Enrichment of rare copy number variation in children with developmental language disorder

Prevalence and heritability of parental-reported speech and/or language difficulties in a Swedish population-based twin sample

Background

Research on genetic and environmental influences on speech and/or language difficulties (SaLD) is sparse, with inconsistent heritability estimates. We aimed to estimate the prevalence of parental reported SaLD and the relative contributions of genetic and environmental factors for the phenotype using a Swedish population-based twin sample. We hypothesized that there would be a stronger genetic than environmental effect on SaLD.

Methods

Data were collected from The Child and Adolescent Twin Study in Sweden. The study sample included 16,774 twin pairs (16,946 males, 16,602 females), of which 5141 were monozygotic, 5861 dizygotic (DZ), and 5772 opposite-sex DZ pairs. The language items in the Autism-Tics, Attention-Deficit Hyperactivity Disorder, and other Comorbidities inventory were used to categorize individuals as having parental-reported SaLD. A classical twin design was used to estimate the relative contribution of genetic and environmental factors to the liability of SaLD.

Results

The prevalence of SaLD was 7.85% (95% confidence interval (CI) [7.57%-8.15%]) and 7.27% (95% CI [6.99%-7.55%]) when excluding individuals with autism and intellectual disability (ID). We also found that SaLD were significantly more prevalent in males than females with a ratio of 2:1. The heritability was estimated to be 75% (95% CI [67%-83%]) for SaLD. Shared environment played a significant role with an estimated contribution of 22% (95% CI [14%-30%]). The heritability estimate was reduced to 70% but with overlapping CI when excluding individuals with autism and ID.

Conclusions

We provide evidence that SaLD is common in the population and under strong genetic influence. Future studies should focus on mapping the genetic architecture of SaLD and related disorders.

Using rare genetic mutations to revisit structural brain asymmetry

Asymmetry between the left and right hemisphere is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variants, which typically exert small effects on brain-related phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We designed a pattern-learning approach to dissect the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior data fusion highlights the consequences of genetically controlled brain lateralization on uniquely human cognitive capacities.

Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder

Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.

Genetic outcomes in children with developmental language disorder: a systematic review

Introduction

Developmental language disorder (DLD) is a common childhood condition negatively influencing communication and psychosocial development. An increasing number of pathogenic variants or chromosomal anomalies possibly related to DLD have been identified. To provide a base for accurate clinical genetic diagnostic work-up for DLD patients, understanding the specific genetic background is crucial. This study aims to give a systematic literature overview of pathogenic variants or chromosomal anomalies causative for DLD in children.

Methods

We conducted a systematic search in PubMed and Embase on available literature related to the genetic background of diagnosed DLD in children. Included papers were critically appraised before data extraction. An additional search in OMIM was performed to see if the described DLD genes are associated with a broader clinical spectrum.

Results

The search resulted in 15,842 papers. After assessing eligibility, 47 studies remained, of which 25 studies related to sex chromosome aneuploidies and 15 papers concerned other chromosomal anomalies (SCAs) and/or Copy Number Variants (CNVs), including del15q13.1-13.3 and del16p11.2. The remaining 7 studies displayed a variety of gene variants. 45 (candidate) genes related to language development, including FOXP2, GRIN2A, ERC1, and ATP2C2. After an additional search in the OMIM database, 22 of these genes were associated with a genetic disorder with a broader clinical spectrum, including intellectual disability, epilepsy, and/or autism.

Conclusion

Our study illustrates that DLD can be related to SCAs and specific CNV's. The reported (candidate) genes (n = 45) in the latter category reflect the genetic heterogeneity and support DLD without any comorbidities and syndromic language disorder have an overlapping genetic etiology.

Using rare genetic mutations to revisit structural brain asymmetry

Asymmetry between the left and right brain is a key feature of brain organization. Hemispheric functional specialization underlies some of the most advanced human-defining cognitive operations, such as articulated language, perspective taking, or rapid detection of facial cues. Yet, genetic investigations into brain asymmetry have mostly relied on common variant studies, which typically exert small effects on brain phenotypes. Here, we leverage rare genomic deletions and duplications to study how genetic alterations reverberate in human brain and behavior. We quantitatively dissected the impact of eight high-effect-size copy number variations (CNVs) on brain asymmetry in a multi-site cohort of 552 CNV carriers and 290 non-carriers. Isolated multivariate brain asymmetry patterns spotlighted regions typically thought to subserve lateralized functions, including language, hearing, as well as visual, face and word recognition. Planum temporale asymmetry emerged as especially susceptible to deletions and duplications of specific gene sets. Targeted analysis of common variants through genome-wide association study (GWAS) consolidated partly diverging genetic influences on the right versus left planum temporale structure. In conclusion, our gene-brain-behavior mapping highlights the consequences of genetically controlled brain lateralization on human-defining cognitive traits.

Developmental language disorder - a comprehensive study of more than 46,000 individuals

Developmental language disorder (DLD) is characterized by enduring low language abilities with a significant functional impact, in the absence of biomedical conditions in which language impairment is part of a complex of impairments. There is a lack of awareness of DLD even among healthcare professionals. Here we estimated the prevalence of DLD and its links to reading and learning difficulties and physical and mental health in the Danish Blood Donor Study (N = 46,547), where DLD-related information is based on questionnaires (self-report). We compared the questionnaire-derived DLD status with the relevant language-related diagnoses from hospital registers. We also investigated the genetic architecture of DLD in a subset of the cohort (N = 18,380). DLD was significantly associated with reading and learning difficulties and poorer mental and physical health. DLD prevalence was 3.36%-3.70% based on questionnaires, compared with 0.04% in hospital registers. Our genetic analyses identified one genome-wide significant locus, but not a significant heritability estimate. Our study shows that DLD has health-related implications that may last into adulthood, and that DLD may be undiagnosed in general healthcare. Furthermore, DLD is likely more genetically heterogeneous than narrower developmental language phenotypes. Our results emphasize the need to raise awareness of DLD and consider criteria for molecular studies of DLD to reduce case heterogeneity.

Behaviors related to autism spectrum disorder in children with developmental language disorder and children with 22q11.2 deletion syndrome

Background and Aim

Children with Developmental Language Disorder (DLD) are at an increased risk to develop behaviors associated with Autism Spectrum Disorder (ASD). The relationship between early language difficulties and the occurrence of ASD-related behaviors in DLD is poorly understood. One factor that may hinder progress in understanding this relationship is the etiological heterogeneity of DLD. We therefore study this relationship in an etiologically homogeneous group of children, who share phenotypic characteristics with children with DLD: children with the 22q11.2 Deletion Syndrome (22q11DS). We compare children with 22q11DS, to children with DLD and age-matched typically developing children (TD).

Method

44 children with 22q11DS, 65 children with DLD and 81 TD children, between 3.0-6.5 years old, participated in a longitudinal cohort study that included a baseline measure and a follow-up measure with a 1-year interval. A parental questionnaire (SRS-2) was used to measure the incidence of behaviors in two key behavioral domains associated with ASD: Social Communication and Interaction and Restricted Repetitive Behaviors and Interests. At baseline, we assessed children's expressive and receptive language abilities as well as their intellectual functioning with standardized tests. We compared the distribution of ASD-related behaviors between the three groups. We used regression analyses to investigate whether language abilities at baseline predict ASD-related behavior at follow-up, accounting for ASD-related behavior at baseline, demographic variables and intellectual functioning.

Results

Both the children with 22q11DS and the children with DLD displayed significantly more ASD-related behaviors than the TD children. Over 30% of children in both clinical groups had scores exceeding the subclinical threshold for ASD in both behavioral domains. Both in 22q11DS and DLD, baseline receptive language scores were negatively correlated with ASD-related behaviors 1 year later, when controlling for baseline SRS-scores. However, this association was statistically significant only in children with 22q11DS, even when controlled for IQ-scores, and it was significantly stronger as than in the TD group. The strength of the association did not differ significantly between 22q11DS and DLD.

Conclusion

Both children with 22q11DS and children with DLD present with elevated rates of ASD-related behaviors at a preschool-age. Only in children with 22q11DS we observed that weaker receptive language skills were related to increased behavioral problems in the domain of social communication and interaction one year later.

Implications

Our findings indicate that relations between early language impairment and other behavioral phenotypes may be more feasible to detect in a subgroup of children with a homogeneous etiology, than in a group of children with a heterogeneous etiology (such as children with DLD). Our results in 22q11DS reveal that receptive language is especially important in predicting the occurrence of ASD-related behaviors. Future research is needed to determine to what extent receptive language predicts the occurrence of ASD-related behaviors in children with DLD, especially among those children with DLD with the weakest receptive language. Clinically, screening for ASD-related behaviors in children with developmental language difficulties is recommended from a young age, especially among children with receptive language difficulties.

The Genetic and Molecular Basis of Developmental Language Disorder: A Review

Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.

A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures

At least 5% of children present unexpected difficulties in expressing and understanding spoken language. This condition is highly heritable and often co-occurs with other neurodevelopmental disorders such as dyslexia and ADHD. Through an exome sequencing analysis, we identified a rare missense variant (chr16:84405221, GRCh38.p12) in the ATP2C2 gene. ATP2C2 was implicated in language disorders by linkage and association studies, and exactly the same variant was reported previously in a different exome sequencing study for language impairment (LI). We followed up this finding by genotyping the mutation in cohorts selected for LI and comorbid disorders. We found that the variant had a higher frequency in LI cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). Additionally, we observed that carriers of the rare variant identified from a general population cohort (N = 42, ALSPAC cohort) presented, as a group, lower scores on a range of reading and language-related measures compared to controls (N = 1825; minimum P = 0.002 for non-word reading). ATP2C2 encodes for an ATPase (SPCA2) that transports calcium and manganese ions into the Golgi lumen. Our functional characterization suggested that the rare variant influences the ATPase activity of SPCA2. Thus, our results further support the role of ATP2C2 locus in language-related phenotypes and pinpoint the possible effects of a specific rare variant at molecular level.

Genome-Wide Association Study of Motor Coordination

The ability to finely control our movement is key to achieving many of the educational milestones and life-skills we develop throughout our lives. Despite the centrality of coordination to early development, there is a vast gap in our understanding of the underlying biology. Like most complex traits, both genetics and environment influence motor coordination, however, the specific genes, early environmental risk factors and molecular pathways are unknown. Previous studies have shown that about 5% of school-age children experience unexplained difficulties with motor coordination. These children are said to have Developmental Coordination Disorder (DCD). For children with DCD, these motor coordination difficulties significantly impact their everyday life and learning. DCD is associated with poorer academic achievement, reduced quality of life, it can constrain career opportunities and increase the risk of mental health issues in adulthood. Despite the high prevalence of coordination difficulties, many children remain undiagnosed by healthcare professionals. Compounding under-diagnosis in the clinic, research into the etiology of DCD is severely underrepresented in the literature. Here we present the first genome-wide association study to examine the genetic basis of early motor coordination in the context of motor difficulties. Using data from the Avon Longitudinal Study of Parents and Children we generate a derived measure of motor coordination from four components of the Movement Assessment Battery for Children, providing an overall measure of coordination across the full range of ability. We perform the first genome-wide association analysis focused on motor coordination (N = 4542). No single nucleotide polymorphisms (SNPs) met the threshold for genome-wide significance, however, 59 SNPs showed suggestive associations. Three regions contained multiple suggestively associated SNPs, within five preliminary candidate genes: IQSEC1, LRCC1, SYNJ2B2, ADAM20, and ADAM21. Association to the gene IQSEC1 suggests a potential link to axon guidance and dendritic projection processes as a potential underlying mechanism of motor coordination difficulties. This represents an interesting potential mechanism, and whilst further validation is essential, it generates a direct window into the biology of motor coordination difficulties. This research has identified potential biological drivers of DCD, a first step towards understanding this common, yet neglected neurodevelopmental disorder.

Description and prediction of reading decoding skills in Swedish children with Developmental Language Disorder

AIM

Research is lacking in terms of reading decoding skills among clinical samples of Swedish-speaking children with Developmental Language Disorder (DLD).

METHOD

The present cross-sectional study included a sample of 61 children (8-12 years) with DLD attending school language units, years 1 to 5. Our purpose was to study reading decoding skills and predictors for decoding, such as a phonological processing skill (nonword repetition), working memory, and a family history of literacy problems.

RESULTS

The results on a combined measure of the word and nonword decoding indicated that only 18% of the children had age-adequate decoding skills. The proportion of age-adequate decoders did not change noticeably with the school year. The participants' decoding skills showed larger deviations to test norm means with higher school years. Hierarchical regression analysis showed that the best predictors of decoding skills were measures of working memory and nonword repetition, followed by school year. These factors significantly contributed to the variance in decoding among our sample of children with DLD. A family history of literacy problems made no contribution to the variance. Conclusions: The findings emphasize the necessity of assessing and following up on literacy development in children with DLD.

Past-tense inflection of non-verbs: a potential clinical marker of developmental language disorder in Swedish children

AIM

In this paper, we explore the performance of past-tense inflection of non-verbs (NVI) in children with developmental language disorder (DLD) and in typically developing controls, to investigate its accuracy as a clinical marker for Swedish-speaking children with DLD. Further, we investigate the relationship between NVI, nonword-repetition, and family history.

METHODS

The sample consists of 36 children with DLD (mean age 9;5 years) and 60 controls (mean age 9;2 years).

RESULTS

The DLD group performed significantly lower than the controls on the NVI task, with a large effect size of the difference (d = 1.52). Analysis of the clinical accuracy of NVI resulted in 80.6% sensitivity and 76.6% specificity. NVI was significantly and moderately associated with nonword-repetition in the controls, but not in the DLD group. A positive family history, 80.6% in the DLD group and 6.9% in the controls, was associated with lower performance on NVI. When controlling for group (DLD and controls), a non-significant association between family history and performance on the NVI task was found.

CONCLUSIONS

NVI is a potential clinical marker of DLD in Swedish school-aged children, but the current NVI task does not reach the level of being acceptable. Further development of the NVI task is warranted to improve its accuracy.

Genetic pathways involved in human speech disorders

Rare genetic variants that disrupt speech development provide entry points for deciphering the neurobiological foundations of key human capacities. The value of this approach is illustrated by FOXP2, a transcription factor gene that was implicated in speech apraxia, and subsequently investigated using human cell-based systems and animal models. Advances in next-generation sequencing, coupled to de novo paradigms, facilitated discovery of etiological variants in additional genes in speech disorder cohorts. As for other neurodevelopmental syndromes, gene-driven studies show blurring of boundaries between diagnostic categories, with some risk genes shared across speech disorders, intellectual disability and autism. Convergent evidence hints at involvement of regulatory genes co-expressed in early human brain development, suggesting that etiological pathways could be amenable for investigation in emerging neural models such as cerebral organoids.

Copy number variation burden does not predict severity of neurodevelopmental phenotype in children with a sex chromosome trisomy

Sex chromosome trisomies (SCTs) (XXX, XXY, and XYY karyotypes) are associated with an elevated risk of neurodevelopmental disorders. The range of severity of the phenotype is substantial. We considered whether this variable outcome was related to the presence of copy number variants (CNVs)-stretches of duplicated or deleted DNA. A sample of 125 children with an SCT were compared with 181 children of normal karyotype who had been given the same assessments. First, we compared the groups on measures of overall CNV burden: number of CNVs, total span of CNVs, and likely functional impact (probability of loss-of-function intolerance, pLI, summed over CNVs). Differences between groups were small relative to within-group variance and not statistically significant on overall test. Next, we considered whether a measure of general neurodevelopmental impairment was predicted by pLI summed score, SCT versus comparison group, or the interaction between them. There was a substantial effect of SCT/comparison status but the pLI score was not predictive of outcomes in either group. We conclude that variable presence of CNVs is not a likely explanation for the wide phenotypic variation in children with SCTs. We discuss methodological challenges of testing whether CNVs are implicated in causing neurodevelopmental problems.

Appropriateness of array-CGH in the ADHD clinics: A comparative study

Attention deficit hyperactivity disorder (ADHD) is one of the most common neurodevelopmental disorder with a worldwide prevalence of about 5%. The disorder is characterized by inattentive, hyperactive and impulsive behavior and is often comorbid with other neuropsychiatric conditions. Array comparative genomic hybridization (array-CGH) testing has been proved to be useful to detect chromosomal aberrations in several neuropsychiatric conditions including autism spectrum disorders (ASD) and intellectual disability (ID). The usefulness of array-CGH in the ADHD clinics is still debated and no conclusive evidence has been reached to date. We performed array-CGH in 98 children and adolescents divided in two similarly sized groups according to the clinical diagnosis: (a) one group diagnosed with ADHD as primary diagnosis; (b) the other group in which ADHD was co-morbid with ASD and/or ID. We detected pathogenetic and likely pathogenetic copy number variants (CNVs) in 12% subjects in which ADHD was co-morbid with autism and/or intellectual disability and in 8.5% subjects diagnosed with ADHD as primary diagnosis. Detection of CNVs of unknown clinical significance was similar in the two groups being 27% and 32%, respectively. Benign and likely benign CNVs accounted for 61% and 59.5% in the first and second group, respectively. Differences in the diagnostic yield were not statistically significant between the two groups (P > .05). Our data strongly suggest that array-CGH (a) is a valuable diagnostic tool to detect clinically significant CNVs in individuals with ADHD even in the absence of comorbidity with ASD and/or ID and (b) should be implemented routinely in the ADHD clinics.