BackgroundThere are limited reports of the use of whole exome sequencing (WES) as a clinical diagnostic tool. Moreover, there are no reports addressing the cost burden associated with genetic tests performed prior to WES.ObjectiveWe demonstrate the performance characteristics of WES in a pediatric setting by describing our patient cohort, calculating the diagnostic yield, and detailing the patients for whom clinical management was altered. Moreover, we examined the potential cost-effectiveness of WES by examining the cost burden of diagnostic workups.MethodsTo determine the clinical utility of our hospital’s clinical WES, we performed a retrospective review of the first 40 cases. We utilized dual bioinformatics analyses pipelines based on commercially available software and in-house tools.ResultsOf the first 40 clinical cases, we identified genetic defects in 12 (30%) patients, of which 47% of the mutations were previously unreported in the literature. Among the 12 patients with positive findings, seven have autosomal dominant disease and five have autosomal recessive disease. Ninety percent of the cohort opted to receive secondary findings and of those, secondary medical actionable results were returned in three cases. Among these positive cases, there are a number of novel mutations that are being reported here. The diagnostic workup included a significant number of genetic tests with microarray and single-gene sequencing being the most popular tests. Significantly, genetic diagnosis from WES led to altered patient medical management in positive cases.ConclusionWe demonstrate the clinical utility of WES by establishing the clinical diagnostic rate and its impact on medical management in a large pediatric center. The cost-effectiveness of WES was demonstrated by ending the diagnostic odyssey in positive cases. Also, in some cases it may be most cost-effective to directly perform WES. WES provides a unique glimpse into the complexity of genetic disorders.

CNOT1 is a member of the CCR4-NOT complex, which is a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. We report on 39 individuals with heterozygous de novo CNOT1 variants, including missense, splice site, and nonsense variants, who present with a clinical spectrum of intellectual disability, motor delay, speech delay, seizures, hypotonia, and behavioral problems. To link CNOT1 dysfunction to the neurodevelopmental phenotype observed, we generated variant-specific Drosophila models, which showed learning and memory defects upon CNOT1 knockdown. Introduction of human wild-type CNOT1 was able to rescue this phenotype, whereas mutants could not or only partially, supporting our hypothesis that CNOT1 impairment results in neurodevelopmental delay. Furthermore, the genetic interaction with autism-spectrum genes, such as ASH1L, DYRK1A, MED13, and SHANK3, was impaired in our Drosophila models. Molecular characterization of CNOT1 variants revealed normal CNOT1 expression levels, with both mutant and wild-type alleles expressed at similar levels. Analysis of protein-protein interactions with other members indicated that the CCR4-NOT complex remained intact. An integrated omics approach of patient-derived genomics and transcriptomics data suggested only minimal effects on endonucleolytic nonsense-mediated mRNA decay components, suggesting that de novo CNOT1 variants are likely haploinsufficient hypomorph or neomorph, rather than dominant negative. In summary, we provide strong evidence that de novo CNOT1 variants cause neurodevelopmental delay with a wide range of additional co-morbidities. Whereas the underlying pathophysiological mechanism warrants further analysis, our data demonstrate an essential and central role of the CCR4-NOT complex in human brain development.Master regulators controlling development include, but are not limited to, paired box (PAX) proteins, 1 SRY-related HMG-box (SOX) proteins, 2 and the relatively unknown CCR4-NOT protein complex. 3 Although the full spectrum of functional diversity for the CCR4-NOT complex has not yet been established, it has already become apparent that it is active on all levels of gene expression, from accessibility of the DNA to translation and degradation of mRNA. 4

Purpose: A few de novo missense variants in the cytoplasmic FMRP-interacting protein 2 (CYFIP2) gene have recently been described as a novel cause of severe intellectual disability, seizures, and hypotonia in 18 individuals, with p.Arg87 substitutions in the majority. Methods: We assembled data from 19 newly identified and all 18 previously published individuals with CYFIP2 variants. By structural modeling and investigation of WAVE-regulatory complex (WRC)-mediated actin polymerization in six patient fibroblast lines we assessed the impact of CYFIP2 variants on the WRC. Results: Sixteen of 19 individuals harbor two previously described and 11 novel (likely) disease-associated missense variants. We report p.Asp724 as second mutational hotspot (4/19 cases). Genotype-phenotype correlation confirms a consistently severe phenotype in p.Arg87 patients but a more variable phenotype in p. Asp724 and other substitutions. Three individuals with milder phenotypes carry putative loss-of-function variants, which remain of unclear pathogenicity. Structural modeling predicted missense variants to disturb interactions within the WRC or impair CYFIP2 stability. Consistent with its role in WRC-mediated actin polymerization we substantiate aberrant regulation of the actin cytoskeleton in patient fibroblasts. Conclusion: Our study expands the clinical and molecular spectrum of CYFIP2-related neurodevelopmental disorder and provides evidence for aberrant WRC-mediated actin dynamics as contributing cellular pathomechanism.

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Enzyme-based newborn screening for Mucopolysaccharidosis type I (MPS I) has a high false-positive rate due to the prevalence of pseudodeficiency alleles, often resulting in unnecessary and costly follow up. The glycosaminoglycans (GAGs), dermatan sulfate (DS) and heparan sulfate (HS) are both substrates for α-l-iduronidase (IDUA). These GAGs are elevated in patients with MPS I and have been shown to be promising biomarkers for both primary and second-tier testing. Since February 2016, we have measured DS and HS in 1213 specimens submitted on infants at risk for MPS I based on newborn screening. Molecular correlation was available for 157 of the tested cases. Samples from infants with MPS I confirmed by IDUA molecular analysis all had significantly elevated levels of DS and HS compared to those with confirmed pseudodeficiency and/or heterozygosity. Analysis of our testing population and correlation with molecular results identified few discrepant outcomes and uncovered no evidence of false-negative cases. We have demonstrated that blood spot GAGs analysis accurately discriminates between patients with confirmed MPS I and false-positive cases due to pseudodeficiency or heterozygosity and increases the specificity of newborn screening for MPS I.

Objective: To identify trajectories of depression symptoms in mothers of children with cancer from diagnosis/relapse through 5 years and examine maternal factors at diagnosis/relapse predicting membership in these trajectories. Method: Mothers (n ϭ 327; M age ϭ 37.6 years, SD ϭ 7.7 years; 85.9% White) reported depression symptoms near the time of their child's diagnosis/relapse and then again at 1-, 3-, and 5-years postdiagnosis/relapse. Mothers also reported perceived stress, coping (primary control, secondary control, and disengagement coping), and spirituality near the time of diagnosis. Latent class growth analysis was used to identify latent trajectories of depression symptoms, and a 3-step multinomial logistic regression tested covariate predictors of membership in the trajectories. Results: Three trajectories were identified: "low depression symptoms" (63.3%), "moderate depression symptoms" (31.5%), and "high depression symptoms" (5.2%). Mothers who used more primary and secondary control coping were more likely to be in the low depression symptom trajectory as compared with the moderate (OR ϭ 1.64, p ϭ .024 and OR ϭ 1.38, p ϭ .013, respectively) or high trajectories (OR ϭ 1.99, p ϭ .008 and OR ϭ 1.81, p ϭ .001, respectively). Conclusions: Although mothers of children with cancer generally displayed improved mental health further from diagnosis, mothers with more depression symptoms after diagnosis/ relapse displayed substantial stability in depression symptoms over the 5 years. Mothers of children with cancer may benefit from early screening of mental health and coping strategies, as well as interventions to bolster effective coping for those with elevated depression symptoms.

Objective: The majority of childhood cancer survivors develop at least one late effect subsequent to treatment (e.g., cardiovascular disease, obesity). Consistent engagement in recommended health behaviors may mitigate some of these conditions. Researchers have identified early survivorship as a teachable moment, yet few studies have examined positive health behaviors during this period. Methods: Families of children with cancer (ages 5–17) were initially recruited following a diagnosis or relapse of cancer. Three years post-diagnosis, survivors (n=82, Mage=13.3, SD=3.7) and their mothers (n=103, Mage=41.1, SD=7.6) completed a questionnaire assessing exercise, dietary, and sleep patterns among survivors. A follow-up assessment was conducted two years later. Mixed models tested change in health behavior over time. Results: At three- and five-years post-diagnosis, mother and self-report indicated that few survivors engaged in appropriate levels of low-intensity exercise, fruit/vegetable intake, and dairy consumption. However, most survivors engaged in recommended levels of high intensity exercise, fast food restriction, and sleep. Health behaviors remained stable over time, except for mother report of sleep duration, which decreased (b=−0.6, p<.001). Brain tumor diagnosis predicted a larger decrease in self-report of sleep duration compared to other diagnoses (p=.04). Income predicted fast food intake such that higher income was associated with decreased intake over time, whereas lower income was associated with increased intake (p=.04). Conclusions: During early survivorship, several health behaviors fell short of expectations for exercise and diet and did not improve upon reaching five years post-diagnosis. Providers should evaluate survivors’ health behaviors, including sleep, early and often, intervening when necessary.

Background-As clinical exome sequencing (CES) becomes more common, understanding which patients are most likely to benefit and in what manner is critical for the general pediatrics community to appreciate. Methods-523 patients referred to the Pediatric Genetics clinic at Michigan Medicine were systematically phenotyped by presence or absence of abnormalities for 13 body/organ systems by a Clinical Genetics team. All patients then underwent CES. Results-Overall, 30% of patients who underwent CES had an identified pathogenic mutation. The most common phenotypes were developmental delay (83%), neuromuscular system abnormalities (81%), and multiple congenital anomalies (42%). 67% of patients had a variant of uncertain significance (VUS) or gene of uncertain significance (GUS); 23% had no variants reported. There was a significant difference in the average number of body systems affected Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: