Publications by authors named "Kristin D Kernohan"

39 Publications

Whole genome sequencing reveals biallelic PLA2G6 mutations in siblings with cerebellar atrophy and cap myopathy.

Clin Genet 2021 Feb 11. Epub 2021 Feb 11.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1111/cge.13935DOI Listing
February 2021

Histone H3.3 beyond cancer: Germline mutations in cause a previously unidentified neurodegenerative disorder in 46 patients.

Authors:
Laura Bryant Dong Li Samuel G Cox Dylan Marchione Evan F Joiner Khadija Wilson Kevin Janssen Pearl Lee Michael E March Divya Nair Elliott Sherr Brieana Fregeau Klaas J Wierenga Alexandrea Wadley Grazia M S Mancini Nina Powell-Hamilton Jiddeke van de Kamp Theresa Grebe John Dean Alison Ross Heather P Crawford Zoe Powis Megan T Cho Marcia C Willing Linda Manwaring Rachel Schot Caroline Nava Alexandra Afenjar Davor Lessel Matias Wagner Thomas Klopstock Juliane Winkelmann Claudia B Catarino Kyle Retterer Jane L Schuette Jeffrey W Innis Amy Pizzino Sabine Lüttgen Jonas Denecke Tim M Strom Kristin G Monaghan Zuo-Fei Yuan Holly Dubbs Renee Bend Jennifer A Lee Michael J Lyons Julia Hoefele Roman Günthner Heiko Reutter Boris Keren Kelly Radtke Omar Sherbini Cameron Mrokse Katherine L Helbig Sylvie Odent Benjamin Cogne Sandra Mercier Stephane Bezieau Thomas Besnard Sebastien Kury Richard Redon Karit Reinson Monica H Wojcik Katrin Õunap Pilvi Ilves A Micheil Innes Kristin D Kernohan Gregory Costain M Stephen Meyn David Chitayat Elaine Zackai Anna Lehman Hilary Kitson Martin G Martin Julian A Martinez-Agosto Stan F Nelson Christina G S Palmer Jeanette C Papp Neil H Parker Janet S Sinsheimer Eric Vilain Jijun Wan Amanda J Yoon Allison Zheng Elise Brimble Giovanni Battista Ferrero Francesca Clementina Radio Diana Carli Sabina Barresi Alfredo Brusco Marco Tartaglia Jennifer Muncy Thomas Luis Umana Marjan M Weiss Garrett Gotway K E Stuurman Michelle L Thompson Kirsty McWalter Constance T R M Stumpel Servi J C Stevens Alexander P A Stegmann Kristian Tveten Arve Vøllo Trine Prescott Christina Fagerberg Lone Walentin Laulund Martin J Larsen Melissa Byler Robert Roger Lebel Anna C Hurst Joy Dean Samantha A Schrier Vergano Jennifer Norman Saadet Mercimek-Andrews Juanita Neira Margot I Van Allen Nicola Longo Elizabeth Sellars Raymond J Louie Sara S Cathey Elly Brokamp Delphine Heron Molly Snyder Adeline Vanderver Celeste Simon Xavier de la Cruz Natália Padilla J Gage Crump Wendy Chung Benjamin Garcia Hakon H Hakonarson Elizabeth J Bhoj

Sci Adv 2020 Dec 2;6(49). Epub 2020 Dec 2.

Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A () or with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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http://dx.doi.org/10.1126/sciadv.abc9207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821880PMC
December 2020

Newborn Screening for Spinal Muscular Atrophy: Ontario Testing and Follow-up Recommendations.

Can J Neurol Sci 2020 Oct 16:1-8. Epub 2020 Oct 16.

Children's Hospital of Eastern Ontario Research Institute, Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.

Background: Spinal muscular atrophy (SMA) is characterized by the progressive loss of motor neurons causing muscle atrophy and weakness. Nusinersen, the first effective SMA therapy was approved by Health Canada in June 2017 and has been added to the provincial formulary of all but one Canadian province. Access to this effective therapy has triggered the inclusion of SMA in an increasing number of Newborn Screening (NBS) programs. However, the range of disease-modifying SMN2 gene copy numbers encountered in survival motor neuron 1 (SMN1)-null individuals means that neither screen-positive definition nor resulting treatment decisions can be determined by SMN1 genotype alone. We outline an approach to this challenge, one that specifically addresses the case of SMA newborns with four copies of SMN2.

Objectives: To develop a standardized post-referral evaluation pathway for babies with a positive SMA NBS screen result.

Methods: An SMA NBS pilot trial in Ontario using first-tier MassARRAY and second-tier multi-ligand probe amplification (MLPA) was launched in January 2020. Prior to this, Ontario pediatric neuromuscular disease and NBS experts met to review the evidence regarding the diagnosis and treatment of children with SMA as it pertained to NBS. A post-referral evaluation algorithm was developed, outlining timelines for patient retrieval and management.

Conclusions: Ontario's pilot NBS program has created a standardized path to facilitate early diagnosis of SMA and initiation of treatment. The goal is to provide timely access to those SMA infants in need of therapy to optimize motor function and prolong survival.
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http://dx.doi.org/10.1017/cjn.2020.229DOI Listing
October 2020

A splice variant in expands the clinical and genetic spectrum of Harel-Yoon syndrome.

Neurol Genet 2020 Aug 3;6(4):e452. Epub 2020 Jun 3.

Division of Neurology (I.H., H.J.M.), Children's Hospital of Eastern Ontario, Children's Hospital of Eastern Ontario Research Institute (H.J.M., Y.I., D.A.D.), University of Ottawa; Newborn Screen Ontario (K.D.K.), Ottawa; Department of Clinical Genetics (J.L., D.A.D.), and Division of Metabolics (M.A.L.), Children's Hospital of Eastern Ontario, University of Ottawa.

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http://dx.doi.org/10.1212/NXG.0000000000000452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286657PMC
August 2020

Early infantile epileptic encephalopathy due to biallelic pathogenic variants in PIGQ: Report of seven new subjects and review of the literature.

J Inherit Metab Dis 2020 11 3;43(6):1321-1332. Epub 2020 Aug 3.

Research Center, CHU Sainte Justine, University of Montreal, Montreal, Quebec, Canada.

We investigated seven children from six families to expand the phenotypic spectrum associated with an early infantile epileptic encephalopathy caused by biallelic pathogenic variants in the phosphatidylinositol glycan anchor biosynthesis class Q (PIGQ) gene. The affected children were all identified by clinical or research exome sequencing. Clinical data, including EEGs and MRIs, was comprehensively reviewed and flow cytometry and transfection experiments were performed to investigate PIGQ function. Pathogenic biallelic PIGQ variants were associated with increased mortality. Epileptic seizures, axial hypotonia, developmental delay and multiple congenital anomalies were consistently observed. Seizure onset occurred between 2.5 months and 7 months of age and varied from treatable seizures to recurrent episodes of status epilepticus. Gastrointestinal issues were common and severe, two affected individuals had midgut volvulus requiring surgical correction. Cardiac anomalies including arrythmias were observed. Flow cytometry using granulocytes and fibroblasts from affected individuals showed reduced expression of glycosylphosphatidylinositol (GPI)-anchored proteins. Transfection of wildtype PIGQ cDNA into patient fibroblasts rescued this phenotype. We expand the phenotypic spectrum of PIGQ-related disease and provide the first functional evidence in human cells of defective GPI-anchoring due to pathogenic variants in PIGQ.
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http://dx.doi.org/10.1002/jimd.12278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7689772PMC
November 2020

New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases.

Annu Rev Genomics Hum Genet 2020 08 13;21:351-372. Epub 2020 Apr 13.

CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada; email:

Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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http://dx.doi.org/10.1146/annurev-genom-083118-015345DOI Listing
August 2020

p21 protein-activated kinase 1 is associated with severe regressive autism, and epilepsy.

Clin Genet 2019 11 13;96(5):449-455. Epub 2019 Aug 13.

Department of Pediatrics, Dalhousie University and IWK Health Centre, Halifax, Nova Scotia, Canada.

The p21-activated kinase (PAK) family of proteins function as key effectors of RHO family GTPases in mammalian cells to regulate many pathways including Ras/Raf/MEK/ERK and Wnt/β-catenin, amongst others. Here we report an individual with a novel autosomal dominant disorder characterized by severe regressive autism, intellectual disability, and epilepsy. Exome sequencing of the proband and her parents revealed a de novo variant in the PAK1 gene ([NM_001128620] c.362C>T/p.Pro121Leu). Studies in patient cells showed a clear effect on PAK1 protein function, including altered phosphorylation of targets (JNK and ERK), decreased abundance of β-catenin, and concomitant altered expression downstream of these key regulators. Our findings add PAK1 to the list of PAK proteins and kinases which when mutated cause rare genetic diseases.
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http://dx.doi.org/10.1111/cge.13618DOI Listing
November 2019

A Novel Mutation in MARS in a Patient with Charcot-Marie-Tooth Disease, Axonal, Type 2U with Congenital Onset.

J Neuromuscul Dis 2019 ;6(3):333-339

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.

Charcot-Marie-Tooth disease is a phenotypically and genetically heterogeneous group of disorders affecting both motor and sensory neurons. Exome sequencing has driven discovery of genes responsible for Charcot-Marie-Tooth disease with more than 70 genes now associated with this neuromuscular disease. The MARS gene was recently reported as the cause of Charcot-Marie-Tooth 2U, a slowly progressive axonal sensorimotor polyneuropathy with adult-onset reported in six patients. We report here a patient with a progressive, early childhood-onset, motor-predominant form of Charcot-Marie-Tooth disease. Exome sequencing identified a novel MARS variant (c.1189G>A; p.Ala397Thr) that was not present in her unaffected mother; her unaffected father was unavailable. Further studies using structural modeling and a yeast humanization assay support pathogenicity of the variant. Our study expands the phenotype of Charcot-Marie-Tooth 2U, while highlighting the utility of functional assays to evaluate variant pathogenicity.
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http://dx.doi.org/10.3233/JND-190404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889022PMC
February 2020

PDXK mutations cause polyneuropathy responsive to pyridoxal 5'-phosphate supplementation.

Ann Neurol 2019 08 1;86(2):225-240. Epub 2019 Jul 1.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.

Objective: To identify disease-causing variants in autosomal recessive axonal polyneuropathy with optic atrophy and provide targeted replacement therapy.

Methods: We performed genome-wide sequencing, homozygosity mapping, and segregation analysis for novel disease-causing gene discovery. We used circular dichroism to show secondary structure changes and isothermal titration calorimetry to investigate the impact of variants on adenosine triphosphate (ATP) binding. Pathogenicity was further supported by enzymatic assays and mass spectroscopy on recombinant protein, patient-derived fibroblasts, plasma, and erythrocytes. Response to supplementation was measured with clinical validated rating scales, electrophysiology, and biochemical quantification.

Results: We identified biallelic mutations in PDXK in 5 individuals from 2 unrelated families with primary axonal polyneuropathy and optic atrophy. The natural history of this disorder suggests that untreated, affected individuals become wheelchair-bound and blind. We identified conformational rearrangement in the mutant enzyme around the ATP-binding pocket. Low PDXK ATP binding resulted in decreased erythrocyte PDXK activity and low pyridoxal 5'-phosphate (PLP) concentrations. We rescued the clinical and biochemical profile with PLP supplementation in 1 family, improvement in power, pain, and fatigue contributing to patients regaining their ability to walk independently during the first year of PLP normalization.

Interpretation: We show that mutations in PDXK cause autosomal recessive axonal peripheral polyneuropathy leading to disease via reduced PDXK enzymatic activity and low PLP. We show that the biochemical profile can be rescued with PLP supplementation associated with clinical improvement. As B is a cofactor in diverse essential biological pathways, our findings may have direct implications for neuropathies of unknown etiology characterized by reduced PLP levels. ANN NEUROL 2019;86:225-240.
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http://dx.doi.org/10.1002/ana.25524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6772106PMC
August 2019

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

Nat Med 2019 06 3;25(6):911-919. Epub 2019 Jun 3.

Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases. This includes muscle biopsies from patients with undiagnosed rare muscle disorders, and cultured fibroblasts from patients with mitochondrial disorders. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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http://dx.doi.org/10.1038/s41591-019-0457-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634302PMC
June 2019

Neu-Laxova syndrome presenting prenatally with increased nuchal translucency and cystic hygroma: The utility of exome sequencing in deciphering the diagnosis.

Am J Med Genet A 2019 05 5;179(5):813-816. Epub 2019 Mar 5.

Regional Genetics Program, CHEO, University of Ottawa, Ottawa, Ontario, Canada.

Neu-Laxova syndrome (NLS) is a lethal autosomal recessive microcephaly syndrome associated with intrauterine growth restriction (IUGR) and multiple congenital anomalies. Clinical features include central nervous system malformations, joint contractures, ichthyosis, edema, and dysmorphic facial features. Biallelic pathogenic variants in either the PHGDH or PSAT1 genes have been shown to cause NLS. Using exome sequencing, we aimed to identify the underlying genetic diagnosis in three fetuses (from one family) with prenatal skin edema, severe IUGR, micrognathia, renal anomalies, and arthrogryposis and identified a homozygous c.1A>C (p.Met1?, NM_006623.3) variant in the PHGDH gene. Loss of the translation start codon is a novel genetic mechanism for the development of NLS. Prenatal diagnosis of NLS is challenging and few reports describe the fetal pathology. Fetal neuropathologic examination revealed: delayed brain development, congenital agenesis of the corticospinal tracts, and hypoplasia of the hippocampus, cerebellum and brainstem. Each pregnancy also showed increased nuchal translucency (NT) or cystic hygroma. While NLS is rare, it may be a cause of recurrent increased NT/cystic hygroma. This finding provides further support that cystic hygroma has many different genetic causes and that exome sequencing may shed light on the underlying genetic diagnoses in this group of prenatal patients.
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http://dx.doi.org/10.1002/ajmg.a.61076DOI Listing
May 2019

Clinical delineation of GTPBP2-associated neuro-ectodermal syndrome: Report of two new families and review of the literature.

Clin Genet 2019 05 19;95(5):601-606. Epub 2019 Mar 19.

Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

The GTPBP2 gene encodes a guanosine triphosphate (GTP)-binding protein of unknown function. Biallelic loss-of-function variants in the GTPBP2 gene have been previously reported in association with a neuro-ectodermal clinical presentation in six individuals from four unrelated families. Here, we provide detailed descriptions of three additional individuals from two unrelated families in the context of the previous literature. Both families carry nonsense variants in GTPBP2: homozygous p.(Arg470*) and compound heterozygous p.(Arg432*)/p.(Arg131*). Key features of this clinically recognizable condition include prenatal onset microcephaly, tone abnormalities, and movement disorders, epilepsy, dysmorphic features, retinal dysfunction, ectodermal dysplasia, and brain iron accumulation. Our findings suggest that some aspects of the clinical presentation appear to be age-related; brain iron accumulation may appear only after childhood, and the ectodermal findings and peripheral neuropathy are most prominent in older individuals. In addition, we present prenatal and neonatal findings as well as the first Caucasian and black African families with GTPBP2 biallelic variants. The individuals described herein provide valuable additional phenotypic information about this rare, novel, and progressive neuroectodermal condition.
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http://dx.doi.org/10.1111/cge.13523DOI Listing
May 2019

PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights.

Brain 2019 03;142(3):542-559

British Columbia Children's Hospital Research Institute, Vancouver, BC, Canada.

Biallelic pathogenic variants in PLPBP (formerly called PROSC) have recently been shown to cause a novel form of vitamin B6-dependent epilepsy, the pathophysiological basis of which is poorly understood. When left untreated, the disease can progress to status epilepticus and death in infancy. Here we present 12 previously undescribed patients and six novel pathogenic variants in PLPBP. Suspected clinical diagnoses prior to identification of PLPBP variants included mitochondrial encephalopathy (two patients), folinic acid-responsive epilepsy (one patient) and a movement disorder compatible with AADC deficiency (one patient). The encoded protein, PLPHP is believed to be crucial for B6 homeostasis. We modelled the pathogenicity of the variants and developed a clinical severity scoring system. The most severe phenotypes were associated with variants leading to loss of function of PLPBP or significantly affecting protein stability/PLP-binding. To explore the pathophysiology of this disease further, we developed the first zebrafish model of PLPHP deficiency using CRISPR/Cas9. Our model recapitulates the disease, with plpbp-/- larvae showing behavioural, biochemical, and electrophysiological signs of seizure activity by 10 days post-fertilization and early death by 16 days post-fertilization. Treatment with pyridoxine significantly improved the epileptic phenotype and extended lifespan in plpbp-/- animals. Larvae had disruptions in amino acid metabolism as well as GABA and catecholamine biosynthesis, indicating impairment of PLP-dependent enzymatic activities. Using mass spectrometry, we observed significant B6 vitamer level changes in plpbp-/- zebrafish, patient fibroblasts and PLPHP-deficient HEK293 cells. Additional studies in human cells and yeast provide the first empirical evidence that PLPHP is localized in mitochondria and may play a role in mitochondrial metabolism. These models provide new insights into disease mechanisms and can serve as a platform for drug discovery.
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http://dx.doi.org/10.1093/brain/awy346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391652PMC
March 2019

Lysosomal dysfunction in hypomyelinating leukodystrophy.

Neurol Genet 2018 Dec 13;4(6):e288. Epub 2018 Nov 13.

Children's Hospital of Eastern Ontario Research Institute (Y.I., T.H., S.B., K.M.B., D.A.D., K.D.K.), Ottawa, Ontario, Canada; Division of Neurology (S.V.), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Institute for Molecular Bioscience (C.S.), University of Queensland, St. Lucia, Queensland, Australia; and Department of Child Neurology (N.I.W.), VU University Medical Center, and Amsterdam Neuroscience, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1212/NXG.0000000000000288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317987PMC
December 2018

Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects.

Am J Hum Genet 2018 11;103(5):727-739

Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK. Electronic address:

Primary defects in motile cilia result in dysfunction of the apparatus responsible for generating fluid flows. Defects in these mechanisms underlie disorders characterized by poor mucus clearance, resulting in susceptibility to chronic recurrent respiratory infections, often associated with infertility; laterality defects occur in about 50% of such individuals. Here we report biallelic variants in LRRC56 (known as oda8 in Chlamydomonas) identified in three unrelated families. The phenotype comprises laterality defects and chronic pulmonary infections. High-speed video microscopy of cultured epithelial cells from an affected individual showed severely dyskinetic cilia but no obvious ultra-structural abnormalities on routine transmission electron microscopy (TEM). Further investigation revealed that LRRC56 interacts with the intraflagellar transport (IFT) protein IFT88. The link with IFT was interrogated in Trypanosoma brucei. In this protist, LRRC56 is recruited to the cilium during axoneme construction, where it co-localizes with IFT trains and is required for the addition of dynein arms to the distal end of the flagellum. In T. brucei carrying LRRC56-null mutations, or a variant resulting in the p.Leu259Pro substitution corresponding to the p.Leu140Pro variant seen in one of the affected families, we observed abnormal ciliary beat patterns and an absence of outer dynein arms restricted to the distal portion of the axoneme. Together, our findings confirm that deleterious variants in LRRC56 result in a human disease and suggest that this protein has a likely role in dynein transport during cilia assembly that is evolutionarily important for cilia motility.
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http://dx.doi.org/10.1016/j.ajhg.2018.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218757PMC
November 2018

ClinPred: Prediction Tool to Identify Disease-Relevant Nonsynonymous Single-Nucleotide Variants.

Am J Hum Genet 2018 10 13;103(4):474-483. Epub 2018 Sep 13.

Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada.

Advances in high-throughput DNA sequencing have revolutionized the discovery of variants in the human genome; however, interpreting the phenotypic effects of those variants is still a challenge. While several computational approaches to predict variant impact are available, their accuracy is limited and further improvement is needed. Here, we introduce ClinPred, an efficient tool for identifying disease-relevant nonsynonymous variants. Our predictor incorporates two machine learning algorithms that use existing pathogenicity scores and, notably, benefits from inclusion of normal population allele frequency from the gnomAD database as an input feature. Another major strength of our approach is the use of ClinVar-a rapidly growing database that allows selection of confidently annotated disease-causing variants-as a training set. Compared to other methods, ClinPred showed superior accuracy for predicting pathogenicity, achieving the highest area under the curve (AUC) score and increasing both the specificity and sensitivity in different test datasets. It also obtained the best performance according to various other metrics. Moreover, ClinPred performance remained robust with respect to disease type (cancer or rare disease) and mechanism (gain or loss of function). Importantly, we observed that adding allele frequency as a predictive feature-as opposed to setting fixed allele frequency cutoffs-boosts the performance of prediction. We provide pre-computed ClinPred scores for all possible human missense variants in the exome to facilitate its use by the community.
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http://dx.doi.org/10.1016/j.ajhg.2018.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6174354PMC
October 2018

Diagnostic clarity of exome sequencing following negative comprehensive panel testing in the neonatal intensive care unit.

Am J Med Genet A 2018 07;176(7):1688-1691

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1002/ajmg.a.38838DOI Listing
July 2018

Periodic breathing in patients with NALCN mutations.

J Hum Genet 2018 Oct 3;63(10):1093-1096. Epub 2018 Jul 3.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.

Biallelic mutations in NALCN are responsible for infantile hypotonia with psychomotor retardation and characteristic facies 1 (IHPRF1). Common features of this condition include severe neonatal-onset hypotonia and profound global developmental delay. Given the rarity of this condition, long-term natural history studies are limited. Here, we present a 9-year-old male with a homozygous nonsense mutation in NALCN (c.3910C>T, p.Arg1304X) leading to profound intellectual disability, seizures, feeding difficulties, and significant periodic breathing. Breathing irregularity was also reported in three previous patients; similar to our patient, those children demonstrated periodic breathing that was characterized by alternating apneic periods with deep, rapid breathing. As the phenotype associated with NALCN mutations continues to be delineated, attention should be given to abnormal respiratory patterns, which may be an important distinguishing feature of this condition.
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http://dx.doi.org/10.1038/s10038-018-0484-1DOI Listing
October 2018

De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures.

Am J Hum Genet 2018 07 28;103(1):144-153. Epub 2018 Jun 28.

NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK. Electronic address:

Next-generation sequencing has been invaluable in the elucidation of the genetic etiology of many subtypes of intellectual disability in recent years. Here, using exome sequencing and whole-genome sequencing, we identified three de novo truncating mutations in WAS protein family member 1 (WASF1) in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected by Matchmaker Exchange were c.1516C>T (p.Arg506Ter), which occurs in three unrelated individuals, c.1558C>T (p.Gln520Ter), and c.1482delinsGCCAGG (p.Ile494MetfsTer23). All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1 and a defect in actin remodeling. This study provides evidence that de novo heterozygous mutations in WASF1 cause a rare form of intellectual disability.
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http://dx.doi.org/10.1016/j.ajhg.2018.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037130PMC
July 2018

Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes.

Am J Hum Genet 2018 01;102(1):156-174

Department of Pathology and Laboratory Medicine, Western University, London, ON N6A5C1, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada. Electronic address:

Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.
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http://dx.doi.org/10.1016/j.ajhg.2017.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5777983PMC
January 2018

Evaluation of exome filtering techniques for the analysis of clinically relevant genes.

Hum Mutat 2018 02 14;39(2):197-201. Epub 2017 Dec 14.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.

A significant challenge facing clinical translation of exome sequencing is meaningful and efficient variant interpretation. Each exome contains ∼500 rare coding variants; laboratories must systematically and efficiently identify which variant(s) contribute to the patient's phenotype. In silico filtering is an approach that reduces analysis time while decreasing the chances of incidental findings. We retrospectively assessed 55 solved exomes using available datasets as in silico filters: Online Mendelian Inheritance in Man (OMIM), Orphanet, Human Phenotype Ontology (HPO), and Radboudumc University Medical Center curated panels. We found that personalized panels produced using HPO terms for each patient had the highest success rate (100%), while producing considerably less variants to assess. HPO panels also captured multiple diagnoses in the same individual. We conclude that custom HPO-derived panels are an efficient and effective way to identify clinically relevant exome variants.
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http://dx.doi.org/10.1002/humu.23374DOI Listing
February 2018

A de novo mutation in RPL10 causes a rare X-linked ribosomopathy characterized by syndromic intellectual disability and epilepsy: A new case and review of the literature.

Eur J Med Genet 2018 Feb 21;61(2):89-93. Epub 2017 Oct 21.

Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.

Intellectual disability (ID) affects 1-2% of the general population and up to 50% of those with ID are estimated to have an underlying genetic cause. Next-generation sequencing provides an efficient means to identify the molecular causes of monogenic forms of ID. Here we present an 18 year old male with severe ID, absent speech, microcephaly, ataxia, dysmorphic facial features, and a refractory, early-onset seizure disorder. Exome sequencing revealed a rare de novo mutation in the X-linked gene RPL10 (c.232A > G, p.K78E). Previous reports of inherited mutations in RPL10 have suggested a role for the gene in neurodevelopment and the individual reported shows marked similarities to three members of a family with the same mutation reported in the literature. The p.K78E substitution appears to be associated with severe microcephaly, seizures, hearing loss, growth retardation, cardiac defects, and dysmorphic facial features. This is the first instance that a de novo mutation in RPL10 has been reported.
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http://dx.doi.org/10.1016/j.ejmg.2017.10.011DOI Listing
February 2018

Yunis-Varón syndrome caused by biallelic VAC14 mutations.

Eur J Hum Genet 2017 09 21;25(9):1049-1054. Epub 2017 Jun 21.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.

Yunis-Varón syndrome (YVS) is an autosomal recessive disorder comprising skeletal anomalies, dysmorphism, global developmental delay and intracytoplasmic vacuolation in brain and other tissues. All hitherto-reported pathogenic variants affect FIG4, a lipid phosphatase involved in phosphatidylinositol (3,5)-bisphosphate [PtdIns(3,5)P] metabolism. FIG4 interacts with PIKfyve, a lipid kinase, via the adapter protein VAC14; all subunits of the resulting complex are essential for PtdIns(3,5)P synthesis in the endolysosomal membrane compartment. Here, we present the case of a female neonate with clinical features of YVS and normal FIG4 sequencing; exome sequencing identified biallelic rare coding variants in VAC14. Cultured patient fibroblasts exhibited a YVS-like vacuolation phenotype ameliorated in a dose-dependent fashion by ML-SA1, a pharmacological activator of the lysosomal PtdIns(3,5)P effector TRPML1. The patient developed a diffuse leukoencephalopathy with loss of the normal N-acetylaspartate spectrographic peak and presence of a large abnormal peak consistent with myoinositol. We report that VAC14 is a second gene for Yunis-Varón syndrome.
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http://dx.doi.org/10.1038/ejhg.2017.99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5558182PMC
September 2017

H3.1 K36M mutation in a congenital-onset soft tissue neoplasm.

Pediatr Blood Cancer 2017 Dec 16;64(12). Epub 2017 May 16.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.

We describe a patient who presented with a congenital soft tissue lesion initially diagnosed as infantile fibromatosis at 15 days of age. Unusually, the mass demonstrated malignant progression leading to death at 20 months of age. Biological progression to malignancy is not known to occur in fibromatosis, and fibrosarcoma is not known to progress from a benign lesion. Whole-exome sequencing of the tumor identified a driver mutation in histone H3.1 at lysine (K)36. Our findings support the link between oncohistones and infantile soft tissue tumors and provide additional evidence for the oncogenic effects of p.K36M in H3 variants.
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http://dx.doi.org/10.1002/pbc.26633DOI Listing
December 2017

Compound heterozygous mutations in the gene PIGP are associated with early infantile epileptic encephalopathy.

Hum Mol Genet 2017 05;26(9):1706-1715

Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec H3T1C5, Canada.

There are over 150 known human proteins which are tethered to the cell surface via glycosylphosphatidylinositol (GPI) anchors. These proteins play a variety of important roles in development, and particularly in neurogenesis. Not surprisingly, mutations in the GPI anchor biosynthesis and remodeling pathway cause a number of developmental disorders. This group of conditions has been termed inherited GPI deficiencies (IGDs), a subgroup of congenital disorders of glycosylation; they present with variable phenotypes, often including seizures, hypotonia and intellectual disability. Here, we report two siblings with compound heterozygous variants in the gene phosphatidylinositol glycan anchor biosynthesis, class P (PIGP) (NM_153681.2: c.74T > C;p.Met25Thr and c.456delA;p.Glu153AsnFs*34). PIGP encodes a subunit of the enzyme that catalyzes the first step of GPI anchor biosynthesis. Both children presented with early-onset refractory seizures, hypotonia, and profound global developmental delay, reminiscent of other IGD phenotypes. Functional studies with patient cells showed reduced PIGP mRNA levels, and an associated reduction of GPI-anchored cell surface proteins, which was rescued by exogenous expression of wild-type PIGP. This work associates mutations in the PIGP gene with a novel autosomal recessive IGD, and expands our knowledge of the role of PIG genes in human development.
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http://dx.doi.org/10.1093/hmg/ddx077DOI Listing
May 2017

Identification of epigenetic signature associated with alpha thalassemia/mental retardation X-linked syndrome.

Epigenetics Chromatin 2017 10;10:10. Epub 2017 Mar 10.

Department of Pathology and Lab Medicine, Western University, London, ON Canada.

Background: Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene . The mechanisms involved in the ATR-X pathology are not completely understood, but may involve epigenetic modifications. ATRX has been linked to the regulation of histone H3 and DNA methylation, while mutations in the gene may lead to the downstream epigenetic and transcriptional effects. Elucidating the underlying epigenetic mechanisms altered in ATR-X will provide a better understanding about the pathobiology of this disease, as well as provide novel diagnostic biomarkers.

Results: We performed genome-wide DNA methylation assessment of the peripheral blood samples from 18 patients with ATR-X and compared it to 210 controls. We demonstrated the evidence of a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of ATRX patients, which was corroborated by targeted bisulfite sequencing experiments. Although genomically represented, differentially methylated regions showed evidence of preferential clustering in pericentromeric and telometric chromosomal regions, areas where ATRX has multiple functions related to maintenance of heterochromatin and genomic integrity.

Conclusion: Most significant methylation changes in the 14 genomic loci provide a unique epigenetic signature for this syndrome that may be used as a highly sensitive and specific diagnostic biomarker to support the diagnosis of ATR-X, particularly in patients with phenotypic complexity and in patients with gene sequence variants of unknown significance.
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http://dx.doi.org/10.1186/s13072-017-0118-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345252PMC
January 2018

Whole-transcriptome sequencing in blood provides a diagnosis of spinal muscular atrophy with progressive myoclonic epilepsy.

Hum Mutat 2017 06 28;38(6):611-614. Epub 2017 Mar 28.

Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.

At least 15% of the disease-causing mutations affect mRNA splicing. Many splicing mutations are missed in a clinical setting due to limitations of in silico prediction algorithms or their location in noncoding regions. Whole-transcriptome sequencing is a promising new tool to identify these mutations; however, it will be a challenge to obtain disease-relevant tissue for RNA. Here, we describe an individual with a sporadic atypical spinal muscular atrophy, in whom clinical DNA sequencing reported one pathogenic ASAH1 mutation (c.458A>G;p.Tyr153Cys). Transcriptome sequencing on patient leukocytes identified a highly significant and atypical ASAH1 isoform not explained by c.458A>G(p<10 ). Subsequent Sanger-sequencing identified the splice mutation responsible for the isoform (c.504A>C;p.Lys168Asn) and provided a molecular diagnosis of autosomal-recessive spinal muscular atrophy with progressive myoclonic epilepsy. Our findings demonstrate the utility of RNA sequencing from blood to identify splice-impacting disease mutations for nonhematological conditions, providing a diagnosis for these otherwise unsolved patients.
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http://dx.doi.org/10.1002/humu.23211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889109PMC
June 2017

Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1) gene.

Hum Mutat 2017 05 6;38(5):511-516. Epub 2017 Mar 6.

Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.

Deleterious variants in the same gene present in two or more families with overlapping clinical features provide convincing evidence of a disease-gene association; this can be a challenge in the study of ultrarare diseases. To facilitate the identification of additional families, several groups have created "matching" platforms. We describe four individuals from three unrelated families "matched" by GeneMatcher and MatchMakerExchange. Individuals had microcephaly, developmental delay, epilepsy, and recessive mutations in TRIT1. A single homozygous mutation in TRIT1 associated with similar features had previously been reported in one family. The identification of these individuals provides additional evidence to support TRIT1 as the disease-causing gene and interprets the variants as "pathogenic." TRIT1 functions to modify mitochondrial tRNAs and is necessary for protein translation. We show that dysfunctional TRIT1 results in decreased levels of select mitochondrial proteins. Our findings confirm the TRIT1 disease association and advance the phenotypic and molecular understanding of this disorder.
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http://dx.doi.org/10.1002/humu.23196DOI Listing
May 2017

Identification of a methylation profile for DNMT1-associated autosomal dominant cerebellar ataxia, deafness, and narcolepsy.

Clin Epigenetics 2016 5;8:91. Epub 2016 Sep 5.

Department of Pathology and Lab Medicine, Western University, London, Ontario Canada.

Background: DNA methylation is an essential epigenetic mark, controlled by DNA methyltransferase (DNMT) proteins, which regulates chromatin structure and gene expression throughout the genome. In this study, we describe a family with adult-onset autosomal dominant cerebellar ataxia with deafness and narcolepsy (ADCA-DN) caused by mutations in the maintenance methyltransferase DNMT1 and assess the DNA methylation profile of these individuals.

Results: We report a family with six individuals affected with ADCA-DN; specifically, patients first developed hearing loss and ataxia, followed by narcolepsy, and cognitive decline. We identified a heterozygous DNMT1 variant, c.1709C>T [p.Ala570Val] by Sanger sequencing, which had been previously reported as pathogenic for ADCA-DN and segregated with disease in the family. DNA methylation analysis by high-resolution genome-wide DNA methylation array identified a decrease in CpGs with 0-10 % methylation and 80-95 % methylation and a concomitant increase in sites with 10-30 % methylation and >95 % methylation. This pattern suggests an increase in methylation of normally unmethylated regions, such as promoters and CpG islands, as well as further methylation of highly methylated gene bodies and intergenic regions. Furthermore, a regional analysis identified 82 hypermethylated loci with consistent robust differences across ≥5 consecutive probes compared to our large reference cohort.

Conclusions: This report identifies robust changes in the DNA methylation patterns in ADCA-DN patients, which is an important step towards elucidating disease pathogenesis.
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http://dx.doi.org/10.1186/s13148-016-0254-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011850PMC
April 2017

Autosomal-Recessive Intellectual Disability with Cerebellar Atrophy Syndrome Caused by Mutation of the Manganese and Zinc Transporter Gene SLC39A8.

Am J Hum Genet 2015 Dec;97(6):886-93

Institute of Human Genetics, FAU Erlangen-Nürnberg, Erlangen 91054, Germany. Electronic address:

Manganese (Mn) and zinc (Zn) are essential divalent cations used by cells as protein cofactors; various human studies and animal models have demonstrated the importance of Mn and Zn for development. Here we describe an autosomal-recessive disorder in six individuals from the Hutterite community and in an unrelated Egyptian sibpair; the disorder is characterized by intellectual disability, developmental delay, hypotonia, strabismus, cerebellar atrophy, and variable short stature. Exome sequencing in one affected Hutterite individual and the Egyptian family identified the same homozygous variant, c.112G>C (p.Gly38Arg), affecting a conserved residue of SLC39A8. The affected Hutterite and Egyptian individuals did not share an extended common haplotype, suggesting that the mutation arose independently. SLC39A8 is a member of the solute carrier gene family known to import Mn, Zn, and other divalent cations across the plasma membrane. Evaluation of these two metal ions in the affected individuals revealed variably low levels of Mn and Zn in blood and elevated levels in urine, indicating renal wasting. Our findings identify a human Mn and Zn transporter deficiency syndrome linked to SLC39A8, providing insight into the roles of Mn and Zn homeostasis in human health and development.
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http://dx.doi.org/10.1016/j.ajhg.2015.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678439PMC
December 2015