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Thys L, Beysen D, Ceulemans B, Kenis S, Dielman C, Roelens F, Reyniers E, Mateiu L, Janssens K, Meuwissen M. The Genetic Puzzle of Cerebral Palsy: Results of a Monocentric Study. Pediatr Neurol 2024; 161:1-8. [PMID: 39213953 DOI: 10.1016/j.pediatrneurol.2024.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Cerebral palsy (CP) is the most frequent cause of motor impairment in children. Although perinatal asphyxia was long considered to be the leading cause of CP, recent studies demonstrate its causation in only around one in 10 individuals with CP. Instead, genetic causes are increasingly demonstrated. We systematically performed clinical phenotyping and genetic investigations in a monocentric CP cohort, aiming to gain insight into the contribution of genetic variants in CP and its different subtypes. METHODS Chromosomal microarray and/or trio exome sequencing were systematically performed in 337 individuals with CP between September 2017 and August 2022. Deep phenotyping was performed through clinical multidisciplinary evaluation and review of medical files. RESULTS Genetic analyses resulted in an overall diagnostic yield of 38.3% (129 of 337). In cases with one or more comorbidities (intellectual disability, epilepsy, autism spectrum disorder), the yield increased to almost 50%. Functional enrichment analysis showed over-representation of the following pathways: genetic imprinting, DNA modification, liposaccharide metabolic process, neuron projection guidance, and axon development. CONCLUSIONS Genetic analyses in our CP cohort, the largest monocentric study to date, demonstrated a diagnostic yield of 38.3%, highlighting the importance of genetic testing in CP. The diagnosis of a genetic disorder is essential for prognosis and clinical follow-up, as well as for family counseling. Pathway analysis points to dysregulation of general developmental and metabolic processes as well as neuronal development and function. Unraveling the role of these pathways in CP pathogenesis is instrumental for the identification of CP candidate genes as well as potential therapeutic targets.
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Affiliation(s)
- Liene Thys
- Department of Pediatric Neurology, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Diane Beysen
- Department of Pediatric Neurology, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Sandra Kenis
- Department of Pediatric Neurology, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Charlotte Dielman
- Department of Pediatrics, Queen Paola Children's Hospital, Wilrijk, Belgium
| | - Filip Roelens
- Department of Pediatrics, AZ Delta Hospital, Roeselare, Belgium
| | - Edwin Reyniers
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Ligia Mateiu
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Katrien Janssens
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium
| | - Marije Meuwissen
- Center of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem/Wilrijk, Belgium.
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Smal N, Majdoub F, Janssens K, Reyniers E, Meuwissen MEC, Ceulemans B, Northrup H, Hill JB, Liu L, Errichiello E, Gana S, Strong A, Rohena L, Franciskovich R, Murali CN, Huybrechs A, Sulem T, Fridriksdottir R, Sulem P, Stefansson K, Bai Y, Rosenfeld JA, Lalani SR, Streff H, Kooy RF, Weckhuysen S. Burden re-analysis of neurodevelopmental disorder cohorts for prioritization of candidate genes. Eur J Hum Genet 2024:10.1038/s41431-024-01661-4. [PMID: 38965372 DOI: 10.1038/s41431-024-01661-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/12/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
This study aimed to uncover novel genes associated with neurodevelopmental disorders (NDD) by leveraging recent large-scale de novo burden analysis studies to enhance a virtual gene panel used in a diagnostic setting. We re-analyzed historical trio-exome sequencing data from 745 individuals with NDD according to the most recent diagnostic standards, resulting in a cohort of 567 unsolved individuals. Next, we designed a virtual gene panel containing candidate genes from three large de novo burden analysis studies in NDD and prioritized candidate genes by stringent filtering for ultra-rare de novo variants with high pathogenicity scores. Our analysis revealed an increased burden of de novo variants in our selected candidate genes within the unsolved NDD cohort and identified qualifying de novo variants in seven candidate genes: RIF1, CAMK2D, RAB11FIP4, AGO3, PCBP2, LEO1, and VCP. Clinical data were collected from six new individuals with de novo or inherited LEO1 variants and three new individuals with de novo PCBP2 variants. Our findings add additional evidence for LEO1 as a risk gene for autism and intellectual disability. Furthermore, we prioritize PCBP2 as a candidate gene for NDD associated with motor and language delay. In summary, by leveraging de novo burden analysis studies, employing a stringent variant filtering pipeline, and engaging in targeted patient recruitment, our study contributes to the identification of novel genes implicated in NDDs.
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Affiliation(s)
- Noor Smal
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Fatma Majdoub
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Medical Genetics Department, University Hedi Chaker Hospital of Sfax, University of Sfax, Sfax, Tunisia
| | - Katrien Janssens
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics, University Hospital Antwerp, Drie Eikenstraat 655, Edegem, 2650, Belgium
| | - Edwin Reyniers
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics, University Hospital Antwerp, Drie Eikenstraat 655, Edegem, 2650, Belgium
| | - Marije E C Meuwissen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics, University Hospital Antwerp, Drie Eikenstraat 655, Edegem, 2650, Belgium
| | - Berten Ceulemans
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Jeremy B Hill
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Lingying Liu
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Edoardo Errichiello
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Luis Rohena
- Division of Medical Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX, USA
- Department of Pediatrics, Long School of Medicine-UT Health San Antonio, San Antonio, TX, USA
| | - Rachel Franciskovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - An Huybrechs
- Department of Pediatrics, Heilig Hart Ziekenhuis, Lier, Belgium
| | - Telma Sulem
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | | | - Yan Bai
- GeneDx, Gaithersburg, MD, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.
- Department of Neurology, University Hospital Antwerp, Antwerp, Belgium.
- µNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium.
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3
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Huybrechts Y, Appelman-Dijkstra NM, Steenackers E, Van Beylen W, Mortier G, Hendrickx G, Van Hul W. A Mosaic Variant in CTNNB1/β-catenin as a Novel Cause for Osteopathia Striata With Cranial Sclerosis. J Clin Endocrinol Metab 2024; 109:1891-1898. [PMID: 38173341 DOI: 10.1210/clinem/dgad757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]
Abstract
CONTEXT Osteopathia striata with cranial sclerosis (OSCS) is a rare bone disorder with X-linked dominant inheritance, characterized by a generalized hyperostosis in the skull and long bones and typical metaphyseal striations in the long bones. So far, loss-of-function variants in AMER1 (also known as WTX or FAM123B), encoding the APC membrane recruitment protein 1 (AMER1), have been described as the only molecular cause for OSCS. AMER1 promotes the degradation of β-catenin via AXIN stabilization, acting as a negative regulator of the WNT/β-catenin signaling pathway, a central pathway in bone formation. OBJECTIVE In this study, we describe a Dutch adult woman with an OSCS-like phenotype, namely, generalized high bone mass and characteristic metaphyseal striations, but no genetic variant affecting AMER1. RESULTS Whole exome sequencing led to the identification of a mosaic missense variant (c.876A > C; p.Lys292Asn) in CTNNB1, coding for β-catenin. The variant disrupts an amino acid known to be crucial for interaction with AXIN, a key factor in the β-catenin destruction complex. Western blotting experiments demonstrate that the p.Lys292Asn variant does not significantly affect the β-catenin phosphorylation status, and hence stability in the cytoplasm. Additionally, luciferase reporter assays were performed to investigate the effect of p.Lys292Asn β-catenin on canonical WNT signaling. These studies indicate an average 70-fold increase in canonical WNT signaling activity by p.Lys292Asn β-catenin. CONCLUSION In conclusion, this study indicates that somatic variants in the CTNNB1 gene could explain the pathogenesis of unsolved cases of osteopathia striata.
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Affiliation(s)
- Yentl Huybrechts
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Natasha M Appelman-Dijkstra
- Department of Internal Medicine, Division Endocrinology, Leiden University Medical Center, 2300 Leiden, The Netherlands
| | - Ellen Steenackers
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Wouter Van Beylen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
- Center for Human Genetics, University Hospital Leuven, 3000 Leuven, Belgium
| | - Gretl Hendrickx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
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4
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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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5
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Karagianni K, Bibi A, Madé A, Acharya S, Parkkonen M, Barbalata T, Srivastava PK, de Gonzalo-Calvo D, Emanueli C, Martelli F, Devaux Y, Dafou D, Nossent AY. Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102085. [PMID: 38192612 PMCID: PMC10772297 DOI: 10.1016/j.omtn.2023.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Alisia Madé
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Shubhra Acharya
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
| | - Mikko Parkkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Teodora Barbalata
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
| | | | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | | | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - A. Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
| | - on behalf of EU-CardioRNA COST Action CA17129
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
- National Heart & Lung Institute, Imperial College London, London, UK
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
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6
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Huyghebaert J, Mateiu L, Elinck E, Van Rossem KE, Christiaenssen B, D'Incal CP, McCormack MK, Lazzarini A, Vandeweyer G, Kooy RF. Identification of a DLG3 stop mutation in the MRX20 family. Eur J Hum Genet 2024; 32:317-323. [PMID: 38273165 PMCID: PMC10923781 DOI: 10.1038/s41431-024-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Here, we identified the causal mutation in the MRX20 family, one of the larger X-linked pedigrees that have been described in which no gene had been identified up till now. In 1995, the putative disease gene had been mapped to the pericentromeric region on the X chromosome, but no follow-up studies were performed. Here, whole exome sequencing (WES) on two affected and one unaffected family member revealed the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) that segregated with the affected individuals in the family. DLG3 mutations have been consequently associated with intellectual disability and are a plausible explanation for the clinical abnormalities observed in this family. In addition, we identified two other variants co-segregating with the phenotype: a stop gain mutation in SSX1 (c.358G>T/p.(Glu120Ter)) (NM_001278691.2) and a nonsynonymous SNV in USP27X (c.56 A>G/p.(Gln19Arg)) (NM_001145073.3). RNA sequencing revealed 14 differentially expressed genes (p value < 0.1) in 7 affected males compared to 4 unaffected males of the family, including four genes known to be associated with neurological disorders. Thus, in this paper we identified the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) as likely responsible for the phenotype observed in the MRX20 family.
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Affiliation(s)
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Michael K McCormack
- Department of Psychiatry, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Department of Cell Biology and Neurosciences, Virtua Health College of Medicine and Life Sciences of Rowan University, Stratford, NJ, 08084, USA
| | - Alice Lazzarini
- Department of Neurology, Rutgers University-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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7
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De Wachter M, Schoonjans AS, Weckhuysen S, Van Schil K, Löfgren A, Meuwissen M, Jansen A, Ceulemans B. From diagnosis to treatment in genetic epilepsies: Implementation of precision medicine in real-world clinical practice. Eur J Paediatr Neurol 2024; 48:46-60. [PMID: 38039826 DOI: 10.1016/j.ejpn.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 07/20/2023] [Accepted: 11/11/2023] [Indexed: 12/03/2023]
Abstract
The implementation of whole exome sequencing (WES) has had a major impact on the diagnostic yield of genetic testing in individuals with epilepsy. The identification of a genetic etiology paves the way to precision medicine: an individualized treatment approach, based on the disease pathophysiology. The aim of this retrospective cohort study was to: (1) determine the diagnostic yield of WES in a heterogeneous cohort of individuals with epilepsy referred for genetic testing in a real-world clinical setting, (2) investigate the influence of epilepsy characteristics on the diagnostic yield, (3) determine the theoretical yield of treatment changes based on genetic diagnosis and (4) explore the barriers to implementation of precision medicine. WES was performed in 247 individuals with epilepsy, aged between 7 months and 68 years. In 34/247 (14 %) a (likely) pathogenic variant was identified. In 7/34 (21 %) of these individuals the variant was found using a HPO-based filtering. Diagnostic yield was highest for individuals with an early onset of epilepsy (39 %) or in those with a developmental and epileptic encephalopathy (34 %). Precision medicine was a theoretical possibility in 20/34 (59 %) of the individuals with a (likely) pathogenic variant but implemented in only 11/34 (32 %). The major barrier to implementation of precision treatment was the limited availability or reimbursement of a given drug. These results confirm the potential impact of genetic analysis on treatment choices, but also highlight the hurdles to the implementation of precision medicine. To optimize precision medicine in real-world practice, additional endeavors are needed: unifying definitions of precision medicine, establishment of publicly accessible databases that include data on the functional effect of gene variants, increasing availability and reimbursement of precision therapeutics, and broadening access to innovative clinical trials.
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Affiliation(s)
- Matthias De Wachter
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium.
| | - An-Sofie Schoonjans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium
| | - Sarah Weckhuysen
- Department of Neurology, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium; Applied&Translational Neurogenomics Group, VIB-CMN, VIB, UAntwerpen, Universiteitsplein 1, 2610, Wilrijk, Belgium; Translational Neurosciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kristof Van Schil
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium
| | - Ann Löfgren
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium
| | - Anna Jansen
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium; Translational Neurosciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Drie eikenstraat 655, 2650, Edegem, Belgium
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8
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Rosenblum J, Van der Veeken L, Aertsen M, Meuwissen M, Jansen AC. Abnormal fetal ultrasound leading to the diagnosis of ADNP syndrome. Eur J Med Genet 2023; 66:104855. [PMID: 37758165 DOI: 10.1016/j.ejmg.2023.104855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/12/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
ADNP syndrome, also known as the Helsmoortel-Van der Aa syndrome (HVDAS), is a neurodevelopmental disorder characterized by hypotonia, developmental delay, and intellectual disability. Diagnosis is typically made postnatally, and little is known about prenatal presentation of the disorder. We report a child who presented with intrauterine growth restriction, proportionate microcephaly, and an abnormal skull shape on fetal ultrasound. Whole exome sequencing performed on amniotic fluid cells showed a de novo pathogenic variant in the ADNP gene, corresponding to a diagnosis of ADNP syndrome.
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Affiliation(s)
- Jessica Rosenblum
- Department of Medical Genetics, Antwerp University Hospital, Belgium.
| | | | - Michael Aertsen
- Department of Radiology, University Hospitals Leuven, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, Antwerp University Hospital, Belgium
| | - Anna C Jansen
- Department of Pediatric Neurology, Antwerp University Hospital, Belgium; Translational Neurosciences, University of Antwerp, Belgium
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Perik MHAM, Govaerts E, Laga S, Goovaerts I, Saenen J, Van Craenenbroeck E, Meester JAN, Luyckx I, Rodrigus I, Verstraeten A, Van Laer L, Loeys BL. Variable clinical expression of a Belgian TGFB3 founder variant suggests the presence of a genetic modifier. Front Genet 2023; 14:1251675. [PMID: 37719708 PMCID: PMC10500191 DOI: 10.3389/fgene.2023.1251675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Background: TGFB3 variants cause Loeys-Dietz syndrome type 5, a syndromic form of thoracic aortic aneurysm and dissection. The exact disease phenotype is hard to delineate because of few identified cases and highly variable clinical representation. Methodology: We provide the results of a haplotype analysis and a medical record review of clinical features of 27 individuals from 5 different families, originating from the Campine region in Flanders, carrying the NM_003239.5(TGFB3):c.787G>C p.(Asp263His) likely pathogenic variant, dbSNP:rs796051886, ClinVar:203492. The Asp263 residue is essential for integrin binding to the Arg-Gly-Asp (RGD) motif of the TGFβ3-cytokine. Results: The haplotype analysis revealed a shared haplotype of minimum 1.92 Mb and maximum 4.14 Mb, suggesting a common founder originating >400 years ago. Variable clinical features included connective tissue manifestations, non-aneurysmal cardiovascular problems such as hypertrophic cardiomyopathy, bicuspid aortic valve, mitral valve disease, and septal defects. Remarkably, only in 4 out of the 27 variant-harboring individuals, significant aortic involvement was observed. In one family, a 31-year-old male presented with type A dissection. In another family, the male proband (65 years) underwent a Bentall procedure because of bicuspid aortic valve insufficiency combined with sinus of Valsalva of 50 mm, while an 80-year-old male relative had an aortic diameter of 43 mm. In a third family, the father of the proband (75 years) presented with ascending aortic aneurysm (44 mm). Conclusion: The low penetrance (15%) of aortic aneurysm/dissection suggests that haploinsufficiency alone by the TGFB3 variant may not result in aneurysm development but that additional factors are required to provoke the aneurysm phenotype.
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Affiliation(s)
- Melanie H. A. M. Perik
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | | | - Steven Laga
- Department of Cardiac Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Inge Goovaerts
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium
| | - Johan Saenen
- Department of Cardiology, Antwerp University Hospital, Antwerp, Belgium
| | | | - Josephina A. N. Meester
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ilse Luyckx
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Inez Rodrigus
- Department of Cardiac Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Aline Verstraeten
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Lut Van Laer
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L. Loeys
- Cardiogenomics and Functional Genomics, Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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10
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Tessler I, Albuisson J, Piñeiro-Sabarís R, Verstraeten A, Kamber Kaya HE, Siguero-Álvarez M, Goudot G, MacGrogan D, Luyckx I, Shpitzen S, Levin G, Kelman G, Reshef N, Mananet H, Holdcraft J, Muehlschlegel JD, Peloso GM, Oppenheim O, Cheng C, Mazzella JM, Andelfinger G, Mital S, Eriksson P, Billon C, Heydarpour M, Dietz HC, Jeunemaitre X, Leitersdorf E, Sprinzak D, Blacklow SC, Body SC, Carmi S, Loeys B, de la Pompa JL, Gilon D, Messas E, Durst R. Novel Association of the NOTCH Pathway Regulator MIB1 Gene With the Development of Bicuspid Aortic Valve. JAMA Cardiol 2023; 8:721-731. [PMID: 37405741 PMCID: PMC10323766 DOI: 10.1001/jamacardio.2023.1469] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 04/21/2023] [Indexed: 07/06/2023]
Abstract
Importance Nonsyndromic bicuspid aortic valve (nsBAV) is the most common congenital heart valve malformation. BAV has a heritable component, yet only a few causative genes have been identified; understanding BAV genetics is a key point in developing personalized medicine. Objective To identify a new gene for nsBAV. Design, Setting, and Participants This was a comprehensive, multicenter, genetic association study based on candidate gene prioritization in a familial cohort followed by rare and common association studies in replication cohorts. Further validation was done using in vivo mice models. Study data were analyzed from October 2019 to October 2022. Three cohorts of patients with BAV were included in the study: (1) the discovery cohort was a large cohort of inherited cases from 29 pedigrees of French and Israeli origin; (2) the replication cohort 1 for rare variants included unrelated sporadic cases from various European ancestries; and (3) replication cohort 2 was a second validation cohort for common variants in unrelated sporadic cases from Europe and the US. Main Outcomes and Measures To identify a candidate gene for nsBAV through analysis of familial cases exome sequencing and gene prioritization tools. Replication cohort 1 was searched for rare and predicted deleterious variants and genetic association. Replication cohort 2 was used to investigate the association of common variants with BAV. Results A total of 938 patients with BAV were included in this study: 69 (7.4%) in the discovery cohort, 417 (44.5%) in replication cohort 1, and 452 (48.2%) in replication cohort 2. A novel human nsBAV gene, MINDBOMB1 homologue MIB1, was identified. MINDBOMB1 homologue (MIB1) is an E3-ubiquitin ligase essential for NOTCH-signal activation during heart development. In approximately 2% of nsBAV index cases from the discovery and replication 1 cohorts, rare MIB1 variants were detected, predicted to be damaging, and were significantly enriched compared with population-based controls (2% cases vs 0.9% controls; P = .03). In replication cohort 2, MIB1 risk haplotypes significantly associated with nsBAV were identified (permutation test, 1000 repeats; P = .02). Two genetically modified mice models carrying Mib1 variants identified in our cohort showed BAV on a NOTCH1-sensitized genetic background. Conclusions and Relevance This genetic association study identified the MIB1 gene as associated with nsBAV. This underscores the crucial role of the NOTCH pathway in the pathophysiology of BAV and its potential as a target for future diagnostic and therapeutic intervention.
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Affiliation(s)
- Idit Tessler
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
- Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Juliette Albuisson
- Genetics Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, National Referral Center for Rare Vascular Diseases, VASCERN MSA European Reference Center, Paris, France
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Platform of Transfer in Cancer Biology, Georges François Leclerc Cancer –UNICANCER, Dijon, France
- Genomic and Immunotherapy Medical Institute, Dijon, France
| | - Rebeca Piñeiro-Sabarís
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hatem Elif Kamber Kaya
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Marcos Siguero-Álvarez
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Guillaume Goudot
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Vascular Medicine Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- French Research Consortium RHU STOP-AS, Rouen, France
| | - Donal MacGrogan
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Ilse Luyckx
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Shoshana Shpitzen
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Galina Levin
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Guy Kelman
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- The Jerusalem Center for Personalized Computational Medicine, Jerusalem, Israel
| | - Noga Reshef
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- The Jerusalem Center for Personalized Computational Medicine, Jerusalem, Israel
| | - Hugo Mananet
- Platform of Transfer in Cancer Biology, Georges François Leclerc Cancer –UNICANCER, Dijon, France
- Genomic and Immunotherapy Medical Institute, Dijon, France
| | - Jake Holdcraft
- Department of Anesthesiology, Boston University School of Medicine, Boston, Massachusetts
| | | | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Olya Oppenheim
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Charles Cheng
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Vascular Medicine Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- French Research Consortium RHU STOP-AS, Rouen, France
| | - Jean-Michael Mazzella
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Vascular Medicine Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de Montreal, Montreal, Quebec, Canada
| | - Seema Mital
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Per Eriksson
- Cardiovascular Medicine Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institute, Karolinska University Hospital, Solna, Sweden
| | - Clarisse Billon
- Genetics Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, National Referral Center for Rare Vascular Diseases, VASCERN MSA European Reference Center, Paris, France
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
| | - Mahyar Heydarpour
- Department of Medicine, Division of Endocrinology, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Harry C. Dietz
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xavier Jeunemaitre
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Vascular Medicine Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Eran Leitersdorf
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Sprinzak
- School of Neurobiology, Biochemistry and Biophysics, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Simon C. Body
- Department of Anesthesiology, Boston University School of Medicine, Boston, Massachusetts
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bart Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - José Luis de la Pompa
- Intercellular Signaling in Cardiovascular Development & Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Ciber de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain
| | - Dan Gilon
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
| | - Emmanuel Messas
- Université Paris Cité, INSERM, U970 PARCC, Paris, France
- Vascular Medicine Department, Assistance Publique–Hȏpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- French Research Consortium RHU STOP-AS, Rouen, France
| | - Ronen Durst
- Cardiology Department, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, the Hebrew University, Jerusalem, Israel
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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11
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De Ridder W, de Vries G, Van Schil K, Deconinck T, Mouly V, Straub V, Baets J. A homozygous loss of function variant in POPDC3: From invalidating exercise intolerance to a limb-girdle muscular dystrophy phenotype. Neuromuscul Disord 2023; 33:432-439. [PMID: 37104941 DOI: 10.1016/j.nmd.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023]
Abstract
Recessive pathogenic variants in POPDC3 have recently been associated with the rare limb-girdle muscular dystrophy (LGMD) subtype LGMDR26. We studied three siblings and a distantly related individual with a skeletal muscle disorder, harboring the c.486-6T>A splice site variant in POPDC3 in homozygosity. Immunohistochemistry, western blot, and mRNA experiments on patients' skeletal muscle tissue as well as on patients' myoblasts were performed to study the pathogenicity of the predicted loss of function mechanism of the variant. Patients mainly presented with invalidating myalgia and exercise intolerance and limited to no segmentary muscle weakness. CK levels were markedly elevated in all patients. A loss of function mechanism at the RNA level was shown (r.485_486insauag, p.Ile163*). Muscle biopsies performed in three out of four patients showed non-specific myopathic features with a marked type 2 fiber predominance and the presence of a large number of severely atrophic fibers with pyknotic nuclear clumps. We show that skeletal muscle symptoms in LGMDR26 may range from an overt late juvenile to young adult-onset limb-girdle muscular dystrophy phenotype to severe exercise intolerance and myalgia, with consistently highly elevated CK levels. We further prove a clear LOF mechanism of POPDC3 in this rare disorder.
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Affiliation(s)
- Willem De Ridder
- Translational Neurosciences and Peripheral Neuropathy Group, University of Antwerp, Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Neuromuscular Reference Centre, Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Antwerp B-2650, Belgium.
| | - Geert de Vries
- Translational Neurosciences and Peripheral Neuropathy Group, University of Antwerp, Antwerp, Belgium
| | - Kristof Van Schil
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Tine Deconinck
- Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, Paris F-75013, France
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jonathan Baets
- Translational Neurosciences and Peripheral Neuropathy Group, University of Antwerp, Antwerp, Belgium; Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium; Department of Neurology, Neuromuscular Reference Centre, Antwerp University Hospital, Drie Eikenstraat 655, Edegem, Antwerp B-2650, Belgium
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12
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Implementation of Exome Sequencing in Prenatal Diagnostics: Chances and Challenges. Diagnostics (Basel) 2023; 13:diagnostics13050860. [PMID: 36900003 PMCID: PMC10000387 DOI: 10.3390/diagnostics13050860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
Whole exome sequencing (WES) has become part of the postnatal diagnostic work-up of both pediatric and adult patients with a range of disorders. In the last years, WES is slowly being implemented in the prenatal setting as well, although some hurdles remain, such as quantity and quality of input material, minimizing turn-around times, and ensuring consistent interpretation and reporting of variants. We present the results of 1 year of prenatal WES in a single genetic center. Twenty-eight fetus-parent trios were analyzed, of which seven (25%) showed a pathogenic or likely pathogenic variant that explained the fetal phenotype. Autosomal recessive (4), de novo (2) and dominantly inherited (1) mutations were detected. Prenatal rapid WES allows for a timely decision-making in the current pregnancy, adequate counseling with the possibility of preimplantation or prenatal genetic testing in future pregnancies and screening of the extended family. With a diagnostic yield in selected cases of 25% and a turn-around time under 4 weeks, rapid WES shows promise for becoming part of pregnancy care in fetuses with ultrasound anomalies in whom chromosomal microarray did not uncover the cause.
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13
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Hendrickx G, Boudin E, Steenackers E, Collet C, Mortier GR, Geneviève D, Van Hul W. A recessive form of craniodiaphyseal dysplasia caused by a homozygous missense variant in SP7/Osterix. Bone 2023; 167:116633. [PMID: 36436818 DOI: 10.1016/j.bone.2022.116633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Gretl Hendrickx
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, 2650 Edegem, Belgium; Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, 2650 Edegem, Belgium
| | - Ellen Steenackers
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, 2650 Edegem, Belgium
| | - Corinne Collet
- INSERM U1132 and Université de Paris, Reference Centre for Rare Bone Diseases, Hospital Robert Debré, F-75010 Paris, France
| | - Geert R Mortier
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, 2650 Edegem, Belgium; Laboratory for Skeletal Dysplasia Research, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium; Center for Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - David Geneviève
- Montpellier University and INSERM U1183, Montpellier, France; Competence Center for Bone Diseases, Clinical Genetics Unit, Montpellier University Hospital, Montpellier, France
| | - Wim Van Hul
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, 2650 Edegem, Belgium.
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14
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Naesens L, Nemegeer J, Roelens F, Vallaeys L, Meuwissen M, Janssens K, Verloo P, Ogunjimi B, Hemelsoet D, Hoste L, Roels L, De Bruyne M, De Baere E, Van Dorpe J, Dendooven A, Sieben A, Rice GI, Kerre T, Beyaert R, Uggenti C, Crow YJ, Tavernier SJ, Maelfait J, Haerynck F. Mutations in RNU7-1 Weaken Secondary RNA Structure, Induce MCP-1 and CXCL10 in CSF, and Result in Aicardi-Goutières Syndrome with Severe End-Organ Involvement. J Clin Immunol 2022; 42:962-974. [PMID: 35320431 PMCID: PMC9402729 DOI: 10.1007/s10875-022-01209-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/07/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Aicardi-Goutières syndrome (AGS) is a type I interferonopathy usually characterized by early-onset neurologic regression. Biallelic mutations in LSM11 and RNU7-1, components of the U7 small nuclear ribonucleoprotein (snRNP) complex, have been identified in a limited number of genetically unexplained AGS cases. Impairment of U7 snRNP function results in misprocessing of replication-dependent histone (RDH) pre-mRNA and disturbance of histone occupancy of nuclear DNA, ultimately driving cGAS-dependent type I interferon (IFN-I) release. OBJECTIVE We performed a clinical, genetic, and immunological workup of 3 unrelated patients with uncharacterized AGS. METHODS Whole exome sequencing (WES) and targeted Sanger sequencing of RNU7-1 were performed. Primary fibroblasts were used for mechanistic studies. IFN-I signature and STAT1/2 phosphorylation were assessed in peripheral blood. Cytokines were profiled on serum and cerebrospinal fluid (CSF). Histopathology was examined on brain and kidney tissue. RESULTS Sequencing revealed compound heterozygous RNU7-1 mutations, resulting in impaired RDH pre-mRNA processing. The 3' stem-loop mutations reduced stability of the secondary U7 snRNA structure. A discrete IFN-I signature in peripheral blood was paralleled by MCP-1 (CCL2) and CXCL10 upregulation in CSF. Histopathological analysis of the kidney showed thrombotic microangiopathy. We observed dysregulated STAT phosphorylation upon cytokine stimulation. Clinical overview of all reported patients with RNU7-1-related disease revealed high mortality and high incidence of organ involvement compared to other AGS genotypes. CONCLUSIONS Targeted RNU7-1 sequencing is recommended in genetically unexplained AGS cases. CSF cytokine profiling represents an additional diagnostic tool to identify aberrant IFN-I signaling. Clinical follow-up of RNU7-1-mutated patients should include screening for severe end-organ involvement including liver disease and nephropathy.
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Affiliation(s)
- Leslie Naesens
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Josephine Nemegeer
- VIB-UGent Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Filip Roelens
- Department of Pediatrics, Algemeen Ziekenhuis Delta, 8800, Roeselare, Belgium
| | - Lore Vallaeys
- Department of Pediatrics, Algemeen Ziekenhuis Groeninge, 8500, Kortrijk, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, 2000, Antwerp, Belgium
- Department of Medical Genetics, Antwerp University Hospital, 2650, Antwerp, Belgium
| | - Katrien Janssens
- Department of Medical Genetics, University of Antwerp, 2000, Antwerp, Belgium
- Department of Medical Genetics, Antwerp University Hospital, 2650, Antwerp, Belgium
| | - Patrick Verloo
- Department of Pediatrics, Division of Pediatric Neurology, University Hospital Ghent, 9000, Ghent, Belgium
| | - Benson Ogunjimi
- Department of Pediatrics, Antwerp University Hospital, 2650, Edegem, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610, Antwerp, Belgium
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Levi Hoste
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Lisa Roels
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, 9000, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Pathology, Antwerp University Hospital, 9000, Ghent, Belgium
| | - Anne Sieben
- Department of Neurology, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Pathology, Antwerp University Hospital, 9000, Ghent, Belgium
| | - Gillian I Rice
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Tessa Kerre
- Department of Hematology, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
| | - Rudi Beyaert
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Laboratory of Molecular Signal Transduction in Inflammation, VIB, 9052, Ghent, Belgium
| | - Carolina Uggenti
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
- Laboratory of Neurogenetics and Neuroinflammation, University of Paris, Imagine Institute, Paris, France
| | - Simon J Tavernier
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
- VIB-UGent Center for Inflammation Research, Laboratory of Molecular Signal Transduction in Inflammation, VIB, 9052, Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, 9052, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052, Ghent, Belgium
| | - Filomeen Haerynck
- Department of Internal Medicine and Pediatrics, Ghent University, 9000, Ghent, Belgium.
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, 9000, Ghent, Belgium.
- Department of Pediatric Pulmonology, Infectious Diseases and Immunology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent, Belgium.
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15
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Shestak AG, Makarov LM, Komoliatova VN, Kolesnikova IV, Skorodumova LO, Generozov EV, Zaklyazminskaya EV. Coexistence of Two Rare Genetic Variants in Canonical and Non-canonical Exons of SCN5A: A Potential Source of Misinterpretation. Front Genet 2021; 12:722291. [PMID: 34552620 PMCID: PMC8450431 DOI: 10.3389/fgene.2021.722291] [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: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Primary cardiac channelopathies are a group of diseases wherein the role of DNA testing in aiding diagnosis and treatment-based decision-making is gaining increasing attention. However, in some cases, evaluating the pathogenicity of new variants is still challenging. We report an accurate multistage assessment of a rare genetic variant in the SCN5A gene using next-generation sequencing (NGS) techniques and Sanger sequencing. Female sportsman (14 years old) underwent genetic counseling and DNA testing due to QT interval prolongation registered during ECG Holter monitoring. Genetic testing of the proband was performed in two independent laboratories. Primary DNA testing was performed by WES using the Ion ProtonTM System. Target panel sequencing of 11 genes was performed using PGM Ion Torrent. Search for variants in non-canonical and canonical exons 6 was performed by Sanger sequencing. The cascade familial screening and control re-sequencing were provided for proband with identified genetic variant p.S216L (g.38655290G>A, NM_198056.2:c.647C>T, and rs41276525) in the canonical exon 6 of the SCN5A gene after receiving data from another laboratory. Control Sanger and NGS sequencing revealed the absence p.S216L in the canonical exon 6 and confirmed the presence of p.S216L (g.38655522G>A, c.647C>T, and rs201002736) in the non-canonical exon 6 of the SCN5A gene. The identified variant was re-interpreted. The non-canonical transcripts of the exon 6 of the SCN5A gene is poorly represented in cardiac tissue (gnomAD). The detected variant was found in proband's healthy mother. The correct interpretation of genetic data requires close cooperation between clinicians and researchers. It can help to avoid financial costs and stress for proband's and families.
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Affiliation(s)
- Anna G Shestak
- Russian National Research Center of Surgery Named After B.V. Petrovsky, Moscow, Russia
| | - Leonid M Makarov
- Center for Syncope and Cardiac Arrhythmias in Children and Adolescents of the Federal Medical Biological Agency, Moscow, Russia
| | - Vera N Komoliatova
- Center for Syncope and Cardiac Arrhythmias in Children and Adolescents of the Federal Medical Biological Agency, Moscow, Russia
| | - Irina V Kolesnikova
- Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
| | - Liubov O Skorodumova
- Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
| | - Edward V Generozov
- Federal Research and Clinical Center of Physical Chemical Medicine of the Federal Medical Biological Agency, Moscow, Russia
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16
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Rodrigues Bento J, Feben C, Kempers M, van Rij M, Woiski M, Devriendt K, De Catte L, Baldewijns M, Alaerts M, Meester J, Verstraeten A, Hendson W, Loeys B. Two novel presentations of KCNMA1-related pathology--Expanding the clinical phenotype of a rare channelopathy. Mol Genet Genomic Med 2021; 9:e1797. [PMID: 34499417 PMCID: PMC8580096 DOI: 10.1002/mgg3.1797] [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: 11/24/2020] [Revised: 05/19/2021] [Accepted: 08/13/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND KCNMA1 mutations have recently been associated with a wide range of dysmorphological, gastro-intestinal, cardiovascular, and neurological manifestations. METHODS Whole exome sequencing was performed in order to identify the underlying pathogenic mutation in two cases presenting with diverse phenotypical manifestations that did not fit into well-known clinical entities. RESULTS In an 8-year-old boy presenting with severe aortic dilatation, facial dysmorphism, and overgrowth at birth a de novo p.Gly375Arg KCNMA1 mutation was identified which has been reported previously in association with gingival hypertrophy, aortic dilatation, and developmental delay. Additionally, in a 30-week-old fetus with severe growth retardation and duodenal atresia a de novo p.Pro805Leu KCNMA1 mutation was identified. The latter has also been reported before in a boy with severe neurological manifestations, including speech delay, developmental delay, and cerebellar dysfunction. CONCLUSION The current report presents the first antenatal presentation of a pathogenic KCNMA1 mutation and confirms the specific association of the p.Gly375Arg variant with early onset aortic root dilatation, gingival hypertrophy, and neonatal overgrowth.
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Affiliation(s)
- Jotte Rodrigues Bento
- Centre of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service & The School of Pathology, University of the Witwatersrand, Johannesburg-Braamfontein, South Africa
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van Rij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Gynaecology and Obstetrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mallory Woiski
- Department of Gynaecology and Obstetrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Koenraad Devriendt
- Department of Human Genetics, Catholic University of Leuven, Leuven, Belgium
| | - Luc De Catte
- Department of Gynaecology and Obstetrics, Catholic University of Leuven, Leuven, Belgium
| | - Marcella Baldewijns
- Department of Gynaecology and Obstetrics, Catholic University of Leuven, Leuven, Belgium
| | - Maaike Alaerts
- Centre of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Josephina Meester
- Centre of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Aline Verstraeten
- Centre of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Willy Hendson
- Department of Paediatrics, Rahima Moosa Mother and Child Hospital & The University of the Witwatersrand, Johannesburg-Braamfontein, South Africa
| | - Bart Loeys
- Centre of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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17
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Pandey P, Gao Y, Kingsford C. VariantStore: an index for large-scale genomic variant search. Genome Biol 2021; 22:231. [PMID: 34412679 PMCID: PMC8375130 DOI: 10.1186/s13059-021-02442-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 07/27/2021] [Indexed: 11/18/2022] Open
Abstract
Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system. We show the scalability of VariantStore by indexing genomic variants from the TCGA project in 4 h and the 1000 Genomes project in 3 h. Querying for variants in a gene takes between 0.002 and 3 seconds using memory only 10% of the size of the full representation.
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Affiliation(s)
- Prashant Pandey
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Yinjie Gao
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Carl Kingsford
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
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18
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Novel LOX Variants in Five Families with Aortic/Arterial Aneurysm and Dissection with Variable Connective Tissue Findings. Int J Mol Sci 2021; 22:ijms22137111. [PMID: 34281165 PMCID: PMC8269155 DOI: 10.3390/ijms22137111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Thoracic aortic aneurysm and dissection (TAAD) is a major cause of cardiovascular morbidity and mortality. Loss-of-function variants in LOX, encoding the extracellular matrix crosslinking enzyme lysyl oxidase, have been reported to cause familial TAAD. Using a next-generation TAAD gene panel, we identified five additional probands carrying LOX variants, including two missense variants affecting highly conserved amino acids in the LOX catalytic domain and three truncating variants. Connective tissue manifestations are apparent in a substantial fraction of the variant carriers. Some LOX variant carriers presented with TAAD early in life, while others had normal aortic diameters at an advanced age. Finally, we identified the first patient with spontaneous coronary artery dissection carrying a LOX variant. In conclusion, our data demonstrate that loss-of-function LOX variants cause a spectrum of aortic and arterial aneurysmal disease, often combined with connective tissue findings.
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19
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Beysen D, De Cordt C, Dielman C, Ogunjimi B, Dandelooy J, Reyniers E, Janssens K, Meuwissen MME. Genetic Testing Contributes to Diagnosis in Cerebral Palsy: Aicardi-Goutières Syndrome as an Example. Front Neurol 2021; 12:617813. [PMID: 33967934 PMCID: PMC8100223 DOI: 10.3389/fneur.2021.617813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/18/2021] [Indexed: 11/13/2022] Open
Abstract
Cerebral palsy (CP) is a non-progressive neurodevelopmental disorder characterized by motor impairments, often accompanied by co-morbidities such as intellectual disability, epilepsy, visual and hearing impairment and speech and language deficits. Despite the established role of hypoxic–ischemic injury in some CP cases, several studies suggest that birth asphyxia is actually an uncommon cause, accounting for <10% of CP cases. For children with CP in the absence of traditional risk factors, a genetic basis to their condition is increasingly suspected. Several recent studies indeed confirm copy number variants and single gene mutations with large genetic heterogeneity as an etiology in children with CP. Here, we report three patients with spastic cerebral palsy and a genetically confirmed diagnosis of Aicardi-Goutières syndrome (AGS), with highly variable phenotypes ranging from clinically suggestive to non-specific symptomatology. Our findings suggest that AGS may be a rather common cause of CP, that frequently remains undiagnosed without additional genetic testing, as in only one case a clinical suspicion of AGS was raised. Our data show that a diagnosis of AGS must be considered in cases with spastic CP, even in the absence of characteristic brain abnormalities. Importantly, a genetic diagnosis of AGS may have significant therapeutic consequences, as targeted therapies are being developed for type 1 interferonopathies, the group of diseases to which AGS belongs. Our findings demonstrate the importance of next generation sequencing in CP patients without an identifiable cause, since targeted diagnostic testing is hampered by the often non-specific presentation.
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Affiliation(s)
- Diane Beysen
- Department of Pediatric Neurology, Antwerp University Hospital, Edegem, Belgium
| | - Chania De Cordt
- Department of Pediatrics, Antwerp University Hospital, Edegem, Belgium
| | - Charlotte Dielman
- Department of Pediatric Neurology, Ziekenhuis Netwerk Antwerpen Queen Paola Children's Hospital, Wilrijk, Belgium
| | - Benson Ogunjimi
- Department of Pediatrics, Antwerp University Hospital, Edegem, Belgium.,Center for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium.,Department of Pediatrics, Ziekenhuis Netwerk Antwerpen Paola Children's Hospital, Wilrijk, Belgium
| | - Julie Dandelooy
- Department of Dermatology, Antwerp University Hospital, Edegem, Belgium
| | - Edwin Reyniers
- Center for Medical Genetics, Antwerp University Hospital, Edegem, Belgium
| | - Katrien Janssens
- Center for Medical Genetics, University of Antwerp, Wilrijk, Belgium
| | - Marije M E Meuwissen
- Center for Medical Genetics, Antwerp University Hospital, Edegem, Belgium.,Center for Medical Genetics, University of Antwerp, Wilrijk, Belgium
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20
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Arora I, Tollefsbol TO. Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. Methods 2021; 187:92-103. [PMID: 32941995 PMCID: PMC7914156 DOI: 10.1016/j.ymeth.2020.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression by modulating the packaging of DNA in the nucleus. A plethora of studies have emphasized the importance of analyzing epigenetics data through genome-wide studies and high-throughput approaches, thereby providing key insights towards epigenetics-based diseases such as cancer. Recent advancements have been made towards translating epigenetics research into a high throughput approach such as genome-scale profiling. Amongst all, bioinformatics plays a pivotal role in achieving epigenetics-related computational studies. Despite significant advancements towards epigenomic profiling, it is challenging to understand how various epigenetic modifications such as chromatin modifications and DNA methylation regulate gene expression. Next-generation sequencing (NGS) provides accurate and parallel sequencing thereby allowing researchers to comprehend epigenomic profiling. In this review, we summarize different computational methods such as machine learning and other bioinformatics tools, publicly available databases and resources to identify key modifications associated with epigenetic machinery. Additionally, the review also focuses on understanding recent methodologies related to epigenome profiling using NGS methods ranging from library preparation, different sequencing platforms and analytical techniques to evaluate various epigenetic modifications such as DNA methylation and histone modifications. We also provide detailed information on bioinformatics tools and computational strategies responsible for analyzing large scale data in epigenetics.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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21
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Peeters S, Declerck K, Thomas M, Boudin E, Beckers D, Chivu O, Heinrichs C, Devriendt K, de Zegher F, Van Hul W, Vanden Berghe W, De Schepper J, Rooman R, Mortier G. DNA Methylation Profiling and Genomic Analysis in 20 Children with Short Stature Who Were Born Small for Gestational Age. J Clin Endocrinol Metab 2020; 105:5873625. [PMID: 32685970 DOI: 10.1210/clinem/dgaa465] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE In a significant proportion of children born small for gestational age (SGA) with failure of catch-up growth, the etiology of short stature remains unclear after routine diagnostic workup. We wanted to investigate if extensive analysis of the (epi)genome can unravel the cause of growth failure in a significant portion of these children. PATIENTS AND METHODS Twenty SGA children treated with GH because of short stature were selected from the BELGROW database of the Belgian Society for Pediatric Endocrinology and Diabetology for exome sequencing, single-nucleotide polymorphism (SNP) array and genome-wide methylation analysis to identify the (epi)genetic cause. First-year response to GH was compared with the response of SGA patients in the KIGS database. RESULTS We identified (likely) pathogenic variants in 4 children (from 3 families) using exome sequencing and found pathogenic copy number variants in 2 probands using SNP array. In a child harboring a NSD1-containing microduplication, we identified a DNA methylation signature that is opposite to the genome-wide DNA methylation signature of Sotos syndrome. Moreover, we observed multilocus imprinting disturbances in 2 children in whom no other genomic alteration could be identified. Five of 6 children with a genetic diagnosis had an "above average" response to GH. CONCLUSIONS The study indicates that a more advanced approach with deep genotyping can unravel unexpected (epi)genomic alterations in SGA children with persistent growth failure. Most SGA children with a genetic diagnosis had a good response to GH treatment.
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Affiliation(s)
- Silke Peeters
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Muriel Thomas
- Belgian Society for Pediatric Endocrinology and Diabetology, Brussels, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dominique Beckers
- Unité d'Endocrinologie Pédiatrique, CHU Namur, Université catholique de Louvain, Yvoir, Belgium and Department of Pediatrics, University Hospital Leuven, Leuven, Belgium
| | - Olimpia Chivu
- Department of Pediatrics, Clinique de l'Espérance, Saint-Nicolas, Belgium
| | - Claudine Heinrichs
- Paediatric Endocrinology Unit, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Brussels, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University of Leuven and the University Hospital Leuven, Leuven, Belgium
| | - Francis de Zegher
- Department of Development & Regeneration, University of Leuven, Leuven, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jean De Schepper
- Department of Pediatrics, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium and Department of Pediatrics, Universitair Ziekenhuis Gent, Ghent, Belgium
| | | | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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22
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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23
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De Ridder R, Boudin E, Zillikens MC, Ibrahim J, van der Eerden BCJ, Van Hul W, Mortier G. A multi-omics approach expands the mutational spectrum of MAP2K1-related melorheostosis. Bone 2020; 137:115406. [PMID: 32387835 DOI: 10.1016/j.bone.2020.115406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/26/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022]
Abstract
Melorheostosis is a very rare sclerosing bone dysplasia characterized by asymmetrical and progressive cortical hyperostosis, usually with involvement of soft tissues surrounding the lesions. Recently Kang et al. identified somatic mosaicism for variants (p.Gln56Pro, p.Lys57Asn, or p.Lys57Glu) in the negative regulatory domain of MAP2K1, resulting in increased ERK1/2 signalling in affected tissues. In our study, we employed several sequencing technologies to unravel genetic variants (only present in affected tissues) from four sporadic melorheostosis patients. In the exome of two patients, we identified the same variants (p.K57N and p.K57E) as previously described by Kang et al. WGS and RNAseq analysis in a third patient demonstrated the presence of a novel variant (p.Cys121Ser) in the catalytic domain of MAP2K1. In addition, gene set enrichment analysis of the transcriptome data demonstrated upregulation of proliferative pathways. Interestingly, increased proliferation of MAP2K1 p.Lys57Asn-positive osteoblasts has been reported by Kang et al. The variants located in the hotspot region of the negative regulatory domain as well as this newly identified p.Cys121Ser variant have all been classified as MAP2K1 variants that can constitutively activate the downstream effector Erk. Finally, in a fourth patient with classical radiographic features of melorheostosis, no pathogenic variants could be identified in MAP2K1 or the other candidate genes for melorheostosis (SMAD3; LEMD3; KRAS). In conclusion, our study strongly suggests that not only somatic variants in the regulatory domain of MAP2K1 but also in the catalytic domain can cause melorheostosis. Our observations confirm that mutations in MAP2K1 are a major cause of melorheostosis and also suggest further locus heterogeneity for this disorder.
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Affiliation(s)
- Raphaël De Ridder
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Eveline Boudin
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - M Carola Zillikens
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Joe Ibrahim
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Bram C J van der Eerden
- Division of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Wim Van Hul
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium.
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24
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Khoshnevisan R, Anderson M, Babcock S, Anderson S, Illig D, Marquardt B, Sherkat R, Schröder K, Moll F, Hollizeck S, Rohlfs M, Walz C, Adibi P, Rezaei A, Andalib A, Koletzko S, Muise AM, Snapper SB, Klein C, Thiagarajah JR, Kotlarz D. NOX1 Regulates Collective and Planktonic Cell Migration: Insights From Patients With Pediatric-Onset IBD and NOX1 Deficiency. Inflamm Bowel Dis 2020; 26:1166-1176. [PMID: 32064493 PMCID: PMC7365810 DOI: 10.1093/ibd/izaa017] [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] [Received: 06/23/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genetic defects of pediatric-onset inflammatory bowel disease (IBD) provide critical insights into molecular factors controlling intestinal homeostasis. NOX1 has been recently recognized as a major source of reactive oxygen species (ROS) in human colonic epithelial cells. Here we assessed the functional consequences of human NOX1 deficiency with respect to wound healing and epithelial migration by studying pediatric IBD patients presenting with a stop-gain mutation in NOX1. METHODS Functional characterization of the NOX1 variant included ROS generation, wound healing, 2-dimensional collective chemotactic migration, single-cell planktonic migration in heterologous cell lines, and RNA scope and immunohistochemistry of paraffin-embedded patient tissue samples. RESULTS Using exome sequencing, we identified a stop-gain mutation in NOX1 (c.160C>T, p.54R>*) in patients with pediatric-onset IBD. Our studies confirmed that loss-of-function of NOX1 causes abrogated ROS activity, but they also provided novel mechanistic insights into human NOX1 deficiency. Cells that were NOX1-mutant showed impaired wound healing and attenuated 2-dimensional collective chemotactic migration. High-resolution microscopy of the migrating cell edge revealed a reduced density of filopodial protrusions with altered focal adhesions in NOX1-deficient cells, accompanied by reduced phosphorylation of p190A. Assessment of single-cell planktonic migration toward an epidermal growth factor gradient showed that NOX1 deficiency is associated with altered migration dynamics with loss of directionality and altered cell-cell interactions. CONCLUSIONS Our studies on pediatric-onset IBD patients with a rare sequence variant in NOX1 highlight that human NOX1 is involved in regulating wound healing by altering epithelial cytoskeletal dynamics at the leading edge and directing cell migration.
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Affiliation(s)
- Razieh Khoshnevisan
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany,Department of Immunology, Medical Faculty, Isfahan University of Medical Sciences, Isfahan, Iran,Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael Anderson
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephen Babcock
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sierra Anderson
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - David Illig
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Benjamin Marquardt
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Roya Sherkat
- Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Franziska Moll
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany
| | - Sebastian Hollizeck
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Meino Rohlfs
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christoph Walz
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Peyman Adibi
- Integrative Functional Gastroenterology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Abbas Rezaei
- Department of Immunology, Medical Faculty, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Alireza Andalib
- Department of Immunology, Medical Faculty, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sibylle Koletzko
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada,Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada,Division of Gastroenterology, Brigham and Women’s Hospital, Boston, Massachusetts, USA,PEDI-CODE Consortium, Boston, Massachusetts, USA
| | - Scott B Snapper
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany,Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada,VEO-IBD Consortium, Munich, Germany
| | - Christoph Klein
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jay R Thiagarajah
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada,PEDI-CODE Consortium, Boston, Massachusetts, USA,Address correspondence to: Daniel Kotlarz, MD, PhD, Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, D-80337 Munich, Germany (); Jay R. Thiagarajah, MD, PhD, Boston Children’s Hospital, Division of Gastroenterology, EN605, 300 Longwood Avenue, Boston, MA 02115, USA ()
| | - Daniel Kotlarz
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany,Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA,SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada,Address correspondence to: Daniel Kotlarz, MD, PhD, Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital, Ludwig-Maximilians-Universität München, Lindwurmstrasse 4, D-80337 Munich, Germany (); Jay R. Thiagarajah, MD, PhD, Boston Children’s Hospital, Division of Gastroenterology, EN605, 300 Longwood Avenue, Boston, MA 02115, USA ()
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Voet J, Ceulemans B, Kooy F, Meuwissen MEC. PUM1
haploinsufficiency is associated with syndromic neurodevelopmental delay and epilepsy. Am J Med Genet A 2020; 182:591-594. [DOI: 10.1002/ajmg.a.61463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/28/2019] [Accepted: 11/12/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Julie Voet
- Department of PediatricsAntwerp University Hospital Edegem Belgium
| | - Berten Ceulemans
- Department of Pediatric NeurologyAntwerp University Hospital Edegem Belgium
- Department of Pediatric NeurologyUniversity of Antwerp Edegem Belgium
| | - Frank Kooy
- Center for Medical GeneticsAntwerp University Hospital Edegem Belgium
- Center for Medical GeneticsUniversity of Antwerp Edegem Belgium
| | - Marije E. C. Meuwissen
- Center for Medical GeneticsAntwerp University Hospital Edegem Belgium
- Center for Medical GeneticsUniversity of Antwerp Edegem Belgium
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AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting. BMC Med Genomics 2020; 13:17. [PMID: 32019565 PMCID: PMC7001226 DOI: 10.1186/s12920-020-0668-3] [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: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking. RESULTS With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals. CONCLUSION Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.
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Van Der Steen N, Zwaenepoel K, Mazzaschi G, A. Luirink R, P. Geerke D, Op de Beeck K, Hermans C, Tiseo M, Van Schil P, Lardon F, Germonpré P, Rolfo C, Giovannetti E, J. Peters G, Pauwels P. The Role of c-Met as a Biomarker and Player in Innate and Acquired Resistance in Non-Small-Cell Lung Cancer: Two New Mutations Warrant Further Studies. Molecules 2019; 24:E4443. [PMID: 31817278 PMCID: PMC6943481 DOI: 10.3390/molecules24244443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/21/2022] Open
Abstract
The c-Met receptor is a therapeutically actionable target in non-small-cell lung cancer (NSCLC), with one approved drug and several agents in development. Most suitable biomarkers for patient selection include c-Met amplification and exon-14 skipping. Our retrospective study focused on the frequency of different c-Met aberrations (overexpression, amplification and mutations) in 153 primary, therapy-naïve resection samples and their paired metastases, from Biobank@UZA. Furthermore, we determined the correlation of c-Met expression with clinicopathological factors, Epidermal Growth Factor Receptor (EGFR)-status and TP53 mutations. Our results showed that c-Met expression levels in primary tumors were comparable to their respective metastases. Five different mutations were detected by deep sequencing: three (E168D, S203T, N375S) previously described and two never reported (I333T, G783E). I333T, a new mutation in the Sema(phorin) domain of c-Met, might influence the binding of antibodies targeting the HGF-binding domain, potentially causing innate resistance. E168D and S203T mutations showed a trend towards a correlation with high c-Met expression (p = 0.058). We found a significant correlation between c-MET expression, EGFR expression (p = 0.010) and EGFR mutations (p = 0.013), as well as a trend (p = 0.057) with regards to TP53 mutant activity. In conclusion this study demonstrated a strong correlation between EGFR mutations, TP53 and c-Met expression in therapy-naïve primary resection samples. Moreover, we found two new c-Met mutations that warrant further studies.
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Affiliation(s)
- Nele Van Der Steen
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
- Department of Medical Oncology, VU University Medical Center, CCA 1.42, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
| | - Karen Zwaenepoel
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - Giulia Mazzaschi
- Department of Medicine and Surgery, University of Parma and Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy; (G.M.); (M.T.)
| | - Rosa A. Luirink
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; (R.A.L.); (D.P.G.)
| | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands; (R.A.L.); (D.P.G.)
| | - Ken Op de Beeck
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Antwerp, Belgium
| | - Christophe Hermans
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma and Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy; (G.M.); (M.T.)
| | - Paul Van Schil
- Department of Thoracic and Vascular Surgery, University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium;
| | - Filip Lardon
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
| | - Paul Germonpré
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Department of Pneumology, AZ Maria Middelares, Kliniekstraat 27, 9050 Gentbrugge, Belgium
| | - Christian Rolfo
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Phase I-Early Clinical Trials Unit, Oncology Department, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
- Thoracic Medical Oncology, Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 20742, USA
| | - Elisa Giovannetti
- Department of Medical Oncology, VU University Medical Center, CCA 1.42, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, Via Giovannini 13, San Giuliano Terme, I-56017 Pisa, Italy
| | - Godefridus J. Peters
- Department of Medical Oncology, VU University Medical Center, CCA 1.42, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands;
- Department of Biochemistry, Medical University of Gdansk, 80-844 Gdansk, Poland
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (N.V.D.S.); (K.Z.); (K.O.d.B.); (C.H.); (F.L.); (P.G.); (C.R.)
- Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
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28
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Flex E, Martinelli S, Van Dijck A, Ciolfi A, Cecchetti S, Coluzzi E, Pannone L, Andreoli C, Radio FC, Pizzi S, Carpentieri G, Bruselles A, Catanzaro G, Pedace L, Miele E, Carcarino E, Ge X, Chijiwa C, Lewis MES, Meuwissen M, Kenis S, Van der Aa N, Larson A, Brown K, Wasserstein MP, Skotko BG, Begtrup A, Person R, Karayiorgou M, Roos JL, Van Gassen KL, Koopmans M, Bijlsma EK, Santen GWE, Barge-Schaapveld DQCM, Ruivenkamp CAL, Hoffer MJV, Lalani SR, Streff H, Craigen WJ, Graham BH, van den Elzen APM, Kamphuis DJ, Õunap K, Reinson K, Pajusalu S, Wojcik MH, Viberti C, Di Gaetano C, Bertini E, Petrucci S, De Luca A, Rota R, Ferretti E, Matullo G, Dallapiccola B, Sgura A, Walkiewicz M, Kooy RF, Tartaglia M. Aberrant Function of the C-Terminal Tail of HIST1H1E Accelerates Cellular Senescence and Causes Premature Aging. Am J Hum Genet 2019; 105:493-508. [PMID: 31447100 DOI: 10.1016/j.ajhg.2019.07.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 07/10/2019] [Indexed: 02/03/2023] Open
Abstract
Histones mediate dynamic packaging of nuclear DNA in chromatin, a process that is precisely controlled to guarantee efficient compaction of the genome and proper chromosomal segregation during cell division and to accomplish DNA replication, transcription, and repair. Due to the important structural and regulatory roles played by histones, it is not surprising that histone functional dysregulation or aberrant levels of histones can have severe consequences for multiple cellular processes and ultimately might affect development or contribute to cell transformation. Recently, germline frameshift mutations involving the C-terminal tail of HIST1H1E, which is a widely expressed member of the linker histone family and facilitates higher-order chromatin folding, have been causally linked to an as-yet poorly defined syndrome that includes intellectual disability. We report that these mutations result in stable proteins that reside in the nucleus, bind to chromatin, disrupt proper compaction of DNA, and are associated with a specific methylation pattern. Cells expressing these mutant proteins have a dramatically reduced proliferation rate and competence, hardly enter into the S phase, and undergo accelerated senescence. Remarkably, clinical assessment of a relatively large cohort of subjects sharing these mutations revealed a premature aging phenotype as a previously unrecognized feature of the disorder. Our findings identify a direct link between aberrant chromatin remodeling, cellular senescence, and accelerated aging.
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Affiliation(s)
- Elisabetta Flex
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium; Department of Neurology, Antwerp University Hospital, Edegem, 2650 Belgium
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Serena Cecchetti
- Microscopy Area, Core Facilities, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Elisa Coluzzi
- Department of Science, University Roma Tre, Rome, 00146 Italy
| | - Luca Pannone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, 00161 Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Giovanna Carpentieri
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy; Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, 00161 Italy
| | | | - Lucia Pedace
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Elena Carcarino
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy; Current affiliation: Cordeliers Research Centre, Inserm 1138, Sorbonne Université, Paris, 75006 France
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Current affiliation: Department of Genetics and Genomic Sciences, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chieko Chijiwa
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium
| | - Sandra Kenis
- Department of Neurology, Antwerp University Hospital, Edegem, 2650 Belgium
| | | | - Austin Larson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kathleen Brown
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Melissa P Wasserstein
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10467, USA
| | - Brian G Skotko
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02114, USA
| | | | | | - Maria Karayiorgou
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - J Louw Roos
- Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, 0001 South Africa
| | - Koen L Van Gassen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3508 AB the Netherlands
| | - Marije Koopmans
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, 3508 AB the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | | | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2300 RC the Netherlands
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Daan J Kamphuis
- Departement of Neurology, Reinier de Graaf Ziekenhuis, Delft, 2600 GA the Netherlands
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, 50406 Estonia; Institute of Clinical Medicine, University of Tartu, Tartu, 50406 Estonia; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Monica H Wojcik
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clara Viberti
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Enrico Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Simona Petrucci
- Department of Clinical and Molecular Medicine, Sapienza University, Rome, 00189 Italy; Division of Medical Genetics, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, 71013 Italy
| | - Alessandro De Luca
- Division of Medical Genetics, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, 71013 Italy
| | - Rossella Rota
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, 00146 Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University, Rome, 00161 Italy; Istituto Neuromed, IRCCS, Pozzilli, 86077 Italy
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, Turin, 10126 Italy; Italian Institute for Genomic Medicine, Turin, 10126 Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy
| | - Antonella Sgura
- Department of Science, University Roma Tre, Rome, 00146 Italy
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Current affiliation: National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, 2650 Belgium.
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, 00146 Italy.
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Demeulenaere S, Beysen D, De Veuster I, Reyniers E, Kooy F, Meuwissen M. Novel BRPF1 mutation in a boy with intellectual disability, coloboma, facial nerve palsy and hypoplasia of the corpus callosum. Eur J Med Genet 2019; 62:103691. [DOI: 10.1016/j.ejmg.2019.103691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/11/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
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30
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De Ridder R, Boudin E, Vandeweyer G, Devogelaer JP, Fransen E, Mortier G, Van Hul W. Genetic Variation in RIN3 in the Belgian Population Supports Its Involvement in the Pathogenesis of Paget's Disease of Bone and Modifies the Age of Onset. Calcif Tissue Int 2019; 104:613-621. [PMID: 30726512 DOI: 10.1007/s00223-019-00530-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/28/2019] [Indexed: 12/24/2022]
Abstract
Paget's disease of bone (PDB) is a common, late-onset bone disorder characterized by focal increase of bone turnover. Mutations in the SQSTM1 gene are found in up to 40% of patients and recent GWAS have led to novel associations with several loci. RIN3, the candidate gene located at the associated 14q32 locus, has recently been studied in a British cohort to elucidate its contribution to the pathogenesis. In this study, we performed a genetic screening of RIN3 in an unrelated cohort to validate these findings and to further explore genetic variation in this gene in the context of PDB. In our screening, we examined the 5' untranslated region (UTR), the exonic regions and the intron-exon boundaries of the gene in a control cohort and a patient cohort. Our findings show clustering of variation similar to the British cohort and support a protective role for common genetic variation (rs117068593, p.R279C) in the proline-rich region and a functionally relevant role for rare genetic variation in the domains that mediate binding and activation of its interaction partner, Rab5. Additive regression models, fitted for the common variants, validated the association of the rs117068593 variant with the disease (OR+/+ 0.315; OR+/- 0.562). In addition, our analyses revealed a potentially modifying effect of this variant on the age of onset of the disease. In conclusion, our findings support the involvement of genetic variation in RIN3 in PDB and suggest a role for RIN3 as a potential modifier of the age of onset of the disease.
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Affiliation(s)
- Raphaël De Ridder
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Eveline Boudin
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Geert Vandeweyer
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Jean-Pierre Devogelaer
- Department of Rheumatology, Saint-Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium
| | - Wim Van Hul
- Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Prins Boudewijnlaan 43, Edegem, 2650, Antwerp, Belgium.
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Alzu'bi AA, Zhou L, Watzlaf VJM. Genetic Variations and Precision Medicine. PERSPECTIVES IN HEALTH INFORMATION MANAGEMENT 2019; 16:1a. [PMID: 31019429 PMCID: PMC6462879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The time and costs associated with the sequencing of a human genome have decreased significantly in recent years. Many people have chosen to have their genomes sequenced to receive genomics-based personalized healthcare services. To reach the goal of genomics-based precision medicine, health information management (HIM) professionals need to manage and analyze patients' genomic data. Two important pieces of information from the genome sequence are the risk of genetic diseases and the specific medication or pharmacogenomic results for the individual patient, both of which are linked to a patient's genetic variations. In this review article, we introduce genetic variations, including their data types, relevant databases, and some currently available analysis methods and systems. HIM professionals can choose to use these databases, methods, and systems in the management and analysis of patients' genomic data.
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Affiliation(s)
- Amal Adel Alzu'bi
- The Department of Computer Information Systems at Jordan University of Science and Technology in Irbid, Jordan
| | - Leming Zhou
- The Department of Health Information Management at the University of Pittsburgh in Pittsburgh, PA
| | - Valerie J M Watzlaf
- The Department of Health Information Management at the University of Pittsburgh in Pittsburgh, PA
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Vandamme T, Beyens M, Boons G, Schepers A, Kamp K, Biermann K, Pauwels P, De Herder WW, Hofland LJ, Peeters M, Van Camp G, Op de Beeck K. Hotspot DAXX, PTCH2 and CYFIP2 mutations in pancreatic neuroendocrine neoplasms. Endocr Relat Cancer 2019; 26:1-12. [PMID: 30021865 DOI: 10.1530/erc-18-0120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/20/2022]
Abstract
Mutations in DAXX/ATRX, MEN1 and genes involved in the phosphoinositide-3-kinase/Akt/mammalian target of rapamycin (PI3K/Akt/mTOR) pathway have been implicated in pancreatic neuroendocrine neoplasms (pNENs). However, mainly mutations present in the majority of tumor cells have been identified, while proliferation-driving mutations could be present only in small fractions of the tumor. This study aims to identify high- and low-abundance mutations in pNENs using ultra-deep targeted resequencing. Formalin-fixed paraffin-embedded matched tumor-normal tissue of 38 well-differentiated pNENs was sequenced using a HaloPlex targeted resequencing panel. Novel amplicon-based algorithms were used to identify both single nucleotide variants (SNVs) and insertion-deletions (indels) present in >10% of reads (high abundance) and in <10% of reads (low abundance). Found variants were validated by Sanger sequencing. Sequencing resulted in 416,711,794 reads with an average target base coverage of 2663 ± 1476. Across all samples, 32 high-abundance somatic, 3 germline and 30 low-abundance mutations were withheld after filtering and validation. Overall, 92% of high-abundance and 84% of low-abundance mutations were predicted to be protein damaging. Frequently, mutated genes were MEN1, DAXX, ATRX, TSC2, PI3K/Akt/mTOR and MAPK-ERK pathway-related genes. Additionally, recurrent alterations on the same genomic position, so-called hotspot mutations, were found in DAXX, PTCH2 and CYFIP2. This first ultra-deep sequencing study highlighted genetic intra-tumor heterogeneity in pNEN, by the presence of low-abundance mutations. The importance of the ATRX/DAXX pathway was confirmed by the first-ever pNEN-specific protein-damaging hotspot mutation in DAXX. In this study, both novel genes, including the pro-apoptotic CYFIP2 gene and hedgehog signaling PTCH2, and novel pathways, such as the MAPK-ERK pathway, were implicated in pNEN.
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Affiliation(s)
- T Vandamme
- Center of Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
- Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M Beyens
- Center of Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - G Boons
- Center of Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - A Schepers
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - K Kamp
- Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - K Biermann
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - P Pauwels
- Department of Pathology, University of Antwerp, Antwerp, Belgium
| | - W W De Herder
- Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L J Hofland
- Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - M Peeters
- Center of Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - G Van Camp
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - K Op de Beeck
- Center of Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
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Boons G, Vandamme T, Peeters M, Beyens M, Driessen A, Janssens K, Zwaenepoel K, Roeyen G, Van Camp G, Op de Beeck K. Cell-Free DNA From Metastatic Pancreatic Neuroendocrine Tumor Patients Contains Tumor-Specific Mutations and Copy Number Variations. Front Oncol 2018; 8:467. [PMID: 30443491 PMCID: PMC6221938 DOI: 10.3389/fonc.2018.00467] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022] Open
Abstract
Background: Detection of tumor-specific alterations in cell-free DNA (cfDNA) has proven valuable as a liquid biopsy for several types of cancer. So far, use of cfDNA remains unexplored for pancreatic neuroendocrine tumor (PNET) patients. Methods: From 10 PNET patients, fresh frozen tumor tissue, buffy coat and plasma samples were collected. Whole-exome sequencing of primary tumor and germline DNA was performed to identify tumor-specific variants and copy number variations (CNVs). Subsequently, tumor-specific variants were quantified in plasma cfDNA with droplet digital PCR. In addition, CNV analysis of cfDNA was performed using shallow whole-genome sequencing. Results: Tumor-specific variants were detected in perioperative plasma samples of two PNET patients, at variant allele fractions (VAFs) of respectively 19 and 21%. Both patients had metastatic disease at time of surgery, while the other patients presented with localized disease. In the metastatic patients, CNV profiles of tumor tissue and cfDNA were significantly correlated. A follow-up plasma sample of a metastatic patient demonstrated an increased VAF (57%) and an increased chromosomal instability, in parallel with an increase in tumor burden. Conclusions: We are the first to report the presence of tumor-specific genetic alterations in cfDNA of metastatic PNET patients and their evolution during disease progression. Additionally, CNV analysis in cfDNA shows potential as a liquid biopsy.
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Affiliation(s)
- Gitta Boons
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Timon Vandamme
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
- Department of Oncology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
- Section of Endocrinology, Department of Internal Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium
- Department of Oncology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Matthias Beyens
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ann Driessen
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Katrien Janssens
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Karen Zwaenepoel
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Geert Roeyen
- Department of Hepatobiliary, Endocrine and Transplantation Surgery, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Guy Van Camp
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ken Op de Beeck
- Center for Oncological Research, University of Antwerp, Antwerp, Belgium
- Center of Medical Genetics Antwerp, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
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Hylebos M, Op de Beeck K, Pauwels P, Zwaenepoel K, van Meerbeeck JP, Van Camp G. Tumor-specific genetic variants can be detected in circulating cell-free DNA of malignant pleural mesothelioma patients. Lung Cancer 2018; 124:19-22. [PMID: 30268460 DOI: 10.1016/j.lungcan.2018.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Patients diagnosed with malignant pleural mesothelioma (MPM) face a poor prognosis, with an overall survival plateauing at a median of one year. This can be explained by difficulties in early diagnosis, effective treatment and treatment monitoring. Circulating cell-free tumor DNA (ctDNA) is emerging as an interesting biomarker addressing some of these issues. So far, the development of ctDNA in MPM lags behind that in other tumors. In this study, the possibility of tracing tumor-specific genetic variants, identified in MPM tissue, in circulating DNA of the corresponding patients is investigated. MATERIALS AND METHODS Whole exome sequencing was performed on paired tumor and germline DNA of ten MPM patients, of which five were treatment naïve. For each patient, a tumor-specific variant was selected and traced in tumor, germline and circulating DNA using droplet digital PCR in two independent runs. RESULTS All but one tumor-specific variants, selected after whole exome sequencing, were validated on primary tumor tissue using droplet digital PCR analysis. Patient-specific, selected variants could be detected in circulating DNA of three MPM patients, either in one or both independent droplet digital PCR runs. Mutated fractions in circulating DNA ranged from 0.28 to 0.9%. Interestingly, all patients whose circulating DNA samples contained tumor-specific variants, were treatment naïve. CONCLUSION We demonstrated for the first time the presence of ctDNA within circulating DNA of treatment naïve MPM patients. This finding opens perspectives towards the use of ctDNA as a biomarker for (early and differential) diagnosis, treatment and treatment monitoring of MPM, which all remain challenging.
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Affiliation(s)
- Marieke Hylebos
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Laboratory of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Laboratory of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium
| | - Jan P van Meerbeeck
- Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; Department of Pulmonology/Thoracic Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Antwerp, Belgium.
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43, 2650 Antwerp, Belgium; Center for Oncological Research, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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35
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Cannaerts E, Kempers M, Maugeri A, Marcelis C, Gardeitchik T, Richer J, Micha D, Beauchesne L, Timmermans J, Vermeersch P, Meyten N, Chénier S, van de Beek G, Peeters N, Alaerts M, Schepers D, Van Laer L, Verstraeten A, Loeys B. Novel pathogenic SMAD2 variants in five families with arterial aneurysm and dissection: further delineation of the phenotype. J Med Genet 2018; 56:220-227. [PMID: 29967133 DOI: 10.1136/jmedgenet-2018-105304] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 01/21/2023]
Abstract
BACKGROUND Missense variants in SMAD2, encoding a key transcriptional regulator of transforming growth factor beta signalling, were recently reported to cause arterial aneurysmal disease. OBJECTIVES The aims of the study were to identify the genetic disease cause in families with aortic/arterial aneurysmal disease and to further define SMAD2 genotype-phenotype correlations. METHODS AND RESULTS Using gene panel sequencing, we identified a SMAD2 nonsense variant and four SMAD2 missense variants, all affecting highly conserved amino acids in the MH2 domain. The premature stop codon (c.612dup; p.(Asn205*)) was identified in a marfanoid patient with aortic root dilatation and in his affected father. A p.(Asn318Lys) missense variant was found in a Marfan syndrome (MFS)-like case who presented with aortic root aneurysm and in her affected daughter with marfanoid features and mild aortic dilatation. In a man clinically diagnosed with Loeys-Dietz syndrome (LDS) that presents with aortic root dilatation and marked tortuosity of the neck vessels, another missense variant, p.(Ser397Tyr), was identified. This variant was also found in his affected daughter with hypertelorism and arterial tortuosity, as well as his affected mother. The third missense variant, p.(Asn361Thr), was discovered in a man presenting with coronary artery dissection. Variant genotyping in three unaffected family members confirmed its absence. The last missense variant, p.(Ser467Leu), was identified in a man with significant cardiovascular and connective tissue involvement. CONCLUSION Taken together, our data suggest that heterozygous loss-of-function SMAD2 variants can cause a wide spectrum of autosomal dominant aortic and arterial aneurysmal disease, combined with connective tissue findings reminiscent of MFS and LDS.
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Affiliation(s)
- Elyssa Cannaerts
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie Richer
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Dimitra Micha
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Luc Beauchesne
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Janneke Timmermans
- Department of Cardiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Sébastien Chénier
- CIUSSS de l'Estrie, Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Gerarda van de Beek
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Nils Peeters
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Maaike Alaerts
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dorien Schepers
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart Loeys
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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36
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Hylebos M, Op de Beeck K, van den Ende J, Pauwels P, Lammens M, van Meerbeeck JP, Van Camp G. Molecular analysis of an asbestos-exposed Belgian family with a high prevalence of mesothelioma. Fam Cancer 2018; 17:569-576. [DOI: 10.1007/s10689-018-0095-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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37
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Eilbeck K, Quinlan A, Yandell M. Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet 2017; 18:599-612. [PMID: 28804138 PMCID: PMC5935497 DOI: 10.1038/nrg.2017.52] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When investigating Mendelian disease using exome or genome sequencing, distinguishing disease-causing genetic variants from the multitude of candidate variants is a complex, multidimensional task. Many prioritization tools and online interpretation resources exist, and professional organizations have offered clinical guidelines for review and return of prioritization results. In this Review, we describe the strengths and weaknesses of widely used computational approaches, explain their roles in the diagnostic and discovery process and discuss how they can inform (and misinform) expert reviewers. We place variant prioritization in the wider context of gene prioritization, burden testing and genotype-phenotype association, and we discuss opportunities and challenges introduced by whole-genome sequencing.
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Affiliation(s)
- Karen Eilbeck
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
| | - Aaron Quinlan
- Department of Biomedical Informatics, School of Medicine, University of Utah, 421 Wakara Way, Suite 120, Salt Lake City, Utah 84108, USA
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, School of Medicine, University of Utah, 15 S 2030 E, Salt Lake City, Utah 84112, USA
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Deben C, Op de Beeck K, Van den Bossche J, Jacobs J, Lardon F, Wouters A, Peeters M, Van Camp G, Rolfo C, Deschoolmeester V, Pauwels P. MDM2 SNP309 and SNP285 Act as Negative Prognostic Markers for Non-small Cell Lung Cancer Adenocarcinoma Patients. J Cancer 2017; 8:2154-2162. [PMID: 28819417 PMCID: PMC5560132 DOI: 10.7150/jca.19254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/26/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives: Two functional polymorphisms in the MDM2 promoter region, SNP309T>G and SNP285G>C, have been shown to impact MDM2 expression and cancer risk. Currently available data on the prognostic value of MDM2 SNP309 in non-small cell lung cancer (NSCLC) is contradictory and unavailable for SNP285. The goal of this study was to clarify the role of these MDM2 SNPs in the outcome of NSCLC patients. Materials and Methods: In this study we genotyped SNP309 and SNP285 in 98 NSCLC adenocarcinoma patients and determined MDM2 mRNA and protein levels. In addition, we assessed the prognostic value of these common SNPs on overall and progression free survival, taking into account the TP53 status of the tumor. Results and Conclusion: We found that the SNP285C allele, but not the SNP309G allele, was significantly associated with increased MDM2 mRNA expression levels (p = 0.025). However, we did not observe an association with MDM2 protein levels for SNP285. The SNP309G allele was significantly associated with the presence of wild type TP53 (p = 0.047) and showed a strong trend towards increased MDM2 protein levels (p = 0.068). In addition, patients harboring the SNP309G allele showed a worse overall survival, but only in the presence of wild type TP53. The SNP285C allele was significantly associated with an early age of diagnosis and metastasis. Additionally, the SNP285C allele acted as an independent predictor for worse progression free survival (HR = 3.97; 95% CI = 1.51 - 10.42; p = 0.005). Our data showed that both SNP309 (in the presence of wild type TP53) and SNP285 act as negative prognostic markers for NSCLC patients, implicating a prominent role for these variants in the outcome of these patients.
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Affiliation(s)
- Christophe Deben
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Ken Op de Beeck
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Jolien Van den Bossche
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Julie Jacobs
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - An Wouters
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Guy Van Camp
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Center of Medical Genetics, University of Antwerp & Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Christian Rolfo
- Department of Medical Oncology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium.,Phase-1 Early Clinical Trials Unit, Antwerp University Hospital Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Vanessa Deschoolmeester
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.,Department of Pathology, Antwerp University Hospital, Wilrijkstraat 10, 2650 Edegem, Antwerp, Belgium
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Gillis E, Kumar AA, Luyckx I, Preuss C, Cannaerts E, van de Beek G, Wieschendorf B, Alaerts M, Bolar N, Vandeweyer G, Meester J, Wünnemann F, Gould RA, Zhurayev R, Zerbino D, Mohamed SA, Mital S, Mertens L, Björck HM, Franco-Cereceda A, McCallion AS, Van Laer L, Verhagen JMA, van de Laar IMBH, Wessels MW, Messas E, Goudot G, Nemcikova M, Krebsova A, Kempers M, Salemink S, Duijnhouwer T, Jeunemaitre X, Albuisson J, Eriksson P, Andelfinger G, Dietz HC, Verstraeten A, Loeys BL. Candidate Gene Resequencing in a Large Bicuspid Aortic Valve-Associated Thoracic Aortic Aneurysm Cohort: SMAD6 as an Important Contributor. Front Physiol 2017; 8:400. [PMID: 28659821 PMCID: PMC5469151 DOI: 10.3389/fphys.2017.00400] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/26/2017] [Indexed: 12/30/2022] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect. Although many BAV patients remain asymptomatic, at least 20% develop thoracic aortic aneurysm (TAA). Historically, BAV-related TAA was considered as a hemodynamic consequence of the valve defect. Multiple lines of evidence currently suggest that genetic determinants contribute to the pathogenesis of both BAV and TAA in affected individuals. Despite high heritability, only very few genes have been linked to BAV or BAV/TAA, such as NOTCH1, SMAD6, and MAT2A. Moreover, they only explain a minority of patients. Other candidate genes have been suggested based on the presence of BAV in knockout mouse models (e.g., GATA5, NOS3) or in syndromic (e.g., TGFBR1/2, TGFB2/3) or non-syndromic (e.g., ACTA2) TAA forms. We hypothesized that rare genetic variants in these genes may be enriched in patients presenting with both BAV and TAA. We performed targeted resequencing of 22 candidate genes using Haloplex target enrichment in a strictly defined BAV/TAA cohort (n = 441; BAV in addition to an aortic root or ascendens diameter ≥ 4.0 cm in adults, or a Z-score ≥ 3 in children) and in a collection of healthy controls with normal echocardiographic evaluation (n = 183). After additional burden analysis against the Exome Aggregation Consortium database, the strongest candidate susceptibility gene was SMAD6 (p = 0.002), with 2.5% (n = 11) of BAV/TAA patients harboring causal variants, including two nonsense, one in-frame deletion and two frameshift mutations. All six missense mutations were located in the functionally important MH1 and MH2 domains. In conclusion, we report a significant contribution of SMAD6 mutations to the etiology of the BAV/TAA phenotype.
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Affiliation(s)
- Elisabeth Gillis
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Ajay A Kumar
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Ilse Luyckx
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Christoph Preuss
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de MontrealMontreal, QC, Canada
| | - Elyssa Cannaerts
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Gerarda van de Beek
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Björn Wieschendorf
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium.,Department of Cardiac and Thoracic Vascular Surgery, University Hospital Schleswig-HolsteinLübeck, Germany
| | - Maaike Alaerts
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Nikhita Bolar
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Geert Vandeweyer
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Josephina Meester
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Florian Wünnemann
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de MontrealMontreal, QC, Canada
| | - Russell A Gould
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, United States
| | - Rustam Zhurayev
- Department of Clinical pathology, Lviv National Medical University after Danylo HalytskyLviv, Ukraine
| | - Dmytro Zerbino
- Department of Clinical pathology, Lviv National Medical University after Danylo HalytskyLviv, Ukraine
| | - Salah A Mohamed
- Department of Cardiac and Thoracic Vascular Surgery, University Hospital Schleswig-HolsteinLübeck, Germany
| | - Seema Mital
- Cardiovascular Research, SickKids University HospitalToronto, ON, Canada
| | - Luc Mertens
- Cardiovascular Research, SickKids University HospitalToronto, ON, Canada
| | - Hanna M Björck
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska InstituteStockholm, Sweden
| | - Anders Franco-Cereceda
- Cardiothoracic Surgery Unit, Department of Molecular Medicine and Surgery, Karolinska InstituteStockholm, Sweden
| | - Andrew S McCallion
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, United States
| | - Lut Van Laer
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Judith M A Verhagen
- Department of Clinical Genetics, Erasmus University Medical CenterRotterdam, Netherlands
| | | | - Marja W Wessels
- Department of Clinical Genetics, Erasmus University Medical CenterRotterdam, Netherlands
| | - Emmanuel Messas
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou; Université Paris Descartes, Paris Sorbonne Cité; Institut National de la Santé et de la Recherche Médicale, UMRSParis, France
| | - Guillaume Goudot
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou; Université Paris Descartes, Paris Sorbonne Cité; Institut National de la Santé et de la Recherche Médicale, UMRSParis, France
| | - Michaela Nemcikova
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine-Charles University and Motol University HospitalPrague, Czechia
| | - Alice Krebsova
- Institute of Clinical and Experimental MedicinePrague, Czechia
| | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical CentreNijmegen, Netherlands
| | - Simone Salemink
- Department of Human Genetics, Radboud University Medical CentreNijmegen, Netherlands
| | - Toon Duijnhouwer
- Department of Human Genetics, Radboud University Medical CentreNijmegen, Netherlands
| | - Xavier Jeunemaitre
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou; Université Paris Descartes, Paris Sorbonne Cité; Institut National de la Santé et de la Recherche Médicale, UMRSParis, France
| | - Juliette Albuisson
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou; Université Paris Descartes, Paris Sorbonne Cité; Institut National de la Santé et de la Recherche Médicale, UMRSParis, France
| | - Per Eriksson
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska InstituteStockholm, Sweden
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Université de MontrealMontreal, QC, Canada
| | - Harry C Dietz
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of MedicineBaltimore, MD, United States.,Howard Hughes Medical InstituteBaltimore, MD, United States
| | - Aline Verstraeten
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium
| | - Bart L Loeys
- Faculty of Medicine and Health Sciences, Center of Medical Genetics, University of Antwerp and Antwerp University HospitalAntwerp, Belgium.,Department of Human Genetics, Radboud University Medical CentreNijmegen, Netherlands
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40
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Proost D, Saenen J, Vandeweyer G, Rotthier A, Alaerts M, Van Craenenbroeck EM, Van Crombruggen J, Mortier G, Wuyts W, Vrints C, Del Favero J, Loeys B, Van Laer L. Targeted Next-Generation Sequencing of 51 Genes Involved in Primary Electrical Disease. J Mol Diagn 2017; 19:445-459. [DOI: 10.1016/j.jmoldx.2017.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 01/11/2017] [Indexed: 01/18/2023] Open
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Deben C, Van den Bossche J, Van Der Steen N, Lardon F, Wouters A, de Beeck KO, Hermans C, Jacobs J, Peeters M, Van Camp G, Rolfo C, Deschoolmeester V, Pauwels P. Deep sequencing of the TP53 gene reveals a potential risk allele for non-small cell lung cancer and supports the negative prognostic value of TP53 variants. Tumour Biol 2017; 39:1010428317694327. [PMID: 28240049 DOI: 10.1177/1010428317694327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The TP53 gene remains the most frequently altered gene in human cancer, of which variants are associated with cancer risk, therapy resistance, and poor prognosis in several tumor types. To determine the true prognostic value of TP53 variants in non-small cell lung cancer, this study conducted further research, particularly focusing on subtype and tumor stage. Therefore, we determined the TP53 status of 97 non-small cell lung cancer adenocarcinoma patients using next generation deep sequencing technology and defined the prognostic value of frequently occurring single nucleotide polymorphisms and mutations in the TP53 gene. Inactivating TP53 mutations acted as a predictor for both worse overall and progression-free survival in stage II-IV patients and patients treated with DNA-damaging (neo)adjuvant therapy. In stage I tumors, the Pro-allele of the TP53 R72P polymorphism acted as a predictor for worse overall survival. In addition, we detected the rare R213R (rs1800372, minor allele frequency: 0.0054) polymorphism in 7.2% of the patients and are the first to show the significant association with TP53 mutations in non-small cell lung cancer adenocarcinoma patients (p = 0.003). In conclusion, Our findings show an important role for TP53 variants as negative predictors for the outcome of non-small cell lung cancer adenocarcinoma patients, especially for TP53 inactivating mutations in advanced stage tumors treated with DNA-damaging agents, and provide the first evidence of the R213R G-allele as possible risk factor for non-small cell lung cancer.
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Affiliation(s)
- Christophe Deben
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | | | - Nele Van Der Steen
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Filip Lardon
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - An Wouters
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Ken Op de Beeck
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,3 Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Christophe Hermans
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Julie Jacobs
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Peeters
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,4 Department of Medical Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Guy Van Camp
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,3 Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Christian Rolfo
- 4 Department of Medical Oncology, Antwerp University Hospital, Antwerp, Belgium.,5 Phase-1 Early Clinical Trials Unit, Antwerp University Hospital, Antwerp, Belgium
| | - Vanessa Deschoolmeester
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
| | - Patrick Pauwels
- 1 Center for Oncological Research (CORE), University of Antwerp, Antwerp, Belgium.,2 Department of Pathology, Antwerp University Hospital, Antwerp, Belgium
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van der Werf IM, Van Dijck A, Reyniers E, Helsmoortel C, Kumar AA, Kalscheuer VM, de Brouwer AP, Kleefstra T, van Bokhoven H, Mortier G, Janssens S, Vandeweyer G, Kooy RF. Mutations in two large pedigrees highlight the role of ZNF711 in X-linked intellectual disability. Gene 2016; 605:92-98. [PMID: 27993705 DOI: 10.1016/j.gene.2016.12.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/02/2016] [Accepted: 12/14/2016] [Indexed: 02/04/2023]
Abstract
Intellectual disability (ID) affects approximately 1-2% of the general population and is characterized by impaired cognitive abilities. ID is both clinically as well as genetically heterogeneous, up to 2000 genes are estimated to be involved in the emergence of the disease with various clinical presentations. For many genes, only a few patients have been reported and causality of some genes has been questioned upon the discovery of apparent loss-of-function mutations in healthy controls. Description of additional patients strengthens the evidence for the involvement of a gene in the disease and can clarify the clinical phenotype associated with mutations in a particular gene. Here, we present two large four-generation families with a total of 11 males affected with ID caused by mutations in ZNF711, thereby expanding the total number of families with ID and a ZNF711 mutation to four. Patients with mutations in ZNF711 all present with mild to moderate ID and poor speech accompanied by additional features in some patients, including autistic features and mild facial dysmorphisms, suggesting that ZNF711 mutations cause non-syndromic ID.
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Affiliation(s)
- Ilse M van der Werf
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Edwin Reyniers
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Céline Helsmoortel
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Ajay Anand Kumar
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Arjan Pm de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp and University Hospital Antwerp, Antwerp, Belgium.
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Dominant variants in the splicing factor PUF60 cause a recognizable syndrome with intellectual disability, heart defects and short stature. Eur J Hum Genet 2016; 25:43-51. [PMID: 27804958 DOI: 10.1038/ejhg.2016.133] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 07/28/2016] [Accepted: 08/23/2016] [Indexed: 12/26/2022] Open
Abstract
Verheij syndrome, also called 8q24.3 microdeletion syndrome, is a rare condition characterized by ante- and postnatal growth retardation, microcephaly, vertebral anomalies, joint laxity/dislocation, developmental delay (DD), cardiac and renal defects and dysmorphic features. Recently, PUF60 (Poly-U Binding Splicing Factor 60 kDa), which encodes a component of the spliceosome, has been discussed as the best candidate gene for the Verheij syndrome phenotype, regarding the cardiac and short stature phenotype. To date, only one patient has been reported with a de novo variant in PUF60 that probably affects function (c.505C>T leading to p.(His169Tyr)) associated with DD, microcephaly, craniofacial and cardiac defects. Additional patients were required to confirm the pathogenesis of this association and further delineate the clinical spectrum. Here we report five patients with de novo heterozygous variants in PUF60 identified using whole exome sequencing. Variants included a splice-site variant (c.24+1G>C), a frameshift variant (p.(Ile136Thrfs*31)), two nonsense variants (p.(Arg448*) and p.(Lys301*)) and a missense change (p.(Val483Ala)). All six patients with a PUF60 variant (the five patients of the present study and the unique reported patient) have the same core facial gestalt as 8q24.3 microdeletions patients, associated with DD. Other findings include feeding difficulties (3/6), cardiac defects (5/6), short stature (5/6), joint laxity and/or dislocation (5/6), vertebral anomalies (3/6), bilateral microphthalmia and irido-retinal coloboma (1/6), bilateral optic nerve hypoplasia (2/6), renal anomalies (2/6) and branchial arch defects (2/6). These results confirm that PUF60 is a major driver for the developmental, craniofacial, skeletal and cardiac phenotypes associated with the 8q24.3 microdeletion.
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Abstract
Marfan syndrome is an autosomal dominant connective tissue disorder, predominantly affecting the ocular, skeletal and cardiovascular systems. Here, we present the results of the first genetic testing in 40 Ukrainian Marfan (-like) patients and 10 relatives. We applied a targeted next generation sequencing panel comprising FBN1 and 13 thoracic aortic aneurysm genes. We identified 27 causal mutations in FBN1, obtaining a mutation yield of 67·5%. A significant difference in age at aortic surgery between mutation positive and negative patients was observed. Thus, we conclude that genetic testing is important to identify patients at higher risk for developing life-threatening cardiovascular complications.
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45
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Meester JAN, Vandeweyer G, Pintelon I, Lammens M, Van Hoorick L, De Belder S, Waitzman K, Young L, Markham LW, Vogt J, Richer J, Beauchesne LM, Unger S, Superti-Furga A, Prsa M, Dhillon R, Reyniers E, Dietz HC, Wuyts W, Mortier G, Verstraeten A, Van Laer L, Loeys BL. Loss-of-function mutations in the X-linked biglycan gene cause a severe syndromic form of thoracic aortic aneurysms and dissections. Genet Med 2016; 19:386-395. [PMID: 27632686 PMCID: PMC5207316 DOI: 10.1038/gim.2016.126] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/15/2016] [Indexed: 12/25/2022] Open
Abstract
PURPOSE Thoracic aortic aneurysm and dissection (TAAD) is typically inherited in an autosomal dominant manner, but rare X-linked families have been described. So far, the only known X-linked gene is FLNA, which is associated with the periventricular nodular heterotopia type of Ehlers-Danlos syndrome. However, mutations in this gene explain only a small number of X-linked TAAD families. METHODS We performed targeted resequencing of 368 candidate genes in a cohort of 11 molecularly unexplained Marfan probands. Subsequently, Sanger sequencing of BGN in 360 male and 155 female molecularly unexplained TAAD probands was performed. RESULTS We found five individuals with loss-of-function mutations in BGN encoding the small leucine-rich proteoglycan biglycan. The clinical phenotype is characterized by early-onset aortic aneurysm and dissection. Other recurrent findings include hypertelorism, pectus deformity, joint hypermobility, contractures, and mild skeletal dysplasia. Fluorescent staining revealed an increase in TGF-β signaling, evidenced by an increase in nuclear pSMAD2 in the aortic wall. Our results are in line with those of prior reports demonstrating that Bgn-deficient male BALB/cA mice die from aortic rupture. CONCLUSION In conclusion, BGN gene defects in humans cause an X-linked syndromic form of severe TAAD that is associated with preservation of elastic fibers and increased TGF-β signaling.Genet Med 19 4, 386-395.
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Affiliation(s)
- Josephina A N Meester
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Geert Vandeweyer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Isabel Pintelon
- Department of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Martin Lammens
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium
| | - Lana Van Hoorick
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Simon De Belder
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Kathryn Waitzman
- Department of Pediatric Cardiology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Luciana Young
- Department of Pediatric Cardiology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Larry W Markham
- Divisions of Pediatric and Adult Cardiology, Vanderbilt University, Nashville, Tennessee, USA
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Richer
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Luc M Beauchesne
- Division of Cardiology, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Sheila Unger
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Milan Prsa
- Department of Pediatrics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rami Dhillon
- The Heart Unit, Birmingham Children's Hospital, Birmingham, UK
| | - Edwin Reyniers
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Harry C Dietz
- Howard Hughes Medical Institute, Baltimore, Maryland, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Wim Wuyts
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Aline Verstraeten
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L Loeys
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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Försti A, Kumar A, Paramasivam N, Schlesner M, Catalano C, Dymerska D, Lubinski J, Eils R, Hemminki K. Pedigree based DNA sequencing pipeline for germline genomes of cancer families. Hered Cancer Clin Pract 2016; 14:16. [PMID: 27508007 PMCID: PMC4977614 DOI: 10.1186/s13053-016-0058-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP). RESULTS The variant calling step distinguishes two types of genomic variants: single nucleotide variants (SNVs) and indels, which undergo technical quality control. Mendelian types of variants are assumed to be rare and variants with frequencies higher that 0.1 % are screened out using human 1000 Genomes (Phase 3) and non-TCGA ExAC population data. Segregation in the pedigree allows variants to be present in affected family members and not in old, unaffected ones. The effectiveness of variant segregation depends on the number and relatedness of the family members: if over 5 third-degree (or more distant) relatives are available, the experience has shown that the number of likely variants is reduced from many hundreds to a few tens. These are then subjected to bioinformatics analysis, starting with the combined annotation dependent depletion (CADD) tool, which predicts the likelihood of the variant being deleterious. Different sets of individual tools are used for further evaluation of the deleteriousness of coding variants, 5' and 3' untranslated regions (UTRs), and intergenic variants. CONLUSIONS The likelihood of success of the present genomic pipeline in finding novel high- or medium-penetrant genes depends on many steps but first and foremost, the pedigree needs to be reasonably large and the assignments and diagnoses among the members need to be correct.
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Affiliation(s)
- Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Abhishek Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
- Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
| | - Calogerina Catalano
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
| | - Dagmara Dymerska
- Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
- Department of Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D69120 Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Tan PPC, Rogic S, Zoubarev A, McDonald C, Lui F, Charathsandran G, Jacobson M, Belmadani M, Leong J, Van Rossum T, Portales-Casamar E, Qiao Y, Calli K, Liu X, Hudson M, Rajcan-Separovic E, Lewis MES, Pavlidis P. Interactive Exploration, Analysis, and Visualization of Complex Phenome-Genome Datasets with ASPIREdb. Hum Mutat 2016; 37:719-26. [PMID: 27158917 PMCID: PMC4940263 DOI: 10.1002/humu.23011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/28/2016] [Indexed: 11/10/2022]
Abstract
Identifying variants causal for complex genetic disorders is challenging. With the advent of whole-exome and whole-genome sequencing, computational tools are needed to explore and analyze the list of variants for further validation. Correlating genetic variants with subject phenotype is crucial for the interpretation of the disease-causing mutations. Often such work is done by teams of researchers who need to share information and coordinate activities. To this end, we have developed a powerful, easy to use Web application, ASPIREdb, which allows researchers to search, organize, analyze, and visualize variants and phenotypes associated with a set of human subjects. Investigators can annotate variants using publicly available reference databases and build powerful queries to identify subjects or variants of interest. Functional information and phenotypic associations of these genes are made accessible as well. Burden analysis and additional reporting tools allow investigation of variant properties and phenotype characteristics. Projects can be shared, allowing researchers to work collaboratively to build queries and annotate the data. We demonstrate ASPIREdb's functionality using publicly available data sets, showing how the software can be used to accomplish goals that might otherwise require specialized bioinformatics expertise. ASPIREdb is available at http://aspiredb.chibi.ubc.ca.
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Affiliation(s)
- Powell Patrick Cheng Tan
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Sanja Rogic
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Anton Zoubarev
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Cameron McDonald
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Frances Lui
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Gayathiri Charathsandran
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Matthew Jacobson
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Manuel Belmadani
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Justin Leong
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Thea Van Rossum
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Elodie Portales-Casamar
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Ying Qiao
- Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Kristina Calli
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Xudong Liu
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6 Canada
- Ongwanada Resource Cente, Kingston, Ontario K7L 3N6 Canada
| | - Melissa Hudson
- Department of Psychiatry, Queen's University, Kingston, Ontario K7L 3N6 Canada
| | - Evica Rajcan-Separovic
- Department of Pathology, BC Child and Family Research Institute, University of British Columbia (UBC), 950 West 28th, Room 3060, Vancouver, BC V5Z 4H4, Canada
| | - ME Suzanne Lewis
- Department of Medical Genetics, BC Child and Family Research Institute, UBC, Vancouver, BC V6H 3N1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories and Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
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Chung RH, Tsai WY, Kang CY, Yao PJ, Tsai HJ, Chen CH. FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies. PLoS Comput Biol 2016; 12:e1004980. [PMID: 27272119 PMCID: PMC4894624 DOI: 10.1371/journal.pcbi.1004980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/12/2016] [Indexed: 11/18/2022] Open
Abstract
In disease studies, family-based designs have become an attractive approach to analyzing next-generation sequencing (NGS) data for the identification of rare mutations enriched in families. Substantial research effort has been devoted to developing pipelines for automating sequence alignment, variant calling, and annotation. However, fewer pipelines have been designed specifically for disease studies. Most of the current analysis pipelines for family-based disease studies using NGS data focus on a specific function, such as identifying variants with Mendelian inheritance or identifying shared chromosomal regions among affected family members. Consequently, some other useful family-based analysis tools, such as imputation, linkage, and association tools, have yet to be integrated and automated. We developed FamPipe, a comprehensive analysis pipeline, which includes several family-specific analysis modules, including the identification of shared chromosomal regions among affected family members, prioritizing variants assuming a disease model, imputation of untyped variants, and linkage and association tests. We used simulation studies to compare properties of some modules implemented in FamPipe, and based on the results, we provided suggestions for the selection of modules to achieve an optimal analysis strategy. The pipeline is under the GNU GPL License and can be downloaded for free at http://fampipe.sourceforge.net.
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Affiliation(s)
- Ren-Hua Chung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- * E-mail:
| | - Wei-Yun Tsai
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Chen-Yu Kang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Po-Ju Yao
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hui-Ju Tsai
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
- Department of Public Health, China Medical University, Taichung, Taiwan
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Gueishan, Taoyuan, Taiwan
- Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
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Heterozygous Loss-of-Function Mutations in DLL4 Cause Adams-Oliver Syndrome. Am J Hum Genet 2015; 97:475-82. [PMID: 26299364 DOI: 10.1016/j.ajhg.2015.07.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/29/2015] [Indexed: 12/17/2022] Open
Abstract
Adams-Oliver syndrome (AOS) is a rare developmental disorder characterized by the presence of aplasia cutis congenita (ACC) of the scalp vertex and terminal limb-reduction defects. Cardiovascular anomalies are also frequently observed. Mutations in five genes have been identified as a cause for AOS prior to this report. Mutations in EOGT and DOCK6 cause autosomal-recessive AOS, whereas mutations in ARHGAP31, RBPJ, and NOTCH1 lead to autosomal-dominant AOS. Because RBPJ, NOTCH1, and EOGT are involved in NOTCH signaling, we hypothesized that mutations in other genes involved in this pathway might also be implicated in AOS pathogenesis. Using a candidate-gene-based approach, we prioritized DLL4, a critical NOTCH ligand, due to its essential role in vascular development in the context of cardiovascular features in AOS-affected individuals. Targeted resequencing of the DLL4 gene with a custom enrichment panel in 89 independent families resulted in the identification of seven mutations. A defect in DLL4 was also detected in two families via whole-exome or genome sequencing. In total, nine heterozygous mutations in DLL4 were identified, including two nonsense and seven missense variants, the latter encompassing four mutations that replace or create cysteine residues, which are most likely critical for maintaining structural integrity of the protein. Affected individuals with DLL4 mutations present with variable clinical expression with no emerging genotype-phenotype correlations. Our findings demonstrate that DLL4 mutations are an additional cause of autosomal-dominant AOS or isolated ACC and provide further evidence for a key role of NOTCH signaling in the etiology of this disorder.
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Proost D, Vandeweyer G, Meester JAN, Salemink S, Kempers M, Ingram C, Peeters N, Saenen J, Vrints C, Lacro RV, Roden D, Wuyts W, Dietz HC, Mortier G, Loeys BL, Van Laer L. Performant Mutation Identification Using Targeted Next-Generation Sequencing of 14 Thoracic Aortic Aneurysm Genes. Hum Mutat 2015; 36:808-14. [PMID: 25907466 DOI: 10.1002/humu.22802] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/08/2015] [Indexed: 02/07/2023]
Abstract
At least 14 causative genes have been identified for both syndromic and nonsyndromic forms of thoracic aortic aneurysm/dissection (TAA), an important cause of death in the industrialized world. Molecular confirmation of the diagnosis is increasingly important for gene-tailored patient management but consecutive, conventional molecular TAA gene screening is expensive and labor-intensive. To circumvent these problems, we developed a TAA gene panel for next-generation sequencing of 14 TAA genes. After validation, we applied the assay to 100 Marfan patients. We identified 90 FBN1 mutations, 44 of which were novel. In addition, Multiplex ligation-dependent probe amplification identified large deletions in six of the remaining samples, whereas false-negative results were excluded by Sanger sequencing of FBN1, TGFBR1, and TGFBR2 in the last four samples. Subsequently, we screened 55 syndromic and nonsyndromic TAA patients. We identified causal mutations in 15 patients (27%), one in each of the six following genes: ACTA2, COL3A1, TGFBR1, MYLK, SMAD3, SLC2A10 (homozygous), two in NOTCH1, and seven in FBN1. We conclude that our approach for TAA genetic testing overcomes the intrinsic hurdles of consecutive Sanger sequencing of all candidate genes and provides a powerful tool for the elaboration of clinical phenotypes assigned to different genes.
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Affiliation(s)
- Dorien Proost
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Josephina A N Meester
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Simone Salemink
- Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marlies Kempers
- Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christie Ingram
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Nils Peeters
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Johan Saenen
- Department of Cardiology, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Christiaan Vrints
- Department of Cardiology, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | | | - Dan Roden
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Wim Wuyts
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Harry C Dietz
- McKusick Nathans Institute for Genetic Medicine, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Geert Mortier
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Bart L Loeys
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.,Department of Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lut Van Laer
- Department of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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