Publications by authors named "Melissa T Carter"

49 Publications

SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.

Authors:
Francesca Clementina Radio Kaifang Pang Andrea Ciolfi Michael A Levy Andrés Hernández-García Lucia Pedace Francesca Pantaleoni Zhandong Liu Elke de Boer Adam Jackson Alessandro Bruselles Haley McConkey Emilia Stellacci Stefania Lo Cicero Marialetizia Motta Rosalba Carrozzo Maria Lisa Dentici Kirsty McWalter Megha Desai Kristin G Monaghan Aida Telegrafi Christophe Philippe Antonio Vitobello Margaret Au Katheryn Grand Pedro A Sanchez-Lara Joanne Baez Kristin Lindstrom Peggy Kulch Jessica Sebastian Suneeta Madan-Khetarpal Chelsea Roadhouse Jennifer J MacKenzie Berrin Monteleone Carol J Saunders July K Jean Cuevas Laura Cross Dihong Zhou Taila Hartley Sarah L Sawyer Fabíola Paoli Monteiro Tania Vertemati Secches Fernando Kok Laura E Schultz-Rogers Erica L Macke Eva Morava Eric W Klee Jennifer Kemppainen Maria Iascone Angelo Selicorni Romano Tenconi David J Amor Lynn Pais Lyndon Gallacher Peter D Turnpenny Karen Stals Sian Ellard Sara Cabet Gaetan Lesca Joset Pascal Katharina Steindl Sarit Ravid Karin Weiss Alison M R Castle Melissa T Carter Louisa Kalsner Bert B A de Vries Bregje W van Bon Marijke R Wevers Rolph Pfundt Alexander P A Stegmann Bronwyn Kerr Helen M Kingston Kate E Chandler Willow Sheehan Abdallah F Elias Deepali N Shinde Meghan C Towne Nathaniel H Robin Dana Goodloe Adeline Vanderver Omar Sherbini Krista Bluske R Tanner Hagelstrom Caterina Zanus Flavio Faletra Luciana Musante Evangeline C Kurtz-Nelson Rachel K Earl Britt-Marie Anderlid Gilles Morin Marjon van Slegtenhorst Karin E M Diderich Alice S Brooks Joost Gribnau Ruben G Boers Teresa Robert Finestra Lauren B Carter Anita Rauch Paolo Gasparini Kym M Boycott Tahsin Stefan Barakat John M Graham Laurence Faivre Siddharth Banka Tianyun Wang Evan E Eichler Manuela Priolo Bruno Dallapiccola Lisenka E L M Vissers Bekim Sadikovic Daryl A Scott Jimmy Lloyd Holder Marco Tartaglia

Am J Hum Genet 2021 Feb 9. Epub 2021 Feb 9.

Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy. Electronic address:

Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
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http://dx.doi.org/10.1016/j.ajhg.2021.01.015DOI Listing
February 2021

Rehabilitation therapies in Rett syndrome across the lifespan: A scoping review of human and animal studies.

J Pediatr Rehabil Med 2020 Aug 28. Epub 2020 Aug 28.

Departments of Clinical Neurosciences and Pediatrics, University of Calgary Cumming School of Medicine, Calgary, AB, Canada.

Purpose: To perform a scoping review of the evidence for therapeutic interventions to manage functional impairments associated with Rett syndrome (RTT) throughout the lifespan.

Methods: MEDLINE, EMBASE, PsycINFO, CENTRAL, CINAHL, Scopus and Index to Chiropractic Literature were searched systematically up to December 2019. Two investigators independently reviewed all search results and extracted those that met the inclusion criteria. Human and animal model studies pertaining to therapies that increase functional ability or treat RTT-associated symptoms in all age groups were included. Relevant studies were grouped into intervention categories and rated using the Oxford Centre of Evidence Based Medicine Levels of Evidence. Demographics of participants, interventions, and outcomes were summarized.

Results: Ninety-one articles representing 88 studies met the inclusion criteria, of which 80 were human clinical studies and eight were studies using animal models. Study designs were primarily case series and only six studies involved participants above the age of 40.

Conclusion: A small number of rigorously studied rehabilitation interventions have been published. Published studies aim to address a wide variety of functional impairments. Research regarding implementation of therapies for older patients with RTT is lacking and requires further exploration.
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http://dx.doi.org/10.3233/PRM-200683DOI Listing
August 2020

Tatton-Brown-Rahman syndrome: Six individuals with novel features.

Am J Med Genet A 2020 04 21;182(4):673-680. Epub 2020 Jan 21.

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

Tatton-Brown Rahman syndrome (TBRS) is an overgrowth-intellectual disability syndrome caused by heterozygous variants in DNMT3A. Seventy-eight individuals have been reported with a consistent phenotype of somatic overgrowth, mild to moderate intellectual disability, and similar dysmorphisms. We present six individuals with TBRS, including the youngest individual thus far reported, first individual to be diagnosed with tumor testing and two individuals with variants at the Arg882 domain, bringing the total number of reported cases to 82. Patients reported herein have additional clinical features not previously reported in TBRS. One patient had congenital diaphragmatic hernia. One patient carrying the recurrent p.Arg882His DNMT3A variant, who was previously reported as having a phenotype due to a truncating variant in the CLTC gene, developed a ganglioneuroblastoma at 18 months and T-cell lymphoblastic lymphoma at 6 years of age. Four patients manifested symptoms suggestive of autonomic dysfunction, including central sleep apnea, postural orthostatic hypotension, and episodic vasomotor instability in the extremities. We discuss the molecular and clinical findings in our patients with TBRS in context of existing literature.
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http://dx.doi.org/10.1002/ajmg.a.61475DOI Listing
April 2020

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

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

1The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, 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

Phenotype and mutation expansion of the PTPN23 associated disorder characterized by neurodevelopmental delay and structural brain abnormalities.

Eur J Hum Genet 2020 01 8;28(1):76-87. Epub 2019 Aug 8.

Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10599, USA.

PTPN23 is a His-domain protein-tyrosine phosphatase implicated in ciliogenesis, the endosomal sorting complex required for transport (ESCRT) pathway, and RNA splicing. Until recently, no defined human phenotype had been associated with alterations in this gene. We identified and report a cohort of seven patients with either homozygous or compound heterozygous rare deleterious variants in PTPN23. Combined with four patients previously reported, a total of 11 patients with this disorder have now been identified. We expand the phenotypic and variation spectrum associated with defects in this gene. Patients have strong phenotypic overlap, suggesting a defined autosomal recessive syndrome caused by reduced function of PTPN23. Shared characteristics of affected individuals include developmental delay, brain abnormalities (mainly ventriculomegaly and/or brain atrophy), intellectual disability, spasticity, language disorder, microcephaly, optic atrophy, and seizures. We observe a broad range of variants across patients that are likely strongly reducing the expression or disrupting the function of the protein. However, we do not observe any patients with an allele combination predicted to result in complete loss of function of PTPN23, as this is likely incompatible with life, consistent with reported embryonic lethality in the mouse. None of the observed or reported variants are recurrent, although some have been identified in homozygosis in patients from consanguineous populations. This study expands the phenotypic and molecular spectrum of PTPN23 associated disease and identifies major shared features among patients affected with this disorder, while providing additional support to the important role of PTPN23 in human nervous and visual system development and function.
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http://dx.doi.org/10.1038/s41431-019-0487-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906308PMC
January 2020

Compound heterozygous CACNA1H mutations associated with severe congenital amyotrophy.

Channels (Austin) 2019 12;13(1):153-161

b Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague , Czech Republic.

Neuromuscular disorders encompass a wide range of conditions often associated with a genetic component. In the present study, we report a patient with severe infantile-onset amyotrophy in whom two compound heterozygous variants in the gene CACNA1H encoding for Ca3.2 T-type calcium channels were identified. Functional analysis of Ca3.2 variants revealed several alterations of the gating properties of the channel that were in general consistent with a loss-of-channel function. Taken together, these findings suggest that severe congenital amyoplasia may be related to CACNA1H and would represent a new phenotype associated with mutations in this gene.
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http://dx.doi.org/10.1080/19336950.2019.1614415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527065PMC
December 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

Atypical Rett Syndrome and Intractable Epilepsy With Novel Mutation.

Child Neurol Open 2018 23;5:2329048X18787946. Epub 2018 Aug 23.

Division of Neurology, The Ottawa Hospital Civic Campus, Ottawa, Ontario, Canada.

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http://dx.doi.org/10.1177/2329048X18787946DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6108011PMC
August 2018

Assessing the accuracy of the Modified Checklist for Autism in Toddlers: a systematic review and meta-analysis.

Dev Med Child Neurol 2018 11 11;60(11):1093-1100. Epub 2018 Jul 11.

Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.

Aim: The Modified Checklist for Autism in Toddlers (M-CHAT) could be appropriate for universal screening for autism spectrum disorder (ASD) at 18 months and 24 months. Validation studies, however, reported differences in psychometric properties across sample populations. This meta-analysis summarized its accuracy measures and quantified their change in relation to patient and study characteristics.

Method: Four electronic databases (MEDLINE, PsycINFO, CINAHL, and Embase) were searched to identify articles published between January 2001 and May 2016. Bayesian regression models pooled study-specific measures. Meta-regressions covariates were age at screening, study design, and proportion of males.

Results: On the basis of the 13 studies included, the pooled sensitivity was 0.83 (95% credible interval [CI] 0.75-0.90), specificity was 0.51 (95% CI 0.41-0.61), and positive predictive value was 0.53 (95% CI 0.43-0.63) in high-risk children and 0.06 (95% CI <0.01-0.14) in low-risk children. Sensitivity was higher for screening at 30 months compared with 24 months.

Interpretation: Findings indicate that the M-CHAT performs with low to moderate accuracy in identifying ASD among children with developmental concerns, but there was a lack of evidence on its performance in low-risk children or at age 18 months. Clinicians should account for a child's age and presence of developmental concern when interpreting their M-CHAT score.

What This Paper Adds: The Modified Checklist for Autism in Toddlers (M-CHAT) performs with low-to-moderate accuracy in children with developmental concerns. There is limited evidence supporting its use at 18 months or in low-risk children.
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http://dx.doi.org/10.1111/dmcn.13964DOI Listing
November 2018

Cost-effectiveness of Genome and Exome Sequencing in Children Diagnosed with Autism Spectrum Disorder.

Appl Health Econ Health Policy 2018 Aug;16(4):481-493

Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada.

Background: Genome (GS) and exome sequencing (ES) could potentially identify pathogenic variants with greater sensitivity than chromosomal microarray (CMA) in autism spectrum disorder (ASD) but are costlier and result interpretation can be uncertain. Study objective was to compare the costs and outcomes of four genetic testing strategies in children with ASD.

Methods: A microsimulation model estimated the outcomes and costs (in societal and public payer perspectives in Ontario, Canada) of four genetic testing strategies: CMA for all, CMA for all followed by ES for those with negative CMA and syndromic features (CMA+ES), ES or GS for all.

Results: Compared to CMA, the incremental cost-effectiveness ratio (ICER) per additional child identified with rare pathogenic variants within 18 months of ASD diagnosis was $CAN5997.8 for CMA+ES, $CAN13,504.2 for ES and $CAN10,784.5 for GS in the societal perspective. ICERs were sensitive to changes in ES or GS diagnostic yields, wait times for test results or pre-test genetic counselling, but were robust to changes in the ES or GS costs.

Conclusion: Strategic integration of ES into ASD care could be a cost-effective strategy. Long wait times for genetic services and uncertain utility, both clinical and personal, of sequencing results could limit broader clinical implementation.
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http://dx.doi.org/10.1007/s40258-018-0390-xDOI Listing
August 2018

Cost-Effectiveness of Universal or High-Risk Screening Compared to Surveillance Monitoring in Autism Spectrum Disorder.

J Autism Dev Disord 2018 Sep;48(9):2968-2979

Institute of Heath Policy, Management and Evaluation, University of Toronto, Toronto, Canada.

The American Academy of Pediatrics recommends universal screening for autism spectrum disorder at 18 and 24 months. This study compared the cost-effectiveness of universal or high-risk screening to surveillance monitoring. Simulation models estimated the costs and outcomes from birth to age 6 years. The incremental cost per child diagnosed by 36 months was $41,651.6 for high-risk screening and $757,116.9 for universal screening from the societal perspective. Universal screening may not be a cost-effective approach to increase earlier treatment initiation, as most children initiated treatment after age 60 months. Eliminating wait times resulted in more children initiated treatment by 48 months, but at a high initial cost that may be offset by future cost-savings related to better outcomes.
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http://dx.doi.org/10.1007/s10803-018-3571-4DOI Listing
September 2018

Genotype-phenotype correlations in individuals with pathogenic RERE variants.

Hum Mutat 2018 05 25;39(5):666-675. Epub 2018 Jan 25.

Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas.

Heterozygous variants in the arginine-glutamic acid dipeptide repeats gene (RERE) have been shown to cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart (NEDBEH). Here, we report nine individuals with NEDBEH who carry partial deletions or deleterious sequence variants in RERE. These variants were found to be de novo in all cases in which parental samples were available. An analysis of data from individuals with NEDBEH suggests that point mutations affecting the Atrophin-1 domain of RERE are associated with an increased risk of structural eye defects, congenital heart defects, renal anomalies, and sensorineural hearing loss when compared with loss-of-function variants that are likely to lead to haploinsufficiency. A high percentage of RERE pathogenic variants affect a histidine-rich region in the Atrophin-1 domain. We have also identified a recurrent two-amino-acid duplication in this region that is associated with the development of a CHARGE syndrome-like phenotype. We conclude that mutations affecting RERE result in a spectrum of clinical phenotypes. Genotype-phenotype correlations exist and can be used to guide medical decision making. Consideration should also be given to screening for RERE variants in individuals who fulfill diagnostic criteria for CHARGE syndrome but do not carry pathogenic variants in CHD7.
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http://dx.doi.org/10.1002/humu.23400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5903952PMC
May 2018

Atypical autism in a boy with double duplication of 22q11.2: implications of increasing dosage.

NPJ Genom Med 2017 28;2:28. Epub 2017 Sep 28.

Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, ON Canada.

Duplication of chromosome 22q11.2 (LCR A-D) has been reported at higher frequencies in clinical samples than the general population, but phenotypes vary widely. Triplication (4 copies) is rare, but studying the associated phenotype may provide insight into dosage-sensitivity of the genes in this chromosomal interval. We describe a proband with a triplication, specifically a "double duplication" (two copies per chromosome) of the 22q11.2 region, while his parents and two siblings each have a single duplication (3 copies). The proband had a heart malformation, dysmorphic features, and learning and socialization deficits, whereas the other family members did not. This family illustrates that while duplication of the 22q11.2 may not be sufficient to cause clinically significant neurodevelopmental or health-related phenotypes, triplication of the same region may result in a phenotype characterized by a mild neurodevelopmental disorder, facial dysmorphism, and possibly cardiac anomalies.
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http://dx.doi.org/10.1038/s41525-017-0031-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677976PMC
September 2017

Noncompaction cardiomyopathy in an infant with Walker-Warburg syndrome.

Am J Med Genet A 2017 Nov 5;173(11):3082-3086. Epub 2017 Oct 5.

Division of Medical Genetics, Department of Pediatrics, Kingston General Hospital, Queen's University, Kingston, Canada.

Walker-Warburg syndrome (WWS) is a rare autosomal recessive, congenital muscular dystrophy that is associated with brain and eye anomalies. Several genes encoding proteins involved in α-dystroglycan glycosylation have been implicated in the aetiology of WWS. We describe a patient with nonclassical features of WWS presenting with heart failure related to noncompaction cardiomyopathy resulting in death at 4 months of age. Muscle biopsy revealed absent α-dystroglycan on immunostaining and genetic testing confirmed the diagnosis with two previously described POMT2 mutations. This is the first reported case of WWS syndrome associated with noncompaction cardiomyopathy.
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http://dx.doi.org/10.1002/ajmg.a.38394DOI Listing
November 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.

The Centre for Applied Genomics, 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

PLS3 Mutations in X-Linked Osteoporosis: Clinical and Bone Characteristics of Two Novel Mutations.

Horm Res Paediatr 2017 12;88(3-4):298-304. Epub 2017 Jun 12.

Department of Pediatrics, Division of Endocrinology, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

Background And Objectives: Plastin 3 (PLS3) mutations are associated with an X-linked osteoporosis. Here we describe two new families with novel mutations, including one with a whole gene PLS3 deletion, and review the literature on 9 previously reported cases.

Results: Hemizygous male carriers presented with multiple peripheral bone fractures, low bone mineral density (BMD), and vertebral compression fractures. Heterozygous female carriers did not have a history of fragility fractures, although 1 individual presented with low BMD. Apart from greyish-tinged sclera, no other extraskeletal features of osteogenesis imperfecta were identified. Histomorphometry from a transiliac bone biopsy in one of our index patients demonstrated significantly low trabecular bone volume with increased bone turnover. Bisphosphonate treatment was associated with a reduction in the fracture rate and increased bone density.

Conclusion: Hemizygous mutations in PLS3 may cause a monogenic form of X-linked osteoporosis presenting in childhood with a nonspecific phenotype. No characteristic ocular, dental, or joint abnormalities are defined. When genetic testing is undertaken to investigate for primary causes of bone fragility, we suggest PLS3 be included in order not to miss this diagnosis.
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http://dx.doi.org/10.1159/000477242DOI Listing
June 2018

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.

Nat Neurosci 2017 Apr 6;20(4):602-611. Epub 2017 Mar 6.

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

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.
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http://dx.doi.org/10.1038/nn.4524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501701PMC
April 2017

Implication of LRRC4C and DPP6 in neurodevelopmental disorders.

Am J Med Genet A 2017 Feb 19;173(2):395-406. Epub 2016 Oct 19.

Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.

We performed whole-genome sequencing on an individual from a family with variable psychiatric phenotypes that had a sensory processing disorder, apraxia, and autism. The proband harbored a maternally inherited balanced translocation (46,XY,t(11;14)(p12;p12)mat) that disrupted LRRC4C, a member of the highly specialized netrin G family of axon guidance molecules. The proband also inherited a paternally derived chromosomal inversion that disrupted DPP6, a potassium channel interacting protein. Copy Number (CN) analysis in 14,077 cases with neurodevelopmental disorders and 8,960 control subjects revealed that 60% of cases with exonic deletions in LRRC4C had a second clinically recognizable syndrome associated with variable clinical phenotypes, including 16p11.2, 1q44, and 2q33.1 CN syndromes, suggesting LRRC4C deletion variants may be modifiers of neurodevelopmental disorders. In vitro, functional assessments modeling patient deletions in LRRC4C suggest a negative regulatory role of these exons found in the untranslated region of LRRC4C, which has a single, terminal coding exon. These data suggest that the proband's autism may be due to the inheritance of disruptions in both DPP6 and LRRC4C, and may highlight the importance of the netrin G family and potassium channel interacting molecules in neurodevelopmental disorders. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajmg.a.38021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833302PMC
February 2017

Microcephaly-capillary malformation syndrome: Brothers with a homozygous STAMBP mutation, uncovered by exome sequencing.

Am J Med Genet A 2016 11 17;170(11):3018-3022. Epub 2016 Aug 17.

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

We describe two brothers from a consanguineous family of Egyptian ancestry, presenting with microcephaly, apparent global developmental delay, seizures, spasticity, congenital blindness, and multiple cutaneous capillary malformations. Through exome sequencing, we uncovered a homozygous missense variant in STAMBP (p.K303R) in the two siblings, inherited from heterozygous carrier parents. Mutations in STAMBP are known to cause microcephaly-capillary malformation syndrome (MIC-CAP) and the phenotype in this family is consistent with this diagnosis. We compared the findings in the present brothers with those of earlier reported patients. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/ajmg.a.37845DOI Listing
November 2016

Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay.

Sci Rep 2016 07 1;6:28663. Epub 2016 Jul 1.

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

A challenge in clinical genomics is to predict whether copy number variation (CNV) affecting a gene or multiple genes will manifest as disease. Increasing recognition of gene dosage effects in neurodevelopmental disorders prompted us to develop a computational approach based on critical-exon (highly expressed in brain, highly conserved) examination for potential etiologic effects. Using a large CNV dataset, our updated analyses revealed significant (P < 1.64 × 10(-15)) enrichment of critical-exons within rare CNVs in cases compared to controls. Separately, we used a weighted gene co-expression network analysis (WGCNA) to construct an unbiased protein module from prenatal and adult tissues and found it significantly enriched for critical exons in prenatal (P < 1.15 × 10(-50), OR = 2.11) and adult (P < 6.03 × 10(-18), OR = 1.55) tissues. WGCNA yielded 1,206 proteins for which we prioritized the corresponding genes as likely to have a role in neurodevelopmental disorders. We compared the gene lists obtained from critical-exon and WGCNA analysis and found 438 candidate genes associated with CNVs annotated as pathogenic, or as variants of uncertain significance (VOUS), from among 10,619 developmental delay cases. We identified genes containing CNVs previously considered to be VOUS to be new candidate genes for neurodevelopmental disorders (GIT1, MVB12B and PPP1R9A) demonstrating the utility of this strategy to index the clinical effects of CNVs.
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http://dx.doi.org/10.1038/srep28663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929460PMC
July 2016

Lateral meningocele (Lehman) syndrome: A child with a novel NOTCH3 mutation.

Am J Med Genet A 2016 Apr 11;170A(4):1070-5. Epub 2016 Jan 11.

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

Lateral meningocele syndrome (LMS), or Lehman syndrome, is a rare disorder characterized by multiple lateral spinal meningoceles, distinctive facial features, joint hypermobility and hypotonia, along with skeletal, cardiac, and urogenital anomalies. Heterozygous NOTCH3 mutations affecting the terminal exon 33 were recently reported as causative in six families with LMS. We report a boy with LMS, the fourteenth reported case, with a de novo 80 base pair deletion in exon 33 of NOTCH3. Our patient's prenatal findings, complex cardiac anomalies, and severe feeding difficulties further expand our understanding of this rare condition.
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http://dx.doi.org/10.1002/ajmg.a.37541DOI Listing
April 2016

Whole Genome Sequencing Expands Diagnostic Utility and Improves Clinical Management in Pediatric Medicine.

NPJ Genom Med 2016 Jan;1

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

The standard of care for first-tier clinical investigation of the etiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion-deletions (indels) and single nucleotide variant (SNV) mutations. Whole genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilized WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a 4-fold increase in diagnostic rate over CMA (8%) (p-value = 1.42e-05) alone and >2-fold increase in CMA plus targeted gene sequencing (13%) (p-value = 0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harboring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counseling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.
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http://dx.doi.org/10.1038/npjgenmed.2015.12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447450PMC
January 2016

Triplication of 16p12.1p12.3 associated with developmental and growth delay and distinctive facial features.

Am J Med Genet A 2016 Mar 8;170(3):712-6. Epub 2015 Dec 8.

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

The 16p12 region is particularly prone to genomic disorders due to the large number of low copy repeats [Martin et al., 2004; Nature 432:988-994]. We report two unrelated patients with de novo triplication of 16p12.1p12.3 who had developmental delay and similar facial features. Patient 1 is a 4-year-old male with a congenital heart anomaly, bilateral cryptorchidism, chronic constipation, and developmental delay. Patient 2 is a 12-year-old female with prenatally diagnosed hydronephrosis, hepatobiliary disease, failure to thrive, and developmental delay. Distinctive facial features common to both patients include short palpebral fissures, bulbous nose, thin upper vermillion border, apparently lowset ears, and large ear lobes. We compare the clinical manifestations of our patients with a previously reported patient with triplication of 16p12.2.
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http://dx.doi.org/10.1002/ajmg.a.37483DOI Listing
March 2016

Identification of a homozygous missense mutation in LRP2 and a hemizygous missense mutation in TSPYL2 in a family with mild intellectual disability.

Psychiatr Genet 2016 Apr;26(2):66-73

aMolecular Neuropsychiatry and Development Lab, The Centre for Addiction & Mental Health (CAMH), The Campbell Family Brain Research Institute bDepartment of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children cDepartment of Medicine, Division of Neurology dDepartment of Psychiatry eInstitute of Medical Science, University of Toronto fKrembil Neuroscience Centre, Toronto Western Research Institute, Toronto gDepartment of Psychiatry, Division of Developmental Disabilities, Queen's University, Kingston, Ontario, Canada hAtta-ur-Rehman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.

Non-syndromic autosomal recessive intellectual disability (ID) is a genetically heterogeneous disorder with more than 50 mutated genes to date. ID is characterized by deficits in memory skills and language development with difficulty in learning, problem solving, and adaptive behaviors, and affects ∼ 1% of the population. For detection of disease-causing mutations in such a heterogeneous disorder, homozygosity mapping together with exome sequencing is a powerful approach, as almost all known genes can be assessed simultaneously in a high-throughput manner. In this study, a hemizygous c.786C>G:p.Ile262Met in the testis specific protein Y-encoded-like 2 (TSPYL2) gene and a homozygous c.11335G>A:p.Asp3779Asn in the low-density lipoprotein receptor-related protein 2 (LRP2) gene were detected after genome-wide genotyping and exome sequencing in a consanguineous Pakistani family with two boys with mild ID. Mutations in the LRP2 gene have previously been reported in patients with Donnai-Barrow and Stickler syndromes. LRP2 has also been associated with a 2q locus for autism (AUTS5). The TSPYL2 variant is not listed in any single-nucleotide polymorphism databases, and the LRP2 variant was absent in 400 ethnically matched healthy control chromosomes, and is not listed in single-nucleotide polymorphism databases as a common polymorphism. The LRP2 mutation identified here is located in one of the low-density lipoprotein-receptor class A domains, which is a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism, suggesting that alteration of cholesterol processing pathway can contribute to ID.
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http://dx.doi.org/10.1097/YPG.0000000000000114DOI Listing
April 2016

Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder.

JAMA 2015 Sep;314(9):895-903

Provincial Medical Genetics Program, Eastern Health, St John's, Newfoundland and Labrador, Canada14Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada.

Importance: The use of genome-wide tests to provide molecular diagnosis for individuals with autism spectrum disorder (ASD) requires more study.

Objective: To perform chromosomal microarray analysis (CMA) and whole-exome sequencing (WES) in a heterogeneous group of children with ASD to determine the molecular diagnostic yield of these tests in a sample typical of a developmental pediatric clinic.

Design, Setting, And Participants: The sample consisted of 258 consecutively ascertained unrelated children with ASD who underwent detailed assessments to define morphology scores based on the presence of major congenital abnormalities and minor physical anomalies. The children were recruited between 2008 and 2013 in Newfoundland and Labrador, Canada. The probands were stratified into 3 groups of increasing morphological severity: essential, equivocal, and complex (scores of 0-3, 4-5, and ≥6).

Exposures: All probands underwent CMA, with WES performed for 95 proband-parent trios.

Main Outcomes And Measures: The overall molecular diagnostic yield for CMA and WES in a population-based ASD sample stratified in 3 phenotypic groups.

Results: Of 258 probands, 24 (9.3%, 95%CI, 6.1%-13.5%) received a molecular diagnosis from CMA and 8 of 95 (8.4%, 95%CI, 3.7%-15.9%) from WES. The yields were statistically different between the morphological groups. Among the children who underwent both CMA and WES testing, the estimated proportion with an identifiable genetic etiology was 15.8% (95%CI, 9.1%-24.7%; 15/95 children). This included 2 children who received molecular diagnoses from both tests. The combined yield was significantly higher in the complex group when compared with the essential group (pairwise comparison, P = .002). [table: see text].

Conclusions And Relevance: Among a heterogeneous sample of children with ASD, the molecular diagnostic yields of CMA and WES were comparable, and the combined molecular diagnostic yield was higher in children with more complex morphological phenotypes in comparison with the children in the essential category. If replicated in additional populations, these findings may inform appropriate selection of molecular diagnostic testing for children affected by ASD.
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http://dx.doi.org/10.1001/jama.2015.10078DOI Listing
September 2015

Mutations in the histamine N-methyltransferase gene, HNMT, are associated with nonsyndromic autosomal recessive intellectual disability.

Hum Mol Genet 2015 Oct 23;24(20):5697-710. Epub 2015 Jul 23.

Molecular Neuropsychiatry and Development (MiND) Lab, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada M5T 1R8, Department of Psychiatry, University of Toronto, Toronto, ON, Canada M5T 1R8 and Institute of Medical Science, University of Toronto, Toronto, ON, Canada M5S 1A8

Histamine (HA) acts as a neurotransmitter in the brain, which participates in the regulation of many biological processes including inflammation, gastric acid secretion and neuromodulation. The enzyme histamine N-methyltransferase (HNMT) inactivates HA by transferring a methyl group from S-adenosyl-l-methionine to HA, and is the only well-known pathway for termination of neurotransmission actions of HA in mammalian central nervous system. We performed autozygosity mapping followed by targeted exome sequencing and identified two homozygous HNMT alterations, p.Gly60Asp and p.Leu208Pro, in patients affected with nonsyndromic autosomal recessive intellectual disability from two unrelated consanguineous families of Turkish and Kurdish ancestry, respectively. We verified the complete absence of a functional HNMT in patients using in vitro toxicology assay. Using mutant and wild-type DNA constructs as well as in silico protein modeling, we confirmed that p.Gly60Asp disrupts the enzymatic activity of the protein, and that p.Leu208Pro results in reduced protein stability, resulting in decreased HA inactivation. Our results highlight the importance of inclusion of HNMT for genetic testing of individuals presenting with intellectual disability.
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http://dx.doi.org/10.1093/hmg/ddv286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581600PMC
October 2015

Deletion of 15q11.2(BP1-BP2) region: further evidence for lack of phenotypic specificity in a pediatric population.

Am J Med Genet A 2015 Sep 6;167A(9):2098-102. Epub 2015 May 6.

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

Microdeletion of the BP1-BP2 region at 15q11.2 is a recurrent copy number variant (CNV) frequently found in patients undergoing chromosomal microarray (CMA). Genetic counselling regarding this CNV is challenging due to the wide range of phenotypic presentation in reported patients and lack of general population-based data. As one of the most common reasons for CMA is childhood developmental delay, clinicians need to be cognizant of the inherent ascertainment bias in the literature. We performed a detailed medical record review for 55 patients with this 15q11.2 microdeletion and report the clinical features of the 35 patients for whom information was available. We compared our results to the recent report by Cafferkey et al. in this journal. Our conclusion is that the phenotypic spectrum is too broad and non-specific to constitute a bona fide "syndrome" and that further research must be done to delineate the contribution of this CNV to phenotype.
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http://dx.doi.org/10.1002/ajmg.a.37134DOI Listing
September 2015

Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment.

Hum Mol Genet 2015 Jun 20;24(11):3172-80. Epub 2015 Feb 20.

Institute of Human Genetics and

There are two known mRNA degradation pathways, 3' to 5' and 5' to 3'. We identified likely pathogenic variants in two genes involved in these two pathways in individuals with intellectual disability. In a large family with multiple branches, we identified biallelic variants in DCPS in three affected individuals; a splice site variant (c.636+1G>A) that results in an in-frame insertion of 45 nucleotides and a missense variant (c.947C>T; p.Thr316Met). DCPS decaps the cap structure generated by 3' to 5' exonucleolytic degradation of mRNA. In vitro decapping assays showed an ablation of decapping function for both variants in DCPS. In another family, we identified a homozygous mutation (c.161T>C; p.Phe54Ser) in EDC3 in two affected children. EDC3 stimulates DCP2, which decaps mRNAs at the beginning of the 5' to 3' degradation pathway. In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration. We show that individuals with biallelic mutations in these genes of seemingly central functions are viable and that these possibly lead to impairment of neurological functions linking mRNA decapping to normal cognition. Our results further affirm an emerging theme linking aberrant mRNA metabolism to neurological defects.
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http://dx.doi.org/10.1093/hmg/ddv069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424955PMC
June 2015

Whole-genome sequencing of quartet families with autism spectrum disorder.

Nat Med 2015 Feb 26;21(2):185-91. Epub 2015 Jan 26.

1] The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.

Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics.
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http://dx.doi.org/10.1038/nm.3792DOI Listing
February 2015

Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes.

Hum Mol Genet 2014 May 30;23(10):2752-68. Epub 2013 Dec 30.

The Centre for Applied Genomics.

Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.
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http://dx.doi.org/10.1093/hmg/ddt669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990173PMC
May 2014