Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders.

While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.

Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.

PURPOSE: Pathogenic variants in SETD1B have been associated with a syndromic neurodevelopmental disorder including intellectual disability, language delay, and seizures. To date, clinical features have been described for 11 patients with (likely) pathogenic SETD1B sequence variants. This study aims to further delineate the spectrum of the SETD1B-related syndrome based on characterizing an expanded patient cohort. METHODS: We perform an in-depth clinical characterization of a cohort of 36 unpublished individuals with SETD1B sequence variants, describing their molecular and phenotypic spectrum. Selected variants were functionally tested using in vitro and genome-wide methylation assays. RESULTS: Our data present evidence for a loss-of-function mechanism of SETD1B variants, resulting in a core clinical phenotype of global developmental delay, language delay including regression, intellectual disability, autism and other behavioral issues, and variable epilepsy phenotypes. Developmental delay appeared to precede seizure onset, suggesting SETD1B dysfunction impacts physiological neurodevelopment even in the absence of epileptic activity. Males are significantly overrepresented and more severely affected, and we speculate that sex-linked traits could affect susceptibility to penetrance and the clinical spectrum of SETD1B variants. CONCLUSION: Insights from this extensive cohort will facilitate the counseling regarding the molecular and phenotypic landscape of newly diagnosed patients with the SETD1B-related syndrome.

Identification of microduplications at Xp21.2 and Xq13.1 in neurodevelopmental disorders.

BACKGROUND: Microduplications are a rare cause of disease in X-linked neurodevelopmental disorders but likely have been under reported due challenges in detection and interpretation. METHODS: We performed exome sequencing and subsequent microarray analysis in two families with a neurodevelopmental disorder. RESULTS: Here, we report on two families each with unique inherited microduplications at Xp21.2 and Xq13.1, respectively. In the first family, a 562.8-kb duplication at Xq13.1 covering DLG3, TEX11, SLC7A3, GDPD2, and part KIF4A was identified in a boy whose phenotype was characterized by delayed speech development, mild intellectual disability (ID), mild dysmorphic facial features, a heart defect, and neuropsychiatric symptoms. By interrogating all reported Xq13.1 duplications in individuals affected with a neurodevelopmental disorder, we provide evidence that this genomic region and particularly DLG3 might be sensitive to an increased dosage. In the second family with four affected males, we found a noncontinuous 223- and 204-kb duplication at Xp21.2, of which the first duplication covers exon 6 of IL1RAPL1. The phenotype of the male patients was characterized by delayed speech development, mild to moderate ID, strabismus, and neurobehavioral symptoms. The carrier daughter and her mother had learning difficulties. IL1RAPL1 shows nonrecurrent causal structural variation and is located at a common fragile site (FRAXC), prone to re-arrangement. CONCLUSION: In conclusion, we show that comprehensive clinical and genetic examination of microduplications on the X-chromosome can be helpful in undiagnosed cases of neurodevelopmental disease.

Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland.

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.

Correction: Phenotypic spectrum associated with a CRADD founder variant underlying frontotemporal predominant pachygyria in the Finnish population.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Phenotypic spectrum associated with a CRADD founder variant underlying frontotemporal predominant pachygyria in the Finnish population.

Intellectual disability (ID), megalencephaly, frontal predominant pachygyria, and seizures, previously called "thin" lissencephaly, are reported to be caused by recessive variants in CRADD. Among five families of different ethnicities identified, one homozygous missense variant, c.509G>A p.(Arg170His), was of Finnish ancestry. Here we report on the phenotypic variability associated for this potential CRADD founder variant in 22 Finnish individuals. Exome sequencing was used to identify candidate genes in Finnish patients presenting with ID. Targeted Sanger sequencing and restriction enzyme analysis were applied to screen for the c.509G>A CRADD variant in cohorts from Finland. Detailed phenotyping and genealogical studies were performed. Twenty two patients were identified with the c.509G>A p.(Arg170His) homozygous variant in CRADD. The majority of the ancestors originated from Northeastern Finland indicating a founder effect. The hallmark of the disease is frontotemporal predominant pachygyria with mild cortical thickening. All patients show ID of variable severity. Aggressive behavior was found in nearly half of the patients, EEG abnormalities in five patients and megalencephaly in three patients. This study provides detailed data about the phenotypic spectrum of patients with lissencephaly due to a CRADD variant that affects function. High inter- and intrafamilial phenotypic heterogeneity was identified in patients with pachygyria caused by the homozygous CRADD founder variant. The phenotype variability suggests that additional genetic and/or environmental factors play a role in the clinical presentation. Since frontotemporal pachygyria is the hallmark of the disease, brain imaging studies are essential to support the molecular diagnosis for individuals with ID and a CRADD variant.

Healthcare and guidelines: a population-based survey of recorded medical problems and health surveillance for people with Down syndrome.

BACKGROUND: Medical problems are described in a population of persons with Down syndrome. Health surveillance is compared to the recommendations of national guidelines. METHOD: Case records from the specialised and primary healthcare and disability services were analysed. RESULTS: A wide spectrum of age-specific medical and surgical problems was described. Congenital heart defects and middle ear infections were mostly experienced by younger people, while thyroid disease, epilepsy, and Alzheimer's disease were frequent among older people. Psychiatric disorders and behavioural problems were frequent in all age groups. CONCLUSIONS: Health surveillance remained insufficient, despite the guidelines available. A joint effort by healthcare and disability service providers is required to ensure that the medical needs of people with Down syndrome are adequately met across their entire lifespan. An active provision of healthcare and monitoring for this vulnerable group is needed.

[Update on current care guidelines: appropriate treatment of medical problems associated with Down's syndrome]. / Downin oireyhtymään liittyvien lääketieteellisten ongelmien hyvä hoito.

The lifetime prognosis of people with Down's syndrome has improved. Development of the services that health care and society can offer to such people is ongoing. These guidelines are targeted at defining what is required to further increase the lifespan and quality-of-life of people with Down's syndrome.

Ageing and health status in adults with intellectual disabilities: results of the European POMONA II study.

BACKGROUND: POMONA II was a European Commission public health-funded project. The research questions in this article focus on age-specific differences relating to environmental and lifestyle factors, and the 17 medical conditions measured by the POMONA Checklist of Health Indicators (P15). METHOD: The P15 was completed in a cross-sectional design for a stratified sample of 1,253 adults with ID across 14 European member states. RESULTS: Older people (55+) were more likely to live in larger residential homes. Rates of smoking and use of alcohol were lower than in the general population but were higher with older age. More than 60% of older adults had a sedentary lifestyle. Cataract, hearing disorder, diabetes, hypertension, osteoarthritis/arthrosis, and osteoporosis were positively associated with advancing age; allergies and epilepsy, negatively associated. CONCLUSIONS: Some evidence of health disparities was found for older people with ID, particularly in terms of underdiagnosed or inadequately managed preventable health conditions.

Sampling and ethical issues in a multicenter study on health of people with intellectual disabilities.

OBJECTIVES: To study health inequalities in persons with intellectual disabilities, representative and unbiased samples are needed. Little is known about sample recruitment in this vulnerable group. This study aimed to determine differences in ethical procedures and sample recruitment in a multicenter research on health of persons with intellectual disabilities. Study questions regarded the practical sampling procedure, how ethical consent was obtained in each country, and which person gave informed consent for each study participant. STUDY DESIGN AND SETTING: Exploratory, as part of a multicenter study, in 14 European countries. After developing identical guidelines for all countries, partners collected data on health indicators by orally interviewing 1,269 persons with intellectual disabilities. Subsequently, semistructured interviews were carried out with partners and researchers. RESULTS: Identification of sufficient study participants proved feasible. Sampling frames differed from nationally estimated proportions of persons with intellectual disabilities living with families or in residential settings. Sometimes, people with intellectual disabilities were hard to trace. Consent procedures and legal representation varied broadly. Nonresponse data proved unavailable. CONCLUSION: To build representative unbiased samples of vulnerable groups with limited academic capacities, international consensus on respectful consent procedures and tailored patient information is necessary.

Sensory impairments and health concerns related to the degree of intellectual disability in people with Down syndrome.

The relationship between poor health and cognitive impairment is not fully understood yet. People with Down syndrome are prone to a number of health problems, including congenital heart defect, visual impairment, hearing loss, autoimmune diseases, epilepsy, early-onset Alzheimer's disease and intellectual disability. Our aim was to assess the impact of impaired health on cognitive performance in people with Down syndrome. A series of people with Down syndrome (n=129) were studied for their intellectual disability, sensory impairments and health concerns. The medical and psychological records of all persons with Down syndrome in the Intellectual Disability Service Register of Kainuu from 1970 to 2004 were analysed. The detected health issues were related to the individuals' cognitive levels. Visual impairment, poor dental health and acute neurological disease were associated with the severity of intellectual disability and ageing.

Mental health, behaviour and intellectual abilities of people with Down syndrome.

The mental health, adaptive behaviour and intellectual abilities of people with Down syndrome (n=129) were evaluated in a population-based survey of social and health care records. Females had better cognitive abilities and speech production compared with males. Males had more behavioural problems than females. Behaviour suggestive of attention deficit hyperactivity disorder was often seen in childhood. Depression was diagnosed mainly in adults with mild to moderate intellectual disability. Autistic behaviour was most common in individuals with profound intellectual disability. Elderly people often showed decline of adaptive behaviour associated with Alzheimer's disease. Case descriptions are presented to illustrate the multitude of mental health and behavioural issues seen from childhood to old age in this population.