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Bakey Z, Cabrera OA, Hoefele J, Antony D, Wu K, Stuck MW, Micha D, Eguether T, Smith AO, van der Wel NN, Wagner M, Strittmatter L, Beales PL, Jonassen JA, Thiffault I, Cadieux-Dion M, Boyes L, Sharif S, Tüysüz B, Dunstheimer D, Niessen HWM, Devine W, Lo CW, Mitchison HM, Schmidts M, Pazour GJ. IFT74 variants cause skeletal ciliopathy and motile cilia defects in mice and humans. PLoS Genet 2023; 19:e1010796. [PMID: 37315079 DOI: 10.1371/journal.pgen.1010796] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/23/2023] [Indexed: 06/16/2023] Open
Abstract
Motile and non-motile cilia play critical roles in mammalian development and health. These organelles are composed of a 1000 or more unique proteins, but their assembly depends entirely on proteins synthesized in the cell body and transported into the cilium by intraflagellar transport (IFT). In mammals, malfunction of non-motile cilia due to IFT dysfunction results in complex developmental phenotypes that affect most organs. In contrast, disruption of motile cilia function causes subfertility, disruption of the left-right body axis, and recurrent airway infections with progressive lung damage. In this work, we characterize allele specific phenotypes resulting from IFT74 dysfunction in human and mice. We identified two families carrying a deletion encompassing IFT74 exon 2, the first coding exon, resulting in a protein lacking the first 40 amino acids and two individuals carrying biallelic splice site mutations. Homozygous exon 2 deletion cases presented a ciliary chondrodysplasia with narrow thorax and progressive growth retardation along with a mucociliary clearance disorder phenotype with severely shorted cilia. Splice site variants resulted in a lethal skeletal chondrodysplasia phenotype. In mice, removal of the first 40 amino acids likewise results in a motile cilia phenotype but with little effect on primary cilia structure. Mice carrying this allele are born alive but are growth restricted and developed hydrocephaly in the first month of life. In contrast, a strong, likely null, allele of Ift74 in mouse completely blocks ciliary assembly and causes severe heart defects and midgestational lethality. In vitro studies suggest that the first 40 amino acids of IFT74 are dispensable for binding of other IFT subunits but are important for tubulin binding. Higher demands on tubulin transport in motile cilia compared to primary cilia resulting from increased mechanical stress and repair needs could account for the motile cilia phenotype observed in human and mice.
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Affiliation(s)
- Zeineb Bakey
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
- Human Genetics Department, Radboud University Medical Center Nijmegen and Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
| | - Oscar A Cabrera
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Julia Hoefele
- Institute for Human Genetics, Technical University Munich (TUM), School of Medicine, Munich, Germany
| | - Dinu Antony
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
- Human Genetics Department, Radboud University Medical Center Nijmegen and Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
| | - Kaman Wu
- Human Genetics Department, Radboud University Medical Center Nijmegen and Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
| | - Michael W Stuck
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Dimitra Micha
- Department of Human Genetics, Amsterdam Movement Sciences, Amsterdam UMC, Amsterdam, The Netherlands
| | - Thibaut Eguether
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Abigail O Smith
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
| | - Nicole N van der Wel
- Electron microscopy Center Amsterdam, Department of Medical Biology, VUMC, Amsterdam, The Netherlands
| | - Matias Wagner
- Institute for Human Genetics, Technical University Munich (TUM), School of Medicine, Munich, Germany
| | - Lara Strittmatter
- Electron Microscopy Core, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Philip L Beales
- Genetics and Genomic Medicine Programme, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Julie A Jonassen
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, Massachusetts, United States of America
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, United States of America
| | - Maxime Cadieux-Dion
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, United States of America
| | - Laura Boyes
- West Midlands Genomic Medicine Hub, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Saba Sharif
- West Midlands Genomic Medicine Hub, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Beyhan Tüysüz
- Department of Pediatrics, Division of Pediatric Genetics, Cerrahpasa Medical Faculty, University-Cerrahpasa, Istanbul, Turkey
| | - Desiree Dunstheimer
- Center for Pediatrics and Adolescent Medicine, University Hospital Augsburg, Augsburg, Germany
| | - Hans W M Niessen
- Department of Pathology, Amsterdam University Medical Center (AUMC), Amsterdam, The Netherlands
| | - William Devine
- Department of Developmental Biology, University of Pittsburgh, 8111 Rangos Research Center, Pittsburgh, Pennsylvania, United States of America
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh, 8111 Rangos Research Center, Pittsburgh, Pennsylvania, United States of America
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Programme, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Miriam Schmidts
- Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
- Human Genetics Department, Radboud University Medical Center Nijmegen and Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, The Netherlands
- CIBSS-Center for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Biotech II, Worcester, Massachusetts, United States of America
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2
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Bakey Z, Cabrera OA, Hoefele J, Antony D, Wu K, Stuck MW, Micha D, Eguether T, Smith AO, van der Wel NN, Wagner M, Strittmatter L, Beales PL, Jonassen JA, Thiffault I, Cadieux-Dion M, Boyes L, Sharif S, Tüysüz B, Dunstheimer D, Niessen HW, Devine W, Lo CW, Mitchison HM, Schmidts M, Pazour GJ. IFT74 variants cause skeletal ciliopathy and motile cilia defects in mice and humans. medRxiv 2023:2023.02.23.23286106. [PMID: 36865301 PMCID: PMC9980244 DOI: 10.1101/2023.02.23.23286106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Motile and non-motile cilia are critical to mammalian development and health. Assembly of these organelles depends on proteins synthesized in the cell body and transported into the cilium by intraflagellar transport (IFT). A series of human and mouse IFT74 variants were studied to understand the function of this IFT subunit. Humans missing exon 2, which codes for the first 40 residues, presented an unusual combination of ciliary chondrodysplasia and mucociliary clearance disorders while individuals carrying biallelic splice site variants developed a lethal skeletal chondrodysplasia. In mice, variants thought to remove all Ift74 function, completely block ciliary assembly and result in midgestational lethality. A mouse allele that removes the first 40 amino acids, analogous to the human exon 2 deletion, results in a motile cilia phenotype with mild skeletal abnormalities. In vitro studies suggest that the first 40 amino acids of IFT74 are dispensable for binding of other IFT subunits but are important for tubulin binding. Higher demands on tubulin transport in motile cilia compared to primary cilia could account for the motile cilia phenotype observed in human and mice.
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3
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Lansdon LA, Cadieux-Dion M, Herriges JC, Johnston J, Yoo B, Alaimo JT, Thiffault I, Miller N, Cohen ASA, Repnikova EA, Zhang L, Farooqi MS, Farrow EG, Saunders CJ. Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies. Clin Chem 2022; 68:1177-1183. [DOI: 10.1093/clinchem/hvac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/31/2022] [Indexed: 01/02/2023]
Abstract
Abstract
Background
Laboratories utilizing next-generation sequencing align sequence data to a standardized human reference genome (HRG). Several updated versions, or builds, have been released since the original HRG in 2001, including the Genome Reference Consortium Human Build 38 (GRCh38) in 2013. However, most clinical laboratories still use GRCh37, which was released in 2009. We report our laboratory’s clinical validation of GRCh38.
Methods
Migration to GRCh38 was validated by comparing the coordinates (lifting over) of 9443 internally curated variants from GRCh37 to GRCh38, globally comparing protein coding sequence variants aligned with GRCh37 vs GRCh38 from 917 exomes, assessing genes with known discrepancies, comparing coverage differences, and establishing the analytic sensitivity and specificity of variant detection using Genome in a Bottle data.
Results
Eight discrepancies, due to strand swap or reference base, were observed. Three clinically relevant variants had the GRCh37 alternate allele as the reference allele in GRCh38. A comparison of 88 295 calls between builds identified 8 disease-associated genes with sequence differences: ABO, BNC2, KIZ, NEFL, NR2E3, PTPRQ, SHANK2, and SRD5A2. Discrepancies in coding regions in GRCh37 were resolved in GRCh38.
Conclusions
There were a small number of clinically significant changes between the 2 genome builds. GRCh38 provided improved detection of nucleotide changes due to the resolution of discrepancies present in GRCh37. Implementation of GRCh38 results in more accurate and consistent reporting.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - John C Herriges
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Jeffrey Johnston
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Byunggil Yoo
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Neil Miller
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Bionano Genomics, Inc. , 9540 Towne Centre Dr., Suite 100, San Diego, CA , USA
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Emily G Farrow
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Department of Pediatrics Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
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4
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Cadieux-Dion M, Farrow E, Thiffault I, Cohen ASA, Welsh H, Bartik L, Schwager C, Engleman K, Zhou D, Zhang L, Repnikova E, Amudhavalli SM, Saunders C. Phenotypic expansion and variable expressivity in individuals with JARID2-related intellectual disability: A case series. Clin Genet 2022; 102:136-141. [PMID: 35533077 DOI: 10.1111/cge.14149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Loss of function variants in JARID2 were recently reported in 16 patients with a neurodevelopmental disorder characterized by delays, intellectual and learning disability, autism, behavioral abnormalities, and dysmorphic features. Most cases were de novo, with only one variant inherited from an affected parent. Here, we present 7 additional individuals from 5 families with pathogenic or likely pathogenic JARID2 variants, confirming this gene-disease association and highlighting palatal abnormalities and heart defect as part of the phenotype. In addition, we report inheritance of JARID2 variants from mildly affected parents, demonstrating the variable expressivity of the disease. We also note the high prevalence of intragenic JARID2 copy number variants, emphasizing the importance of exon-level analysis.
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Affiliation(s)
- Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Emily Farrow
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Holly Welsh
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Lauren Bartik
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Caitlin Schwager
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Kendra Engleman
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Dihong Zhou
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Elena Repnikova
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Shivarajan M Amudhavalli
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Carol Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA.,Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, USA
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5
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Cadieux-Dion M, Gannon J, Newell B, Nopper AJ, Jenkins J, Heese B, Saunders C. Delayed diagnosis of holocarboxylase synthetase deficiency in three patients with prominent skin findings. Pediatr Dermatol 2021; 38:655-658. [PMID: 33870574 DOI: 10.1111/pde.14586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/17/2021] [Accepted: 03/07/2021] [Indexed: 11/29/2022]
Abstract
Holocarboxylase deficiency (HLCSD) is caused by biallelic pathogenic variants in HLCS and is associated with poor feeding, emesis, lethargy, seizures, life-threatening metabolic acidosis, and hyperammonemia. Skin involvement in HLCSD is typically described as scaly, erythrodermic, seborrhea-like, or ichthyosiform, but there is a paucity of reports. We report three patients, including two siblings, with HLCSD and significant cutaneous manifestations including ichthyosiform dermatitis and a presentation with features of annular pustular psoriasis. In this report, we show that persistent, unexplained rash, even in the absence of other clinical findings, should warrant consideration and potential workup for HLCSD.
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Affiliation(s)
- Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Jennifer Gannon
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Brandon Newell
- Division of Dermatology, Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Amy Jo Nopper
- Division of Dermatology, Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Janda Jenkins
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Bryce Heese
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Carol Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
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6
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Lansdon LA, Cadieux-Dion M, Yoo B, Miller N, Cohen ASA, Zellmer L, Zhang L, Farrow EG, Thiffault I, Repnikova EA, Cooley LD, Alaimo JT, Porath B, Herriges JC, Saunders CJ, Farooqi MS. Factors Affecting Migration to GRCh38 in Laboratories Performing Clinical Next-Generation Sequencing. J Mol Diagn 2021; 23:651-657. [PMID: 33631350 DOI: 10.1016/j.jmoldx.2021.02.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/30/2021] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
The most recent build of the human reference genome, GRCh38, was released in 2013. However, many laboratories performing next-generation sequencing (NGS) continue to align to GRCh37. Our aim was to assess the number of clinical diagnostic laboratories that have migrated to GRCh38 and discern factors impeding migration for those still using GRCh37. A brief, five-question survey was electronically administered to 71 clinical laboratories offering constitutional NGS-based testing and analyzed categorically. Twenty-eight responses meeting inclusion criteria were collected from 24 academic and four commercial diagnostic laboratories. Most of these (14; 50%) reported volumes of <500 NGS-based tests in 2019. Only two respondents (7%) had already migrated entirely to GRCh38; most laboratories (15; 54%) had no plans to migrate. The two prevailing reasons for not yet migrating were as follows: laboratories did not feel the benefits outweighed the time and monetary costs (14; 50%); and laboratories had insufficient staff to facilitate the migration (12; 43%). These data, although limited, suggest most clinical molecular laboratories are reluctant to migrate to GRCh38, and there appear to be multiple obstacles to overcome before GRCh38 is widely adopted.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Lee Zellmer
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Emily G Farrow
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Missouri
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Linda D Cooley
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Binu Porath
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri
| | - John C Herriges
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Missouri; Department of Pathology, School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri.
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7
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Cadieux-Dion M, Hughes S, Engleman K, Rush ET, Saunders C. Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease. Am J Med Genet A 2021; 185:1515-1518. [PMID: 33559401 DOI: 10.1002/ajmg.a.62113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/21/2022]
Abstract
Nager syndrome epitomizes the acrofacial dysostoses, which are characterized by craniofacial and limb defects. The craniofacial defects include midfacial retrusion, downslanting palpebral fissures, prominent nasal bridge, and micrognathia. Limb malformations typically include hypoplasia or aplasia of radial elements including the thumb. Nager syndrome is caused by haploinsufficiency of SF3B4, encoding a spliceosomal protein called SAP49. Here, we report a patient with a loss of function variant in SF3B4 without acrofacial dysostosis or limb defects, whose reason for referral was developmental and growth delay. This patient is evidence of a broader phenotypic spectrum associated with SF3B4 variants than previously appreciated.
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Affiliation(s)
- Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Kendra Engleman
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Eric T Rush
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, Missouri, USA.,University of Missouri Kansas City, School of Medicine, Kansas City, Missouri, USA
| | - Carol Saunders
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri, USA.,University of Missouri Kansas City, School of Medicine, Kansas City, Missouri, USA.,Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri, USA
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8
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Jedličková I, Cadieux-Dion M, Přistoupilová A, Stránecký V, Hartmannová H, Hodaňová K, Barešová V, Hůlková H, Sikora J, Nosková L, Mušálková D, Vyleťal P, Sovová J, Cossette P, Andermann E, Andermann F, Kmoch S. Autosomal-dominant adult neuronal ceroid lipofuscinosis caused by duplication in DNAJC5 initially missed by Sanger and whole-exome sequencing. Eur J Hum Genet 2020; 28:783-789. [PMID: 31919451 PMCID: PMC7253421 DOI: 10.1038/s41431-019-0567-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 11/09/2022] Open
Abstract
Adult-onset neuronal ceroid lipofuscinoses (ANCL, Kufs disease) are rare hereditary neuropsychiatric disorders characterized by intralysosomal accumulation of ceroid in tissues. The ceroid accumulation primarily affects the brain, leading to neuronal loss and progressive neurodegeneration. Although several causative genes have been identified (DNAJC5, CLN6, CTSF, GRN, CLN1, CLN5, ATP13A2), the genetic underpinnings of ANCL in some families remain unknown. Here we report one family with autosomal dominant (AD) Kufs disease caused by a 30 bp in-frame duplication in DNAJC5, encoding the cysteine-string protein alpha (CSPα). This variant leads to a duplication of the central core motif of the cysteine-string domain of CSPα and affects palmitoylation-dependent CSPα sorting in cultured neuronal cells similarly to two previously described CSPα variants, p.(Leu115Arg) and p.(Leu116del). Interestingly, the duplication was not detected initially by standard Sanger sequencing due to a preferential PCR amplification of the shorter wild-type allele and allelic dropout of the mutated DNAJC5 allele. It was also missed by subsequent whole-exome sequencing (WES). Its identification was facilitated by reanalysis of original WES data and modification of the PCR and Sanger sequencing protocols. Independently occurring variants in the genomic sequence of DNAJC5 encoding the cysteine-string domain of CSPα suggest that this region may be more prone to DNA replication errors and that insertions or duplications within this domain should be considered in unsolved ANCL cases.
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Affiliation(s)
- Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Maxime Cadieux-Dion
- Centre Hospitalier de L´Universite de Montréal, Montréal, QC, Canada
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Helena Hůlková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Pathology, First Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Jakub Sikora
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
- Institute of Pathology, First Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Patrick Cossette
- Centre Hospitalier de L´Universite de Montréal, Montréal, QC, Canada
| | - Eva Andermann
- Montreal Neurological Hospital & Institute, McGill University, Montreal, QC, Canada
| | - Frederick Andermann
- Montreal Neurological Hospital & Institute, McGill University, Montreal, QC, Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic.
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9
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Yan K, Rousseau J, Machol K, Cross LA, Agre KE, Gibson CF, Goverde A, Engleman KL, Verdin H, De Baere E, Potocki L, Zhou D, Cadieux-Dion M, Bellus GA, Wagner MD, Hale RJ, Esber N, Riley AF, Solomon BD, Cho MT, McWalter K, Eyal R, Hainlen MK, Mendelsohn BA, Porter HM, Lanpher BC, Lewis AM, Savatt J, Thiffault I, Callewaert B, Campeau PM, Yang XJ. Deficient histone H3 propionylation by BRPF1-KAT6 complexes in neurodevelopmental disorders and cancer. Sci Adv 2020; 6:eaax0021. [PMID: 32010779 PMCID: PMC6976298 DOI: 10.1126/sciadv.aax0021] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/20/2019] [Indexed: 05/22/2023]
Abstract
Lysine acetyltransferase 6A (KAT6A) and its paralog KAT6B form stoichiometric complexes with bromodomain- and PHD finger-containing protein 1 (BRPF1) for acetylation of histone H3 at lysine 23 (H3K23). We report that these complexes also catalyze H3K23 propionylation in vitro and in vivo. Immunofluorescence microscopy and ATAC-See revealed the association of this modification with active chromatin. Brpf1 deletion obliterates the acylation in mouse embryos and fibroblasts. Moreover, we identify BRPF1 variants in 12 previously unidentified cases of syndromic intellectual disability and demonstrate that these cases and known BRPF1 variants impair H3K23 propionylation. Cardiac anomalies are present in a subset of the cases. H3K23 acylation is also impaired by cancer-derived somatic BRPF1 mutations. Valproate, vorinostat, propionate and butyrate promote H3K23 acylation. These results reveal the dual functionality of BRPF1-KAT6 complexes, shed light on mechanisms underlying related developmental disorders and various cancers, and suggest mutation-based therapy for medical conditions with deficient histone acylation.
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Affiliation(s)
- Kezhi Yan
- Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Justine Rousseau
- Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Quebec H3T 1C5, Canada
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Texas Children’s Hospital, 6701 Fannin Street, Houston, TX 77030, USA
| | - Laura A. Cross
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Katherine E. Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Cynthia Forster Gibson
- Trillium Health Partners, Credit Valley Hospital, Genetics Program, 2200 Eglinton Ave. W, Mississauga, Ontario L5M 2N1, Canada
| | - Anne Goverde
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Kendra L. Engleman
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Hannah Verdin
- Center for Medical Genetics, Ghent University and Ghent University Hospital, C. Heymanslaan 10, B-9000 Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, C. Heymanslaan 10, B-9000 Ghent, Belgium
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Texas Children’s Hospital, 6701 Fannin Street, Houston, TX 77030, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Gary A. Bellus
- Clinical Genetics and Genomic Medicine, Geisinger, 100 N. Academy Ave., Danville, PA 17822, USA
| | - Monisa D. Wagner
- Autism and Developmental Medicine Institute, Geisinger, 120 Hamm Dr., Lewisburg, PA 17837, USA
| | - Rebecca J. Hale
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Natacha Esber
- KAT6A Foundation, 3 Louise Dr., West Nyack, NY 10994, USA
| | - Alan F. Riley
- Texas Children’s Hospital, 6651 Main Street Legacy Tower, 21st Floor Houston, TX 77030, USA
| | | | - Megan T. Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | | | - Roy Eyal
- Kaiser Oakland Medical Center 3600 Broadway, Oakland, CA 94611, USA
| | - Meagan K. Hainlen
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | | | - Hillary M. Porter
- Department of Genetics and Metabolism, Rare Disease Institute, Children’s National Hospital, 111 Michigan Avenue NW, Washington, DC 20010, USA
| | | | - Andrea M. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Texas Children’s Hospital, 6701 Fannin Street, Houston, TX 77030, USA
| | - Juliann Savatt
- Autism and Developmental Medicine Institute, Geisinger, 120 Hamm Dr., Lewisburg, PA 17837, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine and Department of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108, USA
- Faculty of Medicine, University of Missouri Kansas City, Kansas City, MO 64110, USA
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University and Ghent University Hospital, C. Heymanslaan 10, B-9000 Ghent, Belgium
| | - Philippe M. Campeau
- Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Quebec H3T 1C5, Canada
- Corresponding author. (P.M.C.); (X.-J.Y.)
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada
- Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
- McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
- Corresponding author. (P.M.C.); (X.-J.Y.)
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10
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Thiffault I, Cadieux-Dion M, Farrow E, Caylor R, Miller N, Soden S, Saunders C. On the verge of diagnosis: Detection, reporting, and investigation of de novo variants in novel genes identified by clinical sequencing. Hum Mutat 2019; 39:1505-1516. [PMID: 30311385 DOI: 10.1002/humu.23646] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/16/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022]
Abstract
The variable evidence supporting gene-disease associations contributes to the difficulty of accurate variant reporting in a clinical setting. An evidence-based scoring system for evaluating the clinical validity of gene-disease associations, proposed by ClinGen, considers experimental as well as genetic evidence. De novo variants are heavily weighted, given the overall rarity in the genome and their contribution to human disease, however they are reported as "genes of unknown significance" in our center when there is insufficient evidence for the gene-disease assertion. We report a collection of 21 de novo variants in genes of unknown clinical significance ascertained via clinical testing, of which eight of 21 (38%) are predicted to cause loss of function. These genes were subjected to ClinGen scoring to assess the strength of gene-disease relationships. Using a cutoff for moderate high or strong, 10 of 21 genes now have sufficient evidence to qualify as likely pathogenic or pathogenic variants. Sharing such cases with phenotypic data is imperative to strengthen available genetic evidence to ultimately upgrade clinical validity classifications and facilitate accurate molecular diagnosis.
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Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri
| | - Raymond Caylor
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Sarah Soden
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, Missouri
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
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11
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Diets IJ, van der Donk R, Baltrunaite K, Waanders E, Reijnders MRF, Dingemans AJM, Pfundt R, Vulto-van Silfhout AT, Wiel L, Gilissen C, Thevenon J, Perrin L, Afenjar A, Nava C, Keren B, Bartz S, Peri B, Beunders G, Verbeek N, van Gassen K, Thiffault I, Cadieux-Dion M, Huerta-Saenz L, Wagner M, Konstantopoulou V, Vodopiutz J, Griese M, Boel A, Callewaert B, Brunner HG, Kleefstra T, Hoogerbrugge N, de Vries BBA, Hwa V, Dauber A, Hehir-Kwa JY, Kuiper RP, Jongmans MCJ. De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism. Am J Hum Genet 2019; 104:758-766. [PMID: 30929739 PMCID: PMC6451728 DOI: 10.1016/j.ajhg.2019.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 02/21/2019] [Indexed: 01/17/2023] Open
Abstract
By using exome sequencing and a gene matching approach, we identified de novo and inherited pathogenic variants in KDM3B in 14 unrelated individuals and three affected parents with varying degrees of intellectual disability (ID) or developmental delay (DD) and short stature. The individuals share additional phenotypic features that include feeding difficulties in infancy, joint hypermobility, and characteristic facial features such as a wide mouth, a pointed chin, long ears, and a low columella. Notably, two individuals developed cancer, acute myeloid leukemia and Hodgkin lymphoma, in childhood. KDM3B encodes for a histone demethylase and is involved in H3K9 demethylation, a crucial part of chromatin modification required for transcriptional regulation. We identified missense and truncating variants, suggesting that KDM3B haploinsufficiency is the underlying mechanism for this syndrome. By using a hybrid facial-recognition model, we show that individuals with a pathogenic variant in KDM3B have a facial gestalt, and that they show significant facial similarity compared to control individuals with ID. In conclusion, pathogenic variants in KDM3B cause a syndrome characterized by ID, short stature, and facial dysmorphism.
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Affiliation(s)
- Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Roos van der Donk
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Kristina Baltrunaite
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Esmé Waanders
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, 6229HX Maastricht, the Netherlands
| | - Alexander J M Dingemans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | | | - Laurens Wiel
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France; Equipe Génétique des Anomalies du Développement, Université de Bourgogne-France Comté, 21070 Dijon, France
| | - Laurence Perrin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, Centre Hospitalier Universitaire de Dijon, 21079 Dijon, France
| | - Alexandra Afenjar
- APHP, Département de Génétique et Embryologie Médicale, Centre de Référence Déficiences Intellectuelles de Causes Rares, GRC n°19, ConCer-LD, Hôpital Armand Trousseau, 75012 Paris, France
| | - Caroline Nava
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France; Sorbonne Universités, Institut du Cerveau et de la Moelle épinière, ICM, Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique UMR 7225, 75013, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitié-Salpêtrière, Département de Génétique, 75013, Paris, France
| | - Sarah Bartz
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Bethany Peri
- Division of Endocrinology, Children's Hospital of Colorado, Aurora, CO 80045, USA
| | - Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, 1081HV Amsterdam, the Netherlands
| | - Nienke Verbeek
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; University of Missouri, Kansas City School of Medicine, Kansas City, MO 66211, USA
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 66211, USA
| | - Lina Huerta-Saenz
- Children's Mercy Hospital, Kansas City, MO 66211, USA; Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics, Penn State Hershey Children's Hospital, Hershey, PA 17033, USA
| | - Matias Wagner
- Institute of Human Genetics, Technische Universität München, 80333 Munich, Germany; Institute for Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute for Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Vassiliki Konstantopoulou
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Matthias Griese
- Dr. von Hauner Children's Hospital, Division of Pediatric Pneumology, University Hospital Munich, German Center for Lung Research, 80333 Munich, Germany
| | - Annekatrien Boel
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202AZ Maastricht, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Vivian Hwa
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Andrew Dauber
- Division of Endocrinology, Cincinnati Center for Growth Disorders, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Endocrinology, Children's National Health System, Washington, DC 20010, USA
| | - Jayne Y Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands
| | - Marjolijn C J Jongmans
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584CS Utrecht, the Netherlands; Department of Genetics, University Medical Center Utrecht, 3508AB Utrecht, the Netherlands.
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12
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Paradis C, Cadieux-Dion M, Meloche C, Gravel M, Paradis J, Des Roches A, Leclerc G, Cossette P, Begin P. TREX-1-Related Disease Associated with the Presence of Cryofibrinogenemia. J Clin Immunol 2019; 39:118-125. [DOI: 10.1007/s10875-018-0584-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
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13
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Guissart C, Latypova X, Rollier P, Khan TN, Stamberger H, McWalter K, Cho MT, Kjaergaard S, Weckhuysen S, Lesca G, Besnard T, Õunap K, Schema L, Chiocchetti AG, McDonald M, de Bellescize J, Vincent M, Van Esch H, Sattler S, Forghani I, Thiffault I, Freitag CM, Barbouth DS, Cadieux-Dion M, Willaert R, Guillen Sacoto MJ, Safina NP, Dubourg C, Grote L, Carré W, Saunders C, Pajusalu S, Farrow E, Boland A, Karlowicz DH, Deleuze JF, Wojcik MH, Pressman R, Isidor B, Vogels A, Van Paesschen W, Al-Gazali L, Al Shamsi AM, Claustres M, Pujol A, Sanders SJ, Rivier F, Leboucq N, Cogné B, Sasorith S, Sanlaville D, Retterer K, Odent S, Katsanis N, Bézieau S, Koenig M, Davis EE, Pasquier L, Küry S. Dual Molecular Effects of Dominant RORA Mutations Cause Two Variants of Syndromic Intellectual Disability with Either Autism or Cerebellar Ataxia. Am J Hum Genet 2018; 102:744-759. [PMID: 29656859 DOI: 10.1016/j.ajhg.2018.02.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/26/2018] [Indexed: 01/25/2023] Open
Abstract
RORα, the RAR-related orphan nuclear receptor alpha, is essential for cerebellar development. The spontaneous mutant mouse staggerer, with an ataxic gait caused by neurodegeneration of cerebellar Purkinje cells, was discovered two decades ago to result from homozygous intragenic Rora deletions. However, RORA mutations were hitherto undocumented in humans. Through a multi-centric collaboration, we identified three copy-number variant deletions (two de novo and one dominantly inherited in three generations), one de novo disrupting duplication, and nine de novo point mutations (three truncating, one canonical splice site, and five missense mutations) involving RORA in 16 individuals from 13 families with variable neurodevelopmental delay and intellectual disability (ID)-associated autistic features, cerebellar ataxia, and epilepsy. Consistent with the human and mouse data, disruption of the D. rerio ortholog, roraa, causes significant reduction in the size of the developing cerebellum. Systematic in vivo complementation studies showed that, whereas wild-type human RORA mRNA could complement the cerebellar pathology, missense variants had two distinct pathogenic mechanisms of either haploinsufficiency or a dominant toxic effect according to their localization in the ligand-binding or DNA-binding domains, respectively. This dichotomous direction of effect is likely relevant to the phenotype in humans: individuals with loss-of-function variants leading to haploinsufficiency show ID with autistic features, while individuals with de novo dominant toxic variants present with ID, ataxia, and cerebellar atrophy. Our combined genetic and functional data highlight the complex mutational landscape at the human RORA locus and suggest that dual mutational effects likely determine phenotypic outcome.
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Affiliation(s)
- Claire Guissart
- EA7402 Institut Universitaire de Recherche Clinique, and Laboratoire de Génétique Moléculaire, CHU and Université de Montpellier, 34093 Montpellier, France
| | - Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Paul Rollier
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre de référence anomalies du développement CLAD-Ouest, CHU Rennes, 35203 Rennes, France
| | - Tahir N Khan
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Hannah Stamberger
- Division of Neurology, University Hospital Antwerp (UZA), 2610 Antwerp, Belgium; Neurogenetics Group, Center for Molecular Neurology, VIB, 2650 Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2650 Antwerp, Belgium
| | | | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Susanne Kjaergaard
- Chromosome Laboratory, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Sarah Weckhuysen
- Division of Neurology, University Hospital Antwerp (UZA), 2610 Antwerp, Belgium; Neurogenetics Group, Center for Molecular Neurology, VIB, 2650 Antwerp, Belgium; Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, 2650 Antwerp, Belgium
| | - Gaetan Lesca
- Service de génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France; INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, 2 L.Puusepa street, Tartu 51014, Estonia
| | - Lynn Schema
- University of Minnesota-Fairview, Minneapolis, MN 55454, USA
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, JW Goethe University Frankfurt, Deutschordenstraße 50, Frankfurt am Main 60528, Germany
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Julitta de Bellescize
- Epilepsy, Sleep and Pediatric Neurophysiology Department, Hospices Civils, Lyon, 69677 Bron, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Irman Forghani
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB, room 359 (M-860), Miami, FL 33136, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA; University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, JW Goethe University Frankfurt, Deutschordenstraße 50, Frankfurt am Main 60528, Germany
| | - Deborah Sara Barbouth
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB, room 359 (M-860), Miami, FL 33136, USA
| | - Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | | | | | - Nicole P Safina
- University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA; Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire & Génomique, CHU de Rennes, 35033 Rennes, France
| | - Lauren Grote
- University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA; Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Wilfrid Carré
- Laboratoire de Génétique Moléculaire & Génomique, CHU de Rennes, 35033 Rennes, France
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA; University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108, USA
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, 2 L.Puusepa street, Tartu 51014, Estonia
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA; University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, DRF, CEA, Evry, France
| | - Danielle Hays Karlowicz
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, DRF, CEA, Evry, France
| | - Monica H Wojcik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rena Pressman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, 1501 NW 10th Avenue, BRB, room 359 (M-860), Miami, FL 33136, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Annick Vogels
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Wim Van Paesschen
- Department of Neurology, University Hospitals Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
| | | | - Mireille Claustres
- EA7402 Institut Universitaire de Recherche Clinique, and Laboratoire de Génétique Moléculaire, CHU and Université de Montpellier, 34093 Montpellier, France
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, IDIBELL, Gran Via, 199, L'Hospitalet de Llobregat, 08908 Barcelona, and CIBERER U759, Center for Biomedical Research on Rare Diseases, 08908 Barcelona, Spain, Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - François Rivier
- Department of Neuropaediatrics and CR Maladies Neuromusculaires, CHU Montpellier, PhyMedExp, INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Nicolas Leboucq
- Neuroradiologie, CHU de Montpellier, 34090 Montpellier, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Souphatta Sasorith
- EA7402 Institut Universitaire de Recherche Clinique, and Laboratoire de Génétique Moléculaire, CHU and Université de Montpellier, 34093 Montpellier, France
| | - Damien Sanlaville
- Service de génétique, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France; INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Kyle Retterer
- GeneDx, 207 Perry Parkway, Gaithersburg, MD 20877, USA
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre de référence anomalies du développement CLAD-Ouest, CHU Rennes, 35203 Rennes, France; CNRS UMR 6290, Université de Rennes, 2 Avenue du Professeur Léon Bernard, 35043 Rennes, France
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA
| | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France
| | - Michel Koenig
- EA7402 Institut Universitaire de Recherche Clinique, and Laboratoire de Génétique Moléculaire, CHU and Université de Montpellier, 34093 Montpellier, France
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre Référence "Déficiences Intellectuelles de causes rares" (CRDI), Centre de référence anomalies du développement CLAD-Ouest, CHU Rennes, 35203 Rennes, France
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France; l'institut du thorax, INSERM, CNRS, UNIV Nantes, 44007 Nantes, France.
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14
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Monlong J, Girard SL, Meloche C, Cadieux-Dion M, Andrade DM, Lafreniere RG, Gravel M, Spiegelman D, Dionne-Laporte A, Boelman C, Hamdan FF, Michaud JL, Rouleau G, Minassian BA, Bourque G, Cossette P. Global characterization of copy number variants in epilepsy patients from whole genome sequencing. PLoS Genet 2018; 14:e1007285. [PMID: 29649218 PMCID: PMC5978987 DOI: 10.1371/journal.pgen.1007285] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/24/2018] [Accepted: 03/04/2018] [Indexed: 12/17/2022] Open
Abstract
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.
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Affiliation(s)
- Jean Monlong
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
| | - Simon L. Girard
- Department of Human Genetics, McGill University, Montréal, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Caroline Meloche
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Maxime Cadieux-Dion
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, Missouri, United States of America
| | - Danielle M. Andrade
- Epilepsy Genetics Program, Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Ron G. Lafreniere
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Micheline Gravel
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Cyrus Boelman
- Division of Neurology, BC Children’s Hospital, Vancouver, Canada
| | | | | | - Guy Rouleau
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
- McGill University and Génome Québec Innovation Center, Montréal, Canada
- * E-mail: (GB); (PC)
| | - Patrick Cossette
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- * E-mail: (GB); (PC)
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15
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Cadieux-Dion M, Safina NP, Engleman K, Saunders C, Repnikova E, Raje N, Canty K, Farrow E, Miller N, Zellmer L, Thiffault I. Novel heterozygous pathogenic variants in CHUK in a patient with AEC-like phenotype, immune deficiencies and 1q21.1 microdeletion syndrome: a case report. BMC Med Genet 2018. [PMID: 29523099 PMCID: PMC5845372 DOI: 10.1186/s12881-018-0556-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Ectodermal dysplasias (ED) are a group of diseases that affects the development or function of the teeth, hair, nails and exocrine and sebaceous glands. One type of ED, ankyloblepharon-ectodermal defects-cleft lip/palate syndrome (AEC or Hay-Wells syndrome), is an autosomal dominant disease characterized by the presence of skin erosions affecting the palms, soles and scalp. Other clinical manifestations include ankyloblepharon filiforme adnatum, cleft lip, cleft palate, craniofacial abnormalities and ectodermal defects such as sparse wiry hair, nail changes, dental changes, and subjective hypohydrosis. CASE PRESENTATION We describe a patient presenting clinical features reminiscent of AEC syndrome in addition to recurrent infections suggestive of immune deficiency. Genetic testing for TP63, IRF6 and RIPK4 was negative. Microarray analysis revealed a 2 MB deletion on chromosome 1 (1q21.1q21.2). Clinical exome sequencing uncovered compound heterozygous variants in CHUK; a maternally-inherited frameshift variant (c.1365del, p.Arg457Aspfs*6) and a de novo missense variant (c.1388C > A, p.Thr463Lys) on the paternal allele. CONCLUSIONS To our knowledge, this is the fourth family reported with CHUK-deficiency and the second patient with immune abnormalities. This is the first case of CHUK-deficiency with compound heterozygous pathogenic variants, including one variant that arose de novo. In comparison to cases found in the literature, this patient demonstrates a less severe phenotype than previously described.
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Affiliation(s)
- Maxime Cadieux-Dion
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.
| | - Nicole P Safina
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA.,University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA
| | - Kendra Engleman
- Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, USA.,University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA
| | - Elena Repnikova
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Nikita Raje
- Pediatric Allergy, Asthma and Immunology Clinic, Children's Mercy Hospitals, Kansas City, MO, USA
| | - Kristi Canty
- Dermatology Clinic, Children's Mercy Hospitals, Kansas City, MO, USA
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Lee Zellmer
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA.,Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, MO, USA
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16
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Hamdan FF, Myers CT, Cossette P, Lemay P, Spiegelman D, Laporte AD, Nassif C, Diallo O, Monlong J, Cadieux-Dion M, Dobrzeniecka S, Meloche C, Retterer K, Cho MT, Rosenfeld JA, Bi W, Massicotte C, Miguet M, Brunga L, Regan BM, Mo K, Tam C, Schneider A, Hollingsworth G, FitzPatrick DR, Donaldson A, Canham N, Blair E, Kerr B, Fry AE, Thomas RH, Shelagh J, Hurst JA, Brittain H, Blyth M, Lebel RR, Gerkes EH, Davis-Keppen L, Stein Q, Chung WK, Dorison SJ, Benke PJ, Fassi E, Corsten-Janssen N, Kamsteeg EJ, Mau-Them FT, Bruel AL, Verloes A, Õunap K, Wojcik MH, Albert DV, Venkateswaran S, Ware T, Jones D, Liu YC, Mohammad SS, Bizargity P, Bacino CA, Leuzzi V, Martinelli S, Dallapiccola B, Tartaglia M, Blumkin L, Wierenga KJ, Purcarin G, O’Byrne JJ, Stockler S, Lehman A, Keren B, Nougues MC, Mignot C, Auvin S, Nava C, Hiatt SM, Bebin M, Shao Y, Scaglia F, Lalani SR, Frye RE, Jarjour IT, Jacques S, Boucher RM, Riou E, Srour M, Carmant L, Lortie A, Major P, Diadori P, Dubeau F, D’Anjou G, Bourque G, Berkovic SF, Sadleir LG, Campeau PM, Kibar Z, Lafrenière RG, Girard SL, Mercimek-Mahmutoglu S, Boelman C, Rouleau GA, Scheffer IE, Mefford HC, Andrade DM, Rossignol E, Minassian BA, Michaud JL, Michaud JL. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Am J Hum Genet 2017; 101:664-685. [PMID: 29100083 DOI: 10.1016/j.ajhg.2017.09.008] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/11/2017] [Indexed: 12/30/2022] Open
Abstract
Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques L Michaud
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada; Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada; Department of Pediatrics, Université de Montréal, Montreal, QC H3T1C5, Canada.
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17
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Berkovic SF, Staropoli JF, Carpenter S, Oliver KL, Kmoch S, Anderson GW, Damiano JA, Hildebrand MS, Sims KB, Cotman SL, Bahlo M, Smith KR, Cadieux-Dion M, Cossette P, Jedličková I, Přistoupilová A, Mole SE. Diagnosis and misdiagnosis of adult neuronal ceroid lipofuscinosis (Kufs disease). Neurology 2016; 87:579-84. [PMID: 27412140 DOI: 10.1212/wnl.0000000000002943] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 04/29/2016] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE To critically re-evaluate cases diagnosed as adult neuronal ceroid lipofuscinosis (ANCL) in order to aid clinicopathologic diagnosis as a route to further gene discovery. METHODS Through establishment of an international consortium we pooled 47 unsolved cases regarded by referring centers as ANCL. Clinical and neuropathologic experts within the Consortium established diagnostic criteria for ANCL based on the literature to assess each case. A panel of 3 neuropathologists independently reviewed source pathologic data. Cases were given a final clinicopathologic classification of definite ANCL, probable ANCL, possible ANCL, or not ANCL. RESULTS Of the 47 cases, only 16 fulfilled the Consortium's criteria of ANCL (5 definite, 2 probable, 9 possible). Definitive alternate diagnoses were made in 10, including Huntington disease, early-onset Alzheimer disease, Niemann-Pick disease, neuroserpinopathy, prion disease, and neurodegeneration with brain iron accumulation. Six cases had features suggesting an alternate diagnosis, but no specific condition was identified; in 15, the data were inadequate for classification. Misinterpretation of normal lipofuscin as abnormal storage material was the commonest cause of misdiagnosis. CONCLUSIONS Diagnosis of ANCL remains challenging; expert pathologic analysis and recent molecular genetic advances revealed misdiagnoses in >1/3 of cases. We now have a refined group of cases that will facilitate identification of new causative genes.
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Affiliation(s)
- Samuel F Berkovic
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK.
| | - John F Staropoli
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Stirling Carpenter
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Karen L Oliver
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Stanislav Kmoch
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Glenn W Anderson
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - John A Damiano
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Michael S Hildebrand
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Katherine B Sims
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Susan L Cotman
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Melanie Bahlo
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Katherine R Smith
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Maxime Cadieux-Dion
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Patrick Cossette
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Ivana Jedličková
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
| | - Anna Přistoupilová
- From the Epilepsy Research Centre, Department of Medicine (S.F.B., K.L.O., J.A.D., M.S.H.), University of Melbourne, Austin Health, Heidelberg, Australia; Biogen, Inc. (J.F.S.), Cambridge, MA; Department of Pathology (S.C.), Centro Hospitalar São João, Porto, Portugal; Institute of Inherited Metabolic Disorders (S.K., I.J., A.P.), First Faculty of Medicine, Charles University in Prague; General University Hospital in Prague (S.K.), Czech Republic; Great Ormond Street Hospital for Children NHS Foundation Trust (G.W.A.), London, UK; Center for Human Genetic Research and Department of Neurology (K.B.S., S.L.C.), Harvard Medical School, Massachusetts General Hospital, Boston; Population Health and Immunity Division (M.B., K.R.S.), The Walter and Eliza Hall Institute of Medical Research; Departments of Mathematics and Statistics and Medical Biology (M.B.), University of Melbourne, Australia; Centre de Recherche du Centre Hospitalier de l'Université de Montréal (M.C.-D., P.C.), University of Montreal, Canada; and MRC Laboratory for Cell Biology (S.E.M.), Department of Genetics, Evolution & Environment and UCL Institute of Child Health, University College London, UK
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Cadieux-Dion M, Turcotte-Gauthier M, Noreau A, Martin C, Meloche C, Gravel M, Drouin CA, Rouleau GA, Nguyen DK, Cossette P. Expanding the clinical phenotype associated with ELOVL4 mutation: study of a large French-Canadian family with autosomal dominant spinocerebellar ataxia and erythrokeratodermia. JAMA Neurol 2014; 71:470-5. [PMID: 24566826 DOI: 10.1001/jamaneurol.2013.6337] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The autosomal dominant spinocerebellar ataxias (SCAs) are a complex group of neurodegenerative disorders with significant genetic heterogeneity. Despite the identification of 20 SCA genes, the cause of the disorder in a significant proportion of families with SCA remains unexplained. In 1972, a French-Canadian family segregating a combination of SCA and erythrokeratodermia variabilis (EKV) in an autosomal dominant fashion was described. OBJECTIVE To map and identify the causative gene in this large family with SCA and EKV using a combination of linkage analysis and whole-exome sequencing. DESIGN, SETTING, AND PARTICIPANTS A total of 32 individuals from the family have undergone complete neurologic and dermatologic examinations. MAIN OUTCOMES AND MEASURES Mutations in ELOVL4 have been reported in families with macular degeneration. Recently, homozygous mutations were found in patients with ichthyosis, spastic paraplegia, and severe neurodevelopmental defects. In the present study, we report on a heterozygote mutation in ELOVL4 in affected individuals from the family with SCA and EKV. The mutation segregates with a milder phenotype consisting of early-onset patches of erythema and hyperkeratosis, as well as SCA manifesting in the fourth or fifth decade of life. RESULTS We describe the mapping and the identification of a c.504G>C transversion in ELOVL4 resulting in the p.L168F substitution. We also provide clinical characterization of the phenotypes in 19 mutation carriers. CONCLUSIONS AND RELEVANCE We report, to our knowledge, the first mutation in ELOVL4 that is associated with SCA and EKV. This gene encodes a member of the elongase family, which is responsible for the elongation of very long-chain fatty acids (at least 26 carbons). These fatty acids participate in a wide variety of physiological functions, including skin barrier formation and peroxisome β-oxidation. Overall, these results provide additional insight into the pathogenesis of these complex neurodegenerative disorders.
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Affiliation(s)
- Maxime Cadieux-Dion
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Maude Turcotte-Gauthier
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Anne Noreau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Caroline Martin
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Caroline Meloche
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Micheline Gravel
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | | | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Dang Khoa Nguyen
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
| | - Patrick Cossette
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Notre Dame Hospital, University of Montreal, Montreal, Quebec, Canada
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Pickles S, Cadieux-Dion M, Alvarez JI, Lécuyer MA, Peyrard SL, Destroismaisons L, St-Onge L, Terouz S, Cossette P, Prat A, Vande Velde C. Endo-MitoEGFP mice: a novel transgenic mouse with fluorescently marked mitochondria in microvascular endothelial cells. PLoS One 2013; 8:e74603. [PMID: 24019971 PMCID: PMC3760848 DOI: 10.1371/journal.pone.0074603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 08/05/2013] [Indexed: 12/18/2022] Open
Abstract
Blood vessel-specific fluorescent transgenic mice are excellent tools to study the development of the vasculature and angiogenic processes. There is growing interest in the biological processes relevant to endothelial cells but limited tools exist to selectively evaluate subcellular functions of this cell type in vivo. Here, we report a novel transgenic animal model that expresses mitochondrially targeted enhanced green fluorescent protein (EGFP) via the Hb9 promoter, a homeobox transcription factor with limited known involvement in the vasculature. Random integration of the transgene, containing the entire mouse Hb9 promoter, was found to be expressed in a variety of vascularised tissues. Further inspection revealed that Mito-EGFP localizes to the endothelial cells (ECs) of a subset of microvascular blood vessels, especially in the central nervous system (CNS), heart, spleen, thymus, lymph nodes and skin. We demonstrate the utility of this novel transgenic mouse, named Endo-MitoEGFP, in the detection, imaging, and isolation of microvascular ECs and evaluation of EC mitochondrial function isolated from adult animals. These transgenic mice will be useful to studies of ECs in development, physiology, and pathology.
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Affiliation(s)
- Sarah Pickles
- Centre d'Excellence en Neuromique de l'Université de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Université de Montréal, Montréal, Quebec, Canada ; Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
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20
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Corradi A, Fadda M, Piton A, Patry L, Marte A, Rossi P, Cadieux-Dion M, Gauthier J, Lapointe L, Mottron L, Valtorta F, Rouleau GA, Fassio A, Benfenati F, Cossette P. SYN2 is an autism predisposing gene: loss-of-function mutations alter synaptic vesicle cycling and axon outgrowth. Hum Mol Genet 2013; 23:90-103. [PMID: 23956174 PMCID: PMC3857945 DOI: 10.1093/hmg/ddt401] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An increasing number of genes predisposing to autism spectrum disorders (ASDs) has been identified, many of which are implicated in synaptic function. This 'synaptic autism pathway' notably includes disruption of SYN1 that is associated with epilepsy, autism and abnormal behavior in both human and mice models. Synapsins constitute a multigene family of neuron-specific phosphoproteins (SYN1-3) present in the majority of synapses where they are implicated in the regulation of neurotransmitter release and synaptogenesis. Synapsins I and II, the major Syn isoforms in the adult brain, display partially overlapping functions and defects in both isoforms are associated with epilepsy and autistic-like behavior in mice. In this study, we show that nonsense (A94fs199X) and missense (Y236S and G464R) mutations in SYN2 are associated with ASD in humans. The phenotype is apparent in males. Female carriers of SYN2 mutations are unaffected, suggesting that SYN2 is another example of autosomal sex-limited expression in ASD. When expressed in SYN2 knockout neurons, wild-type human Syn II fully rescues the SYN2 knockout phenotype, whereas the nonsense mutant is not expressed and the missense mutants are virtually unable to modify the SYN2 knockout phenotype. These results identify for the first time SYN2 as a novel predisposing gene for ASD and strengthen the hypothesis that a disturbance of synaptic homeostasis underlies ASD.
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Affiliation(s)
- Anna Corradi
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV 3, Genova 16132, Italy
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21
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Cadieux-Dion M, Andermann E, Lachance-Touchette P, Ansorge O, Meloche C, Barnabé A, Kuzniecky RI, Andermann F, Faught E, Leonberg S, Damiano JA, Berkovic SF, Rouleau GA, Cossette P. Recurrent mutations inDNAJC5cause autosomal dominant Kufs disease. Clin Genet 2012; 83:571-5. [DOI: 10.1111/cge.12020] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/12/2012] [Accepted: 09/12/2012] [Indexed: 01/23/2023]
Affiliation(s)
- M Cadieux-Dion
- CHUM Research Center; University of Montreal; Montreal; Quebec; Canada
| | - E Andermann
- Montreal Neurological Institute; McGill University; Montreal; Quebec; Canada
| | | | - O Ansorge
- Department of Neuropathology; John Radcliffe Hospital; Oxford; UK
| | - C Meloche
- CHUM Research Center; University of Montreal; Montreal; Quebec; Canada
| | - A Barnabé
- Montreal Neurological Institute; McGill University; Montreal; Quebec; Canada
| | - RI Kuzniecky
- Department of Neurology; Langone Medical Center, New York University; New York; NY; USA
| | - F Andermann
- Montreal Neurological Institute; McGill University; Montreal; Quebec; Canada
| | - E Faught
- Emory University School of Medicine; Atlanta; GA; USA
| | - S Leonberg
- Rutgers Medical School and Cooper Hospital/University Medical Center; Camden; NJ; USA
| | - JA Damiano
- Epilepsy Research Center; University of Melbourne, Austin Health; Heidelberg; VIC; 3084; Australia
| | - SF Berkovic
- Epilepsy Research Center; University of Melbourne, Austin Health; Heidelberg; VIC; 3084; Australia
| | - GA Rouleau
- CHUM Research Center; University of Montreal; Montreal; Quebec; Canada
| | - P Cossette
- CHUM Research Center; University of Montreal; Montreal; Quebec; Canada
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