Estimation of Parental Effects Using Polygenic Scores

Non-random Mating Patterns in Education, Mental, and Somatic Health: A Population Study on Within- and Cross-Trait Associations

Partners resemble each other on many traits, such as health and education. The traits are usually studied one by one in data from established couples and with potential participation bias. We studied all Norwegian parents who had their first child between 2016 and 2020 (N=187,926) and the siblings of these parents. We analysed grade point averages at age 16 (GPA), educational attainment (EA), and medical records with diagnostic data on 10 mental and 10 somatic health conditions measured 10 to 5 years before childbirth. We found stronger partner similarity in mental (median r=0.14) than in somatic health conditions (median r=0.04), with ubiquitous cross-trait correlations for mental health conditions (median r=0.13). GPA correlated 0.43 and EA 0.47 between partners. High GPA or EA was associated with better mental (median r=-0.16) and somatic (median r=-0.08) health in partners. Elevated correlations for mental health (median r=0.25) in established couples indicated convergence. Analyses of siblings and in-laws revealed deviations from direct assortment, suggesting instead indirect assortment based on related traits. Adjusting for GPA and EA reduced partner correlations in health with 30-40%. This has implications for the distribution of risk factors among children, for genetic studies, and for studies of intergenerational transmission.

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.

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.

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.

The challenges of sociogenomics make it more, not less, worthy of careful and innovative investigation

Influences on social traits involve a tangled interplay of genetic, social, and environmental factors. Moreover, there is increasing awareness that gene-environment correlations are real and potentially measurable. Such gene-environment correlations can mislead if they are uncontrolled and genetic associations are interpreted as being purely because of direct genetic effects. This complexity is cause for more and better investigation, not a reason to refrain from researching one of the potentially important factors (genetics) influencing trait variation.

Preliminary Evidence for Genetic Nurture in Depression and Neuroticism Through Polygenic Scores

Importance

Modeling genetic nurture (ie, the effects of parental genotypes through influences on the environment experienced by their children) is essential to accurately disentangle genetic and environmental influences on phenotypic variance. However, these influences are often ignored in both epidemiologic and genetic studies of depression.

Objective

To estimate the association of genetic nurture with depression and neuroticism.

Design, Setting, and Participants

This cross-sectional study jointly modeled parental and offspring polygenic scores (PGSs) across 9 traits to test for the association of genetic nurture with lifetime broad depression and neuroticism using data from nuclear families in the UK Biobank, with data collected between 2006 and 2019. A broad depression phenotype was measured in 38 702 offspring from 20 905 independent nuclear families, with most of these participants also reporting neuroticism scores. Parental genotypes were imputed from sibships or parent-offspring duos and used to calculate parental PGSs. Data were analyzed between March 2021 and January 2023.

Main Outcomes and Measures

Estimates of genetic nurture and direct genetic regression coefficients on broad depression and neuroticism.

Results

This study of 38 702 offspring with data on broad depression (mean [SD] age, 55.5 [8.2] years at study entry; 58% female) found limited preliminary evidence for a statistically significant association of genetic nurture with lifetime depression and neuroticism in adults. The estimated regression coefficient of the parental depression PGS on offspring neuroticism (β = 0.04, SE = 0.02, P = 6.63 × 10-3) was estimated to be approximately two-thirds (66%) that of the offspring's depression PGS (β = 0.06, SE = 0.01, P = 6.13 × 10-11). Evidence for an association between parental cannabis use disorder PGS and offspring depression was also found (β = 0.08, SE = 0.03, P = .02), which was estimated to be 2 times greater than the association between the offspring's cannabis use disorder PGS and their own depression status (β = 0.04, SE = 0.02, P = .07).

Conclusions and Relevance

The results of this cross-sectional study highlight the potential for genetic nurture to bias results from epidemiologic and genetic studies on depression or neuroticism and, with further replication and larger samples, identify potential avenues for future prevention and intervention efforts.

Environment-by-PGS Interaction in the Classical Twin Design: An Application to Childhood Anxiety and Negative Affect

One type of genotype-environment interaction occurs when genetic effects on a phenotype are moderated by an environment; or when environmental effects on a phenotype are moderated by genes. Here we outline these types of genotype-environment interaction models, and propose a test of genotype-environment interaction based on the classical twin design, which includes observed genetic variables (polygenic scores: PGSs) that account for part of the genetic variance of the phenotype. We introduce environment-by-PGS interaction and the results of a simulation study to address statistical power and parameter recovery. Next, we apply the model to empirical data on anxiety and negative affect in children. The power to detect environment-by-PGS interaction depends on the heritability of the phenotype, and the strength of the PGS. The simulation results indicate that under realistic conditions of sample size, heritability and strength of the interaction, the environment-by-PGS model is a viable approach to detect genotype-environment interaction. In 7-year-old children, we defined two PGS based on the largest genetic association studies for 2 traits that are genetically correlated to childhood anxiety and negative affect, namely major depression (MDD) and intelligence (IQ). We find that common environmental influences on negative affect are amplified for children with a lower IQ-PGS.

Estimation of indirect genetic effects and heritability under assortative mating

Both direct genetic effects (effects of alleles in an individual on that individual) and indirect genetic effects - effects of alleles in an individual (e.g. parents) on another individual (e.g. offspring) - can contribute to phenotypic variation and genotype-phenotype associations. Here, we consider a phenotype affected by direct and parental indirect genetic effects under assortative mating at equilibrium. We generalize classical theory to derive a decomposition of the equilibrium phenotypic variance in terms of direct and indirect genetic effect components. We extend this theory to show that popular methods for estimating indirect genetic effects or 'genetic nurture' through analysis of parental and offspring polygenic predictors (called polygenic indices or scores - PGIs or PGSs) are substantially biased by assortative mating. We propose an improved method for estimating indirect genetic effects while accounting for assortative mating that can also correct heritability estimates for bias due to assortative mating. We validate our method in simulations and apply it to PGIs for height and educational attainment (EA), estimating that the equilibrium heritability of height is 0.699 (S.E. = 0.075 ) and finding no evidence for indirect genetic effects on height. We estimate a very high correlation between parents' underlying genetic components for EA, 0.755 (S.E. = 0.035), which is inconsistent with twin based estimates of the heritability of EA, possibly due to confounding in the EA PGI and/or in twin studies. We implement our method in the software package snipar, enabling researchers to apply the method to data including observed and/or imputed parental genotypes. We provide a theoretical framework for understanding the results of PGI analyses and a practical methodology for estimating heritability and indirect genetic effects while accounting for assortative mating.

Maximizing the value of twin studies in health and behaviour

In the classical twin design, researchers compare trait resemblance in cohorts of identical and non-identical twins to understand how genetic and environmental factors correlate with resemblance in behaviour and other phenotypes. The twin design is also a valuable tool for studying causality, intergenerational transmission, and gene-environment correlation and interaction. Here we review recent developments in twin studies, recent results from twin studies of new phenotypes and recent insights into twinning. We ask whether the results of existing twin studies are representative of the general population and of global diversity, and we conclude that stronger efforts to increase representativeness are needed. We provide an updated overview of twin concordance and discordance for major diseases and mental disorders, which conveys a crucial message: genetic influences are not as deterministic as many believe. This has important implications for public understanding of genetic risk prediction tools, as the accuracy of genetic predictions can never exceed identical twin concordance rates.

Annual Research Review: Towards a deeper understanding of nature and nurture: combining family-based quasi-experimental methods with genomic data

Distinguishing between the effects of nature and nurture constitutes a major research goal for those interested in understanding human development. It is known, for example, that many parent traits predict mental health outcomes in children, but the causal processes underlying such associations are often unclear. Family-based quasi-experimental designs such as sibling comparison, adoption and extended family studies have been used for decades to distinguish the genetic transmission of risk from the environmental effects family members potentially have on one another. Recently, these designs have been combined with genomic data, and this combination is fuelling a range of exciting methodological advances. In this review we explore these advances - highlighting the ways in which they have been applied to date and considering what they are likely to teach us in the coming years about the aetiology and intergenerational transmission of psychopathology.

Disentangling the influences of parental genetics on offspring's cognition, education, and psychopathology via genetic and phenotypic pathways

BACKGROUND

Specific pathways of intergenerational transmission of behavioral traits remain unclear. Here, we aim to investigate how parental genetics influence offspring cognition, educational attainment, and psychopathology in youth.

METHODS

Participants for the discovery sample were 2,189 offspring (aged 6-14 years), 1898 mothers and 1,017 fathers who underwent genotyping, psychiatric, and cognitive assessments. We calculated polygenic scores (PGS) for cognition, educational attainment, attention-deficit hyperactivity disorder (ADHD), and schizophrenia for the trios. Phenotypes studied included educational and cognitive measures, ADHD and psychotic symptoms. We used a stepwise approach and multiple mediation models to analyze the effect of parental PGS on offspring traits via offspring PGS and parental phenotype. Significant results were replicated in a sample of 1,029 adolescents, 363 mothers, and 307 fathers.

RESULTS

Maternal and paternal PGS for cognition influenced offspring general intelligence and executive function via offspring PGS (genetic pathway) and parental education (phenotypic pathway). Similar results were found for parental PGS for educational attainment and offspring reading and writing skills. These pathways fully explained associations between parental PGS and offspring phenotypes, without residual direct association. Associations with maternal, but not paternal, PGS were replicated. No associations were found between parental PGS for psychopathology and offspring specific symptoms.

CONCLUSIONS

Our findings indicate that parental genetics influences offspring cognition and educational attainment by genetic and phenotypic pathways, suggesting the expression of parental phenotypes partially explain the association between parental genetic risk and offspring outcomes. Multiple mediations might represent an effective approach to disentangle distinct pathways for intergenerational transmission of behavioral traits.

Behaviour genetics and sleep: A narrative review of the last decade of quantitative and molecular genetic research in humans

During the last decade quantitative and molecular genetic research on sleep has increased considerably. New behavioural genetics techniques have marked a new era for sleep research. This paper provides a summary of the most important findings from the last ten years, on the genetic and environmental influences on sleep and sleep disorders and their associations with health-related variables (including anxiety and depression) in humans. In this review we present a brief summary of the main methods in behaviour genetic research (such as twin and genome-wide association studies). We then discuss key research findings on: genetic and environmental influences on normal sleep and sleep disorders, as well as on the association between sleep and health variables (highlighting a substantial role for genes in individual differences in sleep and their associations with other variables). We end by discussing future lines of enquiry and drawing conclusions, including those focused on problems and misconceptions associated with research of this type. In this last decade our knowledge about genetic and environmental influences on sleep and its disorders has expanded. Both, twin and genome-wide association studies show that sleep and sleep disorders are substantially influenced by genetic factors and for the very first time multiple specific genetic variants have been associated with sleep traits and disorders.

Using Genomic Structural Equation Modeling to Partition the Genetic Covariance Between Birthweight and Cardiometabolic Risk Factors into Maternal and Offspring Components in the Norwegian HUNT Study

The Barker Hypothesis posits that adverse intrauterine environments result in fetal growth restriction and increased risk of cardiometabolic disease through developmental compensations. Here we introduce a new statistical model using the genomic SEM software that is capable of simultaneously partitioning the genetic covariation between birthweight and cardiometabolic traits into maternally mediated and offspring mediated contributions. We model the covariance between birthweight and later life outcomes, such as blood pressure, non-fasting glucose, blood lipids and body mass index in the Norwegian HUNT study, consisting of 15,261 mother-eldest offspring pairs with genetic and phenotypic data. Application of this model showed some evidence for maternally mediated effects of systolic blood pressure on offspring birthweight, and pleiotropy between birthweight and non-fasting glucose mediated through the offspring genome. This underscores the importance of genetic links between birthweight and cardiometabolic phenotypes and offer alternative explanations to environmentally based hypotheses for the phenotypic correlation between these variables.

The Genetically Informed Neurobiology of Addiction (GINA) model

Addictions are heritable and unfold dynamically across the lifespan. One prominent neurobiological theory proposes that substance-induced changes in neural circuitry promote the progression of addiction. Genome-wide association studies have begun to characterize the polygenic architecture undergirding addiction liability and revealed that genetic loci associated with risk can be divided into those associated with a general broad-spectrum liability to addiction and those associated with drug-specific addiction risk. In this Perspective, we integrate these genomic findings with our current understanding of the neurobiology of addiction to propose a new Genetically Informed Neurobiology of Addiction (GINA) model.

The estimation of environmental and genetic parental influences

Parents share half of their genes with their children, but they also share background social factors and actively help shape their child's environment - making it difficult to disentangle genetic and environmental causes of parent-offspring similarity. While adoption and extended twin family designs have been extremely useful for distinguishing genetic and nongenetic parental influences, these designs entail stringent assumptions about phenotypic similarity between relatives and require samples that are difficult to collect and therefore are typically small and not publicly shared. Here, we describe these traditional designs, as well as modern approaches that use large, publicly available genome-wide data sets to estimate parental effects. We focus in particular on an approach we recently developed, structural equation modeling (SEM)-polygenic score (PGS), that instantiates the logic of modern PGS-based methods within the flexible SEM framework used in traditional designs. Genetically informative designs such as SEM-PGS rely on different and, in some cases, less rigid assumptions than traditional approaches; thus, they allow researchers to capitalize on new data sources and answer questions that could not previously be investigated. We believe that SEM-PGS and similar approaches can lead to improved insight into how nature and nurture combine to create the incredible diversity underlying human behavior.

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

Understanding how parents' cognitive and non-cognitive skills influence offspring education is essential for educational, family and economic policy. We use genetics (GWAS-by-subtraction) to assess a latent, broad non-cognitive skills dimension. To index parental effects controlling for genetic transmission, we estimate indirect parental genetic effects of polygenic scores on childhood and adulthood educational outcomes, using siblings (N = 47,459), adoptees (N = 6407), and parent-offspring trios (N = 2534) in three UK and Dutch cohorts. We find that parental cognitive and non-cognitive skills affect offspring education through their environment: on average across cohorts and designs, indirect genetic effects explain 36-40% of population polygenic score associations. However, indirect genetic effects are lower for achievement in the Dutch cohort, and for the adoption design. We identify potential causes of higher sibling- and trio-based estimates: prenatal indirect genetic effects, population stratification, and assortative mating. Our phenotype-agnostic, genetically sensitive approach has established overall environmental effects of parents' skills, facilitating future mechanistic work.

Using adopted individuals to partition indirect maternal genetic effects into prenatal and postnatal effects on offspring phenotypes

Maternal genetic effects can be defined as the effect of a mother's genotype on the phenotype of her offspring, independent of the offspring's genotype. Maternal genetic effects can act via the intrauterine environment during pregnancy and/or via the postnatal environment. In this manuscript, we present a simple extension to the basic adoption design that uses structural equation modelling (SEM) to partition maternal genetic effects into prenatal and postnatal effects. We examine the power, utility and type I error rate of our model using simulations and asymptotic power calculations. We apply our model to polygenic scores of educational attainment and birth weight associated variants, in up to 5,178 adopted singletons, 943 trios, 2687 mother-offspring pairs, 712 father-offspring pairs and 347,980 singletons from the UK Biobank. Our results show the expected pattern of maternal genetic effects on offspring birth weight, but unexpectedly large prenatal maternal genetic effects on offspring educational attainment. Sensitivity and simulation analyses suggest this result may be at least partially due to adopted individuals in the UK Biobank being raised by their biological relatives. We show that accurate modelling of these sorts of cryptic relationships is sufficient to bring type I error rate under control and produce asymptotically unbiased estimates of prenatal and postnatal maternal genetic effects. We conclude that there would be considerable value in following up adopted individuals in the UK Biobank to determine whether they were raised by their biological relatives, and if so, to precisely ascertain the nature of these relationships. These adopted individuals could then be incorporated into informative statistical genetics models like the one described in our manuscript to further elucidate the genetic architecture of complex traits and diseases.

Evaluating indirect genetic effects of siblings using singletons

Estimating effects of parental and sibling genotypes (indirect genetic effects) can provide insight into how the family environment influences phenotypic variation. There is growing molecular genetic evidence for effects of parental phenotypes on their offspring (e.g. parental educational attainment), but the extent to which siblings affect each other is currently unclear. Here we used data from samples of unrelated individuals, without (singletons) and with biological full-siblings (non-singletons), to investigate and estimate sibling effects. Indirect genetic effects of siblings increase (or decrease) the covariance between genetic variation and a phenotype. It follows that differences in genetic association estimates between singletons and non-singletons could indicate indirect genetic effects of siblings if there is no heterogeneity in other sources of genetic association between singletons and non-singletons. We used UK Biobank data to estimate polygenic score (PGS) associations for height, BMI and educational attainment in self-reported singletons (N = 50,143) and non-singletons (N = 328,549). The educational attainment PGS association estimate was 12% larger (95% C.I. 3%, 21%) in the non-singleton sample than in the singleton sample, but the height and BMI PGS associations were consistent. Birth order data suggested that the difference in educational attainment PGS associations was driven by individuals with older siblings rather than firstborns. The relationship between number of siblings and educational attainment PGS associations was non-linear; PGS associations were 24% smaller in individuals with 6 or more siblings compared to the rest of the sample (95% C.I. 11%, 38%). We estimate that a 1 SD increase in sibling educational attainment PGS corresponds to a 0.025 year increase in the index individual's years in schooling (95% C.I. 0.013, 0.036). Our results suggest that older siblings may influence the educational attainment of younger siblings, adding to the growing evidence that effects of the environment on phenotypic variation partially reflect social effects of germline genetic variation in relatives.

Mendelian imputation of parental genotypes improves estimates of direct genetic effects

Effects estimated by genome-wide association studies (GWASs) include effects of alleles in an individual on that individual (direct genetic effects), indirect genetic effects (for example, effects of alleles in parents on offspring through the environment) and bias from confounding. Within-family genetic variation is random, enabling unbiased estimation of direct genetic effects when parents are genotyped. However, parental genotypes are often missing. We introduce a method that imputes missing parental genotypes and estimates direct genetic effects. Our method, implemented in the software package snipar (single-nucleotide imputation of parents), gives more precise estimates of direct genetic effects than existing approaches. Using 39,614 individuals from the UK Biobank with at least one genotyped sibling/parent, we estimate the correlation between direct genetic effects and effects from standard GWASs for nine phenotypes, including educational attainment (r = 0.739, standard error (s.e.) = 0.086) and cognitive ability (r = 0.490, s.e. = 0.086). Our results demonstrate substantial confounding bias in standard GWASs for some phenotypes.

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects.

Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

We conduct a genome-wide association study (GWAS) of educational attainment (EA) in a sample of ~3 million individuals and identify 3,952 approximately uncorrelated genome-wide-significant single-nucleotide polymorphisms (SNPs). A genome-wide polygenic predictor, or polygenic index (PGI), explains 12-16% of EA variance and contributes to risk prediction for ten diseases. Direct effects (i.e., controlling for parental PGIs) explain roughly half the PGI's magnitude of association with EA and other phenotypes. The correlation between mate-pair PGIs is far too large to be consistent with phenotypic assortment alone, implying additional assortment on PGI-associated factors. In an additional GWAS of dominance deviations from the additive model, we identify no genome-wide-significant SNPs, and a separate X-chromosome additive GWAS identifies 57.

Modeling assortative mating and genetic similarities between partners, siblings, and in-laws

Assortative mating on heritable traits can have implications for the genetic resemblance between siblings and in-laws in succeeding generations. We studied polygenic scores and phenotypic data from pairs of partners (n = 26,681), siblings (n = 2,170), siblings-in-law (n = 3,905), and co-siblings-in-law (n = 1,763) in the Norwegian Mother, Father and Child Cohort Study. Using structural equation models, we estimated associations between measurement error-free latent genetic and phenotypic variables. We found evidence of genetic similarity between partners for educational attainment (r_g = 0.37), height (r_g = 0.13), and depression (r_g = 0.08). Common genetic variants associated with educational attainment correlated between siblings above 0.50 (r_g = 0.68) and between siblings-in-law (r_g = 0.25) and co-siblings-in-law (r_g = 0.09). Indirect assortment on secondary traits accounted for partner similarity in education and depression, but not in height. Comparisons between the genetic similarities of partners and siblings indicated that genetic variances were in intergenerational equilibrium. This study shows genetic similarities between extended family members and that assortative mating has taken place for several generations.

Causal Inference with Genetic Data: Past, Present, and Future

The set of methods discussed in this collection has emerged from the convergence of two scientific fields-genetics and causal inference. In this introduction, we discuss relevant aspects of each field and show how their convergence arises from the natural experiments that genetics offer. We present introductory concepts useful to readers unfamiliar with genetically informed methods for causal inference. We conclude that existing applications and foreseeable developments should ensure that we rapidly reap the rewards of this relatively new field, not only in terms of our understanding of human disease and development, but also in terms of tangible translational applications.

Indirect Genetic Effects: A Cross-disciplinary Perspective on Empirical Studies

Indirect genetic effects (IGE) occur when an individual's phenotype is influenced by genetic variation in conspecifics. Opportunities for IGE are ubiquitous, and, when present, IGE have profound implications for behavioral, evolutionary, agricultural, and biomedical genetics. Despite their importance, the empirical study of IGE lags behind the development of theory. In large part, this lag can be attributed to the fact that measuring IGE, and deconvoluting them from the direct genetic effects of an individual's own genotype, is subject to many potential pitfalls. In this Perspective, we describe current challenges that empiricists across all disciplines will encounter in measuring and understanding IGE. Using ideas and examples spanning evolutionary, agricultural, and biomedical genetics, we also describe potential solutions to these challenges, focusing on opportunities provided by recent advances in genomic, monitoring, and phenotyping technologies. We hope that this cross-disciplinary assessment will advance the goal of understanding the pervasive effects of conspecific interactions in biology.

What Do We Know About the Genetic Architecture of Psychopathology?

In the second half of the twentieth century, twin and family studies established beyond a reasonable doubt that all forms of psychopathology are substantially heritable and highly polygenic. These conclusions were simultaneously an important theoretical advance and a difficult methodological obstacle, as it became clear that heritability is universal and undifferentiated across forms of psychopathology, and the radical polygenicity of genetic effects limits the biological insight provided by genetically informed studies at the phenotypic level. The paradigm-shifting revolution brought on by the Human Genome Project has recapitulated the great methodological promise and the profound theoretical difficulties of the twin study era. We review these issues using the rubric of genetic architecture, which we define as a search for specific genetic insight that adds to the general conclusion that psychopathology is heritable and polygenic. Although significant problems remain, we see many promising avenues for progress.

Expected final online publication date for the Annual Review of Clinical Psychology, Volume 18 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetic and environmental contributions to IQ in adoptive and biological families with 30-year-old offspring

While adoption studies have provided key insights into the influence of the familial environment on IQ scores of adolescents and children, few have followed adopted offspring long past the time spent living in the family home. To improve confidence about the extent to which shared environment exerts enduring effects on IQ, we estimated genetic and environmental effects on adulthood IQ in a unique sample of 486 biological and adoptive families. These families, tested previously on measures of IQ when offspring averaged age 15, were assessed a second time nearly two decades later ( M offspring age = 32 years). We estimated the proportions of the variance in IQ attributable to environmentally mediated effects of parental IQs, sibling-specific shared environment, and gene-environment covariance to be .01 [95% CI .00, .02], .04 [95% CI .00, .15], and .03 [95% CI .00, .07] respectively; these components jointly accounted for 8 percent of the IQ variance in adulthood. The heritability was estimated to be .42 [95% CI .21, .64]. Together, these findings provide further evidence for the predominance of genetic influences on adult intelligence over any other systematic source of variation.

Twin studies to GWAS: there and back again

The field of human behavioral genetics has come full circle. It began by using twin/family studies to estimate the relative importance of genetic and environmental influences. As large-scale genotyping became cost-effective, genome-wide association studies (GWASs) yielded insights about the nature of genetic influences and new methods that use GWAS data to estimate heritability and genetic correlations invigorated the field. Yet these newer GWAS methods have not replaced twin/family studies. In this review, we discuss the strengths and weaknesses of the two approaches with respect to characterizing genetic and environmental influences, measurement of behavioral phenotypes, and evaluation of causal models, with a particular focus on cognitive neuroscience. This discussion highlights how twin/family studies and GWAS complement and mutually reinforce one another.

Robust genetic nurture effects on education: A systematic review and meta-analysis based on 38,654 families across 8 cohorts

Similarities between parents and offspring arise from nature and nurture. Beyond this simple dichotomy, recent genomic studies have uncovered "genetic nurture" effects, whereby parental genotypes influence offspring outcomes via environmental pathways rather than genetic transmission. Such genetic nurture effects also need to be accounted for to accurately estimate "direct" genetic effects (i.e., genetic effects on a trait originating in the offspring). Empirical studies have indicated that genetic nurture effects are particularly relevant to the intergenerational transmission of risk for child educational outcomes, which are, in turn, associated with major psychological and health milestones throughout the life course. These findings have yet to be systematically appraised across contexts. We conducted a systematic review and meta-analysis to quantify genetic nurture effects on educational outcomes. A total of 12 studies comprising 38,654 distinct parent(s)-offspring pairs or trios from 8 cohorts reported 22 estimates of genetic nurture effects. Genetic nurture effects on offspring's educational outcomes (βgenetic nurture = 0.08, 95% CI [0.07, 0.09]) were smaller than direct genetic effects (βdirect genetic = 0.17, 95% CI [0.13, 0.20]). Findings were largely consistent across studies. Genetic nurture effects originating from mothers and fathers were of similar magnitude, highlighting the need for a greater inclusion of fathers in educational research. Genetic nurture effects were largely explained by observed parental education and socioeconomic status, pointing to their role in environmental pathways shaping child educational outcomes. Findings provide consistent evidence that environmentally mediated parental genetic influences contribute to the intergenerational transmission of educational outcomes, in addition to effects due to genetic transmission.

The Associations of Polygenic Scores for Risky Behaviors and Parenting Behaviors with Adolescent Externalizing Problems

The current study focused on longitudinal effects of genetics and parental behaviors and their interplay on externalizing behaviors in a panel study following individuals from adolescence to young adulthood. The nationally representative sample of Add Health participants of European ancestry included N = 4142 individuals, measured on three occasions. Parenting was operationalized as experiences with child maltreatment and maternal closeness. Externalizing problems were operationalized as alcohol use, cannabis use, and antisocial behaviors. Genetic effects were operationalized as a polygenic score (PGS) of risky behaviors. The results showed significant effects for child maltreatment, maternal closeness, and PGS, above and beyond other factors and previous levels of externalizing behaviors. Furthermore, maternal closeness was found to negatively correlate with PGS. No significant interaction effects of parenting and PGS were found. The results underscore the joint independent effects of parenting and genetics on the change in externalizing behaviors from adolescence to young adulthood.

RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset

Motivation

Polygenic scores (PGS) aim to genetically predict complex traits at an individual level. PGS are typically trained on genome-wide association summary statistics and require an independent test dataset to tune parameters. More recent methods allow parameters to be tuned on the training data, removing the need for independent test data, but approaches are computationally intensive. Based on fine-mapping principles, we present RápidoPGS, a flexible and fast method to compute PGS requiring summary-level Genome-wide association studies (GWAS) datasets only, with little computational requirements and no test data required for parameter tuning.

Results

We show that RápidoPGS performs slightly less well than two out of three other widely used PGS methods (LDpred2, PRScs and SBayesR) for case–control datasets, with median r² difference: -0.0092, -0.0042 and 0.0064, respectively, but up to 17 000-fold faster with reduced computational requirements. RápidoPGS is implemented in R and can work with user-supplied summary statistics or download them from the GWAS catalog.

Availability and implementation

Our method is available with a GPL license as an R package from CRAN and GitHub.

Supplementary information

Supplementary data are available at Bioinformatics online.