VACTERL association etiology: The impact of de novo and rare copy number variations

Copy number variations (CNVs), either DNA gains or losses, have been found at common regions throughout the human genome. Most CNVs neither have a pathogenic significance nor result in disease-related phenotypes but, instead, reflect the normal population variance. However, larger CNVs, which often arise de novo, are frequently associated with human disease. A genetic contribution has long been suspected in VACTERL (Vertebral, Anal, Cardiac, TracheoEsophageal fistula, Renal and Limb anomalies) association. The anomalies observed in this association overlap with several monogenetic conditions associated with mutations in specific genes, e.g. Townes Brocks (SALL1), Feingold syndrome (MYCN) or Fanconi anemia. So far VACTERL association has typically been considered a diagnosis of exclusion. Identifying recurrent or de novo genomic variations in individuals with VACTERL association could make it easier to distinguish VACTERL association from other syndromes and could provide insight into disease mechanisms. Sporadically, de novo CNVs associated with VACTERL are described in literature. In addition to this literature review of genomic variation in published VACTERL association patients, we describe CNVs present in 68 VACTERL association patients collected in our institution. De novo variations (>30 kb) are absent in our VACTERL association cohort. However, we identified recurrent rare CNVs which, although inherited, could point to mechanisms or biological processes contributing to this constellation of developmental defects

Copy number variations in 375 patients with oesophageal atresia and/or tracheoesophageal fistula

Oesophageal atresia (OA) with or without tracheoesophageal fistula (TOF) are rare anatomical congenital malformations whose cause is unknown in over 90% of patients. A genetic background is suggested, and among the reported genetic defects are copy number variations (CNVs). We hypothesized that CNVs contribute to OA/TOF development. Quantifying their prevalence could aid in genetic diagnosis and clinical care strategies. Therefore, we profiled 375 patients in a combined Dutch, American and German cohort via genomic microarray and compared the CNV profiles with their unaffected parents and published control cohorts. We identified 167 rare CNVs containing genes (frequency<0.0005 in our in-house cohort). Eight rare CNVs - in six patients - were de novo, including one CNV previously associated with oesophageal disease. (hg19 chr7:g.(143820444-143839360)-(159119486-159138663)del) 1.55% of isolated OA/TOF patients and 1.62% of patients with additional congenital anomalies had de novo CNVs. Furthermore, three (15q13.3, 16p13.3 and 22q11.2) susceptibility loci were identified based on their overlap with known OA/TOF-associated CNV syndromes and overlap with loci in published CNV association case-control studies in developmental delay. Our study suggests that CNVs contribute to OA/TOF development. In addition to the identified likely deleterious de novo CNVs, we detected 167 rare CNVs. Although not directly disease-causing, these CNVs might be of interest, as they can act as a modifier in a multiple hit model, or as the second hit in a recessive condition

Artificial neural network trained on smartphone behavior can trace epileptiform activity in epilepsy

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The connectivity index: An effective metric for grading epileptogenicity

OBJECTIVE The aim of this study was to investigate the performance of a metric of functional connectivity to classify and grade the excitability of brain regions based on evoked potentials in response to single-pulse electrical stimulation (SPES). METHODS Patients who underwent 1-Hz frequency stimulation at prospectively selected contacts between 2003 and 2014 at the Yale Comprehensive Epilepsy Center were included. The stimulated contacts were classified as the seizure onset zone (SOZ), highly irritative zone (possibly epileptogenic irritative zone [IZp]), and control contacts not involved in the epileptic activity. Response contacts were classified as SOZ, active interictal irritative zone (IZ), quiet, or other. The normalized number of responses was defined as the number of contacts with any evoked responses divided by the total number of recorded contacts, and the normalized distance is the ratio of the average distance between the site of stimulation and sites of evoked responses to the average distances between the site of stimulation and all other recording contacts. A new metric that the authors labeled the connectivity index (CI) is defined as the product of the 2 values. RESULTS A total of 57 stimulation sessions in 22 patients were analyzed. The CI of the SOZ was higher than for control contacts (median CI of 0.74 vs 0.16, p = 0.0002). The evoked responses after stimulation of SOZ were seen at further distances compared to control (median normalized distance 0.96 vs 0.62, p = 0.0005). It was 1.8 times more likely that a response would be recorded at the SOZ than in nonepileptic contacts after stimulation of a control site. Habitual seizures were triggered in 27% of patients and 35% of SOZ contacts (median stimulation intensity 4 mA) but in none of the control or IZp contacts. Non-SOZ contacts in multifocal or poor surgical outcome cases had a higher CI than non-SOZ contacts in patients with localizable onsets (median CI of 0.5 vs 0.12, p = 0.04). There was a correlation between the stimulation current intensity and the normalized number of evoked responses (r = + 0.49, p = 0.01) but not with distance (r = + 0.1, p = 0.64). CONCLUSIONS The authors found enhanced connectivity when stimulating the SOZ compared to stimulating control contacts; responses were more distant as well. Habitual auras and seizures provoked by SPES were highly predictive of brain sites involved in seizure generation.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Stromal Fat4 acts non-autonomously with Dchs1/2 to restrict the nephron progenitor pool

International audienceRegulation of the balance between progenitor self-renewal and differentiation is crucial to development. In the mammalian kidney, reciprocal signalling between three lineages (stromal, mesenchymal and ureteric) ensures correct nephron progenitor self-renewal and differentiation. Loss of either the atypical cadherin FAT4 or its ligand Dachsous 1 (DCHS1) results in expansion of the mesenchymal nephron progenitor pool, called the condensing mesenchyme (CM). This has been proposed to be due to misregulation of the Hippo kinase pathway transcriptional co-activator YAP. Here, we use tissue-specific deletions to prove that FAT4 acts non-autonomously in the renal stroma to control nephron progenitors. We show that loss of Yap from the CM in Fat4-null mice does not reduce the expanded CM, indicating that FAT4 regulates the CM independently of YAP. Analysis of Six2(-/-);Fat4(-/-) double mutants demonstrates that excess progenitors in Fat4 mutants are dependent on Six2, a crucial regulator of nephron progenitor self-renewal. Electron microscopy reveals that cell organisation is disrupted in Fat4 mutants. Gene expression analysis demonstrates that the expression of Notch and FGF pathway components are altered in Fat4 mutants. Finally, we show that Dchs1, and its paralogue Dchs2, function in a partially redundant fashion to regulate the number of nephron progenitors. Our data support a model in which FAT4 in the stroma binds to DCHS1/2 in the mouse CM to restrict progenitor self-renewal

Delta rhythm in wakefulness: Evidence from intracranial recordings in human beings

A widely accepted view is that wakefulness is a state in which the entire cortical mantle is persistently activated, and therefore desynchronized. Consequently, the EEG is dominated by low-amplitude, high-frequency fluctuations. This view is currently under revision because the 1-4 Hz delta rhythm is often evident during "quiet" wakefulness in rodents and nonhuman primates. Here we used intracranial EEG recordings to assess the occurrence of delta rhythm in 18 awake human beings. Our recordings reveal rhythmic delta during wakefulness at 10% of all recording sites. Delta rhythm could be observed in a single cortical lobe or in multiple lobes. Sites with high delta could flip between high and low delta power or could be in a persistently high delta state. Finally, these sites were rarely identified as the sites of seizure onset. Thus rhythmic delta can dominate the background operation and activity of some neocortical circuits in awake human beings.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Identification of Critical Regions and Candidate Genes for Cardiovascular Malformations and Cardiomyopathy Associated with Deletions of Chromosome 1p36

Genetics of disease, diagnosis and treatmen