Publications by authors named "Gregory Costain"

62 Publications

Novel heterozygous variants in cause different anterior segment dysgenesis phenotypes in monozygotic twins.

Ophthalmic Genet 2021 May 14:1-7. Epub 2021 May 14.

Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada.

Background: Since bi-allelic variants in the gene were first discovered in 2011 to be associated with anterior segment dysgenesis, a spectrum of ophthalmologic and systemic clinical manifestations has been described. This manuscript reports two distinct clinical phenotypes in monozygotic twin sisters, including the previously unreported ocular manifestation of bilateral primary aphakia, associated with novel compound heterozygous variants in the gene.

Materials And Methods: We used genome sequencing to study a non-consanguineous family with monozygotic twin sister probands: one presenting with bilateral microphthalmia, primary aphakia, total corneal opacification, congenital glaucoma, and complex systemic comorbidities; the other with anterior persistent fetal vasculature in the right eye, and Peters anomaly type 2 with cataract and iris coloboma in the left eye but no systemic issues. These findings were compared to published reports of -related ocular diseases upon comprehensive review of prior literature.

Results: In both affected sisters, genome sequencing identified two novel heterozygous variants in in the gene: c.1569_1570insT, predicting p.(Thr524TyrfsTer53), and c.3206 C > A, predicting p.(Ala1069Asp), respectively. No other potentially diagnostic variants were identified in any other genes.

Conclusions: This report on two novel compound heterozygous variants in the gene associated with previously unreported clinical manifestations further expands the genotypic and phenotypic spectrum associated with this gene. Our finding of distinctive clinical phenotypes associated with identical compound heterozygous variants in monozygotic twins emphasizes the significant clinical variability that can occur, suggesting a potential role for stochastic developmental and/or epigenetic factors in the ultimate pathophysiologic pathway.
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http://dx.doi.org/10.1080/13816810.2021.1925929DOI Listing
May 2021

ATP1A2- and ATP1A3-associated early profound epileptic encephalopathy and polymicrogyria.

Brain 2021 Apr 21. Epub 2021 Apr 21.

Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence, Italy.

Constitutional heterozygous mutations of ATP1A2 and ATP1A3, encoding for two distinct isoforms of the Na+/K+-ATPase (NKA) alpha-subunit, have been associated with familial hemiplegic migraine (ATP1A2), alternating hemiplegia of childhood (ATP1A2/A3), rapid-onset dystonia-parkinsonism, cerebellar ataxia-areflexia-progressive optic atrophy, and relapsing encephalopathy with cerebellar ataxia (all ATP1A3). A few reports have described single individuals with heterozygous mutations of ATP1A2/A3 associated with severe childhood epilepsies. Early lethal hydrops fetalis, arthrogryposis, microcephaly, and polymicrogyria have been associated with homozygous truncating mutations in ATP1A2. We investigated the genetic causes of developmental and epileptic encephalopathies variably associated with malformations of cortical development in a large cohort and identified 22 patients with de novo or inherited heterozygous ATP1A2/A3 mutations. We characterized clinical, neuroimaging and neuropathological findings, performed in silico and in vitro assays of the mutations' effects on the NKA-pump function, and studied genotype-phenotype correlations. Twenty-two patients harboured 19 distinct heterozygous mutations of ATP1A2 (six patients, five mutations) and ATP1A3 (16 patients, 14 mutations, including a mosaic individual). Polymicrogyria occurred in 10 (45%) patients, showing a mainly bilateral perisylvian pattern. Most patients manifested early, often neonatal, onset seizures with a multifocal or migrating pattern. A distinctive, 'profound' phenotype, featuring polymicrogyria or progressive brain atrophy and epilepsy, resulted in early lethality in seven patients (32%). In silico evaluation predicted all mutations to be detrimental. We tested 14 mutations in transfected COS-1 cells and demonstrated impaired NKA-pump activity, consistent with severe loss of function. Genotype-phenotype analysis suggested a link between the most severe phenotypes and lack of COS-1 cell survival, and also revealed a wide continuum of severity distributed across mutations that variably impair NKA-pump activity. We performed neuropathological analysis of the whole brain in two individuals with polymicrogyria respectively related to a heterozygous ATP1A3 mutation and a homozygous ATP1A2 mutation and found close similarities with findings suggesting a mainly neural pathogenesis, compounded by vascular and leptomeningeal abnormalities. Combining our report with other studies, we estimate that ∼5% of mutations in ATP1A2 and 12% in ATP1A3 can be associated with the severe and novel phenotypes that we describe here. Notably, a few of these mutations were associated with more than one phenotype. These findings assign novel, 'profound' and early lethal phenotypes of developmental and epileptic encephalopathies and polymicrogyria to the phenotypic spectrum associated with heterozygous ATP1A2/A3 mutations and indicate that severely impaired NKA pump function can disrupt brain morphogenesis.
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http://dx.doi.org/10.1093/brain/awab052DOI Listing
April 2021

Genome sequencing broadens the range of contributing variants with clinical implications in schizophrenia.

Transl Psychiatry 2021 Feb 1;11(1):84. Epub 2021 Feb 1.

Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.

The range of genetic variation with potential clinical implications in schizophrenia, beyond rare copy number variants (CNVs), remains uncertain. We therefore analyzed genome sequencing data for 259 unrelated adults with schizophrenia from a well-characterized community-based cohort previously examined with chromosomal microarray for CNVs (none with 22q11.2 deletions). We analyzed these genomes for rare high-impact variants considered causal for neurodevelopmental disorders, including single-nucleotide variants (SNVs) and small insertions/deletions (indels), for potential clinical relevance based on findings for neurodevelopmental disorders. Also, we investigated a novel variant type, tandem repeat expansions (TREs), in 45 loci known to be associated with monogenic neurological diseases. We found several of these variants in this schizophrenia population suggesting that these variants have a wider clinical spectrum than previously thought. In addition to known pathogenic CNVs, we identified 11 (4.3%) individuals with clinically relevant SNVs/indels in genes converging on schizophrenia-relevant pathways. Clinical yield was significantly enriched in females and in those with broadly defined learning/intellectual disabilities. Genome analyses also identified variants with potential clinical implications, including TREs (one in DMPK; two in ATXN8OS) and ultra-rare loss-of-function SNVs in ZMYM2 (a novel candidate gene for schizophrenia). Of the 233 individuals with no pathogenic CNVs, we identified rare high-impact variants (i.e., clinically relevant or with potential clinical implications) for 14 individuals (6.0%); some had multiple rare high-impact variants. Mean schizophrenia polygenic risk score was similar between individuals with and without clinically relevant rare genetic variation; common variants were not sufficient for clinical application. These findings broaden the individual and global picture of clinically relevant genetic risk in schizophrenia, and suggest the potential translational value of genome sequencing as a single genetic technology for schizophrenia.
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http://dx.doi.org/10.1038/s41398-021-01211-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7851385PMC
February 2021

Within-family influences on dimensional neurobehavioral traits in a high-risk genetic model.

Psychol Med 2021 Jan 14:1-9. Epub 2021 Jan 14.

Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.

Background: Genotype-first and within-family studies can elucidate factors that contribute to psychiatric illness. Combining these approaches, we investigated the patterns of influence of parental scores, a high-impact variant, and schizophrenia on dimensional neurobehavioral phenotypes implicated in major psychiatric disorders.

Methods: We quantitatively assessed cognitive (FSIQ, VIQ, PIQ), social, and motor functioning in 82 adult individuals with a de novo 22q11.2 deletion (22 with schizophrenia), and 148 of their unaffected parents. We calculated within-family correlations and effect sizes of the 22q11.2 deletion and schizophrenia, and used linear regressions to assess contributions to neurobehavioral measures.

Results: Proband-parent intra-class correlations (ICC) were significant for cognitive measures (e.g. FSIQ ICC = 0.549, p < 0.0001), but not for social or motor measures. Compared to biparental scores, the 22q11.2 deletion conferred significant impairments for all phenotypes assessed (effect sizes -1.39 to -2.07 s.d.), strongest for PIQ. There were further decrements in those with schizophrenia. Regression models explained up to 37.7% of the variance in IQ and indicated that for proband IQ, parental IQ had larger effects than schizophrenia.

Conclusions: This study, for the first time, disentangles the impact of a high-impact variant from the modifying effects of parental scores and schizophrenia on relevant neurobehavioral phenotypes. The robust proband-parent correlations for cognitive measures, independent of the impact of the 22q11.2 deletion and of schizophrenia, suggest that, for certain phenotypes, shared genetic variation plays a significant role in expression. Molecular genetic and predictor studies are needed to elucidate shared factors and their contribution to psychiatric illness in this and other high-risk groups.
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http://dx.doi.org/10.1017/S0033291720005279DOI Listing
January 2021

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

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

Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany.

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

Genome sequencing identifies a rare case of moderate Zellweger spectrum disorder caused by a defect: Case report and literature review.

Mol Genet Metab Rep 2020 Dec 19;25:100664. Epub 2020 Oct 19.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.

Defects in are associated with a severe neonatal-lethal form of Zellweger spectrum disorder. We report two moderately affected siblings whose clinical and biochemical phenotypes expand the reported spectrum of -related disease. Genome sequencing of an adolescent male with progressive movement disorder, spasticity and neurodegeneration, and previous non-diagnostic plasma very-long chain fatty acid analysis, revealed a homozygous likely pathogenic missense variant in [c.991G > A; p.(Gly331Arg)]. A younger sibling with significant motor decline since the age of three years was also subsequently found to be homozygous for the familial variant. A comprehensive review of the scientific literature identified three additional families with non-lethal infantile- or childhood-onset -related disease, which together with this clinical report illustrate the potential for highly variable disease severity. Our findings demonstrate the diagnostic utility of genome-wide sequencing for identifying clinically and biochemically heterogeneous inherited metabolic disorders such as the peroxisome biogenesis disorders.
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http://dx.doi.org/10.1016/j.ymgmr.2020.100664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7578253PMC
December 2020

Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity.

JAMA Netw Open 2020 09 1;3(9):e2018109. Epub 2020 Sep 1.

Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.

Importance: Children with medical complexity (CMC) represent a growing population in the pediatric health care system, with high resource use and associated health care costs. A genetic diagnosis can inform prognosis, anticipatory care, management, and reproductive planning. Conventional genetic testing strategies for CMC are often costly, time consuming, and ultimately unsuccessful.

Objective: To evaluate the analytical and clinical validity of genome sequencing as a comprehensive diagnostic genetic test for CMC.

Design, Setting, And Participants: In this cohort study of the prospective use of genome sequencing and comparison with standard-of-care genetic testing, CMC were recruited from May 1, 2017, to November 30, 2018, from a structured complex care program based at a tertiary care pediatric hospital in Toronto, Canada. Recruited CMC had at least 1 chronic condition, technology dependence (child is dependent at least part of each day on mechanical ventilators, and/or child requires prolonged intravenous administration of nutritional substances or drugs, and/or child is expected to have prolonged dependence on other device-based support), multiple subspecialist involvement, and substantial health care use. Review of the care plans for 545 CMC identified 143 suspected of having an undiagnosed genetic condition. Fifty-four families met inclusion criteria and were interested in participating, and 49 completed the study. Probands, similarly affected siblings, and biological parents were eligible for genome sequencing.

Exposures: Genome sequencing was performed using blood-derived DNA from probands and family members using established methods and a bioinformatics pipeline for clinical genome annotation.

Main Outcomes And Measures: The primary study outcome was the diagnostic yield of genome sequencing (proportion of CMC for whom the test result yielded a new diagnosis).

Results: Genome sequencing was performed for 138 individuals from 49 families of CMC (29 male and 20 female probands; mean [SD] age, 7.0 [4.5] years). Genome sequencing detected all genomic variation previously identified by conventional genetic testing. A total of 15 probands (30.6%; 95% CI 19.5%-44.6%) received a new primary molecular genetic diagnosis after genome sequencing. Three individuals had novel diseases and an additional 9 had either ultrarare genetic conditions or rare genetic conditions with atypical features. At least 11 families received diagnostic information that had clinical management implications beyond genetic and reproductive counseling.

Conclusions And Relevance: This study suggests that genome sequencing has high analytical and clinical validity and can result in new diagnoses in CMC even in the setting of extensive prior investigations. This clinical population may be enriched for ultrarare and novel genetic disorders. Genome sequencing is a potentially first-tier genetic test for CMC.
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http://dx.doi.org/10.1001/jamanetworkopen.2020.18109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7509619PMC
September 2020

A novel intronic variant in UBE3A identified by genome sequencing in a patient with an atypical presentation of Angelman syndrome.

Am J Med Genet A 2020 09 11;182(9):2145-2151. Epub 2020 Jul 11.

Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.

Angelman syndrome (AS) is a genetic neurodevelopmental disorder caused by loss or deficient expression of UBE3A on the maternally inherited allele. In 10-15% of individuals with a clinical diagnosis of AS, a molecular diagnosis cannot be established with conventional testing. We describe a 13-year-old male with an atypical presentation of AS, who was found to have a novel, maternally inherited, intronic variant in UBE3A (c.3-12T>A) using genome sequencing (GS). Targeted sequencing of RNA isolated from blood confirmed the creation of a new acceptor splice site. These GS results ended a six-year diagnostic odyssey and revealed a 50% recurrence risk for the unaffected parents. This case illustrates a previously unreported splicing variant causing AS. Intronic variants identifiable by GS may account for a proportion of individuals who are suspected of having well-known genetic disorders despite negative prior genetic testing.
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http://dx.doi.org/10.1002/ajmg.a.61740DOI Listing
September 2020

Cell-based analysis of CAD variants identifies individuals likely to benefit from uridine therapy.

Genet Med 2020 10 28;22(10):1598-1605. Epub 2020 May 28.

Genome Dynamics and Function Program, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain.

Purpose: Pathogenic autosomal recessive variants in CAD, encoding the multienzymatic protein initiating pyrimidine de novo biosynthesis, cause a severe inborn metabolic disorder treatable with a dietary supplement of uridine. This condition is difficult to diagnose given the large size of CAD with over 1000 missense variants and the nonspecific clinical presentation. We aimed to develop a reliable and discerning assay to assess the pathogenicity of CAD variants and to select affected individuals that might benefit from uridine therapy.

Methods: Using CRISPR/Cas9, we generated a human CAD-knockout cell line that requires uridine supplements for survival. Transient transfection of the knockout cells with recombinant CAD restores growth in absence of uridine. This system determines missense variants that inactivate CAD and do not rescue the growth phenotype.

Results: We identified 25 individuals with biallelic variants in CAD and a phenotype consistent with a CAD deficit. We used the CAD-knockout complementation assay to test a total of 34 variants, identifying 16 as deleterious for CAD activity. Combination of these pathogenic variants confirmed 11 subjects with a CAD deficit, for whom we describe the clinical phenotype.

Conclusions: We designed a cell-based assay to test the pathogenicity of CAD variants, identifying 11 CAD-deficient individuals who could benefit from uridine therapy.
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http://dx.doi.org/10.1038/s41436-020-0833-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521996PMC
October 2020

Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor.

Front Mol Neurosci 2020 11;13:12. Epub 2020 Feb 11.

Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia.

Multiple TREX mRNA export complex subunits (e.g., THOC1, THOC2, THOC5, THOC6, THOC7) have now been implicated in neurodevelopmental disorders (NDDs), neurodegeneration and cancer. We previously implicated missense and splicing-defective variants in NDDs and a broad range of other clinical features. Here we report 10 individuals from nine families with rare missense variants including the first case of a recurrent variant (p.Arg77Cys), and an additional individual with an intragenic microdeletion (Del-Ex37-38). missense variant testing and patient-derived cell line data from current and published studies show 9 of the 14 missense THOC2 variants result in reduced protein stability. The splicing-defective and deletion variants result in a loss of small regions of the C-terminal THOC2 RNA binding domain (RBD). Interestingly, reduced stability of THOC2 variant proteins has a flow-on effect on the stability of the multi-protein TREX complex; specifically on the other NDD-associated THOC subunits. Our current, expanded cohort refines the core phenotype of THOC2 NDDs to language disorder and/or ID, with a variable severity, and disorders of growth. A subset of affected individuals' has severe-profound ID, persistent hypotonia and respiratory abnormalities. Further investigations to elucidate the pathophysiological basis for this severe phenotype are warranted.
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http://dx.doi.org/10.3389/fnmol.2020.00012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026477PMC
February 2020

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion.

Mol Psychiatry 2020 Feb 3. Epub 2020 Feb 3.

Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (p = 6.73 × 10). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.
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http://dx.doi.org/10.1038/s41380-020-0654-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396297PMC
February 2020

A large data resource of genomic copy number variation across neurodevelopmental disorders.

NPJ Genom Med 2019 7;4:26. Epub 2019 Oct 7.

Hamilton Health Sciences, Ron Joyce Children's Health Centre, Hamilton, On Canada.

Copy number variations (CNVs) are implicated across many neurodevelopmental disorders (NDDs) and contribute to their shared genetic etiology. Multiple studies have attempted to identify shared etiology among NDDs, but this is the first genome-wide CNV analysis across autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), and obsessive-compulsive disorder (OCD) at once. Using microarray (Affymetrix CytoScan HD), we genotyped 2,691 subjects diagnosed with an NDD (204 SCZ, 1,838 ASD, 427 ADHD and 222 OCD) and 1,769 family members, mainly parents. We identified rare CNVs, defined as those found in <0.1% of 10,851 population control samples. We found clinically relevant CNVs (broadly defined) in 284 (10.5%) of total subjects, including 22 (10.8%) among subjects with SCZ, 209 (11.4%) with ASD, 40 (9.4%) with ADHD, and 13 (5.6%) with OCD. Among all NDD subjects, we identified 17 (0.63%) with aneuploidies and 115 (4.3%) with known genomic disorder variants. We searched further for genes impacted by different CNVs in multiple disorders. Examples of NDD-associated genes linked across more than one disorder (listed in order of occurrence frequency) are , , , , , , , , , , and long non-coding RNAs: and . We demonstrated that CNVs impacting the same genes could potentially contribute to the etiology of multiple NDDs. The CNVs identified will serve as a useful resource for both research and diagnostic laboratories for prioritization of variants.
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http://dx.doi.org/10.1038/s41525-019-0098-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6779875PMC
October 2019

Clinical Application of Targeted Next-Generation Sequencing Panels and Whole Exome Sequencing in Childhood Epilepsy.

Neuroscience 2019 10 2;418:291-310. Epub 2019 Sep 2.

Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada. Electronic address:

Genetic diagnosis of childhood epilepsy is crucial to provide disease-specific treatments. This report describes the genetic landscape of childhood epilepsy revealed by targeted next-generation sequencing panels for epilepsy (TNGSP-E) and whole exome sequencing (WES). In this retrospective cohort study, TNGSP-E and/or WES were applied to identify underlying genetic diagnoses in children seen in a single Pediatric Epilepsy Genetics Clinic. We reviewed electronic patient charts for phenotypes and biochemical, genetic, and neuroimaging investigations. Forty-four different genetic diagnoses were confirmed in 71 of 197 patients (36%; 95% CI 29.3%-43.2%). The diagnostic yield of WES (37%) was 1.9-fold greater than the diagnostic yield of TNGSP-E (19.0%; P=.0018). The number of genes included in TNGSP-E was not correlated with whether or not the test resulted in a diagnosis (Pearson's R=-0.02, P=.8). Inherited metabolic disorders accounted for 13% of the genetic diagnoses, despite abnormal metabolic investigations being an exclusion criteria. There was a direct treatment implication in 6% of patients with inherited metabolic disorders including pyridoxine dependent epilepsy, glucose transporter 1 deficiency and neuronal ceroid lipofuscinosis type 2. Additionally, there might be some treatment implications in 30% of patients with genetic diagnoses including SCN1A, SCN2A, SCN8A, and KCNQ2 associated epilepsies by application of effective anti-epileptic drugs or the ketogenic diet therapy. The high diagnostic yield of clinical molecular genetic investigations and their disease-specific treatment implications highlight the importance of genetic diagnosis in childhood epilepsy. We recommend a stepwise diagnostic algorithm including metabolic investigations for treatable disorders, chromosomal microarray analysis, TNGSP-E, and WES.
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http://dx.doi.org/10.1016/j.neuroscience.2019.08.016DOI Listing
October 2019

Reply: IREB2-associated neurodegeneration.

Brain 2019 08;142(8):e41

Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.

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http://dx.doi.org/10.1093/brain/awz185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6658843PMC
August 2019

Absence of iron-responsive element-binding protein 2 causes a novel neurodegenerative syndrome.

Brain 2019 05;142(5):1195-1202

Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

Disruption of cellular iron homeostasis can contribute to neurodegeneration. In mammals, two iron-regulatory proteins (IRPs) shape the expression of the iron metabolism proteome. Targeted deletion of Ireb2 in a mouse model causes profoundly disordered iron metabolism, leading to functional iron deficiency, anemia, erythropoietic protoporphyria, and a neurodegenerative movement disorder. Using exome sequencing, we identified the first human with bi-allelic loss-of-function variants in the gene IREB2 leading to an absence of IRP2. This 16-year-old male had neurological and haematological features that emulate those of Ireb2 knockout mice, including neurodegeneration and a treatment-resistant choreoathetoid movement disorder. Cellular phenotyping at the RNA and protein level was performed using patient and control lymphoblastoid cell lines, and established experimental assays. Our studies revealed functional iron deficiency, altered post-transcriptional regulation of iron metabolism genes, and mitochondrial dysfunction, as observed in the mouse model. The patient's cellular abnormalities were reversed by lentiviral-mediated restoration of IRP2 expression. These results confirm that IRP2 is essential for regulation of iron metabolism in humans, and reveal a previously unrecognized subclass of neurodegenerative disease. Greater understanding of how the IRPs mediate cellular iron distribution may ultimately provide new insights into common and rare neurodegenerative processes, and could result in novel therapies.
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http://dx.doi.org/10.1093/brain/awz072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487337PMC
May 2019

Rare copy number variations affecting the synaptic gene DMXL2 in neurodevelopmental disorders.

J Neurodev Disord 2019 02 7;11(1). Epub 2019 Feb 7.

The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.

Background: Ultra-rare genetic variants, including non-recurrent copy number variations (CNVs) affecting important dosage-sensitive genes, are important contributors to the etiology of neurodevelopmental disorders (NDDs). Pairing family-based whole-genome sequencing (WGS) with detailed phenotype data can enable novel gene associations in NDDs.

Methods: We performed WGS of six members from a three-generation family, where three individuals each had a spectrum of features suggestive of a NDD. CNVs and sequence-level variants were identified and further investigated in disease and control databases.

Results: We identified a novel 252-kb deletion at 15q21 that overlaps the synaptic gene DMXL2 and the gene GLDN. The microdeletion segregated in NDD-affected individuals. Additional rare inherited and de novo sequence-level variants were found that may also be involved, including a missense change in GRIK5. Multiple CNVs and loss-of-function sequence variants affecting DMXL2 were discovered in additional unrelated individuals with a range of NDDs.

Conclusions: Disruption of DMXL2 may predispose to NDDs including autism spectrum disorder. The robust interpretation of private variants requires a multifaceted approach that incorporates multigenerational pedigrees and genome-wide and population-scale data.
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http://dx.doi.org/10.1186/s11689-019-9263-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366120PMC
February 2019

De novo missense variants in RAC3 cause a novel neurodevelopmental syndrome.

Genet Med 2019 04 8;21(4):1021-1026. Epub 2018 Oct 8.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.

Purpose: RAC3 is an underexamined member of the Rho GTPase gene family that is expressed in the developing brain and linked to key cellular functions. De novo missense variants in the homolog RAC1 were recently associated with developmental disorders. In the RAC subfamily, transforming missense changes at certain shared residues have been observed in human cancers and previously characterized in experimental studies. The purpose of this study was to determine whether constitutional dysregulation of RAC3 is associated with human disease.

Methods: We discovered a RAC3 variant in the index case using genome sequencing, and searched for additional variants using international data-sharing initiatives. Functional effects of the variants were assessed using a multifaceted approach generalizable to most clinical laboratory settings.

Results: We rapidly identified five individuals with de novo monoallelic missense variants in RAC3, including one recurrent change. Every participant had severe intellectual disability and brain malformations. In silico protein modeling, and prior in vivo and in situ experiments, supported a transforming effect for each of the three different RAC3 variants. All variants were observed in databases of somatic variation in cancer.

Conclusions: Missense variants in RAC3 cause a novel brain disorder, likely through a mechanism of constitutive protein activation.
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http://dx.doi.org/10.1038/s41436-018-0323-yDOI Listing
April 2019

Haploinsufficiency of vascular endothelial growth factor related signaling genes is associated with tetralogy of Fallot.

Genet Med 2019 04 20;21(4):1001-1007. Epub 2018 Sep 20.

Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.

Purpose: To determine disease-associated single-gene variants in conotruncal defects, particularly tetralogy of Fallot (TOF).

Methods: We analyzed for rare loss-of-function and deleterious variants in FLT4 (VEGFR3) and other genes in the vascular endothelial growth factor (VEGF) pathway, as part of a genome sequencing study involving 175 adults with TOF from a single site.

Results: We identified nine (5.1%) probands with novel FLT4 variants: seven loss-of-function, including an 8-kb deletion, and two predicted damaging. In ten other probands we found likely disruptive variants in VEGF-related genes: KDR (VEGFR2; two stopgain and two nonsynonymous variants), VEGFA, FGD5, BCAR1, IQGAP1, FOXO1, and PRDM1. Detection of VEGF-related variants (19/175, 10.9%) was associated with an increased prevalence of absent pulmonary valve (26.3% vs. 3.4%, p < 0.0001) and right aortic arch (52.6% vs. 29.1%, p = 0.029). Extracardiac anomalies were rare. In an attempt to replicate findings, we identified three loss-of-function or damaging variants in FLT4, KDR, and IQGAP1 in ten independent families with TOF.

Conclusion: Loss-of-function variants in FLT4 and KDR contribute substantially to the genetic basis of TOF. The findings support dysregulated VEGF signaling as a novel mechanism contributing to the pathogenesis of TOF.
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http://dx.doi.org/10.1038/s41436-018-0260-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752294PMC
April 2019

Challenges in Diagnosing Rare Genetic Causes of Common In Utero Presentations: Report of Two Patients with Mucolipidosis Type II (I-Cell Disease).

J Pediatr Genet 2018 Sep 9;7(3):134-137. Epub 2018 Mar 9.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

Traditional approaches to prenatal genetic diagnosis for common presentations such as short femurs or intrauterine growth restriction are imperfect, and whole-exome sequencing is an emerging option. Mucolipidosis type II (I-cell disease) is an ultra-rare autosomal recessive lysosomal storage disorder with the potential for prenatal-onset skeletal and placental manifestations. We describe the prenatal signs in two recent unrelated patients with confirmed diagnoses soon after birth. In both cases, parents were consanguineous but there was no known family history of mucolipidosis type II. False reassurance was provided after negative testing for another disease with overlapping prenatal manifestations already present in one of the families, emphasizing that offspring of consanguineous parents can be at risk for more than one recessive condition. Our experience illustrates the potential advantages in expanding prenatal applications of WES for the identification of rare single gene disorders in offspring of consanguineous unions.
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http://dx.doi.org/10.1055/s-0038-1636995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6087473PMC
September 2018

Reappraisal of Reported Genes for Sudden Arrhythmic Death: Evidence-Based Evaluation of Gene Validity for Brugada Syndrome.

Circulation 2018 09;138(12):1195-1205

Toronto General Hospital Research Institute, University of Toronto, Ontario, Canada (S.U., M.H.G.).

Background: Implicit in the genetic evaluation of patients with suspected genetic diseases is the assumption that the genes evaluated are causative for the disease based on robust scientific and statistical evidence. However, in the past 20 years, considerable variability has existed in the study design and quality of evidence supporting reported gene-disease associations, raising concerns of the validity of many published disease-causing genes. Brugada syndrome (BrS) is an arrhythmia syndrome with a risk of sudden death. More than 20 genes have been reported to cause BrS and are assessed routinely on genetic testing panels in the absence of a systematic, evidence-based evaluation of the evidence supporting the causality of these genes.

Methods: We evaluated the clinical validity of genes tested by diagnostic laboratories for BrS by assembling 3 gene curation teams. Using an evidence-based semiquantitative scoring system of genetic and experimental evidence for gene-disease associations, curation teams independently classified genes as demonstrating limited, moderate, strong, or definitive evidence for disease causation in BrS. The classification of curator teams was reviewed by a clinical domain expert panel that could modify the classifications based on their independent review and consensus.

Results: Of 21 genes curated for clinical validity, biocurators classified only 1 gene ( SCN5A) as definitive evidence, whereas all other genes were classified as limited evidence. After comprehensive review by the clinical domain Expert panel, all 20 genes classified as limited evidence were reclassified as disputed with regard to any assertions of disease causality for BrS.

Conclusions: Our results contest the clinical validity of all but 1 gene clinically tested and reported to be associated with BrS. These findings warrant a systematic, evidence-based evaluation for reported gene-disease associations before use in patient care.
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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.035070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6147087PMC
September 2018

Periodic reanalysis of whole-genome sequencing data enhances the diagnostic advantage over standard clinical genetic testing.

Eur J Hum Genet 2018 05 16;26(5):740-744. Epub 2018 Feb 16.

Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.

Whole-genome sequencing (WGS) as a first-tier diagnostic test could transform medical genetic assessments, but there are limited data regarding its clinical use. We previously showed that WGS could feasibly be deployed as a single molecular test capable of a higher diagnostic rate than current practices, in a prospectively recruited cohort of 100 children meeting criteria for chromosomal microarray analysis. In this study, we report on the added diagnostic yield with re-annotation and reanalysis of these WGS data ~2 years later. Explanatory variants have been discovered in seven (10.9%) of 64 previously undiagnosed cases, in emerging disease genes like HMGA2. No new genetic diagnoses were made by any other method in the interval period as part of ongoing clinical care. The results increase the cumulative diagnostic yield of WGS in the study cohort to 41%. This represents a greater than 5-fold increase over the chromosomal microarrays, and a greater than 3-fold increase over all the clinical genetic testing ordered in practice. These findings highlight periodic reanalysis as yet another advantage of genomic sequencing in heterogeneous disorders. We recommend reanalysis of an individual's genome-wide sequencing data every 1-2 years until diagnosis, or sooner if their phenotype evolves.
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http://dx.doi.org/10.1038/s41431-018-0114-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945683PMC
May 2018

Impact of IQ on the diagnostic yield of chromosomal microarray in a community sample of adults with schizophrenia.

Genome Med 2017 11 30;9(1):105. Epub 2017 Nov 30.

Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, Canada, M5S 2S1.

Background: Schizophrenia is a severe psychiatric disorder associated with IQ deficits. Rare copy number variations (CNVs) have been established to play an important role in the etiology of schizophrenia. Several of the large rare CNVs associated with schizophrenia have been shown to negatively affect IQ in population-based controls where no major neuropsychiatric disorder is reported. The aim of this study was to examine the diagnostic yield of microarray testing and the functional impact of genome-wide rare CNVs in a community ascertained cohort of adults with schizophrenia and low (< 85) or average (≥ 85) IQ.

Methods: We recruited 546 adults of European ancestry with schizophrenia from six community psychiatric clinics in Canada. Each individual was assigned to the low or average IQ group based on standardized tests and/or educational attainment. We used rigorous methods to detect genome-wide rare CNVs from high-resolution microarray data. We compared the burden of rare CNVs classified as pathogenic or as a variant of unknown significance (VUS) between each of the IQ groups and the genome-wide burden and functional impact of rare CNVs after excluding individuals with a pathogenic CNV.

Results: There were 39/546 (7.1%; 95% confidence interval [CI] = 5.2-9.7%) schizophrenia participants with at least one pathogenic CNV detected, significantly more of whom were from the low IQ group (odds ratio [OR] = 5.01 [2.28-11.03], p = 0.0001). Secondary analyses revealed that individuals with schizophrenia and average IQ had the lowest yield of pathogenic CNVs (n = 9/325; 2.8%), followed by those with borderline intellectual functioning (n = 9/130; 6.9%), non-verbal learning disability (n = 6/29; 20.7%), and co-morbid intellectual disability (n = 15/62; 24.2%). There was no significant difference in the burden of rare CNVs classified as a VUS between any of the IQ subgroups. There was a significantly (p=0.002) increased burden of rare genic duplications in individuals with schizophrenia and low IQ that persisted after excluding individuals with a pathogenic CNV.

Conclusions: Using high-resolution microarrays we were able to demonstrate for the first time that the burden of pathogenic CNVs in schizophrenia differs significantly between IQ subgroups. The results of this study have implications for clinical practice and may help inform future rare variant studies of schizophrenia using next-generation sequencing technologies.
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http://dx.doi.org/10.1186/s13073-017-0488-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708103PMC
November 2017

Enzyme replacement therapy in perinatal hypophosphatasia: Case report of a negative outcome and lessons for clinical practice.

Mol Genet Metab Rep 2018 Mar 7;14:22-26. Epub 2017 Nov 7.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.

Enzyme replacement therapy (ERT) is a newly approved disease-modifying treatment for hypophosphatasia (HPP), a rare metabolic bone disorder. With an orphan drug and ultra-rare disease, sharing information about responders and non-responders is particularly important, as any one centre's familiarity with its use will be limited. Nearly all published data in infants and very young children with life-threatening HPP are from three small clinical trials that have reported generally positive outcomes. We describe in detail a patient with perinatal HPP for whom treatment with ERT was not successful. Lessons learned from this case can inform clinical decision-making and provide topics for the research agenda. We also discuss practical and ethical challenges related to treatment of an ultra-rare disease with an expensive new medication in a publicly funded healthcare system.
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http://dx.doi.org/10.1016/j.ymgmr.2017.10.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681336PMC
March 2018

Genome-wide sequencing expands the phenotypic spectrum of EP300 variants.

Eur J Med Genet 2018 Mar 10;61(3):125-129. Epub 2017 Nov 10.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada. Electronic address:

Many disease genes are defined by their role in causing specific clinically recognizable syndromes. Heterozygous loss of function of the gene EP300 is responsible for a minority of cases of Rubinstein-Taybi syndrome (RSTS). With the application of whole-exome sequencing and whole-genome sequencing, there is the potential to discover new genotype-phenotype correlations. The purpose of this case series is to describe three unrelated females without classic manifestations of RSTS who were unexpectedly found on genome-wide sequencing to have likely pathogenic variants in EP300. These individuals expand our knowledge of the disease spectrum by virtue of their very rare or novel clinical features. Results are placed within the context of all prior published EP300 cases not ascertained by targeted testing, which are disproportionately female compared with a cohort identified because of a clinical suspicion of RSTS (p = 0.01). There are implications for diagnosis, management, and genetic counselling of individuals with EP300-related disease.
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http://dx.doi.org/10.1016/j.ejmg.2017.11.002DOI Listing
March 2018

Genomic Disorders in Psychiatry-What Does the Clinician Need to Know?

Curr Psychiatry Rep 2017 Sep 20;19(11):82. Epub 2017 Sep 20.

Clinical Genetics Research Program, Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, Toronto, ON, M5S 2S1, Canada.

Purpose Of Review: The purpose of this review is to summarize the role of genomic disorders in various psychiatric conditions and to highlight important recent advances in the field that are of potential clinical relevance.

Recent Findings: Genomic disorders are caused by large rare recurrent deletions and duplications at certain chromosomal "hotspots" (e.g., 22q11.2, 16p11.2, 15q11-q13, 1q21.1, 15q13.3) across the genome. Most overlap multiple genes, affect development, and are associated with variable cognitive and other neuropsychiatric expression. Although individually rare, genomic disorders collectively account for a significant minority of intellectual disability, autism spectrum disorder, and schizophrenia. Genome-wide chromosomal microarray analysis is capable of detecting all genomic disorders in a single test, offering the first opportunity for routine clinical genetic testing in psychiatric practice.
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http://dx.doi.org/10.1007/s11920-017-0831-5DOI Listing
September 2017

Improved diagnostic yield compared with targeted gene sequencing panels suggests a role for whole-genome sequencing as a first-tier genetic test.

Genet Med 2018 04 3;20(4):435-443. Epub 2017 Aug 3.

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada.

PurposeGenetic testing is an integral diagnostic component of pediatric medicine. Standard of care is often a time-consuming stepwise approach involving chromosomal microarray analysis and targeted gene sequencing panels, which can be costly and inconclusive. Whole-genome sequencing (WGS) provides a comprehensive testing platform that has the potential to streamline genetic assessments, but there are limited comparative data to guide its clinical use.MethodsWe prospectively recruited 103 patients from pediatric non-genetic subspecialty clinics, each with a clinical phenotype suggestive of an underlying genetic disorder, and compared the diagnostic yield and coverage of WGS with those of conventional genetic testing.ResultsWGS identified diagnostic variants in 41% of individuals, representing a significant increase over conventional testing results (24%; P = 0.01). Genes clinically sequenced in the cohort (n = 1,226) were well covered by WGS, with a median exonic coverage of 40 × ±8 × (mean ±SD). All the molecular diagnoses made by conventional methods were captured by WGS. The 18 new diagnoses made with WGS included structural and non-exonic sequence variants not detectable with whole-exome sequencing, and confirmed recent disease associations with the genes PIGG, RNU4ATAC, TRIO, and UNC13A.ConclusionWGS as a primary clinical test provided a higher diagnostic yield than conventional genetic testing in a clinically heterogeneous cohort.
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http://dx.doi.org/10.1038/gim.2017.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895460PMC
April 2018

Rare Genome-Wide Copy Number Variation and Expression of Schizophrenia in 22q11.2 Deletion Syndrome.

Am J Psychiatry 2017 11 28;174(11):1054-1063. Epub 2017 Jul 28.

From the Dalglish Family 22q Clinic, Department of Psychiatry, University Health Network, Toronto; the Department of Psychiatry and Toronto General Research Institute, University Health Network, Toronto; the Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto; the Department of Psychiatry, University of Toronto, Toronto; the Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto; the Centre for Applied Genomics and Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto; the Medical Genetics Residency Training Program, University of Toronto, Toronto; the Department of Psychiatry and Psychology, Maastricht University, Maastricht, the Netherlands; the Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia; the Departments of Pediatrics and of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia; the Centre for Human Genetics, University of Leuven (KU Leuven), Leuven, Belgium; the Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales; the Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin; the Department of Child and Adolescent Psychiatry, King's College London; the Department of Psychiatry, Tel Aviv University, Tel Aviv, Israel; the Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles; Office Médico-Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, Geneva; the Department of Psychiatry and Behavioral Sciences, Upstate Medical University, State University of New York, Syracuse; Département de Génétique Médicale, Centre Hospitalier Universitaire de Marseille - Hôpital de la Timone, Marseilles, France; the Department of Pediatrics, Duke University, Durham, N.C.; the Department of Psychology, University of Newcastle, Newcastle, Australia; the Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands; the Department of Human Genetics, Emory University, Atlanta; Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile; the Department of Psychiatry and Behavioral Sciences, UC Davis, Sacramento, Calif.; Molecular Genetics and McLaughlin Centre, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto; the Department of Genetics, Albert Einstein College of Medicine, Bronx, N.Y.; and Genome Diagnostics, Department of Paediatric Laboratory Medicine, the Hospital for Sick Children, Toronto.

Objective: Chromosome 22q11.2 deletion syndrome (22q11.2DS) is associated with a more than 20-fold increased risk for developing schizophrenia. The aim of this study was to identify additional genetic factors (i.e., "second hits") that may contribute to schizophrenia expression.

Method: Through an international consortium, the authors obtained DNA samples from 329 psychiatrically phenotyped subjects with 22q11.2DS. Using a high-resolution microarray platform and established methods to assess copy number variation (CNV), the authors compared the genome-wide burden of rare autosomal CNV, outside of the 22q11.2 deletion region, between two groups: a schizophrenia group and those with no psychotic disorder at age ≥25 years. The authors assessed whether genes overlapped by rare CNVs were overrepresented in functional pathways relevant to schizophrenia.

Results: Rare CNVs overlapping one or more protein-coding genes revealed significant between-group differences. For rare exonic duplications, six of 19 gene sets tested were enriched in the schizophrenia group; genes associated with abnormal nervous system phenotypes remained significant in a stepwise logistic regression model and showed significant interactions with 22q11.2 deletion region genes in a connectivity analysis. For rare exonic deletions, the schizophrenia group had, on average, more genes overlapped. The additional rare CNVs implicated known (e.g., GRM7, 15q13.3, 16p12.2) and novel schizophrenia risk genes and loci.

Conclusions: The results suggest that additional rare CNVs overlapping genes outside of the 22q11.2 deletion region contribute to schizophrenia risk in 22q11.2DS, supporting a multigenic hypothesis for schizophrenia. The findings have implications for understanding expression of psychotic illness and herald the importance of whole-genome sequencing to appreciate the overall genomic architecture of schizophrenia.
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http://dx.doi.org/10.1176/appi.ajp.2017.16121417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665703PMC
November 2017

The importance of copy number variation in congenital heart disease.

NPJ Genom Med 2016 Sep;1:16031

Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.

Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD. These include and inherited variants at established (chromosome 22q11.2), emerging (chromosome 1q21.1), and novel loci across the genome. Variable expression of rare CNVs provides support for the notion of a genetic spectrum of CHD that crosses traditional anatomic classification boundaries. Clinical genetic testing using genome-wide technologies (e.g., chromosomal microarray analysis) is increasingly employed in prenatal, paediatric and adult settings. CNV discoveries in CHD have translated to changes to clinical management, prognostication and genetic counselling. The convergence of findings at individual gene and at pathway levels is shedding light on the mechanisms that govern human cardiac morphogenesis. These clinical and research advances are helping to inform whole-genome sequencing, the next logical step in delineating the genetic architecture of CHD.
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http://dx.doi.org/10.1038/npjgenmed.2016.31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5505728PMC
September 2016

Homozygous mutation in PRUNE1 in an Oji-Cree male with a complex neurological phenotype.

Am J Med Genet A 2017 Mar;173(3):740-743

Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Ontario, Canada.

The PRUNE1 gene encodes a member of the phosphoesterases (DHH) protein superfamily that is highly expressed in the human fetal brain and involved in the regulation of cell migration. Homozygous or compound heterozygous PRUNE1 mutations were recently identified in five individuals with brain malformations from four families. We present a case of a 2-year-old male with a complex neurological phenotype and abnormalities on brain MRI. Re-annotation of clinical whole-exome sequencing data revealed a homozygous likely pathogenic variant in PRUNE1 (c.521-2A>G). These results further delineate a new PRUNE1-related syndrome, and highlight the importance of periodic data re-annotation in individuals who remain without a diagnosis after undergoing genome-wide testing. © 2017 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajmg.a.38066DOI Listing
March 2017

Neuropsychiatric aspects of 22q11.2 deletion syndrome: considerations in the prenatal setting.

Prenat Diagn 2017 Jan 14;37(1):61-69. Epub 2016 Nov 14.

The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.

Most major neuropsychiatric outcomes of concern to families are not detectable by prenatal ultrasound. The introduction of genome-wide chromosomal microarray analysis to prenatal clinical diagnostic testing has increased the detection of pathogenic 22q11.2 deletions, which cause the most common genomic disorder. The recent addition of this and other microdeletions to non-invasive prenatal screening methods using cell-free fetal DNA has further propelled interest in outcomes. Conditions associated with 22q11.2 deletions include intellect ranging from intellectual disability to average, schizophrenia and other treatable psychiatric conditions, epilepsy, and early-onset Parkinson's disease. However, there is currently no way to predict how severe the lifetime expression will be. Available evidence suggests no major role in these neuropsychiatric outcomes for the congenital cardiac or most other structural anomalies that may be detectable on ultrasound. This article provides an outline of the lifetime neuropsychiatric phenotype of 22q11.2 deletion syndrome that will be useful to clinicians involved in prenatal diagnosis and related genetic counselling. The focus is on information that will be most relevant to two common situations: detection of a 22q11.2 deletion in a fetus or newborn, and new diagnosis of 22q11.2 deletion syndrome in a parent without a previous molecular diagnosis. © 2016 John Wiley & Sons, Ltd.
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http://dx.doi.org/10.1002/pd.4935DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5243851PMC
January 2017