Myriam Srour

Excess of De Novo Deleterious Mutations in Genes Associated with Glutamatergic Systems in Nonsyndromic Intellectual Disability

Little is known about the genetics of nonsyndromic intellectual disability (NSID). We hypothesized that de novo mutations (DNMs) in synaptic genes explain an important fraction of sporadic NSID cases. In order to investigate this possibility, we sequenced 197 genes encoding glutamate receptors and a large subset of their known interacting proteins in 95 sporadic cases of NSID. We found 11 DNMs, including ten potentially deleterious mutations (three nonsense, two splicing, one frameshift, four missense) and one neutral mutation (silent) in eight different genes. Calculation of point-substitution DNM rates per functional and neutral site showed significant excess of functional DNMs compared to neutral ones. De novo truncating and/or splicing mutations in SYNGAP1, STXBP1, and SHANK3 were found in six patients and are likely to be pathogenic. De novo missense mutations were found in KIF1A, GRIN1, CACNG2, and EPB41L1. Functional studies showed that all these missense mutations affect protein function in cell culture systems, suggesting that they may be pathogenic. Sequencing these four genes in 50 additional sporadic cases of NSID identified a second DNM in GRIN1 (c.1679_1681dup/p.Ser560dup). This mutation also affects protein function, consistent with structural predictions. None of these mutations or any other DNMs were identified in these genes in 285 healthy controls. This study highlights the importance of the glutamate receptor complexes in NSID and further supports the role of DNMs in this disorder.

Screening for Developmental Delay in the Setting of a Community Pediatric Clinic: A Prospective Assessment of Parent-Report Questionnaires

OBJECTIVES. Our goal for this study was to prospectively test whether parent-completed questionnaires can be effectively used in the setting of a busy ambulatory pediatric clinic to accurately screen for developmental impairments. Specific objectives included (1) assessing the feasibility of using parent-report instruments in the setting of a community pediatric clinic, (2) evaluating the accuracy of 2 available screening tests (the Ages and Stages Questionnaire and Child Development Inventory), and (3) ascertaining if the pediatricians clinical judgment could be used as a potential modifier. METHODS. Subjects were recruited from the patient population of a community clinic providing primary ambulatory pediatric care. Subjects without previous developmental delay or concerns noted were contacted at the time of their routine 18-month-old visit. Those subjects who agreed to participate were randomly assigned to 1 of 2 groups and completed either the Ages and Stages Questionnaire or Child Development Inventory. The childs pediatrician also completed a brief questionnaire regarding his or her opinion of the childs development. Those children for whom concerns were identified by either questionnaire underwent additional detailed testing by the Battelle Development Inventory, the “gold standard” for the purposes of this study. An equal number of children scoring within the norms of the screening measures also underwent testing with the Battelle Development Inventory. RESULTS. Of the 356 parents contacted, 317 parents (90%) agreed to participate. Most parents correctly completed the Ages and Stages Questionnaire (81%) and the Child Development Inventory (75%). Predictive values were calculated for the Ages and Stages Questionnaire and the Child Development Inventory (sensitivity: 0.67 and 0.50; specificity: 0.39 and 0.86; positive predictive value: 34% and 50%; negative predictive value: 71% and 86%, respectively). Incorporating the physicians opinion regarding the developmental status of the child did not improve the accuracy of the screening questionnaires. CONCLUSIONS. Three important conclusions were reached: (1) parent-completed questionnaires can be feasibly used in the setting of a pediatric clinic; (2) the pediatricians opinion had little effect in ameliorating the accuracy of either questionnaire; and (3) single-point accuracy of these screening instruments in a community setting did not meet the requisite standard for development screening tests as set by current recommendations. This study raises important questions about how developmental screening can be performed, and we recommend additional research to elucidate a successful screening procedure.

De novo mutations in moderate or severe intellectual disability.

Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.

Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development.

The regulated proliferation and differentiation of neural stem cells before the generation and migration of neurons in the cerebral cortex are central aspects of mammalian development. Periventricular neuronal heterotopia, a specific form of mislocalization of cortical neurons, can arise from neuronal progenitors that fail to negotiate aspects of these developmental processes. Here we show that mutations in genes encoding the receptor-ligand cadherin pair DCHS1 and FAT4 lead to a recessive syndrome in humans that includes periventricular neuronal heterotopia. Reducing the expression of Dchs1 or Fat4 within mouse embryonic neuroepithelium increased progenitor cell numbers and reduced their differentiation into neurons, resulting in the heterotopic accumulation of cells below the neuronal layers in the neocortex, reminiscent of the human phenotype. These effects were countered by concurrent knockdown of Yap, a transcriptional effector of the Hippo signaling pathway. These findings implicate Dchs1 and Fat4 upstream of Yap as key regulators of mammalian neurogenesis.

Analysis of Clinical Features Predicting Etiologic Yield in the Assessment of Global Developmental Delay

OBJECTIVE. Global developmental delay is a common reason for presentation for neurologic evaluation. This study examined the role of clinical features in predicting the identification of an underlying cause for a childs global developmental delay. METHODS. Over a 10-year inclusive interval, the case records of all consecutive children <5 years of age referred to a single ambulatory practice setting for global developmental delay were systematically reviewed. The use of clinical features in predicting the identification of a specific underlying cause for a childs delay was tested using χ2 analysis. RESULTS. A total of 261 patients eventually met criteria for study inclusion. Mean age at initial evaluation was 33.6 months. An underlying cause was found in 98 children. Commonest etiologic groupings were genetic syndrome/chromosomal abnormality, intrapartum asphyxia, cerebral dysgenesis, psychosocial deprivation, and toxin exposure. Factors associated with the ability to eventually identify an underlying cause included female gender (40 of 68 vs 58 of 193), abnormal prenatal/perinatal history (52 of 85 vs 46 of 176), absence of autistic features (85 of 159 vs 13 of 102), presence of microcephaly (26 of 40 vs 72 of 221), abnormal neurologic examination (52 of 71 vs 46 of 190), and dysmorphic features (44 of 84 vs 54 of 177). In 113 children without any abnormal features identified on history or physical examination, routine screening investigations (karyotype, fragile X molecular genotyping, and neuroimaging) revealed an underlying etiology in 18. CONCLUSIONS. Etiologic yield in an unselected series of young children with global developmental delay is close to 40% overall and 55% in the absence of any coexisting autistic features. Clinical features are readily apparent that may enhance an expectation of a successful etiologic search. Screening investigations may yield an underlying cause.

KIF1A, an axonal transporter of synaptic vesicles, is mutated in hereditary sensory and autonomic neuropathy type 2

Hereditary sensory and autonomic neuropathy type II (HSANII) is a rare autosomal-recessive disorder characterized by peripheral nerve degeneration resulting in a severe distal sensory loss. Although mutations in FAM134B and the HSN2 exon of WNK1 were associated with HSANII, the etiology of a substantial number of cases remains unexplained. In addition, the functions of WNK1/HSN2 and FAM134B and their role in the peripheral nervous system remain poorly understood. Using a yeast two-hybrid screen, we found that KIF1A, an axonal transporter of synaptic vesicles, interacts with the domain encoded by the HSN2 exon. In parallel to this screen, we performed genome-wide homozygosity mapping in a consanguineous Afghan family affected by HSANII and identified a unique region of homozygosity located on chromosome 2q37.3 and spanning the KIF1A gene locus. Sequencing of KIF1A in this family revealed a truncating mutation segregating with the disease phenotype. Subsequent sequencing of KIF1A in a series of 112 unrelated patients with features belonging to the clinical spectrum of ulcero-mutilating sensory neuropathies revealed truncating mutations in three additional families, thus indicating that mutations in KIF1A are a rare cause of HSANII. Similarly to WNK1 mutations, pathogenic mutations in KIF1A were almost exclusively restricted to an alternatively spliced exon. This study provides additional insights into the molecular pathogenesis of HSANII and highlights the potential biological relevance of alternative splicing in the peripheral sensory nervous system.

Mutations in DCC cause congenital mirror movements.

Humans who display involuntary symmetrical limb movements carry mutations in a gene required for nerve growth across the midline. Mirror movements are involuntary contralateral movements that mirror voluntary ones and are often associated with defects in midline crossing of the developing central nervous system. We studied two large families, one French Canadian and one Iranian, in which isolated congenital mirror movements were inherited as an autosomal dominant trait. We found that affected individuals carried protein-truncating mutations in DCC (deleted in colorectal carcinoma), a gene on chromosome 18q21.2 that encodes a receptor for netrin-1, a diffusible protein that helps guide axon growth across the midline. Functional analysis of the mutant DCC protein from the French Canadian family revealed a defect in netrin-1 binding. Thus, DCC has an important role in lateralization of the human nervous system.

Mutations in C5ORF42 Cause Joubert Syndrome in the French Canadian Population

Joubert syndrome (JBTS) is an autosomal-recessive disorder characterized by a distinctive mid-hindbrain malformation, developmental delay with hypotonia, ocular-motor apraxia, and breathing abnormalities. Although JBTS was first described more than 40 years ago in French Canadian siblings, the causal mutations have not yet been identified in this family nor in most French Canadian individuals subsequently described. We ascertained a cluster of 16 JBTS-affected individuals from 11 families living in the Lower St. Lawrence region. SNP genotyping excluded the presence of a common homozygous mutation that would explain the clustering of these individuals. Exome sequencing performed on 15 subjects showed that nine affected individuals from seven families (including the original JBTS family) carried rare compound-heterozygous mutations in C5ORF42. Two missense variants (c.4006C>T [p.Arg1336Trp] and c.4690G>A [p.Ala1564Thr]) and a splicing mutation (c.7400+1G>A), which causes exon skipping, were found in multiple subjects that were not known to be related, whereas three other truncating mutations (c.6407del [p.Pro2136Hisfs*31], c.4804C>T [p.Arg1602*], and c.7477C>T [p.Arg2493*]) were identified in single individuals. None of the unaffected first-degree relatives were compound heterozygous for these mutations. Moreover, none of the six putative mutations were detected among 477 French Canadian controls. Our data suggest that mutations in C5ORF42 explain a large portion of French Canadian individuals with JBTS.

Array comparative genomic hybridization in global developmental delay.

Objective: Array‐based comparative genomic hybridization (array CGH) is an emerging technology that allows for the genome‐wide detection of DNA copy number changes (CNC) such as deletions or duplications. In this study, array‐based CGH was applied to a consecutive series of children with previously undiagnosed non‐syndromal global developmental delay (GDD) to assess potential etiologic yield. Methods: The children in this study were drawn from a previously reported consecutive series of children with well‐defined GDD. Almost all subjects had undergone prior karyotyping and neuroimaging studies with non‐diagnostic results. Array‐based CGH was undertaken using the SignatureChip® (1887 BACs representing 622 loci) with abnormalities verified by subsequent FISH analysis and testing of parents to distinguish between pathogenic and familial non‐pathogenic variants. Results: On CGH analysis in our study, 6 of 94 children (6.4%) had a causally related pathogenic CNC. Three were sub‐telomeric in location. An analysis of a variety of clinical factors revealed that only the presence of minor dysmorphic features (<3) was predictive of etiologic yield on CGH analysis (4/26 vs. 2/68, P = 0.05). Severity of delay was not found to be predictive. Interpretation: In children with non‐syndromal GDD, array‐based CGH has an etiologic yield of 6.4%. This suggests that this emerging technology may be of diagnostic value when applied subsequent to detailed history, physical examination, and targeted laboratory testing. Array CGH may merit consideration as a first‐tier test in the context of a child with unexplained GDD.

Mutations in TMEM231 cause Joubert syndrome in French Canadians

Background Joubert syndrome (JBTS) is a predominantly autosomal recessive disorder characterised by a distinctive midhindbrain malformation, oculomotor apraxia, breathing abnormalities and developmental delay. JBTS is genetically heterogeneous, involving genes required for formation and function of non-motile cilia. Here we investigate the genetic basis of JBTS in 12 French–Canadian (FC) individuals. Methods and results Exome sequencing in all subjects showed that six of them carried rare compound heterozygous mutations in CC2D2A or C5ORF42, known JBTS genes. In addition, three individuals (two families) were compound heterozygous for the same rare mutations in TMEM231(c.12T>A[p.Tyr4*]; c.625G>A[p.Asp209Asn]). All three subjects showed a severe neurological phenotype and variable presence of polydactyly, retinopathy and renal cysts. These mutations were not detected among 385 FC controls. TMEM231 has been previously shown to localise to the ciliary transition zone, and to interact with several JBTS gene products in a complex involved in the formation of the diffusion barrier between the cilia and plasma membrane. siRNA knockdown of TMEM231 was also shown to affect barrier integrity, resulting in a reduction of cilia formation and ciliary localisation of signalling receptors. Conclusions Our data suggest that mutations in TMEM231 cause JBTS, reinforcing the relationship between this condition and the disruption of the barrier at the ciliary transition zone.