Biology subjects

St Pourcain, B.

Publications and source records attributed to St Pourcain, B..

12 recordsLinked to original sources

bioRxiv2025

Disentangling multivariate relationships between cognition, language and social traits: structures of G, E, and rGE

BackgroundCognitive, language, and social abilities are complex, heritable and intertwined traits shaping childrens development and later mental health. To better understand cross-trait interrelationships, we model here the structures of shared genomic and shared non-genomic/residual (i.e. broadly environmental) influences, and their correlation (rGE), investigating cognitive, language, and social behavioural/communication measures. MethodsData were obtained for unrelated children (8-13 years) from two population-based cohorts: the UK Avon Longitudinal Study of Parents and Children (ALSPAC, N[≤]6,543) and the US Adolescent Brain Cognitive DevelopmentSM (ABCD) Study (N[≤]4,412), and analyses were carried out implementing an extended data-driven genetic-relationship-matrix structural equation modelling (GRM-SEM) approach. ResultsIn ALSPAC, we identified two independent phenotypic domains, each captured by a structurally matching pair consisting of a genomic (A) and a non-genomic/residual (E) factor. The first domain reflected cognitive/language difficulties, with the largest genomic and residual factor loadings ({lambda}A and {lambda}E, respectively) for verbal IQ ({lambda}A=0.73(SE=0.05); {lambda}E=0.57(SE=0.07)). The second domain captured social difficulties, with the largest {lambda}A and {lambda}E for social communication measures ({lambda}A=0.39(SE=0.10); {lambda}E=0.82(SE=0.10)). We identified trait-specific rGE between pairs of A and E factors with different directions of effect (cognition/language rGE=0.89(SE=0.18), social rGE=-0.62(SE=0.17)). rGE patterns were linked to increased measurable A and E contributions for cognition/language difficulties, but decreased contributions for social problems. Analyses in ABCD confirmed the two domains for E and phenotypic structures, although genomic contributions were low. ConclusionsIn childhood, cognitive/language abilities versus social abilities are influenced by distinct genomic and/or environmental factors, potentially interlinked through trait-specific rGE, suggesting differences in developmental processes.

genomics↗

bioRxiv2024

Preschool musicality is associated with school-age communication abilities through genes related to rhythmicity

Early-life musical engagement is an understudied but developmentally important and heritable precursor of later (social) communication and language abilities. This study aims to uncover the aetiological mechanisms linking musical to communication abilities. We derived polygenic scores (PGS) for self-reported beat synchronisation abilities (PGSrhythmicity) in children (N[≤]6,737) from the Avon Longitudinal Study of Parents and Children and tested their association with preschool musical (0.5-5 years) and school-age (social) communication and cognition-related abilities (9-12 years). We further assessed whether relationships between preschool musicality and school-age communication are shared through PGSrhythmicity, using structural equation modelling techniques. PGSrhythmicity were associated with preschool musicality (Nagelkerke-R2=0.70-0.79%), and school-age communication and cognition-related abilities (R2=0.08-0.41%), but not social communication. We identified links between preschool musicality and school-age speech-and syntax-related communication abilities as captured by known genetic influences underlying rhythmicity (shared effect {beta}=0.0065(SE=0.0021), p=0.0016), above and beyond general cognition, strengthening support for early music intervention programmes.

genetics↗

bioRxiv2020

The developmental genetic architecture of vocabulary skills during the first three years of life: Capturing emerging associations with later-life reading and cognition

Individual differences in early-life vocabulary measures are heritable and associated with subsequent reading and cognitive abilities, although the underlying mechanisms are little understood. Here, we (i) investigate the developmental genetic architecture of expressive and receptive vocabulary in toddlerhood and (ii) assess origin and developmental stage of emerging genetic associations with mid-childhood verbal and non-verbal skills. Studying up to 6,524 unrelated children from the population-based Avon Longitudinal Study of Parents and Children (ALSPAC) cohort, we dissected the phenotypic variance of longitudinally assessed early-life vocabulary measures (15-38 months) and later-life reading and cognitive skills (7-8 years) into genetic and residual components, by fitting multivariate structural equation models to genome-wide genetic-relationship matrices. Our findings show that the genetic architecture of early-life vocabulary is dynamic, involving multiple distinct genetic factors. Two of them are developmentally stable and contribute to genetic variation in mid-childhood skills: Genetic links with later-life verbal abilities (reading, verbal intelligence) emerged with expressive vocabulary at 24 months. The underlying genetic factor explained 10.1% variation (path coefficient: 0.32(SE=0.06)) in early language, but also 6.4% (path coefficient: 0.25(SE=0.12)) and 17.9% (path coefficient: 0.42(SE=0.13)) variation in mid-childhood reading and verbal intelligence, respectively. An independent stable genetic factor was identified for receptive vocabulary at 38 months, explaining 2.1% (path coefficient: 0.15(SE=0.07)) phenotypic variation. This genetic factor was also linked to both verbal and non-verbal cognitive abilities in mid-childhood, accounting for 24.7% of the variation in non-verbal intelligence (path coefficient: 0.50(SE=0.08)), 33.0% in reading (path coefficient: 0.57(SE=0.07)) and 36.1% in verbal intelligence (path coefficient: 0.60(0.10)), corresponding to the majority of genetic variance ([≥]66.4%). Thus, the genetic foundations of mid-childhood reading and cognition are diverse. They involve at least two independent genetic factors that emerge at different developmental stages during early language development and may implicate differences in cognitive processes that are already detectable during toddlerhood. Author summaryDifferences in the number of words young children produce (expressive vocabulary) and understand (receptive vocabulary) can be partially explained by genetic factors, and are related to reading and cognitive abilities later in life. Here, we studied genetic influences underlying word production and understanding during early development (15-38 months) and their genetic relationship with mid-childhood reading and cognitive skills (7-8 years), based on longitudinal phenotype measures and genome-wide genetic data from up to 6,524 unrelated children. We showed that vocabulary skills assessed at different stages during early development are influenced by distinct genetic factors, two of which also contribute to genetic variation in mid-childhood skills, suggesting developmental stability: Genetic sources emerging for word production skills at 24 months were linked to subsequent verbal abilities, including mid-childhood reading and verbal intelligence performance. A further independent genetic factor was identified that related to word comprehension at 38 months and also contributed to variation in later verbal as well as non-verbal abilities during mid-childhood. Thus, the genetic foundations of mid-childhood reading and cognition involve at least two independent genetic factors that emerge during early-life langauge development and may implicate differences in overarching cognitive mechanisms.

genetics↗

bioRxiv2020

The Multivariate Genetic Architecture of Literacy-, Language- and Working Memory-related Abilities as Captured by Genome-wide Variation

There is genetic overlap between many measures of literacy, language and phonological working memory (PWM) though our knowledge of multivariate genetic architectures is incomplete. Here, we directly modeled genetic trait interrelationships in unrelated UK youth (8-13 years, N=6,453), as captured by genome-wide relationship matrices, using novel structural equation modeling techniques. We identified, besides shared genetic factors across different domains (explaining 91-97% genetic variance in literacy-related measures such as passage reading fluency, spelling, phonemic awareness, 44% in oral language and 53% in PWM), evidence for distinct cognitive abilities; trait-specific genetic influences ranged between 47% for PWM to 56% for oral language. Among reading fluency measures (non-word, word and passage reading), single-word reading was genetically most diverse. Multivariate genetic and residual covariance patterns showed concordant effect directionality, except for near-zero residual correlations between oral language and literacy-related abilities. These findings suggest differences in etiological mechanisms and trait modifiability even among genetically highly correlated skills.

genetics↗

bioRxiv2019

The amplification of genetic factors for early vocabulary during children's language and literacy development

The heritability of language and literacy skills increases during development. The underlying mechanisms are little understood, and may involve (i) the amplification of early genetic influences and/or (ii) the emergence of novel genetic factors (innovation). Here, we use multivariate structural equation models to quantify these processes, as captured by genome-wide genetic markers. Studying expressive and receptive vocabulary at 38 months and subsequent language, literacy and cognitive skills (7-13 years) in unrelated children (ALSPAC: N[≤]6,092), we found little support for genetic innovation during mid-childhood and adolescence. Instead, genetic factors for early vocabulary, especially those unique to receptive skills, were amplified. Explaining as little as 3.9%(SE=1.8%) variation in early language, the same genetic influences accounted for 25.7%(SE=6.4%) to 45.1%(SE=7.6%) variation in verbal intelligence and literacy skills, but also performance intelligence, capturing the majority of SNP-heritability ([≤]99%). This suggests that complex verbal and non-verbal cognitive skills originate developmentaly in early receptive language.

genetics↗

bioRxiv2019

Genetic Association Study of Childhood Aggression across raters, instruments and age

Childhood aggressive behavior (AGG) has a substantial heritability of around 50%. Here we present a genome-wide association meta-analysis (GWAMA) of childhood AGG, in which all phenotype measures across childhood ages from multiple assessors were included. We analyzed phenotype assessments for a total of 328 935 observations from 87 485 children aged between 1.5 and 18 years, while accounting for sample overlap. We also meta-analyzed within subsets of the data - i.e. within rater, instrument and age. SNP-heritability for the overall meta-analysis (AGGoverall) was 3.31% (SE=0.0038). We found no genome-wide significant SNPs for AGGoverall. The gene-based analysis returned three significant genes: ST3GAL3 (P=1.6E-06), PCDH7 (P=2.0E-06) and IPO13 (P=2.5E-06). All three genes have previously been associated with educational traits. Polygenic scores based on our GWAMA significantly predicted aggression in a holdout sample of children (variance explained = 0.44%) and in retrospectively assessed childhood aggression (variance explained = 0.20%). Genetic correlations (rg) among rater-specific assessment of AGG ranged from rg =0.46 between self- and teacher-assessment to rg =0.81 between mother- and teacher-assessment. We obtained moderate to strong rgs with selected phenotypes from multiple domains, but hardly with any of the classical biomarkers thought to be associated with AGG. Significant genetic correlations were observed with most psychiatric and psychological traits (range |rg| : 0.19 - 1.00), except for obsessive-compulsive disorder. Aggression had a negative genetic correlation (rg =~ -0.5) with cognitive traits and age at first birth. Aggression was strongly genetically correlated with smoking phenotypes (range |rg| : 0.46 - 0.60). The genetic correlations between aggression and psychiatric disorders were weaker for teacher-reported AGG than for mother- and self-reported AGG. The current GWAMA of childhood aggression provides a powerful tool to interrogate the rater-specific genetic etiology of AGG.

genomics↗

bioRxiv2019

Shared polygenetic variation between ASD and ADHD exerts opposite association patterns with educational attainment

Insight into shared polygenetic architectures affects our understanding of neurodevelopmental disorders. Here, we investigate evidence for pleiotropic mechanisms that may explain the comorbidity between Autism Spectrum Disorder (ASD) and Attention-Deficit/Hyperactivity Disorder (ADHD). These complex neurodevelopmental conditions often co-occur, but differ in their polygenetic association patterns, especially with educational attainment (EA), showing discordant association effects. Using multivariable regression analyses and existing genome-wide summary statistics based on 10,610 to 766,345 individuals, we demonstrate that EA-related polygenic variation is shared between ASD and ADHD. We show that different combinations of the same ASD and ADHD risk-increasing alleles can simultaneously re-capture known ASD-related positive and ADHD-related negative associations with EA. Such patterns, although to a lesser degree, were also present for combinations of other psychiatric disorders. These findings suggest pleiotropic mechanisms, where the same polygenic sites can encode multiple independent, even discordant, association patterns without involving distinct loci, and have implications for cross-disorder investigations.

genetics↗

bioRxiv2018

Low-frequency variation in TP53 has large effects on head circumference and intracranial volume

Cranial growth and development affects the closely related traits of head circumference (HC) and intracranial volume (ICV). Here we model the developmental genetic architecture of HC, showing this is genetically stable and correlated with genetic determinants of ICV. Investigating up to 46,000 children and adults of European descent, we identify association with final HC and/or final ICV+HC at 9 novel common and low-frequency loci, illustrating that genetic variation from a wide allele frequency spectrum contributes to cranial growth. The largest effects are reported for low-frequency variants within TP53, with 0.5 cm wider heads in increaser-allele carriers versus non-carriers during mid-childhood.

genetics↗

bioRxiv2018

Genome Wide Association Scan identifies new variants associated with a cognitive predictor of dyslexia.

Developmental dyslexia (DD) is one of the most prevalent learning disorders among children and is characterized by deficits in different cognitive skills, including reading, spelling, short term memory and others. To help unravel the genetic basis of these skills, we conducted a Genome Wide Association Study (GWAS), including nine cohorts of reading-impaired and typically developing children of European ancestry, recruited across different countries (N=2,562-3,468).\n\nWe observed a genome-wide significant effect (p<1x10-8) on rapid automatized naming of letters (RANlet) for variants on 18q12.2 within MIR924HG (micro-RNA 924 host gene; p = 4.73x10-9), and a suggestive association on 8q12.3 within NKAIN3 (encoding a cation transporter; p = 2.25 x10-8). RAN represents one of the best universal predictors of reading fluency across orthographies and linkage to RAN has been previously reported within CELF4 (18q12.2), a gene highly expressed in the fetal brain which is co-expressed with NKAIN3 and predicted to be a target of MIR924. These findings suggest new candidate DD susceptibility genes and provide insights into the genetics and neurobiology of dyslexia.

genomics↗

bioRxiv2018

Disentangling genetic overlap between Attention-Deficit/Hyperactivity Disorder, literacy and language

Interpreting polygenic overlap between ADHD and both literacy- and language-related impairments is challenging as genetic confounding can bias associations. Here, we investigate evidence for links between polygenic ADHD risk and multiple literacy- and language-related abilities (LRAs), assessed in UK children (N[≤]5,919), conditional on genetic effects shared with educational attainment (EA). Genome-wide summary statistics on clinical ADHD and years-of-schooling were obtained from large consortia (N[≤]326,041). ADHD-polygenic scores (ADHD-PGS) were inversely associated with LRAs in ALSPAC, most consistently with reading-related abilities, and explained [≤]1.6% phenotypic variation. Polygenic links were then dissected into both genetic effects shared with and independent of EA using multivariable regressions (MVR), analogous to Mendelian Randomization approaches accounting for mediating effects. Conditional on EA, polygenic ADHD risk remained associated with multiple literacy-related skills, phonemic awareness and verbal intelligence, but not language-related skills such as listening comprehension and non-word repetition. Pooled reading performance showed the strongest overlap with ADHD independent of EA. Using conservative ADHD-instruments (P-threshold<5x10-8) this corresponded to a 0.35 decrease in Z-scores per log-odds in ADHD-liability (P=9.2x10-5). Using subthreshold ADHD-instruments (P-threshold<0.0015), these associations had lower magnitude, but higher predictive accuracy, with a 0.03 decrease in Z-scores (P=1.4x10-6). Polygenic ADHD-effects shared with EA were of equal strength and at least equal magnitude compared to those independent of EA, for all LRAs studied, and only detectable using subthreshold instruments. Thus, ADHD-related polygenic links are highly susceptible to genetic confounding, concealing an ADHD-specific association profile that primarily involves reading-related impairments, but few language-related problems.

genetics↗

bioRxiv2018

DNA methylation mediates genetic liability to non-syndromic cleft lip/palate

BackgroundNon-syndromic cleft lip/palate (nsCL/P) is a complex trait with genetic and environmental risk factors. Around 40 distinct genetic risk loci have been identified for nsCL/P, but many reside in non-protein-coding regions with an unclear function. We hypothesised that one possibility is that the genetic risk variants influence susceptibility to nsCL/P through gene regulation pathways, such as those involving DNA methylation.\n\nMethodsUsing nsCL/P Genome-wide association study summary data and methylation data from four studies, we used Mendelian randomization and joint likelihood mapping to identify putative loci where genetic liability to nsCL/P may be mediated by variation in DNA methylation in blood.\n\nResultsThere was evidence at three independent loci, VAX1 (10q25.3), LOC146880 (17q23.3) and NTN1 (17p13.1), that liability to nsCL/P and variation in DNA methylation might be driven by the same genetic variant. Follow up analyses using DNA methylation data, derived from lip and palate tissue, and gene expression catalogues provided further insight into possible biological mechanisms.\n\nConclusionsGenetic variation may increase liability to nsCL/P by influencing DNA methylation and gene expression at VAX1, LOC146880 and NTN1.

genetics↗

bioRxiv2018

Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology

There is increasing evidence that genetic risk variants for non-syndromic cleft lip/palate (nsCL/P) are also associated with normal-range variation in facial morphology. However, previous analyses are mostly limited to candidate SNPs and findings have not been consistently replicated. Here, we used polygenic risk scores (PRS) to test for genetic overlap between nsCL/P and seven biologically relevant facial phenotypes. Where evidence was found of genetic overlap, we used bidirectional Mendelian randomization (MR) to test the hypothesis that genetic liability to nsCL/P is causally related to implicated facial phenotypes. Across 5,804 individuals of European ancestry from two studies, we found strong evidence, using PRS, of genetic overlap between nsCL/P and philtrum width; a 1 S.D. increase in nsCL/P PRS was associated with a 0.10 mm decrease in philtrum width (95% C.I. 0.054, 0.146; P = 0.00002). Follow-up MR analyses supported a causal relationship; genetic variants for nsCL/P homogeneously cause decreased philtrum width. In addition to the primary analysis, we also identified two novel risk loci for philtrum width at 5q22.2 and 7p15.2 in our Genome-wide Association Study (GWAS) of 6,136 individuals. Our results support a liability threshold model of inheritance for nsCL/P, related to abnormalities in development of the philtrum.

genetics↗