Estimating effects of parents' cognitive and non-cognitive skills on offspring education using polygenic scores

Genome-wide association meta-analysis of age at onset of walking in over 70,000 infants of European ancestry

Age at onset of walking is an important early childhood milestone which is used clinically and in public health screening. In this genome-wide association study meta-analysis of age at onset of walking (N = 70,560 European-ancestry infants), we identified 11 independent genome-wide significant loci. SNP-based heritability was 24.13% (95% confidence intervals = 21.86-26.40) with ~11,900 variants accounting for about 90% of it, suggesting high polygenicity. One of these loci, in gene RBL2, co-localized with an expression quantitative trait locus (eQTL) in the brain. Age at onset of walking (in months) was negatively genetically correlated with ADHD and body-mass index, and positively genetically correlated with brain gyrification in both infant and adult brains. The polygenic score showed out-of-sample prediction of 3-5.6%, confirmed as largely due to direct effects in sib-pair analyses, and was separately associated with volume of neonatal brain structures involved in motor control. This study offers biological insights into a key behavioural marker of neurodevelopment.

The genetics of low and high birthweight and their relationship with cardiometabolic disease

AIMS/HYPOTHESIS

Low birthweight infants are at increased risk not only of mortality, but also of type 2 diabetes mellitus and CVD in later life. At the opposite end of the spectrum, high birthweight infants have increased risk of birth complications, such as shoulder dystocia, neonatal hypoglycaemia and obesity, and similarly increased risk of type 2 diabetes mellitus and CVD. However, previous genome-wide association studies (GWAS) of birthweight in the UK Biobank have primarily focused on individuals within the 'normal' range and have excluded individuals with high and low birthweight (<2.5 kg or >4.5 kg). The aim of this study was to investigate genetic variation associated within the tail ends of the birthweight distribution, to: (1) see whether the genetic factors operating in these regions were different from those that explained variation in birthweight within the normal range; (2) explore the genetic correlation between extremes of birthweight and cardiometabolic disease; and (3) investigate whether analysing the full distribution of birthweight values, including the extremes, improved the ability to detect genuine loci in GWAS.

METHODS

We performed case-control GWAS analysis of low (<2.5 kg) and high (>4.5 kg) birthweight in the UK Biobank using REGENIE software (Nlow=20,947; Nhigh=12,715; Ncontrols=207,506) and conducted three continuous GWAS of birthweight, one including the full range of birthweights, one involving a truncated GWAS including only individuals with birthweights between 2.5 and 4.5 kg and a third GWAS that winsorised birthweight values <2.5 kg and >4.5 kg. Additionally, we performed bivariate linkage disequilibrium (LD) score regression to estimate the genetic correlation between low/normal/high birthweight and cardiometabolic traits.

RESULTS

Bivariate LD score regression analyses suggested that high birthweight had a mostly similar genetic aetiology to birthweight within the normal range (genetic correlation coefficient [rG]=0.91, 95% CI 0.83, 0.99), whereas there was more evidence for a separate set of genes underlying low birthweight (rG=-0.74, 95% CI 0.66, 0.82). Low birthweight was also significantly positively genetically correlated with most cardiometabolic traits and diseases we examined, whereas high birthweight was mostly positively genetically correlated with adiposity and anthropometric-related traits. The winsorisation strategy performed best in terms of locus detection, with the number of independent genome-wide significant associations (p<5×10-8) increasing from 120 genetic variants at 94 loci in the truncated GWAS to 270 genetic variants at 178 loci, including 27 variants at 25 loci that had not been identified in previous birthweight GWAS. This included a novel low-frequency missense variant in the ABCC8 gene, a gene known to be involved in congenital hyperinsulinism, neonatal diabetes mellitus and MODY, that was estimated to be responsible for a 170 g increase in birthweight amongst carriers.

CONCLUSIONS/INTERPRETATION

Our results underscore the importance of genetic factors in the genesis of the phenotypic correlation between birthweight and cardiometabolic traits and diseases.

Intergenerational transmission of polygenic predisposition for neuropsychiatric traits on emotional and behavioural difficulties in childhood

Childhood emotional and behavioural difficulties tend to co-occur and often precede diagnosed neuropsychiatric conditions. Identifying shared and specific risk factors for early-life mental health difficulties is therefore essential for prevention strategies. Here, we examine how parental risk factors shape their offspring's emotional and behavioural symptoms (e.g. feelings of anxiety, and restlessness) using data from 14,959 genotyped family trios from the Norwegian Mother, Father and Child Cohort Study (MoBa). We model maternal reports of emotional and behavioural symptoms, organizing them into general and specific domains. We then investigate the direct (genetically transmitted) and indirect (environmentally mediated) contributions of parental polygenic risk for neuropsychiatric-related traits and whether these are shared across symptoms. We observe evidence consistent with an environmental route to general symptomatology beyond genetic transmission, while also demonstrating domain-specific direct and indirect genetic contributions. These findings improve our understanding of early risk pathways that can be targeted in preventive interventions aiming to interrupt the intergenerational cycle of risk transmission.

Gene-environment correlation: the role of family environment in academic development

Academic achievement is partly heritable and highly polygenic. However, genetic effects on academic achievement are not independent of environmental processes. We investigated whether aspects of the family environment mediated genetic effects on academic achievement across development. Our sample included 5151 children who participated in the Twins Early Development Study, as well as their parents and teachers. Data on academic achievement and family environments (parenting, home environments, and geocoded indices of neighbourhood characteristics) were available at ages 7, 9, 12 and 16. We computed educational attainment polygenic scores (PGS) and further separated genetic effects into cognitive and noncognitive PGS. Three core findings emerged. First, aspects of the family environment, but not the wider neighbourhood context, consistently mediated the PGS effects on achievement across development-accounting for up to 34.3% of the total effect. Family characteristics mattered beyond socio-economic status. Second, family environments were more robustly linked to noncognitive PGS effects on academic achievement than cognitive PGS effects. Third, when we investigated whether environmental mediation effects could also be observed when considering differences between siblings, adjusting for family fixed effects, we found that environmental mediation was nearly exclusively observed between families. This is consistent with the proposition that family environmental contexts contribute to academic development via passive gene-environment correlation processes or genetic nurture. Our results show how parents tend to shape environments that foster their children's academic development partly based on their own genetic disposition, particularly towards noncognitive skills, rather than responding to each child's genetic disposition.

Do polygenic indices capture "direct" effects on child externalizing behavior problems? Within-family analyses in two longitudinal birth cohorts

Failures of self-control can manifest as externalizing behaviors (e.g., aggression, rule-breaking) that have far-reaching negative consequences. Researchers have long been interested in measuring children's genetic risk for externalizing behaviors to inform efforts at early identification and intervention. Drawing on data from the Environmental Risk Longitudinal Twin Study (N = 862 twins) and the Millennium Cohort Study (N = 2,824 parent-child trios), two longitudinal cohorts from the UK, we leveraged molecular genetic data and within-family designs to test for genetic associations with externalizing behavior that are not affected by common sources of environmental influence. We found that a polygenic index (PGI) calculated from genetic variants discovered in previous studies of self-controlled behavior in adults captures direct genetic effects on externalizing problems in children and adolescents when evaluated with rigorous within-family designs (β's = 0.13-0.19 across development). The externalizing behavior PGI can usefully augment psychological studies of the development of self-control.

Using twin-pairs to assess potential bias in polygenic prediction of externalising behaviours across development

Prediction from polygenic scores may be confounded by sources of passive gene-environment correlation (rGE; e.g. population stratification, assortative mating, and environmentally mediated effects of parental genotype on child phenotype). Using genomic data from 10 000 twin pairs, we asked whether polygenic scores from the most recent externalising genome-wide association study predict conduct problems, ADHD symptomology and callous-unemotional traits, and whether these predictions are biased by rGE. We ran regression models including within-family and between-family polygenic scores, to separate the direct genetic influence on a trait from environmental influences that correlate with genes (indirect genetic effects). Findings suggested that this externalising polygenic score is a good index of direct genetic influence on conduct and ADHD-related symptoms across development, with minimal bias from rGE, although the polygenic score predicted less variance in CU traits. Post-hoc analyses showed some indirect genetic effects acting on a common factor indexing stability of conduct problems across time and contexts.

Polygenic prediction of occupational status GWAS elucidates genetic and environmental interplay in intergenerational transmission, careers and health in UK Biobank

Socioeconomic status (SES) impacts health and life-course outcomes. This genome-wide association study (GWAS) of sociologically informed occupational status measures (ISEI, SIOPS, CAMSIS) using the UK Biobank (N = 273,157) identified 106 independent single-nucleotide polymorphisms of which 8 are novel to the study of SES. Genetic correlations with educational attainment (rg = 0.96-0.97) and income (rg = 0.81-0.91) point to a common genetic factor for SES. We observed a 54-57% reduction in within-family predictions compared with population-based predictions, attributed to indirect parental effects (22-27% attenuation) and assortative mating (21-27%) following our calculations. Using polygenic scores from population predictions of 5-10% (incremental R2 = 0.023-0.097 across different approaches and occupational status measures), we showed that (1) cognitive and non-cognitive traits, including scholastic and occupational motivation and aspiration, link polygenic scores to occupational status and (2) 62% of the intergenerational transmission of occupational status cannot be ascribed to genetic inheritance of common variants but other factors such as family environments. Finally, links between genetics, occupation, career trajectory and health are interrelated with parental occupational status.

The Role of Parental Education, Intelligence, and Personality on the Cognitive Abilities of Gifted Children

Several studies have indicated that parental education predicts children's intelligence. In contrast, fewer studies have simultaneously analyzed the role of parental intelligence, education, and personality in shaping their children's giftedness. This study investigated the effects of parental education, cognitive abilities (based on CHC theory), and personality traits (based on the Five-Factor Model) on the expression of gifted children's cognitive abilities. Sixty-five gifted children (IQ ≥ 120) aged 6 to 14 years (M = 9.91 years; SD = 2.24 years) were assessed using the WISC-IV, while parents (65 mothers, M = 44.00 years; SD = 4.20 years, and 61 fathers, M = 45.70 years; SD = 5.40 years) completed the WAIS-IV and the Big-Five Inventory. The results indicated that maternal education was a key predictor of children's Verbal Comprehension Index (VCI) in bivariate analyses, though its effect was not robust in multivariate models. Children's Perceptual Reasoning Index (PRI) was associated with maternal conscientiousness, and fathers' short-term memory (Gsm) emerged as the primary predictor of children's Working Memory Index (WMI). Maternal processing speed (Gs) was the strongest predictor of children's Processing Speed Index (PSI) across both bivariate and multivariate analyses. While personality traits, such as maternal conscientiousness, played a role in facilitating visual-spatial reasoning, their effects were weaker compared to cognitive and educational factors. The findings obtained, which are only partly consistent with data in the literature, highlight the domain-specific influence of parental characteristics on children's giftedness and underscore the need for further research into the interplay of genetic, cognitive, and environmental factors.

Genetic Nurture Effects on Type 2 Diabetes Among Chinese Han Adults: A Family-Based Design

Background/Objectives: Genes and environments were transmitted across generations. Parents' genetics influence the environments of their offspring; these two modes of inheritance can produce a genetic nurture effect, also known as indirect genetic effects. Such indirect effects may partly account for estimated genetic variance in T2D. However, the well-established specific genetic risk factors about genetic nurture effect for T2D are not fully understood. This study aimed to investigate the genetic nurture effect on type 2 diabetes and reveal the potential underlying mechanism using publicly available data. Methods: Whole-genome genotyping data of 881 offspring and/or their parents were collected. We assessed SNP-level, gene-based, and pathway-based associations for different types of genetic effects. Results: Rs3805116 (β: 0.54, p = 4.39 × 10-8) was significant for paternal genetic nurture effects. MRPS33 (p = 1.58 × 10-6), PIH1D2 (p = 6.76 × 10-7), and SD1HD (p = 2.67 × 10-6) revealed significantly positive paternal genetic nurture effects. Five ontologies were identified as enrichment in both direct and indirect genetic effects, including flavonoid metabolic process and antigen processing and presentation via the MHC class Ib pathway. Two pathways were only enriched in paternal genetic nurture effects, including the transforming growth factor beta pathway. Tissue enrichment of type 2 diabetes-associated genes on different genetic effect types was performed using publicly available gene expression data from the Human Protein Atlas database. We observed significant gene enrichment in paternal genetic nurture effects in the gallbladder, smooth muscle, and adrenal gland tissues. Conclusions: MRPS33, PIH1D2, and SD1HD are associated with increased T2D risk through the environment influenced by paternal genotype, suggesting a novel perspective on paternal contributions to the T2D predisposition.

Exome sequencing of UK birth cohorts

Birth cohort studies involve repeated surveys of large numbers of individuals from birth and throughout their lives. They collect information useful for a wide range of life course research domains, and biological samples which can be used to derive data from an increasing collection of omic technologies. This rich source of longitudinal data, when combined with genomic data, offers the scientific community valuable insights ranging from population genetics to applications across the social sciences. Here we present quality-controlled whole exome sequencing data from three UK birth cohorts: the Avon Longitudinal Study of Parents and Children (8,436 children and 3,215 parents), the Millenium Cohort Study (7,667 children and 6,925 parents) and Born in Bradford (8,784 children and 2,875 parents). The overall objective of this coordinated effort is to make the resulting high-quality data widely accessible to the global research community in a timely manner. We describe how the datasets were generated and subjected to quality control at the sample, variant and genotype level. We then present some preliminary analyses to illustrate the quality of the datasets and probe potential sources of bias. We introduce measures of ultra-rare variant burden to the variables available for researchers working on these cohorts, and show that the exome-wide burden of deleterious protein-truncating variants, S het burden, is associated with educational attainment and cognitive test scores. The whole exome sequence data from these birth cohorts (CRAM & VCF files) are available through the European Genome-Phenome Archive, and here we provide guidance for their use.

Examining the role of common variants in rare neurodevelopmental conditions

Although rare neurodevelopmental conditions have a large Mendelian component1, common genetic variants also contribute to risk2,3. However, little is known about how this polygenic risk is distributed among patients with these conditions and their parents nor its interplay with rare variants. It is also unclear whether polygenic background affects risk directly through alleles transmitted from parents to children, or whether indirect genetic effects mediated through the family environment4 also play a role. Here we addressed these questions using genetic data from 11,573 patients with rare neurodevelopmental conditions, 9,128 of their parents and 26,869 controls. Common variants explained around 10% of variance in risk. Patients with a monogenic diagnosis had significantly less polygenic risk than those without, supporting a liability threshold model5. A polygenic score for neurodevelopmental conditions showed only a direct genetic effect. By contrast, polygenic scores for educational attainment and cognitive performance showed no direct genetic effect, but the non-transmitted alleles in the parents were correlated with the child's risk, potentially due to indirect genetic effects and/or parental assortment for these traits4. Indeed, as expected under parental assortment, we show that common variant predisposition for neurodevelopmental conditions is correlated with the rare variant component of risk. These findings indicate that future studies should investigate the possible role and nature of indirect genetic effects on rare neurodevelopmental conditions, and consider the contribution of common and rare variants simultaneously when studying cognition-related phenotypes.

The contribution of attention-deficit/hyperactivity disorder polygenic load to metabolic and cardiovascular health outcomes: a large-scale population and sibling study

Emerging evidence suggests that ADHD is associated with increased risk for metabolic and cardiovascular (cardiometabolic) diseases. However, an understanding of the mechanisms underlying these associations is still limited. In this study we estimated the associations of polygenic scores (PGS) for ADHD with several cardiometabolic diseases and biomarkers. Furthermore, we investigated to what extent the PGS effect was influenced by direct and indirect genetic effects (i.e., shared familial effects). We derived ADHD-PGS in 50,768 individuals aged 18-90 years from the Dutch Lifelines Cohort study. Using generalised estimating equations, we estimated the association of PGS with cardiometabolic diseases, derived from self-report and several biomarkers measured during a physical examination. We additionally ran within-sibling PGS analyses, using fixed effects models, to disentangle direct effects of individuals' own ADHD genetic risk from confounding due to indirect genetic effects of relatives, as well as population stratification. We found that higher ADHD-PGS were statistically significantly associated with several cardiometabolic diseases (R-squared [R2] range = 0.03-0.50%) and biomarkers (related to inflammation, blood pressure, lipid metabolism, amongst others) (R2 range = 0.01-0.16%) (P < 0.05). Adjustment for shared familial factors attenuated the associations between ADHD-PGS and cardiometabolic outcomes (on average 56% effect size reduction), and significant associations only remained for metabolic disease. Overall our findings suggest that increased genetic liability for ADHD confers a small but significant risk increase for cardiometabolic health outcomes in adulthood. These associations were observable in the general population, even in individuals without ADHD diagnosis, and were partly explained by familial factors shared among siblings.

Gene-environment interactions in human health

Gene-environment interactions (G × E), the interplay of genetic variation with environmental factors, have a pivotal impact on human complex traits and diseases. Statistically, G × E can be assessed by determining the deviation from expectation of predictive models based solely on the phenotypic effects of genetics or environmental exposures. Despite the unprecedented, widespread and diverse use of G × E analytical frameworks, heterogeneity in their application and reporting hinders their applicability in public health. In this Review, we discuss study design considerations as well as G × E analytical frameworks to assess polygenic liability dependent on the environment, to identify specific genetic variants exhibiting G × E, and to characterize environmental context for these dynamics. We conclude with recommendations to address the most common challenges and pitfalls in the conceptualization, methodology and reporting of G × E studies, as well as future directions.

Do Children Cause the Cognitive Stimulation they Receive? Modelling the Direction of Causality

We tested the directionality of associations between children's early-life cognitive development and the cognitive stimulation that they received from their parents. Our sample included up to 15,314 children from the Twins Early Development Study (TEDS), who were born between 1994 and 1996 in England and Wales and assessed at ages 3 and 4 years on cognitive development and cognitive stimulation, including singing rhymes, reading books, and playing games. Using genetically informative cross-lagged models, we found consistent, bidirectional effects from cognitive development at age 3 to cognitive stimulation at age 4, and from cognitive stimulation at age 3 to cognitive development at age 4. These cross-lagged longitudinal effects were largely explained by underlying common genetic and shared environmental factors, rather than reflecting causal mechanisms. Our findings emphasize the active role that children play in constructing their own learning experiences.

DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits

Perinatal traits are influenced by fetal and maternal genomes. We investigate the performance of three strategies to detect loci in maternal and fetal genome-wide association studies (GWASs) of the same quantitative trait: (i) the traditional strategy of analysing maternal and fetal GWASs separately; (ii) a two-degree-of-freedom test which combines information from maternal and fetal GWASs; and (iii) a one-degree-of-freedom test where signals from maternal and fetal GWASs are meta-analysed together conditional on estimated sample overlap. We demonstrate that the optimal strategy depends on the extent of sample overlap, correlation between phenotypes, whether loci exhibit fetal and/or maternal effects, and whether these effects are directionally concordant. We apply our methods to summary statistics from a recent GWAS meta-analysis of birth weight. Both the two-degree-of-freedom and meta-analytic approaches increase the number of genetic loci for birth weight relative to separately analysing the scans. Our best strategy identifies an additional 62 loci compared to the most recently published meta-analysis of birth weight. We conclude that whilst the two-degree-of-freedom test may be useful for the analysis of certain perinatal phenotypes, for most phenotypes, a simple meta-analytic strategy is likely to perform best, particularly in situations where maternal and fetal GWASs only partially overlap.

Childhood personality and academic performance: A sibling fixed-effects study

OBJECTIVE

This study investigated the associations between personality traits at age 8 and academic performance between ages 10 and 14, controlling for family confounds.

BACKGROUND

Many studies have shown links between children's personality traits and their school performance. However, we lack evidence on whether these associations remain after genetic and environmental confounders are accounted for.

METHOD

Sibling data from the Norwegian Mother and Child Cohort Study (MoBa) were used (n = 9701). First, we estimated the overall associations between Big Five personality traits and academic performance, including literacy, numeracy, and foreign language. Second, we added sibling fixed effects to remove unmeasured confounders shared by siblings as well as rating bias.

RESULTS

Openness to Experience (between-person β = 0.22 [95% CI: 0.21-0.24]) and Conscientiousness (between-person β = 0.18 [95% CI 0.16-0.20]) were most strongly related to educational performance. Agreeableness (between-person β = 0.06 [95% CI -0.08-0.04]) and Extraversion (between-person β = 0.02 [95% CI 0.00-0.04]) showed small associations with educational performance. Neuroticism had a moderate negative association (between-person β = -0.14 [95% CI -0.15-0.11]). All associations between personality and performance were robust to confounding: the within-family estimates from sibling fixed-effects models overlapped with the between-person effects. Finally, childhood personality was equally predictive of educational performance across ages and genders.

CONCLUSIONS

Although family background is influential for academic achievement, it does not confound associations with personality. Childhood personality traits reflect unbiased and consistent individual differences in educational potential.

The importance of family-based sampling for biobanks

Biobanks aim to improve our understanding of health and disease by collecting and analysing diverse biological and phenotypic information in large samples. So far, biobanks have largely pursued a population-based sampling strategy, where the individual is the unit of sampling, and familial relatedness occurs sporadically and by chance. This strategy has been remarkably efficient and successful, leading to thousands of scientific discoveries across multiple research domains, and plans for the next wave of biobanks are underway. In this Perspective, we discuss the strengths and limitations of a complementary sampling strategy for future biobanks based on oversampling of close genetic relatives. Such family-based samples facilitate research that clarifies causal relationships between putative risk factors and outcomes, particularly in estimates of genetic effects, because they enable analyses that reduce or eliminate confounding due to familial and demographic factors. Family-based biobank samples would also shed new light on fundamental questions across multiple fields that are often difficult to explore in population-based samples. Despite the potential for higher costs and greater analytical complexity, the many advantages of family-based samples should often outweigh their potential challenges.

Pourcain B, Robinson EB, Bourgeron T, Baron-Cohen S, Børglum AD, Martin HC, Warrier V. An axis of genetic heterogeneity in autism is indexed by age at diagnosis and is associated with varying developmental and mental health profiles

There is growing recognition that earliest signs of autism need not clearly manifest in the first three years of life. To what extent is this variation in developmental trajectories associated with age at autism diagnosis? Does the genetic profile of autism vary with age at autism diagnosis? Using longitudinal data from four birth cohorts, we demonstrate that two different trajectories of socio-emotional behaviours are associated with age at diagnosis. We further demonstrate that the age at autism diagnosis is partly heritable (h2 SNP = 0.12, s.e.m = 0.01), and is associated with two moderately correlated (rg = 0.38, s.e.m = 0.07) autism polygenic factors. One of these factors is associated with earlier diagnosis of autism, lower social and communication abilities in early childhood. The second factor is associated with later autism diagnosis, increased socio-emotional difficulties in adolescence, and has moderate to high positive genetic correlations with Attention-Deficit/Hyperactivity Disorder, mental health conditions, and trauma. Overall, our research identifies an axis of heterogeneity in autism, indexed by age at diagnosis, which partly explains heterogeneity in autism and the profiles of co-occurring neurodevelopmental and mental health profiles. Our findings have important implications for how we conceptualise autism and provide one model to explain some of the diversity within autism.

Interaction of family SES with children's genetic propensity for cognitive and noncognitive skills: No evidence of the Scarr-Rowe hypothesis for educational outcomes

This study examines the role of genes and environments in predicting educational outcomes. We test the Scarr-Rowe hypothesis, suggesting that enriched environments enable genetic potential to unfold, and the compensatory advantage hypothesis, proposing that low genetic endowments have less impact on education for children from high socioeconomic status (SES) families. We use a pre-registered design with Netherlands Twin Register data (426 ≤ N individuals ≤ 3875). We build polygenic indexes (PGIs) for cognitive and noncognitive skills to predict seven educational outcomes from childhood to adulthood across three designs (between-family, within-family, and trio) accounting for different confounding sources, totalling 42 analyses. Cognitive PGIs, noncognitive PGIs, and parental education positively predict educational outcomes. Providing partial support for the compensatory hypothesis, 39/42 PGI × SES interactions are negative, with 7 reaching statistical significance under Romano-Wolf and 3 under the more conservative Bonferroni multiple testing corrections (p-value < 0.007). In contrast, the Scarr-Rowe hypothesis lacks empirical support, with just 2 non-significant and 1 significant (not surviving Romano-Wolf) positive interactions. Overall, we emphasise the need for future replication studies in larger samples. Our findings demonstrate the value of merging social-stratification and behavioural-genetic theories to better understand the intricate interplay between genetic factors and social contexts.

Using parent-offspring pairs and trios to estimate indirect genetic effects in education

We investigated indirect genetic effects (IGEs), also known as genetic nurture, in education with a novel approach that uses phased data to include parent-offspring pairs in the transmitted/nontransmitted study design. This method increases the power to detect IGEs, enhances the generalizability of the findings, and allows for the study of effects by parent-of-origin. We validated and applied this method in a family-based subsample of adolescents and adults from the Lifelines Cohort Study in the Netherlands (N = 6147), using the latest genome-wide association study data on educational attainment to construct polygenic scores (PGS). Our results indicated that IGEs play a role in education outcomes in the Netherlands: we found significant associations of the nontransmitted PGS with secondary school level in youth between 13 and 24 years old as well as with education attainment and years of education in adults over 25 years old (β = 0.14, 0.17 and 0.26, respectively), with tentative evidence for larger maternal IGEs. In conclusion, we replicated previous findings and showed that including parent-offspring pairs in addition to trios in the transmitted/nontransmitted design can benefit future studies of parental IGEs in a wide range of outcomes.

Evaluating the causal relationship between educational attainment and mental health

We investigate the causal relationship between educational attainment (EA) and mental health using two research designs. First, we compare the relationship between EA and 18 psychiatric diagnoses within sibship in Dutch national registry data (N=1.7 million), thereby controlling for unmeasured familial factors. Second, we apply two-sample Mendelian Randomization, which uses genetic variants related to EA or psychiatric diagnosis as instrumental variables, to test whether there is a causal relation in either direction. Our results suggest that lower levels of EA causally increase the risk of MDD, ADHD, alcohol dependence, GAD and PTSD diagnoses. We also find evidence of a causal effect of ADHD on EA. For schizophrenia, anorexia nervosa, OCD, and bipolar disorder, results were inconsistent across the different approaches, highlighting the importance of using multiple research designs to understand complex relationships such as between EA and mental health.

More than nature and nurture, indirect genetic effects on children's academic achievement are consequences of dynastic social processes

Families transmit genes and environments across generations. When parents' genetics affect their children's environments, these two modes of inheritance can produce an 'indirect genetic effect'. Such indirect genetic effects may account for up to half of the estimated genetic variance in educational attainment. Here we tested if indirect genetic effects reflect within-nuclear-family transmission ('genetic nurture') or instead a multi-generational process of social stratification ('dynastic effects'). We analysed indirect genetic effects on children's academic achievement in their fifth to ninth years of schooling in N = 37,117 parent-offspring trios in the Norwegian Mother, Father, and Child Cohort Study (MoBa). We used pairs of genetically related families (parents were siblings, children were cousins; N = 10,913) to distinguish within-nuclear-family genetic-nurture effects from dynastic effects shared by cousins in different nuclear families. We found that indirect genetic effects on children's academic achievement cannot be explained by processes that operate exclusively within the nuclear family.

Interpreting population- and family-based genome-wide association studies in the presence of confounding

A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding and can also absorb the "indirect" genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect-size estimates are used in polygenic scores (PGSs). We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding.

Examining intergenerational risk factors for conduct problems using polygenic scores in the Norwegian Mother, Father and Child Cohort Study

The aetiology of conduct problems involves a combination of genetic and environmental factors, many of which are inherently linked to parental characteristics given parents' central role in children's lives across development. It is important to disentangle to what extent links between parental heritable characteristics and children's behaviour are due to transmission of genetic risk or due to parental indirect genetic influences via the environment (i.e., genetic nurture). We used 31,290 genotyped mother-father-child trios from the Norwegian Mother, Father and Child Cohort Study (MoBa), testing genetic transmission and genetic nurture effects on conduct problems using 13 polygenic scores (PGS) spanning psychiatric conditions, substance use, education-related factors, and other risk factors. Maternal or self-reports of conduct problems at ages 8 and 14 years were available for up to 15,477 children. We found significant genetic transmission effects on conduct problems for 12 out of 13 PGS at age 8 years (strongest association: PGS for smoking, β = 0.07, 95% confidence interval = [0.05, 0.08]) and for 4 out of 13 PGS at age 14 years (strongest association: PGS for externalising problems, β = 0.08, 95% confidence interval = [0.05, 0.11]). Conversely, we did not find genetic nurture effects for conduct problems using our selection of PGS. Our findings provide evidence for genetic transmission in the association between parental characteristics and child conduct problems. Our results may also indicate that genetic nurture via traits indexed by our polygenic scores is of limited aetiological importance for conduct problems-though effects of small magnitude or effects via parental traits not captured by the included PGS remain a possibility.

Genetic similarity between relatives provides evidence on the presence and history of assortative mating

Assortative mating - the non-random mating of individuals with similar traits - is known to increase trait-specific genetic variance and genetic similarity between relatives. However, empirical evidence is limited for many traits, and the implications hinge on whether assortative mating has started recently or many generations ago. Here we show theoretically and empirically that genetic similarity between relatives can provide evidence on the presence and history of assortative mating. First, we employed path analysis to understand how assortative mating affects genetic similarity between family members across generations, finding that similarity between distant relatives is more affected than close relatives. Next, we correlated polygenic indices of 47,135 co-parents from the Norwegian Mother, Father, and Child Cohort Study (MoBa) and found genetic evidence of assortative mating in nine out of sixteen examined traits. The same traits showed elevated similarity between relatives, especially distant relatives. Six of the nine traits, including educational attainment, showed greater genetic variance among offspring, which is inconsistent with stable assortative mating over many generations. These results suggest an ongoing increase in familial similarity for these traits. The implications of this research extend to genetic methodology and the understanding of social and economic disparities.

Estimating the impact of transmitted and non-transmitted psychiatric and neurodevelopmental polygenic scores on youth emotional problems

Anxiety and depression (emotional disorders) are familial and heritable, especially when onset is early. However, other cross-generational studies suggest transmission of youth emotional problems is explained by mainly environmental risks. We set out to test the contribution of parental non-transmitted genetic liability, as indexed by psychiatric/neurodevelopmental common polygenic liability, to youth emotional problems using a UK population-based cohort: the Millennium Cohort Study. European (N = 6328) and South Asian (N = 814) ancestries were included, as well as a subset with genomic data from both parents (European: N = 2809; South Asian: N = 254). We examined the association of transmitted (PGST) and non-transmitted polygenic scores (PGSNT) for anxiety, depression, bipolar disorder and neurodevelopmental disorders (attention-deficit/hyperactivity disorder [ADHD], autism spectrum disorder [ASD], schizophrenia) with youth emotional disorder and symptom scores, measured using the parent- and self-reported Strengths and Difficulties Questionnaire emotional subscale at 6 timepoints between ages 3-17 years. In the European sample, PGST for anxiety and depression, but not bipolar disorder, were associated with emotional disorder and symptom scores across all ages, except age 3, with strongest association in adolescence. ADHD and ASD PGST also showed association across ages 11-17 years. In the South Asian sample, evidence for associations between all PGST and outcome measures were weaker. There was weak evidence of association between PGSNT for anxiety and depression and age 17 symptom scores in the South Asian sample, but not in the European sample for any outcome. Overall, PGST for depression, anxiety, ADHD and ASD contributed to youth emotional problems, with stronger associations in adolescence. There was limited support for non-transmitted genetic effects: these findings do not support the hypothesis that parental polygenic psychiatric/neurodevelopmental liability confer risk to offspring emotional problems through non-transmitted rearing/nurture effects.

Using twin-pairs to assess potential bias in polygenic prediction of externalising behaviours across development

Prediction from polygenic scores may be confounded sources of passive gene-environment correlation (rGE; e.g. population stratification, assortative mating, and environmentally mediated effects of parental genotype on child phenotype). Using genomic data from 10,000 twin pairs, we asked whether polygenic scores from the recent externalising genome-wide association study predicted conduct problems, ADHD symptomology and callous-unemotional traits, and whether these predictions are biased by rGE. We ran regression models including within-family and between-family polygenic scores, to separate the direct genetic influence on a trait from environmental influences that correlate with genes (indirect genetic effects). Findings suggested that this externalising polygenic score is a good index of direct genetic influence on conduct and ADHD-related symptoms across development, with minimal bias from rGE, although the polygenic score predicted less variance in CU traits. Post-hoc analyses showed some indirect genetic effects acting on a common factor indexing stability of conduct problems across time and contexts.

Direct and Indirect Genetic Effects on Aggression

Background

Family members resemble each other in their propensity for aggression. In twin studies, approximately 50% of the variance in aggression can be explained by genetic influences. However, if there are genotype-environment correlation mechanisms, such as environmental manifestations of parental and sibling genotypes, genetic influences may partly reflect environmental influences. In this study, we investigated the importance of indirect polygenic score (PGS) effects on aggression.

Methods

We modeled the effect of PGSs based on 3 genome-wide association studies: early-life aggression, educational attainment, and attention-deficit/hyperactivity disorder (ADHD). The associations with aggression were tested in a within- and between-family design (37,796 measures from 7740 individuals, ages 3-86 years [mean = 14.20 years, SE = 12.03], from 3107 families, 55% female) and in a transmitted/nontransmitted PGS design (42,649 measures from 6653 individuals, ages 3-61 years [mean = 11.81 years, SE = 8.68], from 3024 families, 55% female). All participants are enrolled in the Netherlands Twin Register.

Results

We found no evidence for contributions of indirect PGS effects on aggression in either a within- and between-family design or a transmitted/nontransmitted PGS design. Results indicate significant direct effects on aggression for the PGSs based on early-life aggression, educational attainment, and ADHD, although explained variance was low (within- and between-family: early-life aggression R2 = 0.3%, early-life ADHD R2 = 0.6%, educational attainment R2 = 0.7%; transmitted/nontransmitted PGSs: early-life aggression R2 = 0.2%, early-life ADHD R2 = 0.9%, educational attainment R2 = 0.5%).

Conclusions

PGSs included in the current study had a direct (but no indirect) effect on aggression, consistent with results of previous twin and family studies. Further research involving other PGSs for aggression and related phenotypes is needed to determine whether this conclusion generalizes to overall genetic influences on aggression.

Intergenerational effects of parental educational attainment on parenting and childhood educational outcomes: Evidence from MoBa using within-family Mendelian randomization

The intergenerational transmission of educational attainment from parents to their children is one of the most important and studied relationships in social science. Longitudinal studies have found strong associations between parents' and their children's educational outcomes, which could be due to the effects of parents. Here we provide new evidence about whether parents' educational attainment affects their parenting behaviours and children's early educational outcomes using within-family Mendelian randomization and data from 40,879 genotyped parent-child trios from the Norwegian Mother, Father and Child Cohort (MoBa) study. We found evidence suggesting that parents' educational attainment affects their children's educational outcomes from age 5 to 14. More studies are needed to provide more samples of parent-child trios and assess the potential consequences of selection bias and grandparental effects.

Direct and INdirect effects analysis of Genetic lOci (DINGO): A software package to increase the power of locus discovery in GWAS meta-analyses of perinatal phenotypes and traits influenced by indirect genetic effects

Perinatal traits are influenced by genetic variants from both fetal and maternal genomes. Genome-wide association studies (GWAS) of these phenotypes have typically involved separate fetal and maternal scans, however, this approach may be inefficient as it does not utilize the information shared across the individual GWAS. In this manuscript we investigate the performance of three strategies to detect loci in maternal and fetal GWAS of the same trait: (i) the traditional strategy of analysing maternal and fetal GWAS separately; (ii) a novel two degree of freedom test which combines information from maternal and fetal GWAS; and (iii) a novel one degree of freedom test where signals from maternal and fetal GWAS are meta-analysed together conditional on the estimated sample overlap. We demonstrate through a combination of analytical formulae and data simulation that the optimal strategy depends on the extent of sample overlap/relatedness between the maternal and fetal GWAS, the correlation between own and offspring phenotypes, whether loci jointly exhibit fetal and maternal effects, and if so, whether these effects are directionally concordant. We apply our methods to summary results statistics from a recent GWAS meta-analysis of birth weight from deCODE, the UK Biobank and the Early Growth Genetics (EGG) consortium. Both the two degree of freedom (213 loci) and meta-analytic approach (226 loci) dramatically increase the number of robustly associated genetic loci for birth weight relative to separately analysing the scans (183 loci). Our best strategy identifies an additional 62 novel loci compared to the most recent published meta-analysis of birth weight and implicates both known and new biological pathways in the aetiology of the trait. We implement our methods in the online DINGO (Direct and INdirect effects analysis of Genetic lOci) software package, which allows users to perform one and/or two degree of freedom tests easily and computationally efficiently across the genome. We conclude that whilst the novel two degree of freedom test may be particularly useful for the analysis of certain perinatal phenotypes where many loci exhibit discordant maternal and fetal genetic effects, for most phenotypes, a simple meta-analytic strategy is likely to perform best, particularly in situations where maternal and fetal GWAS only partially overlap.

Genetic nurture versus genetic transmission of risk for ADHD traits in the Norwegian Mother, Father and Child Cohort Study

Identifying mechanisms underlying the intergenerational transmission of risk for attention-deficit/hyperactivity disorder (ADHD) traits can inform interventions and provide insights into the role of parents in shaping their children's outcomes. We investigated whether genetic transmission and genetic nurture (environmentally mediated effects) underlie associations between polygenic scores indexing parental risk and protective factors and their offspring's ADHD traits. This birth cohort study included 19,506 genotyped mother-father-offspring trios from the Norwegian Mother, Father and Child Cohort Study. Polygenic scores were calculated for parental factors previously associated with ADHD, including psychopathology, substance use, neuroticism, educational attainment, and cognitive performance. Mothers reported on their 8-year-old children's ADHD traits (n = 9,454 children) using the Parent/Teacher Rating Scale for Disruptive Behaviour Disorders. We found that associations between ADHD maternal and paternal polygenic scores and child ADHD traits decreased significantly when adjusting for the child polygenic score (pΔβ = 9.95 × 10-17 for maternal and pΔβ = 1.48 × 10-14 for paternal estimates), suggesting genetic transmission of ADHD risk. Similar patterns suggesting genetic transmission of risk were observed for smoking, educational attainment, and cognition. The maternal polygenic score for neuroticism remained associated with children's ADHD ratings even after adjusting for the child polygenic score, indicating genetic nurture. There was no robust evidence of genetic nurture for other parental factors. Our findings indicate that the intergenerational transmission of risk for ADHD traits is largely explained by the transmission of genetic variants from parents to offspring rather than by genetic nurture. Observational associations between parental factors and childhood ADHD outcomes should not be interpreted as evidence for predominantly environmentally mediated effects.

Maternal depression and the polygenic p factor: A family perspective on direct and indirect effects

Within-family studies typically assess indirect genetic effects of parents on children, however social support theory points to a critical role of partners and children on women's depression. To address this research gap and account for the high heterogeneity of depression, we calculated a general psychiatric factor using eleven major psychiatric polygenic scores (polygenic p), in up to 25,000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study (MoBa). Multilevel modeling of trio polygenic p was used to distinguish direct and indirect genetic effects on mothers depression during pregnancy (gestational age 17 and 30 weeks), infancy (6 months, 18 months) and early childhood (3 years, 5 years, and 8 years). We found mothers polygenic p predicts their depression symptoms (b = 0.092; 95 % CI [0.087,0.098]), outperforming prediction using a single major depressive disorder polygenic score (b = 0.070, 95 % CI [0.066,0.075]). Jointly modeling trio polygenic p revealed indirect genetic effects of fathers (b = 0.022, 95 % CI [0.014,0.030]) and children (b = 0.021, 95 % CI [0.010,0.037]) on mothers' depression. Our results support the generalizability of polygenic effects across mental health and highlight the role of close family members on women's depression.

Do environmental effects indexed by parental genetic variation influence common psychiatric symptoms in childhood?

Parental genes may indirectly influence offspring psychiatric outcomes through the environment that parents create for their children. These indirect genetic effects, also known as genetic nurture, could explain individual differences in common internalising and externalising psychiatric symptoms during childhood. Advanced statistical genetic methods leverage data from families to estimate the overall contribution of parental genetic nurture effects. This study included up to 10,499 children, 5990 mother-child pairs, and 6,222 father-child pairs from the Norwegian Mother Father and Child Study. Genome-based restricted maximum likelihood (GREML) models were applied using software packages GCTA and M-GCTA to estimate variance in maternally reported depressive, disruptive, and attention-deficit hyperactivity disorder (ADHD) symptoms in 8-year-olds that was explained by direct offspring genetic effects and maternal or paternal genetic nurture. There was no strong evidence of genetic nurture in this sample, although a suggestive paternal genetic nurture effect on offspring depressive symptoms (variance explained (V) = 0.098, standard error (SE) = 0.057) and a suggestive maternal genetic nurture effect on ADHD symptoms (V = 0.084, SE = 0.058) was observed. The results indicate that parental genetic nurture effects could be of some relevance in explaining individual differences in childhood psychiatric symptoms. However, robustly estimating their contribution is a challenge for researchers given the current paucity of large-scale samples of genotyped families with information on childhood psychiatric outcomes.

Interpreting population and family-based genome-wide association studies in the presence of confounding

A central aim of genome-wide association studies (GWASs) is to estimate direct genetic effects: the causal effects on an individual's phenotype of the alleles that they carry. However, estimates of direct effects can be subject to genetic and environmental confounding, and can also absorb the 'indirect' genetic effects of relatives' genotypes. Recently, an important development in controlling for these confounds has been the use of within-family GWASs, which, because of the randomness of Mendelian segregation within pedigrees, are often interpreted as producing unbiased estimates of direct effects. Here, we present a general theoretical analysis of the influence of confounding in standard population-based and within-family GWASs. We show that, contrary to common interpretation, family-based estimates of direct effects can be biased by genetic confounding. In humans, such biases will often be small per-locus, but can be compounded when effect size estimates are used in polygenic scores. We illustrate the influence of genetic confounding on population- and family-based estimates of direct effects using models of assortative mating, population stratification, and stabilizing selection on GWAS traits. We further show how family-based estimates of indirect genetic effects, based on comparisons of parentally transmitted and untransmitted alleles, can suffer substantial genetic confounding. In addition to known biases that can arise in family-based GWASs when interactions between family members are ignored, we show that biases can also arise from gene-by-environment (G×E) interactions when parental genotypes are not distributed identically across interacting environmental and genetic backgrounds. We conclude that, while family-based studies have placed GWAS estimation on a more rigorous footing, they carry subtle issues of interpretation that arise from confounding and interactions.

The Cognitive Profile of Gifted Children Compared to Those of Their Parents: A Descriptive Study Using the Wechsler Scales

The manifestation of performance at the top of a given talent distribution constitutes giftedness. While identifying talented youths based on IQ has been the focus of previous research, examining their cognitive profile is a new endeavor. The present study assessed the IQ and cognitive abilities of a sample of gifted Italian children and compared them to their parents using the Wechsler scales. Fifty-nine gifted children aged 6 to 14 years were administered the WISC-IV while their parents (N = 53 mothers and N = 55 fathers) took the WAIS-IV. The gifted children (IQ ≥ 120) obtained particularly high scores in verbal comprehension (VCI) and visual-perceptual reasoning (PRI). More than two-thirds of the mothers and over half of the fathers also achieved an IQ ≥ 120. The gifted children scored significantly higher than both mothers and fathers in VCI and PRI. The mothers were significantly higher than their children in the processing speed domain. Correlational analyses highlighted that children's IQ was positively related to that of their mothers. In keeping with the literature, the cognitive profile of gifted children was found to vary across cognitive abilities. It follows that the General Ability Index was the WISC-IV index that best matched the potential of gifted youths. Consistent with previous research, our study suggests that intellectual abilities, especially working memory and processing speed, are maintained and presumably passed on from one generation to the next.