoexons, while the splicing defects caused by the recurrent c.5196+1137G>A variant strongly increased upon differentiation of patient-derived induced pluripotent stem cells into retina-like cells. Finally, all splicing defects could be rescued by the administration of antisense oligonucleotides that were designed to specifically block the pseudoexon insertion, including rescue in 3D retinal organoids harboring the c.5196+1137G>A variant. Our data illustrate the importance of intronic variants in ABCA4 and expand the therapeutic possibilities for overcoming splicing defects in Stargardt disease.
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Affiliation(s)
- Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gavin Arno
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK; Great Ormond Street Hospital for Children, London, UK
| | - Ana Fakin
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK; Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Patty P A Dhooge
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nathalie M Bax
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Kwan L Hau
- UCL Institute for Ophthalmology, London, UK
| | - Edward Bloch
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK
| | | | | | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andrew R Webster
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
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118
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Amilpur S, Bhukya R. EDeepSSP: Explainable deep neural networks for exact splice sites prediction. J Bioinform Comput Biol 2020; 18:2050024. [PMID: 32696716 DOI: 10.1142/s0219720020500249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Splice site prediction is crucial for understanding underlying gene regulation, gene function for better genome annotation. Many computational methods exist for recognizing the splice sites. Although most of the methods achieve a competent performance, their interpretability remains challenging. Moreover, all traditional machine learning methods manually extract features, which is tedious job. To address these challenges, we propose a deep learning-based approach (EDeepSSP) that employs convolutional neural networks (CNNs) architecture for automatic feature extraction and effectively predicts splice sites. Our model, EDeepSSP, divulges the opaque nature of CNN by extracting significant motifs and explains why these motifs are vital for predicting splice sites. In this study, experiments have been conducted on six benchmark acceptors and donor datasets of humans, cress, and fly. The results show that EDeepSSP has outperformed many state-of-the-art approaches. EDeepSSP achieves the highest area under the receiver operating characteristic curve (AUC_ROC) and area under the precision-recall curve (AUC_PR) of 99.32% and 99.26% on human donor datasets, respectively. We also analyze various filter activities, feature activations, and extracted significant motifs responsible for the splice site prediction. Further, we validate the learned motifs of our model against known motifs of JASPAR splice site database.
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Affiliation(s)
- Santhosh Amilpur
- Computer Science and Engineering, National Institute of Technology Warangal, Warangal, Telangana 506004, India
| | - Raju Bhukya
- Computer Science and Engineering, National Institute of Technology Warangal, Warangal, Telangana 506004, India
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119
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Morales-Rosado JA, Goel K, Zhang L, Åkerblom A, Baheti S, Black JL, Eriksson N, Wallentin L, James S, Storey RF, Goodman SG, Jenkins GD, Eckloff BW, Bielinski SJ, Sicotte H, Johnson S, Roger VL, Wang L, Weinshilboum R, Klee EW, Rihal CS, Pereira NL. Next-Generation Sequencing of CYP2C19 in Stent Thrombosis: Implications for Clopidogrel Pharmacogenomics. Cardiovasc Drugs Ther 2020; 35:549-559. [PMID: 32623598 DOI: 10.1007/s10557-020-06988-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE Describe CYP2C19 sequencing results in the largest series of clopidogrel-treated cases with stent thrombosis (ST), the closest clinical phenotype to clopidogrel resistance. Evaluate the impact of CYP2C19 genetic variation detected by next-generation sequencing (NGS) with comprehensive annotation and functional studies. METHODS Seventy ST cases on clopidogrel identified from the PLATO trial (n = 58) and Mayo Clinic biorepository (n = 12) were matched 1:1 with controls for age, race, sex, diabetes mellitus, presentation, and stent type. NGS was performed to cover the entire CYP2C19 gene. Assessment of exonic variants involved measuring in vitro protein expression levels. Intronic variants were evaluated for potential splicing motif variations. RESULTS Poor metabolizers (n = 4) and rare CYP2C19*8, CYP2C19*15, and CYP2C19*11 alleles were identified only in ST cases. CYP2C19*17 heterozygote carriers were observed more frequently in cases (n = 29) than controls (n = 18). Functional studies of CYP2C19 exonic variants (n = 11) revealed 3 cases and only 1 control carrying a deleterious variant as determined by in vitro protein expression studies. Greater intronic variation unique to ST cases (n = 169) compared with controls (n = 84) was observed with predictions revealing 13 allele candidates that may lead to a potential disruption of splicing and a loss-of-function effect of CYP2C19 in ST cases. CONCLUSION NGS detected CYP2C19 poor metabolizers and paradoxically greater number of so-called rapid metabolizers in ST cases. Rare deleterious exonic variation occurs in 4%, and potentially disruptive intronic alleles occur in 16% of ST cases. Additional studies are required to evaluate the role of these variants in platelet aggregation and clopidogrel metabolism.
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Affiliation(s)
- Joel A Morales-Rosado
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kashish Goel
- Vanderbilt University School of Medicine, Nashville, TN, 37215, USA
| | - Lingxin Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Axel Åkerblom
- Department of Medical Sciences, Cardiology and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - John L Black
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Niclas Eriksson
- Department of Medical Sciences, Cardiology and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Stefan James
- Department of Medical Sciences, Cardiology and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden
| | - Robert F Storey
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Shaun G Goodman
- St. Michael's Hospital, University of Toronto, Toronto, Canada.,Canadian VIGOUR Centre, University of Alberta , Edmonton, Canada
| | - Gregory D Jenkins
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Suzette J Bielinski
- Division of Epidemiology, Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA
| | - Hugues Sicotte
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen Johnson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Veronique L Roger
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Richard Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Charanjit S Rihal
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Naveen L Pereira
- Department of Cardiovascular Medicine, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
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Huang D, Thompson JA, Charng J, Chelva E, McLenachan S, Chen S, Zhang D, McLaren TL, Lamey TM, Constable IJ, De Roach JN, Aung‐Htut MT, Adams A, Fletcher S, Wilton SD, Chen FK. Phenotype-genotype correlations in a pseudodominant Stargardt disease pedigree due to a novel ABCA4 deletion-insertion variant causing a splicing defect. Mol Genet Genomic Med 2020; 8:e1259. [PMID: 32627976 PMCID: PMC7336727 DOI: 10.1002/mgg3.1259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Deletion-insertion (delins) variants in the retina-specific ATP-binding cassette transporter gene, subfamily A, member 4 (ABCA4) accounts for <1% in Stargardt disease. The consequences of these delins variants on splicing cannot be predicted with certainty without supporting in vitro data. METHODS Candidate ABCA4 variants were revealed by genetic and segregation analysis of a family with pseudodominant Stargardt disease using a commercial panel and Sanger sequencing. RNA extracted from patient-derived fibroblasts was analyzed by RT-PCR to evaluate splicing behavior of the ABCA4 variants. RESULTS Affected members carrying the novel c.6031_6044delinsAGTATTTAACCAATATTT variant in exon 44 presented with contrasting phenotypes; from early-onset cone-rod dystrophy to late-onset macular dystrophy. This variant resulted in a 56-nucleotide deletion in the mutant allele by activation of a cryptic splice acceptor site which disrupts the reading frame and results in a premature termination codon (p.Ile2003LeufsTer41). If translated, the crucial functional domains near the C-terminus would be truncated from the ABCA4 protein. CONCLUSION This work demonstrates the intrafamilial phenotypic variability in a pseudodominant Stargardt disease pedigree and the use of patient-derived fibroblasts to evaluate the effect of a novel ABCA4 delins variant on splicing to complement in silico pathogenicity assessment.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWestern AustraliaAustralia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Centre for Neuromuscular and Neurological DisordersThe University of Western Australia and Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
| | - Enid Chelva
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
| | - Shang‐Chih Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
| | - Dan Zhang
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - Ian J. Constable
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Department of OphthalmologySir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
| | - May Thandar Aung‐Htut
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWestern AustraliaAustralia
- Centre for Neuromuscular and Neurological DisordersThe University of Western Australia and Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
| | - Abbie Adams
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWestern AustraliaAustralia
- Centre for Neuromuscular and Neurological DisordersThe University of Western Australia and Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative TherapeuticsMurdoch UniversityMurdochWestern AustraliaAustralia
- Centre for Neuromuscular and Neurological DisordersThe University of Western Australia and Perron Institute for Neurological and Translational ScienceNedlandsWestern AustraliaAustralia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Australian Inherited Retinal Disease Registry and DNA BankDepartment of Medical Technology and PhysicsSir Charles Gairdner HospitalNedlandsWestern AustraliaAustralia
- Department of OphthalmologyRoyal Perth HospitalPerthWestern AustraliaAustralia
- Department of OphthalmologyPerth Children's HospitalNedlandsWestern AustraliaAustralia
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Monger S, Troup M, Ip E, Dunwoodie SL, Giannoulatou E. Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants. Bioinformatics 2020; 35:4405-4407. [PMID: 30993321 DOI: 10.1093/bioinformatics/btz263] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/31/2019] [Accepted: 04/10/2019] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants. RESULTS We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer. AVAILABILITY AND IMPLEMENTATION Spliceogen is available as a command line tool which accepts VCF/BED inputs and handles both single nucleotide variants (SNVs) and indels (https://github.com/VCCRI/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Steven Monger
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Michael Troup
- Victor Chang Cardiac Research Institute, Sydney, Australia
| | - Eddie Ip
- Victor Chang Cardiac Research Institute, Sydney, Australia.,St Vincent's Clinical School, UNSW Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Sydney, Australia.,St Vincent's Clinical School, UNSW Sydney, Australia.,School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Australia
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Sydney, Australia.,St Vincent's Clinical School, UNSW Sydney, Australia
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Lee D, Zhang J, Liu J, Gerstein M. Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput Biol 2020; 16:e1008006. [PMID: 32584815 PMCID: PMC7343189 DOI: 10.1371/journal.pcbi.1008006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Alternative RNA splicing provides an important means to expand metazoan transcriptome diversity. Contrary to what was accepted previously, splicing is now thought to predominantly take place during transcription. Motivated by emerging data showing the physical proximity of the spliceosome to Pol II, we surveyed the effect of epigenetic context on co-transcriptional splicing. In particular, we observed that splicing factors were not necessarily enriched at exon junctions and that most epigenetic signatures had a distinctly asymmetric profile around known splice sites. Given this, we tried to build an interpretable model that mimics the physical layout of splicing regulation where the chromatin context progressively changes as the Pol II moves along the guide DNA. We used a recurrent-neural-network architecture to predict the inclusion of a spliced exon based on adjacent epigenetic signals, and we showed that distinct spatio-temporal features of these signals were key determinants of model outcome, in addition to the actual nucleotide sequence of the guide DNA strand. After the model had been trained and tested (with >80% precision-recall curve metric), we explored the derived weights of the latent factors, finding they highlight the importance of the asymmetric time-direction of chromatin context during transcription.
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Affiliation(s)
- Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jing Zhang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jason Liu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- Department of Statistics and Data Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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123
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Terkelsen T, Larsen OH, Vang S, Jensen UB, Wikman F. Deleterious mis-splicing of STK11 caused by a novel single-nucleotide substitution in the 3' polypyrimidine tract of intron five. Mol Genet Genomic Med 2020; 8:e1381. [PMID: 32573125 PMCID: PMC7507455 DOI: 10.1002/mgg3.1381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 01/07/2023] Open
Abstract
Background Pathogenic variants in STK11, also designated as LKB1, cause Peutz–Jeghers syndrome, which is a rare autosomal dominant disorder characterized by mucocutaneous pigmentation changes, polyposis, and a high risk of cancer. Methods A male meeting the clinical diagnostic criteria for Peutz–Jeghers syndrome underwent next‐generation sequencing. To validate the predicted splicing impact of a detected STK11 variant, we performed RNA‐Seq on mRNA extracted from patient‐derived Epstein‐Barr virus‐transformed lymphocytes treated with cycloheximide to inhibit nonsense‐mediated decay ex vivo. Results Blood testing identified a novel single‐nucleotide substitution, NM_000455.4:c.735‐10C>A, at the end of the 3′ polypyrimidine tract of intron five in STK11. RNA‐Seq confirmed a predicted eight base pair insertion in the mRNA transcript. Following inhibition of nonsense‐mediated decay, the out‐of‐frame insertion was detected in 50% of all RNA‐Seq reads. This confirmed a strong, deleterious splicing impact of the variant. Conclusion We characterized a novel likely pathogenic germline variant in intron five of STK11 associated with Peutz–Jeghers syndrome. The study highlights RNA‐Seq as a useful supplement in hereditary cancer predisposition testing.
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Affiliation(s)
- Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Ole H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Friedrik Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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Doll J, Hofrichter MAH, Bahena P, Heihoff A, Segebarth D, Müller T, Dittrich M, Haaf T, Vona B. A novel missense variant in MYO3A is associated with autosomal dominant high-frequency hearing loss in a German family. Mol Genet Genomic Med 2020; 8:e1343. [PMID: 32519820 PMCID: PMC7434730 DOI: 10.1002/mgg3.1343] [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: 04/27/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/30/2022] Open
Abstract
Background MYO3A, encoding the myosin IIIA protein, is associated with autosomal recessive and autosomal dominant nonsyndromic hearing loss. To date, only two missense variants located in the motor‐head domain of MYO3A have been described in autosomal dominant families with progressive, mild‐to‐profound sensorineural hearing loss. These variants alter the ATPase activity of myosin IIIA. Methods Exome sequencing of a proband from a three‐generation German family with prelingual, moderate‐to‐profound, high‐frequency hearing loss was performed. Segregation analysis confirmed a dominant inheritance pattern. Regression analysis of mean hearing level thresholds per individual and ear was performed at high‐, mid‐, and low‐frequencies. Results A novel heterozygous missense variant c.716T>C, p.(Leu239Pro) in the kinase domain of MYO3A was identified that is predicted in silico as disease causing. High‐frequency, progressive hearing loss was identified. Conclusion Correlation analysis of pure‐tone hearing thresholds revealed progressive hearing loss, especially in the high‐frequencies. In the present study, we report the first dominant likely pathogenic variant in MYO3A in a European family and further support MYO3A as an autosomal dominant hearing loss gene.
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Affiliation(s)
- Julia Doll
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Paulina Bahena
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Dennis Segebarth
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Tobias Müller
- Institute of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.,Institute of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.,Tübingen Hearing Research Centre, Department of Otolaryngology - Head and Neck Surgery, Eberhard Karls University, Tübingen, Germany
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Santana dos Santos E, Lallemand F, Petitalot A, Caputo SM, Rouleau E. HRness in Breast and Ovarian Cancers. Int J Mol Sci 2020; 21:E3850. [PMID: 32481735 PMCID: PMC7312125 DOI: 10.3390/ijms21113850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. The majority are carcinomas, originating from epithelial cells that are in constant division and subjected to cyclical variations of the estrogen stimulus during the female hormonal cycle, therefore being vulnerable to DNA damage. A portion of breast and ovarian carcinomas arises in the context of DNA repair defects, in which genetic instability is the backdrop for cancer initiation and progression. For these tumors, DNA repair deficiency is now increasingly recognized as a target for therapeutics. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 mutations present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 mutations were only screened on germline DNA, but now they are also searched at the tumor level to personalize treatment. The reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of a HR-deficient signature. Evidence indicates that identifying the mechanism of HR inactivation should improve both genetic counseling and therapeutic response, since they can be useful as new biomarkers of response.
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Affiliation(s)
- Elizabeth Santana dos Santos
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
- Department of Clinical Oncology, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - François Lallemand
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
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Albaradei S, Magana-Mora A, Thafar M, Uludag M, Bajic VB, Gojobori T, Essack M, Jankovic BR. Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA. Gene 2020; 763S:100035. [PMID: 32550561 PMCID: PMC7285987 DOI: 10.1016/j.gene.2020.100035] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Background The accurate identification of the exon/intron boundaries is critical for the correct annotation of genes with multiple exons. Donor and acceptor splice sites (SS) demarcate these boundaries. Therefore, deriving accurate computational models to predict the SS are useful for functional annotation of genes and genomes, and for finding alternative SS associated with different diseases. Although various models have been proposed for the in silico prediction of SS, improving their accuracy is required for reliable annotation. Moreover, models are often derived and tested using the same genome, providing no evidence of broad application, i.e. to other poorly studied genomes. Results With this in mind, we developed the Splice2Deep models for SS detection. Each model is an ensemble of deep convolutional neural networks. We evaluated the performance of the models based on the ability to detect SS in Homo sapiens, Oryza sativa japonica, Arabidopsis thaliana, Drosophila melanogaster, and Caenorhabditis elegans. Results demonstrate that the models efficiently detect SS in other organisms not considered during the training of the models. Compared to the state-of-the-art tools, Splice2Deep models achieved significantly reduced average error rates of 41.97% and 28.51% for acceptor and donor SS, respectively. Moreover, the Splice2Deep cross-organism validation demonstrates that models correctly identify conserved genomic elements enabling annotation of SS in new genomes by choosing the taxonomically closest model. Conclusions The results of our study demonstrated that Splice2Deep both achieved a considerably reduced error rate compared to other state-of-the-art models and the ability to accurately recognize SS in other organisms for which the model was not trained, enabling annotation of poorly studied or newly sequenced genomes. Splice2Deep models are implemented in Python using Keras API; the models and the data are available at https://github.com/SomayahAlbaradei/Splice_Deep.git.
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Key Words
- AUC, area under curve
- AcSS, acceptor splice site
- Acc, accuracy
- Bioinformatics
- CNN, convolutional neural network
- CONV, convolutional layers
- DL, deep learning
- DNA, deoxyribonucleic acid
- DT, decision trees
- Deep-learning
- DoSS, donor splice site
- FC, fully connected layer
- ML, machine learning
- NB, naive Bayes
- NN, neural network
- POOL, pooling layer
- Prediction
- RF, random forest
- RNA, ribonucleic acid
- ReLU, rectified linear unit layer
- SS, splice site
- SVM, support vector machine
- Sn, sensitivity
- Sp, specificity
- Splice sites
- Splicing
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Affiliation(s)
- Somayah Albaradei
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Faculty of Computing and Information Technology, King Abdulaziz University, Saudi Arabia
| | - Arturo Magana-Mora
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Saudi Aramco, EXPEC-ARC, Drilling Technology Team, Dhahran 31311, Saudi Arabia
| | - Maha Thafar
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Faculty of Computers and Information Systems, Taif University, Saudi Arabia
| | - Mahmut Uludag
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Boris R Jankovic
- Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Rasmussen AG, Melikian M, Globa E, Detlefsen S, Rasmussen L, Petersen H, Brusgaard K, Rasmussen AH, Mortensen MB, Christesen HT. The difficult management of persistent, non-focal congenital hyperinsulinism: A retrospective review from a single, tertiary center. Pediatr Diabetes 2020; 21:441-455. [PMID: 31997554 DOI: 10.1111/pedi.12989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 11/14/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/OBJECTIVE Congenital hyperinsulinism (CHI) is a rare, heterogeneous disease with transient or persistent hypoglycemia. Histologically, focal, diffuse, and atypical forms of CHI exist, and at least 11 disease-causing genes have been identified. METHODS We retrospectively evaluated the treatment and outcome of a cohort of 40 patients with non-focal, persistent CHI admitted to the International Hyperinsulinism Center, Denmark, from January 2000 to May 2017. RESULTS Twenty-two patients (55%) could not be managed with medical monotherapy (diazoxide or octreotide) and six (15%) patients developed severe potential side effects to medication. Surgery was performed in 17 (43%) patients with resection of 66% to 98% of the pancreas. Surgically treated patients had more frequently KATP -channel gene mutations (surgical treatment 12/17 vs conservative treatment 6/23, P = .013), highly severe disease (15/17 vs 13/23, P = .025) and clinical onset <30 days of age (15/17 vs 10/23, P = .004). At last follow-up at median 5.3 (range: 0.3-31.3) years of age, 31/40 (78%) patients still received medical treatment, including 12/17 (71%) after surgery. One patient developed diabetes after a 98% pancreatic resection. Problematic treatment status was seen in 7/40 (18%). Only 8 (20%) had clinical remission (three spontaneous, five after pancreatic surgery). Neurodevelopmental impairment (n = 12, 30%) was marginally associated with disease severity (P = .059). CONCLUSIONS Persistent, non-focal CHI remains difficult to manage. Neurological impairment in 30% suggests a frequent failure of prompt and adequate treatment. A high rate of problematic treatment status at follow-up demonstrates an urgent need for new medical treatment modalities.
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Affiliation(s)
- Amalie G Rasmussen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Maria Melikian
- Department of Pediatric Endocrinology, Endrocrine Research Center, Moscow, Russia
| | - Evgenia Globa
- Department of Pediatric Endocrinology, Ukrainian Research Center of Endocrine Surgery, Kyiv, Ukraine
| | - Sönke Detlefsen
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,OPAC, Odense Pancreas Center, Odense University Hospital, Odense, Denmark.,Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Lars Rasmussen
- OPAC, Odense Pancreas Center, Odense University Hospital, Odense, Denmark.,Department of Surgery, Odense University Hospital, Odense, Denmark
| | - Henrik Petersen
- Department of Nuclear Medicine, Odense University Hospital, Odense, Denmark
| | - Klaus Brusgaard
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Annett H Rasmussen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark
| | - Michael B Mortensen
- OPAC, Odense Pancreas Center, Odense University Hospital, Odense, Denmark.,Department of Surgery, Odense University Hospital, Odense, Denmark
| | - Henrik T Christesen
- Hans Christian Andersen Children's Hospital, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,OPAC, Odense Pancreas Center, Odense University Hospital, Odense, Denmark
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Grassi S, Campuzano O, Coll M, Brión M, Arena V, Iglesias A, Carracedo Á, Brugada R, Oliva A. Genetic variants of uncertain significance: How to match scientific rigour and standard of proof in sudden cardiac death? Leg Med (Tokyo) 2020; 45:101712. [PMID: 32361481 DOI: 10.1016/j.legalmed.2020.101712] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/17/2020] [Accepted: 04/21/2020] [Indexed: 02/08/2023]
Abstract
In many SCD cases, in particular in pediatric age, autopsy can be completely negative and then a post-mortem genetic testing (molecular autopsy) is indicated. In NGS era finding new/rare variants is extremely frequent and, when only variants of unknown significance are found, molecular autopsy fails to find a cause of death. We describe the emblematic case of the sudden death of a 7-year-old girl. We performed a full-body micro-CT analysis, an accurate autopsy, a serum tryptase test and toxicological tests. Since the only macroscopic abnormality we found was a myocardial bridging (length: 1,1 cm, thickness: 0,5 cm) of the left anterior descending coronary artery, a molecular autopsy has been performed. NGS analysis on victim DNA detected rare variants in DPP6, MYH7, SCN2B and NOTCH1 and segregation analysis was then achieved. On the basis of ACMG/AMP (clinical) guidelines, all the found variants were classified as of unknown significance. In other words, both the macroscopic and genetic anomalies we found were of uncertain significance and then the autopsy failed to find the cause of the death. Our case raises three main discussion points: (a) economical, ethical and legal limitations of genetic investigation; (b) risk that genetic testing does not succeed in finding a certain cause of the death; (c) absence of specific guidelines to face the problem of VUS in forensic cases.
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Affiliation(s)
- Simone Grassi
- Institute of Public Health, Section of Legal Medicine, Catholic University, Rome, Italy
| | - Oscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro Investigación Biomédica Red Enfermedades Cardiovasculares, Madrid, Spain; Department of Biochemistry and Molecular Genetics, Hospital Clinic, IDIBAPS, Barcelona, Spain
| | - Mònica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - María Brión
- Genetics of Cardiovascular and Ophthalmological Diseases, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain; Genomic Medicine, University of Santiago de Compostela, IDIS, CIBERER, Santiago de Compostela, Spain
| | - Vincenzo Arena
- Institute of Anatomical Pathology, Catholic University, Rome, Italy
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Ángel Carracedo
- Genomic Medicine, University of Santiago de Compostela, IDIS, CIBERER, Santiago de Compostela, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain; Medical Science Department, School of Medicine, University of Girona, Girona, Spain; Centro Investigación Biomédica Red Enfermedades Cardiovasculares, Madrid, Spain; Cardiology Service, Hospital Josep Trueta, Girona, Spain
| | - Antonio Oliva
- Institute of Public Health, Section of Legal Medicine, Catholic University, Rome, Italy.
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In or Out? New Insights on Exon Recognition through Splice-Site Interdependency. Int J Mol Sci 2020; 21:ijms21072300. [PMID: 32225107 PMCID: PMC7177576 DOI: 10.3390/ijms21072300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/13/2020] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
Noncanonical splice-site mutations are an important cause of inherited diseases. Based on in vitro and stem-cell-based studies, some splice-site variants show a stronger splice defect than expected based on their predicted effects, suggesting that other sequence motifs influence the outcome. We investigated whether splice defects due to human-inherited-disease-associated variants in noncanonical splice-site sequences in ABCA4, DMD, and TMC1 could be rescued by strengthening the splice site on the other side of the exon. Noncanonical 5′- and 3′-splice-site variants were selected. Rescue variants were introduced based on an increase in predicted splice-site strength, and the effects of these variants were analyzed using in vitro splice assays in HEK293T cells. Exon skipping due to five variants in noncanonical splice sites of exons in ABCA4, DMD, and TMC1 could be partially or completely rescued by increasing the predicted strengths of the other splice site of the same exon. We named this mechanism “splicing interdependency”, and it is likely based on exon recognition by splicing machinery. Awareness of this interdependency is of importance in the classification of noncanonical splice-site variants associated with disease and may open new opportunities for treatments.
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Volozonoka L, Rots D, Kempa I, Kornete A, Rezeberga D, Gailite L, Miskova A. Genetic landscape of preterm birth due to cervical insufficiency: Comprehensive gene analysis and patient next-generation sequencing data interpretation. PLoS One 2020; 15:e0230771. [PMID: 32214361 PMCID: PMC7098624 DOI: 10.1371/journal.pone.0230771] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/07/2020] [Indexed: 01/10/2023] Open
Abstract
Preterm delivery is both a traumatizing experience for the patient and a burden on the healthcare system. A condition distinguishable by its phenotype in prematurity is cervical insufficiency, where certain cases exhibit a strong genetic component. Despite genomic advancements, little is known about the genetics of human cervix remodeling during pregnancy. Using selected gene approaches, a few studies have demonstrated an association of common gene variants with cervical insufficiency. However, until now, no study has employed comprehensive methods to investigate this important subject matter. In this study, we asked: i) are there genes reliably linked to cervical insufficiency and, if so, what are their roles? and ii) what is the proportion of cases of non-syndromic cervical insufficiency attributable to these genetic variations? We performed next-generation sequencing on 21 patients with a clinical presentation of cervical insufficiency. To assist the sequencing data interpretation, we retrieved all known genes implicated in cervical functioning through a systematic literature analysis and additional gene searches. These genes were then classified according to their relation to the questions being posed by the study. Patients' sequence variants were filtered for pathogenicity and assigned a likelihood of being contributive to phenotype development. Gene extraction and analysis revealed 12 genes primarily linked to cervical insufficiency, the majority of which are known to cause collagenopathies. Ten patients carried disruptive variants potentially contributive to the development of non-syndromic cervical insufficiency. Pathway enrichment analysis of variant genes from our cohort revealed an increased variation burden in genes playing roles in tissue mechanical and biomechanical properties, i.e. collagen biosynthesis and cell-extracellular matrix communications. Consequently, the proposed idea of cervical insufficiency being a subtle form of collagenopathy, now strengthened by our genetic findings, might open up new opportunities for improved patient evaluation and management.
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Affiliation(s)
- Ludmila Volozonoka
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Inga Kempa
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Anna Kornete
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
| | - Dace Rezeberga
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
| | - Linda Gailite
- Scientific Laboratory of Molecular Genetics, Riga Stradins University, Riga, Latvia
| | - Anna Miskova
- Department of Obstetrics and Gynecology, Riga Stradins University, Riga, Latvia
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Wimmer K, Schamschula E, Wernstedt A, Traunfellner P, Amberger A, Zschocke J, Kroisel P, Chen Y, Callens T, Messiaen L. AG-exclusion zone revisited: Lessons to learn from 91 intronic NF1 3' splice site mutations outside the canonical AG-dinucleotides. Hum Mutat 2020; 41:1145-1156. [PMID: 32126153 PMCID: PMC7317903 DOI: 10.1002/humu.24005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/26/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Uncovering frequent motives of action by which variants impair 3′ splice site (3′ss) recognition and selection is essential to improve our understanding of this complex process. Through several mini‐gene experiments, we demonstrate that the pyrimidine (Y) to purine (R) transversion NM_000267.3(NF1):c.1722‐11T>G, although expected to weaken the polypyrimidine tract, causes exon skipping primarily by introducing a novel AG in the AG‐exclusion zone (AGEZ) between the authentic 3′ss AG and the branch point. Evaluation of 90 additional noncanonical intronic NF1 3′ss mutations confirmed that 63% of all mutations and 89% (49/55) of the single‐nucleotide variants upstream of positions ‐3 interrupt the AGEZ. Of these AGEZ‐interrupting mutations, 24/49 lead to exon skipping suggesting that absence of AG in this region is necessary for accurate 3′ss selection already in the initial steps of splicing. The analysis of 91 noncanonical NF1 3′ss mutations also shows that 90% either introduce a novel AG in the AGEZ, cause a Y>R transversion at position ‐3 or remove ≥2 Ys in the AGEZ. We confirm in a validation cohort that these three motives distinguish spliceogenic from splice‐neutral variants with 85% accuracy and, therefore, are generally applicable to select among variants of unknown significance those likely to affect splicing.
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Affiliation(s)
- Katharina Wimmer
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Esther Schamschula
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Annekatrin Wernstedt
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Pia Traunfellner
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Albert Amberger
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Zschocke
- Institute of Human Genetics, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Kroisel
- Diagnostic & Research Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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Kingsmore SF, Ramchandar N, James K, Niemi AK, Feigenbaum A, Ding Y, Benson W, Hobbs C, Nahas S, Chowdhury S, Dimmock D. Mortality in a neonate with molybdenum cofactor deficiency illustrates the need for a comprehensive rapid precision medicine system. Cold Spring Harb Mol Case Stud 2020; 6:a004705. [PMID: 32014857 PMCID: PMC6996516 DOI: 10.1101/mcs.a004705] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/30/2019] [Indexed: 12/31/2022] Open
Abstract
Neonatal encephalopathy with seizures is a presentation in which rapid whole-genome sequencing (rWGS) has shown clinical utility and improved outcomes. We report a neonate who presented on the third day of life with seizures refractory to antiepileptic medications and neurologic and computerized tomographic findings consistent with severe generalized brain swelling. rWGS revealed compound heterozygous variants in the molybdenum cofactor synthesis gene, type 1A (MOCS1 c.*7 + 5G > A and c.377G > A); a provisional diagnosis of molybdenum cofactor deficiency on day of life 4. An emergency investigational new drug application for intravenous replacement of the MOCS1 product, cyclic pyranopterin monophosphate, was considered, but felt unsuitable in light of the severity of disease and delay in the start of treatment. The patient died on day of life 9 despite having a precise molecular diagnosis within the first week of life. This case illustrates that an rWGS-based molecular diagnosis within the first week of life may be insufficient to improve outcomes. However, it did inform clinical decision-making with regard to resuscitation and predicted long-term outcome. We suggest that to achieve optimal reductions in morbidity and mortality, rWGS must be implemented within a comprehensive rapid precision medicine system (CRPM). Akin to newborn screening (NBS), CRPM will have onboarding, diagnosis, and precision medicine implementation components developed in response to patient and parental needs. Education of health-care providers in a learning model in which ongoing data analyses informs system improvement will be essential for optimal effectiveness of CRPM.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Nanda Ramchandar
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
- Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, California 92123, USA
| | - Kiely James
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Anna-Kaisa Niemi
- Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, California 92123, USA
| | - Annette Feigenbaum
- Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, California 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Wendy Benson
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Charlotte Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - Shimul Chowdhury
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
| | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California 92123, USA
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133
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Doll J, Kolb S, Schnapp L, Rad A, Rüschendorf F, Khan I, Adli A, Hasanzadeh A, Liedtke D, Knaup S, Hofrichter MAH, Müller T, Dittrich M, Kong IK, Kim HG, Haaf T, Vona B. Novel Loss-of-Function Variants in CDC14A are Associated with Recessive Sensorineural Hearing Loss in Iranian and Pakistani Patients. Int J Mol Sci 2020; 21:ijms21010311. [PMID: 31906439 PMCID: PMC6982189 DOI: 10.3390/ijms21010311] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022] Open
Abstract
CDC14A encodes the Cell Division Cycle 14A protein and has been associated with autosomal recessive non-syndromic hearing loss (DFNB32), as well as hearing impairment and infertile male syndrome (HIIMS) since 2016. To date, only nine variants have been associated in patients whose initial symptoms included moderate-to-profound hearing impairment. Exome analysis of Iranian and Pakistani probands who both showed bilateral, sensorineural hearing loss revealed a novel splice site variant (c.1421+2T>C, p.?) that disrupts the splice donor site and a novel frameshift variant (c.1041dup, p.Ser348Glnfs*2) in the gene CDC14A, respectively. To evaluate the pathogenicity of both loss-of-function variants, we analyzed the effects of both variants on the RNA-level. The splice variant was characterized using a minigene assay. Altered expression levels due to the c.1041dup variant were assessed using RT-qPCR. In summary, cDNA analysis confirmed that the c.1421+2T>C variant activates a cryptic splice site, resulting in a truncated transcript (c.1414_1421del, p.Val472Leufs*20) and the c.1041dup variant results in a defective transcript that is likely degraded by nonsense-mediated mRNA decay. The present study functionally characterizes two variants and provides further confirmatory evidence that CDC14A is associated with a rare form of hereditary hearing loss.
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Affiliation(s)
- Julia Doll
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Susanne Kolb
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Linda Schnapp
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Aboulfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar 009851, Iran; (A.R.); (A.A.); (A.H.)
- Tübingen Hearing Research Centre, Department of Otorhinolaryngology, Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
| | - Franz Rüschendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany;
| | - Imran Khan
- Department of Chemistry, Bacha Khan University, Charsadda, Khyber Pakhtunkhawa 24420, Pakistan;
| | - Abolfazl Adli
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar 009851, Iran; (A.R.); (A.A.); (A.H.)
| | - Atefeh Hasanzadeh
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar 009851, Iran; (A.R.); (A.A.); (A.H.)
| | - Daniel Liedtke
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Sabine Knaup
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Michaela AH Hofrichter
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Tobias Müller
- Institute of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany;
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
- Institute of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany;
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea;
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha 34110, Qatar;
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; (J.D.); (S.K.); (L.S.); (D.L.); (S.K.); (M.A.H.); (M.D.); (T.H.)
- Tübingen Hearing Research Centre, Department of Otorhinolaryngology, Head and Neck Surgery, Eberhard Karls University, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-7071-29-88154
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Wang R, Wang Z, Wang J, Li S. SpliceFinder: ab initio prediction of splice sites using convolutional neural network. BMC Bioinformatics 2019; 20:652. [PMID: 31881982 PMCID: PMC6933889 DOI: 10.1186/s12859-019-3306-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites with important biological functions. Meanwhile, the dinucleotides occur frequently at the sequences without splice sites, which makes the prediction prone to generate false positives. Most existing tools select all the sequences with the two dimers and then focus on distinguishing the true splice sites from those pseudo ones. Such an approach will lead to a decrease in false positives; however, it will result in non-canonical splice sites missing. Result We have designed SpliceFinder based on convolutional neural network (CNN) to predict splice sites. To achieve the ab initio prediction, we used human genomic data to train our neural network. An iterative approach is adopted to reconstruct the dataset, which tackles the data unbalance problem and forces the model to learn more features of splice sites. The proposed CNN obtains the classification accuracy of 90.25%, which is 10% higher than the existing algorithms. The method outperforms other existing methods in terms of area under receiver operating characteristics (AUC), recall, precision, and F1 score. Furthermore, SpliceFinder can find the exact position of splice sites on long genomic sequences with a sliding window. Compared with other state-of-the-art splice site prediction tools, SpliceFinder generates results in about half lower false positive while keeping recall higher than 0.8. Also, SpliceFinder captures the non-canonical splice sites. In addition, SpliceFinder performs well on the genomic sequences of Drosophila melanogaster, Mus musculus, Rattus, and Danio rerio without retraining. Conclusion Based on CNN, we have proposed a new ab initio splice site prediction tool, SpliceFinder, which generates less false positives and can detect non-canonical splice sites. Additionally, SpliceFinder is transferable to other species without retraining. The source code and additional materials are available at https://gitlab.deepomics.org/wangruohan/SpliceFinder.
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Affiliation(s)
- Ruohan Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China
| | - Zishuai Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China
| | - Jianping Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China.
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong, China.
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135
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Beecroft SJ, Olive M, Quereda LG, Gallano P, Ojanguren I, McLean C, McCombe P, Laing NG, Ravenscroft G. Cylindrical spirals in two families: Clinical and genetic investigations. Neuromuscul Disord 2019; 30:151-158. [PMID: 31952901 DOI: 10.1016/j.nmd.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 01/19/2023]
Abstract
Cylindrical spirals are a rare ultrastructural finding on muscle biopsy, with fewer than 20 reported cases since its first description in 1979. These structures are sometimes observed with tubular aggregates and are thought to comprise longitudinal sarcoplasmic reticulum. While mutations in genes encoding key components of Ca2+ handling (ORAI1 and STIM1) underlie tubular aggregate myopathy, no causative genes have been associated with cylindrical spirals. Here we describe two families with cylindrical spirals on muscle biopsy with a suspected genetic cause. In one family we identified a known truncating variant in EBF3, previously associated with a neurodevelopmental disorder. The affected individuals in this family present with clinical features overlapping with those described for EBF3 disease. An isolated proband in the second family harbours bi-allelic truncating variants in TTN and her clinical course and other features on biopsy are highly concordant for titinopathy. From experimental studies, EBF3 is known to be involved in Ca2+ regulation in muscle, thus EBF3 dysregulation may represent a novel mechanism of impaired Ca2+ handling leading to cylindrical spirals. Additional cases of EBF3 disease or titinopathy with cylindrical spirals need to be identified to support the involvement of these genes in the pathogenesis of cylindrical spirals.
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Affiliation(s)
- Sarah J Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Australia
| | - Montse Olive
- Neuropathology Unit, Department of Pathology and Neuromuscular Unit, Department of Neurology, IDIBELL-Hospital de Bellvitge, Hospitalet de Llobregat, Barcelona 08907, Spain
| | | | - Pia Gallano
- CIBERER, Genetics Department, Hospital Sant Pau, Barcelona 08041, Spain
| | - Isabel Ojanguren
- Department of Pathology, Hospital Germans Trias i Pujol, Badalona 08916, Spain
| | - Catriona McLean
- Victorian Neuromuscular Laboratory, Alfred Health, Commercial Rd, Prahran, VIC 3181, Australia
| | - Pamela McCombe
- The University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Nigel G Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Australia.
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Fadaie Z, Khan M, Del Pozo‐Valero M, Cornelis SS, Ayuso C, Cremers FPM, Roosing S, The ABCA4 study group. Identification of splice defects due to noncanonical splice site or deep-intronic variants in ABCA4. Hum Mutat 2019; 40:2365-2376. [PMID: 31397521 PMCID: PMC6899986 DOI: 10.1002/humu.23890] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 12/25/2022]
Abstract
Pathogenic variants in the ATP-binding cassette transporter A4 (ABCA4) gene cause a continuum of retinal disease phenotypes, including Stargardt disease. Noncanonical splice site (NCSS) and deep-intronic variants constitute a large fraction of disease-causing alleles, defining the functional consequences of which remains a challenge. We aimed to determine the effect on splicing of nine previously reported or unpublished NCSS variants, one near exon splice variant and nine deep-intronic variants in ABCA4, using in vitro splice assays in human embryonic kidney 293T cells. Reverse transcription-polymerase chain reaction and Sanger sequence analysis revealed splicing defects for 12 out of 19 variants. Four deep-intronic variants create pseudoexons or elongate the upstream exon. Furthermore, eight NCSS variants cause a partial deletion or skipping of one or more exons in messenger RNAs. Among the 12 variants, nine lead to premature stop codons and predicted truncated ABCA4 proteins. At least two deep-intronic variants affect splice enhancer and silencer motifs and, therefore, these conserved sequences should be carefully evaluated when predicting the outcome of NCSS and deep-intronic variants.
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Affiliation(s)
- Zeinab Fadaie
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Marta Del Pozo‐Valero
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain
| | - Stéphanie S. Cornelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain
| | - Frans P. M. Cremers
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
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137
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Rowlands CF, Baralle D, Ellingford JM. Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. Cells 2019; 8:E1513. [PMID: 31779139 PMCID: PMC6953098 DOI: 10.3390/cells8121513] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
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Affiliation(s)
- Charlie F Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, MP808, Tremona Road, Southampton SO16 6YD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
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138
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Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks. Comput Biol Med 2019; 116:103558. [PMID: 31783254 DOI: 10.1016/j.compbiomed.2019.103558] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022]
Abstract
Neural models have been able to obtain state-of-the-art performances on several genome sequence-based prediction tasks. Such models take only nucleotide sequences as input and learn relevant features on their own. However, extracting the interpretable motifs from the model remains a challenge. This work explores various existing visualization techniques in their ability to infer relevant sequence information learnt by a recurrent neural network (RNN) on the task of splice junction identification. The visualization techniques have been modulated to suit the genome sequences as input. The visualizations inspect genomic regions at the level of a single nucleotide as well as a span of consecutive nucleotides. This inspection is performed based on the modification of input sequences (perturbation based) or the embedding space (back-propagation based). We infer features pertaining to both canonical and non-canonical splicing from a single neural model. Results indicate that the visualization techniques produce comparable performances for branchpoint detection. However, in the case of canonical donor and acceptor junction motifs, perturbation based visualizations perform better than back-propagation based visualizations, and vice-versa for non-canonical motifs. The source code of our stand-alone SpliceVisuL tool is available at https://github.com/aaiitggrp/SpliceVisuL.
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139
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Marco-Puche G, Lois S, Benítez J, Trivino JC. RNA-Seq Perspectives to Improve Clinical Diagnosis. Front Genet 2019; 10:1152. [PMID: 31781178 PMCID: PMC6861419 DOI: 10.3389/fgene.2019.01152] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/22/2019] [Indexed: 01/22/2023] Open
Abstract
In recent years, high-throughput next-generation sequencing technology has allowed a rapid increase in diagnostic capacity and precision through different bioinformatics processing algorithms, tools, and pipelines. The identification, annotation, and classification of sequence variants within different target regions are now considered a gold standard in clinical genetic diagnosis. However, this procedure lacks the ability to link regulatory events such as differential splicing to diseases. RNA-seq is necessary in clinical routine in order to interpret and detect among others splicing events and splicing variants, as it would increase the diagnostic rate by up to 10-35%. The transcriptome has a very dynamic nature, varying according to tissue type, cellular conditions, and environmental factors that may affect regulatory events such as splicing and the expression of genes or their isoforms. RNA-seq offers a robust technical analysis of this complexity, but it requires a profound knowledge of computational/statistical tools that may need to be adjusted depending on the disease under study. In this article we will cover RNA-seq analyses best practices applied to clinical routine, bioinformatics procedures, and present challenges of this approach.
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Affiliation(s)
| | - Sergio Lois
- Bioinformatics Group, Sistemas Genómicos, Paterna, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center, Madrid, Spain
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140
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Jilani A, Matviychuk D, Blaser S, Dyack S, Mathieu J, Prasad AN, Prasad C, Kyriakopoulou L, Mercimek‐Andrews S. High diagnostic yield of direct Sanger sequencing in the diagnosis of neuronal ceroid lipofuscinoses. JIMD Rep 2019; 50:20-30. [PMID: 31741823 PMCID: PMC6850977 DOI: 10.1002/jmd2.12057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/14/2019] [Accepted: 05/23/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Neuronal ceroid lipofuscinoses are neurodegenerative disorders. To investigate the diagnostic yield of direct Sanger sequencing of the CLN genes, we reviewed Molecular Genetics Laboratory Database for molecular genetic test results of the CLN genes from a single clinical molecular diagnostic laboratory. METHODS We reviewed electronic patient charts. We used consent forms and Research Electronic Data Capture questionnaires for the patients from outside of our Institution. We reclassified all variants in the CLN genes. RESULTS Six hundred and ninety three individuals underwent the direct Sanger sequencing of the CLN genes for the diagnosis of neuronal ceroid lipofuscinoses. There were 343 symptomatic patients and 350 family members. Ninety-one symptomatic patients had molecular genetic diagnosis of neuronal ceroid lipofuscinoses including CLN1 (PPT1) (n = 10), CLN2 (TPP1) (n = 33), CLN3 (n = 17), CLN5 (n = 7), CLN6 (n = 10), CLN7 (MFSD8) (n = 10), and CLN8 (n = 4) diseases. The diagnostic yield of direct Sanger sequencing of CLN genes was 27% in symptomatic patients. We report detailed clinical and investigation results of 33 NCL patients. Juvenile onset CLN1 (PPT1) and adult onset CLN6 diseases were nonclassical phenotypes. CONCLUSION In our study, the diagnostic yield of direct Sanger sequencing was close to diagnostic yield of whole exome sequencing. Developmental regression, cognitive decline, visual impairment and cerebral and/or cerebellar atrophy in brain MRI are significant clinical and neuroimaging denominators to include NCL in the differential diagnosis.
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Affiliation(s)
- Abdulhakim Jilani
- Division of Clinical and Metabolic Genetics, Department of PaediatricsUniversity of Toronto, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Diana Matviychuk
- Division of Genome Diagnostics, Department of Paediatric Laboratory MedicineThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Susan Blaser
- Division of Neuroradiology, Department of Medical ImagingUniversity of Toronto, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Sarah Dyack
- Division of Medical Genetics, Department of Pediatrics, IWK Health CentreUniversity of DalhouiseHalifaxNova ScotiaCanada
| | - Jean Mathieu
- Neuromuscular Disease ClinicUniversity of SherbrookeQuebecCanada
| | - Asuri N. Prasad
- Division of Clinical Neurosciences, Department of Paediatrics, Schulich School of Medicine and DentistryWestern UniversityLondonOntarioCanada
| | - Chitra Prasad
- Division of Medical Genetics Department of Paediatrics, Schulich School of Medicine & DentistryWestern UniversityLondonOntarioCanada
| | - Lianna Kyriakopoulou
- Division of Genome Diagnostics, Department of Paediatric Laboratory MedicineThe Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Paediatric Laboratory Medicine and PathobiologyUniversity of TorontoTorontoOntarioCanada
| | - Saadet Mercimek‐Andrews
- Division of Clinical and Metabolic Genetics, Department of PaediatricsUniversity of Toronto, The Hospital for Sick ChildrenTorontoOntarioCanada
- Genetics and Genome Biology Program, Research InstituteThe Hospital for Sick ChildrenTorontoOntarioCanada
- Institute of Medical SciencesUniversity of TorontoTorontoOntarioCanada
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141
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Prevalence of ABCA4 Deep-Intronic Variants and Related Phenotype in An Unsolved "One-Hit" Cohort with Stargardt Disease. Int J Mol Sci 2019; 20:ijms20205053. [PMID: 31614660 PMCID: PMC6829239 DOI: 10.3390/ijms20205053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023] Open
Abstract
We investigated the prevalence of reported deep-intronic variants in a French cohort of 70 patients with Stargardt disease harboring a monoallelic pathogenic variant on the exonic regions of ABCA4. Direct Sanger sequencing of selected intronic regions of ABCA4 was conducted. Complete phenotypic analysis and correlation with the genotype was performed in case a known intronic pathogenic variant was identified. All other variants found on the analyzed sequences were queried for minor allele frequency and possible pathogenicity by in silico predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G>A in intron 36 (6 subjects), c.4539+2064C>T in intron 30 (4 subjects) and c.4253+43G>A in intron 28 (4 subjects). Even though the phenotype depends on the compound effect of the biallelic variants, a genotype-phenotype correlation suggests that the c.5196+1137G>A was mostly associated with a mild phenotype and the c.4539+2064C>T with a more severe one. A variable effect was instead associated with the variant c.4253+43G>A. In addition, two novel variants, c.768+508A>G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted in silico. Our study calls for a larger cohort analysis including targeted locus sequencing and 3D protein modeling to better understand phenotype-genotype correlations associated with deep-intronic changes and patients’ selection for clinical trials.
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142
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Harris C, Xu W, Grassi L, Wang C, Markle A, Hardman C, Stevens R, Miro-Quesada G, Hatton D, Wang J. Identification and characterization of an IgG sequence variant with an 11 kDa heavy chain C-terminal extension using a combination of mass spectrometry and high-throughput sequencing analysis. MAbs 2019; 11:1452-1463. [PMID: 31570042 PMCID: PMC6816433 DOI: 10.1080/19420862.2019.1667740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein primary structure is a potential critical quality attribute for biotherapeutics. Identifying and characterizing any sequence variants present is essential for product development. A sequence variant ~11 kDa larger than the expected IgG mass was observed by size-exclusion chromatography and two-dimensional liquid chromatography coupled with online mass spectrometry. Further characterization indicated that the 11 kDa was added to the heavy chain (HC) Fc domain. Despite the relatively large mass addition, only one unknown peptide was detected by peptide mapping. To decipher the sequence, the transcriptome of the manufacturing cell line was characterized by Illumina RNA-seq. Transcriptome reconstruction detected an aberrant fusion transcript, where the light chain (LC) constant domain sequence was fused to the 3ʹ end of the HC transcript. Translation of this fusion transcript generated an extended peptide sequence at the HC C-terminus corresponding to the observed 11 kDa mass addition. Nanopore-based genome sequencing showed multiple copies of the plasmid had integrated in tandem with one copy missing the 5ʹ end of the plasmid, deleting the LC variable domain. The fusion transcript was due to read-through of the HC terminator sequence into the adjacent partial LC gene and an unexpected splicing event between a cryptic splice-donor site at the 3ʹ end of the HC and the splice acceptor site at the 5ʹ end of the LC constant domain. Our study demonstrates that combining protein physicochemical characterization with genomic and transcriptomic analysis of the manufacturing cell line greatly improves the identification of sequence variants and understanding of the underlying molecular mechanisms.
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Affiliation(s)
- Claire Harris
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Weichen Xu
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Luigi Grassi
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Chunlei Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Abigail Markle
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Colin Hardman
- Data Science & Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Richard Stevens
- Antibody Discovery and Protein Engineering, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Guillermo Miro-Quesada
- Data & Quantitative Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Diane Hatton
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Jihong Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
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143
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Bryen SJ, Joshi H, Evesson FJ, Girard C, Ghaoui R, Waddell LB, Testa AC, Cummings B, Arbuckle S, Graf N, Webster R, MacArthur DG, Laing NG, Davis MR, Lührmann R, Cooper ST. Pathogenic Abnormal Splicing Due to Intronic Deletions that Induce Biophysical Space Constraint for Spliceosome Assembly. Am J Hum Genet 2019; 105:573-587. [PMID: 31447096 DOI: 10.1016/j.ajhg.2019.07.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022] Open
Abstract
A precise genetic diagnosis is the single most important step for families with genetic disorders to enable personalized and preventative medicine. In addition to genetic variants in coding regions (exons) that can change a protein sequence, abnormal pre-mRNA splicing can be devastating for the encoded protein, inducing a frameshift or in-frame deletion/insertion of multiple residues. Non-coding variants that disrupt splicing are extremely challenging to identify. Stemming from an initial clinical discovery in two index Australian families, we define 25 families with genetic disorders caused by a class of pathogenic non-coding splice variant due to intronic deletions. These pathogenic intronic deletions spare all consensus splice motifs, though they critically shorten the minimal distance between the 5' splice-site (5'SS) and branchpoint. The mechanistic basis for abnormal splicing is due to biophysical constraint precluding U1/U2 spliceosome assembly, which stalls in A-complexes (that bridge the 5'SS and branchpoint). Substitution of deleted nucleotides with non-specific sequences restores spliceosome assembly and normal splicing, arguing against loss of an intronic element as the primary causal basis. Incremental lengthening of 5'SS-branchpoint length in our index EMD case subject defines 45-47 nt as the critical elongation enabling (inefficient) spliceosome assembly for EMD intron 5. The 5'SS-branchpoint space constraint mechanism, not currently factored by genomic informatics pipelines, is relevant to diagnosis and precision medicine across the breadth of Mendelian disorders and cancer genomics.
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144
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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145
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Muiño-Mosquera L, Steijns F, Audenaert T, Meerschaut I, De Paepe A, Steyaert W, Symoens S, Coucke P, Callewaert B, Renard M, De Backer J. Tailoring the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines for the Interpretation of Sequenced Variants in the FBN1 Gene for Marfan Syndrome: Proposal for a Disease- and Gene-Specific Guideline. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e002039. [PMID: 29875124 DOI: 10.1161/circgen.117.002039] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/09/2018] [Indexed: 01/08/2023]
Abstract
BACKGROUND The introduction of next-generation sequencing techniques has substantially increased the identification of new genetic variants and hence the necessity of accurate variant interpretation. In 2015, the American College of Medical Genetics and Genomics and the Association for Molecular Pathology proposed new variant interpretation guidelines. Gene-specific characteristics were, however, not considered, sometimes leading to inconsistent variant interpretation. METHODS To allow a more uniform interpretation of variants in the FBN1 (fibrillin-1) gene, causing Marfan syndrome, we tailored these guidelines to this gene and disease. We adapted 15 of the 28 general criteria and classified 713 FBN1 variants previously identified in our laboratory as causal mutation or variant of uncertain significance according to these adapted guidelines. We then compared the agreement between previous methods and the adapted American College of Medical Genetics and Genomics and the Association for Molecular Pathology criteria. RESULTS Agreement between the methods was 86.4% (K-alpha, 0.6). Application of the tailored guidelines resulted in an increased number of variants of uncertain significance (14.5% to 24.2%). Of the 85 variants that were downscaled to likely benign or variant of uncertain significance, 59.7% were missense variants outside a well-established functional site. Available clinical- or segregation data, necessary to further classify these types of variants, were in many cases insufficient to aid the classification. CONCLUSIONS Our study shows that classification of variants remains challenging and may change over time. Currently, a higher level of evidence is necessary to classify a variant as pathogenic. Gene-specific guidelines may be useful to allow a more precise and uniform interpretation of the variants to accurately support clinical decision-making.
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Affiliation(s)
- Laura Muiño-Mosquera
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.) .,Division of Pediatric Cardiology (L.M.-M.)
| | - Felke Steijns
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Tjorven Audenaert
- Department of Cardiology (T.A., J.D.B.), Ghent University Hospital, Belgium
| | - Ilse Meerschaut
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Anne De Paepe
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Wouter Steyaert
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Sofie Symoens
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Paul Coucke
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Bert Callewaert
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Marjolijn Renard
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.)
| | - Julie De Backer
- Center for Medical Genetics (L.M.-M., F.S., I.M., A.D.P., W.S., S.S., P.C., B.C., M.R., J.D.B.).,Department of Cardiology (T.A., J.D.B.), Ghent University Hospital, Belgium
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146
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A deep intronic splice mutation of STAT3 underlies hyper IgE syndrome by negative dominance. Proc Natl Acad Sci U S A 2019; 116:16463-16472. [PMID: 31346092 DOI: 10.1073/pnas.1901409116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Heterozygous in-frame mutations in coding regions of human STAT3 underlie the only known autosomal dominant form of hyper IgE syndrome (AD HIES). About 5% of familial cases remain unexplained. The mutant proteins are loss-of-function and dominant-negative when tested following overproduction in recipient cells. However, the production of mutant proteins has not been detected and quantified in the cells of heterozygous patients. We report a deep intronic heterozygous STAT3 mutation, c.1282-89C>T, in 7 relatives with AD HIES. This mutation creates a new exon in the STAT3 complementary DNA, which, when overexpressed, generates a mutant STAT3 protein (D427ins17) that is loss-of-function and dominant-negative in terms of tyrosine phosphorylation, DNA binding, and transcriptional activity. In immortalized B cells from these patients, the D427ins17 protein was 2 kDa larger and 4-fold less abundant than wild-type STAT3, on mass spectrometry. The patients' primary B and T lymphocytes responded poorly to STAT3-dependent cytokines. These findings are reminiscent of the impaired responses of leukocytes from other patients with AD HIES due to typical STAT3 coding mutations, providing further evidence for the dominance of the mutant intronic allele. These findings highlight the importance of sequencing STAT3 introns in patients with HIES without candidate variants in coding regions and essential splice sites. They also show that AD HIES-causing STAT3 mutant alleles can be dominant-negative even if the encoded protein is produced in significantly smaller amounts than wild-type STAT3.
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147
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Núñez L, Marrón-Liñares GM, Crespo-Leiro MG, Barge-Caballero E, Álvarez-López E, Suarez-Fuentetaja N, Paniagua-Martin MJ, Pombo J, Muñiz J, Tan CD, Rodríguez ER, Vázquez-Rodríguez JM, Hermida-Prieto M. AGT haplotype in ITGA4 gene is related to antibody-mediated rejection in heart transplant patients. PLoS One 2019; 14:e0219345. [PMID: 31335901 PMCID: PMC6650139 DOI: 10.1371/journal.pone.0219345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/05/2019] [Indexed: 11/29/2022] Open
Abstract
Introduction One of the main problems involved in heart transplantation (HT) is antibody-mediated rejection (AMR). Many aspects of AMR are still unresolved, including its etiology, diagnosis and treatment. In this project, we hypothesize that variants in genes involved in B-cell biology in HT patients can yield diagnostic and prognostic information about AMR. Methods Genetic variants in 61 genes related to B-cell biology were analyzed by next generation sequencing in 46 HT patients, 23 with and 23 without AMR. Results We identified 3 single nucleotide polymorphisms in ITGA4 gene (c.1845G>A, c.2633A>G, and c.2883C>T) that conformed the haplotype AGT-ITGA4. This haplotype is associated with the development of AMR. Moreover, AMR patients with the haplotype AGT-ITGA4 present lower levels of integrin α-4 in serum samples compared to the reference GAC haplotype in control patients. Conclusion We can conclude that polymorphisms in genes related to the biology of B-cells could have an important role in the development of AMR. In fact, the AGT haplotype in ITGA4 gene could potentially increase the risk of AMR.
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Affiliation(s)
- Lucía Núñez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Grecia M. Marrón-Liñares
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - María G. Crespo-Leiro
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Eduardo Barge-Caballero
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Eloy Álvarez-López
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Suarez-Fuentetaja
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - María Jesús Paniagua-Martin
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Jorge Pombo
- Servicio de Anatomía Patológica, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), SERGAS, A Coruña, Spain
| | - Javier Muñiz
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
| | - Carmela D. Tan
- Department of Pathology, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - E. René Rodríguez
- Department of Pathology, The Cleveland Clinic, Cleveland, Ohio, United States of America
| | - José Manuel Vázquez-Rodríguez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC)-CIBERCV, Sergas Universidade da Coruña (UDC), A Coruña, Spain
| | - Manuel Hermida-Prieto
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), A Coruña, Spain
- * E-mail:
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148
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Gao P, Zhang R, Li J. Comprehensive elaboration of database resources utilized in next-generation sequencing-based tumor somatic mutation detection. Biochim Biophys Acta Rev Cancer 2019; 1872:122-137. [PMID: 31265877 DOI: 10.1016/j.bbcan.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022]
Abstract
The rapid evolution of next-generation sequencing (NGS)-based tumor genomic profile detection and the emergence of molecularly targeted therapies have enabled precision oncology. In NGS-based analysis, various types of databases have been developed to perform different functions. However, many problems still exist when using these public databases. Therefore, it is important to better understand the characteristics and limitations of each database and have them complement each other to provide useful clinical evidence for NGS testing. In this review, we elaborate on the important role of databases and their concrete applications in NGS-based somatic mutation detection. We introduce the typically used databases for sequence alignment, variant filtration, and variant interpretation, and compare the differences between the databases with similar functions. Subsequently, we determine the limitations of each database and provide the corresponding solutions. Furthermore, we present an overview diagram to clearly illustrate the database used in the entire NGS-based somatic mutation detection pipeline.
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Affiliation(s)
- Peng Gao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
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149
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Khan M, Cornelis SS, Khan MI, Elmelik D, Manders E, Bakker S, Derks R, Neveling K, van de Vorst M, Gilissen C, Meunier I, Defoort S, Puech B, Devos A, Schulz HL, Stöhr H, Grassmann F, Weber BHF, Dhaenens CM, Cremers FPM. Cost-effective molecular inversion probe-based ABCA4 sequencing reveals deep-intronic variants in Stargardt disease. Hum Mutat 2019; 40:1749-1759. [PMID: 31212395 DOI: 10.1002/humu.23787] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]
Abstract
PURPOSE Stargardt disease (STGD1) is caused by biallelic mutations in ABCA4, but many patients are genetically unsolved due to insensitive mutation-scanning methods. We aimed to develop a cost-effective sequencing method for ABCA4 exons and regions carrying known causal deep-intronic variants. METHODS Fifty exons and 12 regions containing 14 deep-intronic variants of ABCA4 were sequenced using double-tiled single molecule Molecular Inversion Probe (smMIP)-based next-generation sequencing. DNAs of 16 STGD1 cases carrying 29 ABCA4 alleles and of four healthy persons were sequenced using 483 smMIPs. Thereafter, DNAs of 411 STGD1 cases with one or no ABCA4 variant were sequenced. The effect of novel noncoding variants on splicing was analyzed using in vitro splice assays. RESULTS Thirty-four ABCA4 variants previously identified in 16 STGD1 cases were reliably identified. In 155/411 probands (38%), two causal variants were identified. We identified 11 deep-intronic variants present in 62 alleles. Two known and two new noncanonical splice site variants showed splice defects, and one novel deep-intronic variant (c.4539+2065C>G) resulted in a 170-nt mRNA pseudoexon insertion (p.[Arg1514Lysfs*35,=]). CONCLUSIONS smMIPs-based sequence analysis of coding and selected noncoding regions of ABCA4 enabled cost-effective mutation detection in STGD1 cases in previously unsolved cases.
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Affiliation(s)
- Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stéphanie S Cornelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eline Manders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sem Bakker
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Isabelle Meunier
- Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France
| | - Sabine Defoort
- Service d'exploration de la vision et neuro-ophtalmologie, CHRU de Lille, Lille, France
| | - Bernard Puech
- Service d'exploration de la vision et neuro-ophtalmologie, CHRU de Lille, Lille, France
| | - Aurore Devos
- University of Lille, INSERM UMR-S1172, CHU Lille, Biochemistry and Molecular Biology Department, UF Genopathies, Lille, France
| | - Heidi L Schulz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Claire-Marie Dhaenens
- University of Lille, INSERM UMR-S1172, CHU Lille, Biochemistry and Molecular Biology Department, UF Genopathies, Lille, France
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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150
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A novel phenotype with splicing mutation identified in a Chinese family with desminopathy. Chin Med J (Engl) 2019; 132:127-134. [PMID: 30614851 PMCID: PMC6365268 DOI: 10.1097/cm9.0000000000000001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Desminopathy, a hereditary myofibrillar myopathy, mainly results from the desmin gene (DES) mutations. Desminopathy involves various phenotypes, mainly including different cardiomyopathies, skeletal myopathy, and arrhythmia. Combined with genotype, it helps us precisely diagnose and treat for desminopathy. METHODS Sanger sequencing was used to characterize DES variation, and then a minigene assay was used to verify the effect of splice-site mutation on pre-mRNA splicing. Phenotypes were analyzed based on clinical characteristics associated with desminopathy. RESULTS A splicing mutation (c.735+1G>T) in DES was detected in the proband. A minigene assay revealed skipping of the whole exon 3 and transcription of abnormal pre-mRNA lacking 32 codons. Another affected family member who carried the identical mutation, was identified with a novel phenotype of desminopathy, non-compaction of ventricular myocardium. There were 2 different phenotypes varied in cardiomyopathy and skeletal myopathy among the 2 patients, but no significant correlation between genotype and phenotype was identified. CONCLUSIONS We reported a novel phenotype with a splicing mutation in DES, enlarging the spectrum of phenotype in desminopathy. Molecular studies of desminopathy should promote our understanding of its pathogenesis and provide a precise molecular diagnosis of this disorder, facilitating clinical prevention and treatment at an early stage.
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