Genomic analyses in Cornelia de Lange Syndrome and related diagnoses: Novel candidate genes, <scp>genotype–phenotype</scp> correlations and common mechanisms

Cornelia de Lange Syndrome (CdLS) is a rare, dominantly inherited multisystem developmental disorder characterized by highly variable manifestations of growth and developmental delays, upper limb involvement, hypertrichosis, cardiac, gastrointestinal, craniofacial, and other systemic features. Pathogenic variants in genes encoding cohesin complex structural subunits and regulatory proteins (NIPBL, SMC1A, SMC3, HDAC8, and RAD21) are the major pathogenic contributors to CdLS. Heterozygous or hemizygous variants in the genes encoding these five proteins have been found to be contributory to CdLS, with variants in NIPBL accounting for the majority (&gt;60%) of cases, and the only gene identified to date that results in the severe or classic form of CdLS when mutated. Pathogenic variants in cohesin genes other than NIPBL tend to result in a less severe phenotype. Causative variants in additional genes, such as ANKRD11, EP300, AFF4, TAF1, and BRD4, can cause a CdLS‐like phenotype. The common role that these genes, and others, play as critical regulators of developmental transcriptional control has led to the conditions they cause being referred to as disorders of transcriptional regulation (or “DTRs”). Here, we report the results of a comprehensive molecular analysis in a cohort of 716 probands with typical and atypical CdLS in order to delineate the genetic contribution of causative variants in cohesin complex genes as well as novel candidate genes, genotype–phenotype correlations, and the utility of genome sequencing in understanding the mutational landscape in this population

Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features

SOX5 encodes a transcription factor involved in the regulation of chondrogenesis and the development of the nervous system. Despite its important developmental roles, SOX5 disruption has yet to be associated with human disease. We report one individual with a reciprocal translocation breakpoint within SOX5, eight individuals with intragenic SOX5 deletions (four are apparently de novo and one inherited from an affected parent), and seven individuals with larger 12p12 deletions encompassing SOX5. Common features in these subjects include prominent speech delay, intellectual disability, behavior abnormalities, and dysmorphic features. The phenotypic impact of the deletions may depend on the location of the deletion and consequently which of the three major SOX5 protein isoforms are affected. One intragenic deletion involving only untranslated exons was present in a more mildly affected subject, was inherited from a healthy parent and grandparent, and is similar to a deletion found in a control cohort. Therefore, some intragenic SOX5 deletions may have minimal phenotypic effect. Based on the location of the deletions in the subjects compared to the controls, the de novo nature of most of these deletions, and the phenotypic similarities among cases, SOX5 appears to be a dosage-sensitive, developmentally important gene

The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin–Siris syndrome

Purpose: Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods: Clinicians entered clinical data in an extensive web-based survey. Results: 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion: There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features

A National Profile of Children with Down Syndrome: Disease Burden, Access to Care, and Family Impact

Objective: To measure the co-morbidities associated with Down syndrome compared with those in other children with special health care needs (CSHCN). Additionally, to examine reported access to care, family impact, and unmet needs for children with Down syndrome compared with other CSHCN. Study design: An analysis was conducted on the nationally representative 2005 to 2006 National Survey of Children with Special Health Care Needs. Bivariate analyses compared children with Down syndrome with all other CSHCN. Multivariate analyses examined the role of demographic, socioeconomic, and medical factors on measures of care receipt and family impact. Results: An estimated 98 000 CSHCN have Down syndrome nationally. Compared with other CSHCN, children with Down syndrome had a greater number of co-morbid conditions, were more likely to have unmet needs, faced greater family impacts, and were less likely to have access to a medical home. These differences become more pronounced for children without insurance and from low socioeconomic status families. Conclusions: Children with Down syndrome disproportionately face greater disease burden, more negatively pronounced family impacts, and greater unmet needs than other CSHCN. Promoting medical homes at the practice level and use of those services by children with Down syndrome and other CSHCN may help mitigate these family impacts

The metabolic evaluation of the child with an intellectual developmental disorder: Diagnostic algorithm for identification of treatable causes and new digital resource

Intellectual developmental disorders (IDD), characterized by significant impairment of cognitive functions, with limitations of learning, adaptive behavior and skills, are frequent (2.5% of the population affected) and present with significant co-morbidity. The burden of IDD, in terms of emotional suffering and associated health care costs, is significant; prevention and treatment therefore are important A systematic literature review, updated in 2013, identified 89 inborn errors of metabolism (IEMs), which present with IDD as prominent feature and are amenable to causal therapy. Therapeutic effects include improvement and/or stabilization of psychomotor/ cognitive development, behavior/psychiatric disturbances, seizures, neurologic and systemic manifestations. The levels of available evidence for the various treatments range from Level 1b, c (n = 5); Level 2a, b, c (n = 14); Level 4 (n = 53), and Levels 4-5 (n = 27). For a target audience comprising clinical and biochemical geneticists, child neurologists and developmental pediatricians, five experts translated....this data into a 2-tiered diagnostic algorithm: The first tier comprises metabolic "screening" tests in urine and blood, which are relatively accessible, affordable, less invasive, and have the potential to identify 60% of all treatable IEMs. The second tier investigations for the remaining disorders are ordered based on individual clinical signs and symptoms. This algorithm is supported by an App www.treatable-id.org, which comprises up-to-date information on all 89 IEMs, relevant diagnostic tests, therapies and a search function based on signs and symptoms. These recommendations support the clinician in early identification of treatable IEMs in the child with IDD, allowing for timely initiation of therapy with the potential to improve neurodevelopmental outcomes. The need for future studies to determine yield and usefulness of these recommendations, with subsequent updates and improvements to developments in the field, is outlined. (c) 2014 The Authors. Published by Elsevier Inc. All rights reserve

Access to Genetic Counseling for Children with Autism, Down syndrome and Intellectual Disabilities

OBJECTIVE: We examined the need for genetic counseling services (GCS) for families of children with autism spectrum disorder (ASD), Down syndrome (DS), and/or mental retardation (MR) and factors that influence the receipt of needed GCS for those children relative to other children with special health care needs (CSHCN). METHODS: Analysis was conducted on the 2005–2006 National Survey of Children With Special Health Care Needs, a nationally representative sample. Bivariate analyses were conducted by examining need for and receipt of GCS for children with ASD, DS, and/or MR and other CSHCN as well as differences by contextual variables using the health belief model (HBM). Logistic regression analyses were conducted to assess the relative impact of receipt of needed GCS by HBM constructs. RESULTS: Families of children with diagnoses of ASD, DS, and/or MR perceive significantly higher need for GCS than other CSHCN. The presence of a medical home is the single most important factor in facilitating access to GCS, together with the presence of insurance, particularly private or a combination of private and public insurance. As income and education attainment decrease, barriers to GCS rise. CONCLUSIONS: This analysis supports strategies for improving linkages between specialty providers and the medical home at which primary care is delivered. Increased effort should be made to attend to those who experience barriers that result from lack of insurance, poverty, low education, or racial or ethnic differences. Health professionals need to collaborate in developing solutions to underinsurance or lack of insurance for CSHCN

Mapping Disease at an Approximated Individual Level Using Aggregate Data: A Case Study of Mapping New Hampshire Birth Defects

Background: Limited by data availability, most disease maps in the literature are for relatively large and subjectively-defined areal units, which are subject to problems associated with polygon maps. High resolution maps based on objective spatial units are needed to more precisely detect associations between disease and environmental factors. Method: We propose to use a Restricted and Controlled Monte Carlo (RCMC) process to disaggregate polygon-level location data to achieve mapping aggregate data at an approximated individual level. RCMC assigns a random point location to a polygon-level location, in which the randomization is restricted by the polygon and controlled by the background (e.g., population at risk). RCMC allows analytical processes designed for individual data to be applied, and generates high-resolution raster maps. Results: We applied RCMC to the town-level birth defect data for New Hampshire and generated raster maps at the resolution of 100 m. Besides the map of significance of birth defect risk represented by p-value, the output also includes a map of spatial uncertainty and a map of hot spots. Conclusions: RCMC is an effective method to disaggregate aggregate data. An RCMC-based disease mapping maximizes the use of available spatial information, and explicitly estimates the spatial uncertainty resulting from aggregation

Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity

Mutations in KDM5C are an important cause of X-linked intellectual disability in males. KDM5C encodes a histone demethylase, suggesting that alterations in chromatin landscape may contribute to disease. We used primary patient cells and biochemical approaches to investigate the effects of patient mutations on KDM5C expression, stability and catalytic activity. We report and characterize a novel nonsense mutation, c.3223delG (p.V1075Yfs*2), which leads to loss of KDM5C protein. We also characterize two KDM5C missense mutations, c.1439C&gt;T (p.P480L) and c.1204G&gt;T (p.D402Y) that are compatible with protein production, but compromise stability and enzymatic activity. Finally, we demonstrate that a c.2T&gt;C mutation in the translation initiation codon of KDM5C results in translation re-start and production of a N-terminally truncated protein (p.M1_E165del) that is unstable and lacks detectable demethylase activity. Patient fibroblasts do not show global changes in histone methylation but we identify several up-regulated genes, suggesting local changes in chromatin conformation and gene expression. This thorough examination of KDM5C patient mutations demonstrates the utility of examining the molecular consequences of patient mutations on several levels, ranging from enzyme production to catalytic activity, when assessing the functional outcomes of intellectual disability mutations