Genome-wide analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people.

The use of spoken and written language is a fundamental human capacity. Individual differences in reading- and language-related skills are influenced by genetic variation, with twin-based heritability estimates of 30 to 80% depending on the trait. The genetic architecture is complex, heterogeneous, and multifactorial, but investigations of contributions of single-nucleotide polymorphisms (SNPs) were thus far underpowered. We present a multicohort genome-wide association study (GWAS) of five traits assessed individually using psychometric measures (word reading, nonword reading, spelling, phoneme awareness, and nonword repetition) in samples of 13,633 to 33,959 participants aged 5 to 26 y. We identified genome-wide significant association with word reading (rs11208009, P = 1.098 × 10-8) at a locus that has not been associated with intelligence or educational attainment. All five reading-/language-related traits showed robust SNP heritability, accounting for 13 to 26% of trait variability. Genomic structural equation modeling revealed a shared genetic factor explaining most of the variation in word/nonword reading, spelling, and phoneme awareness, which only partially overlapped with genetic variation contributing to nonword repetition, intelligence, and educational attainment. A multivariate GWAS of word/nonword reading, spelling, and phoneme awareness maximized power for follow-up investigation. Genetic correlation analysis with neuroimaging traits identified an association with the surface area of the banks of the left superior temporal sulcus, a brain region linked to the processing of spoken and written language. Heritability was enriched for genomic elements regulating gene expression in the fetal brain and in chromosomal regions that are depleted of Neanderthal variants. Together, these results provide avenues for deciphering the biological underpinnings of uniquely human traits.

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

Individual differences in early-life vocabulary measures are heritable and associated with subsequent reading and cognitive abilities, although the underlying mechanisms are little understood. Here, we (i) investigate the developmental genetic architecture of expressive and receptive vocabulary in early-life and (ii) assess timing of emerging genetic associations with mid-childhood verbal and non-verbal skills. We studied longitudinally assessed early-life vocabulary measures (15-38 months) and later-life verbal and non-verbal skills (7-8 years) in up to 6,524 unrelated children from the population-based Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. We dissected the phenotypic variance of rank-transformed scores into genetic and residual components by fitting multivariate structural equation models to genome-wide genetic-relationship matrices. Our findings show that the genetic architecture of early-life vocabulary involves multiple distinct genetic factors. Two of these genetic factors are developmentally stable and also contribute to genetic variation in mid-childhood skills: One genetic factor emerging with expressive vocabulary at 24 months (path coefficient: 0.32(SE = 0.06)) was also related to later-life reading (path coefficient: 0.25(SE = 0.12)) and verbal intelligence (path coefficient: 0.42(SE = 0.13)), explaining up to 17.9% of the phenotypic variation. A second, independent genetic factor emerging with receptive vocabulary at 38 months (path coefficient: 0.15(SE = 0.07)), was more generally linked to verbal and non-verbal cognitive abilities in mid-childhood (reading path coefficient: 0.57(SE = 0.07); verbal intelligence path coefficient: 0.60(0.10); performance intelligence path coefficient: 0.50(SE = 0.08)), accounting for up to 36.1% of the phenotypic variation and the majority of genetic variance in these later-life traits (≥66.4%). Thus, the genetic foundations of mid-childhood reading and cognitive abilities are diverse. They involve at least two independent genetic factors that emerge at different developmental stages during early language development and may implicate differences in cognitive processes that are already detectable during toddlerhood.

Language and reading impairments are associated with increased prevalence of non-right-handedness.

Handedness has been studied for association with language-related disorders because of its link with language hemispheric dominance. No clear pattern has emerged, possibly because of small samples, publication bias, and heterogeneous criteria across studies. Non-right-handedness (NRH) frequency was assessed in N = 2503 cases with reading and/or language impairment and N = 4316 sex-matched controls identified from 10 distinct cohorts (age range 6-19 years old; European ethnicity) using a priori set criteria. A meta-analysis (Ncases  = 1994) showed elevated NRH % in individuals with language/reading impairment compared with controls (OR = 1.21, CI = 1.06-1.39, p = .01). The association between reading/language impairments and NRH could result from shared pathways underlying brain lateralization, handedness, and cognitive functions.

Pathfinder: a gamified measure to integrate general cognitive ability into the biological, medical, and behavioural sciences.

Genome-wide association (GWA) studies have uncovered DNA variants associated with individual differences in general cognitive ability (g), but these are far from capturing heritability estimates obtained from twin studies. A major barrier to finding more of this 'missing heritability' is assessment--the use of diverse measures across GWA studies as well as time and the cost of assessment. In a series of four studies, we created a 15-min (40-item), online, gamified measure of g that is highly reliable (alpha = 0.78; two-week test-retest reliability = 0.88), psychometrically valid and scalable; we called this new measure Pathfinder. In a fifth study, we administered this measure to 4,751 young adults from the Twins Early Development Study. This novel g measure, which also yields reliable verbal and nonverbal scores, correlated substantially with standard measures of g collected at previous ages (r ranging from 0.42 at age 7 to 0.57 at age 16). Pathfinder showed substantial twin heritability (0.57, 95% CIs = 0.43, 0.68) and SNP heritability (0.37, 95% CIs = 0.04, 0.70). A polygenic score computed from GWA studies of five cognitive and educational traits accounted for 12% of the variation in g, the strongest DNA-based prediction of g to date. Widespread use of this engaging new measure will advance research not only in genomics but throughout the biological, medical, and behavioural sciences.

The developmental origins of genetic factors influencing language and literacy: Associations with early-childhood vocabulary.

BACKGROUND: The heritability of language and literacy skills increases from early-childhood to adolescence. The underlying mechanisms are little understood and may involve (a) the amplification of genetic influences contributing to early language abilities, and/or (b) the emergence of novel genetic factors (innovation). Here, we investigate the developmental origins of genetic factors influencing mid-childhood/early-adolescent language and literacy. We evaluate evidence for the amplification of early-childhood genetic factors for vocabulary, in addition to genetic innovation processes. METHODS: Expressive and receptive vocabulary scores at 38 months, thirteen language- and literacy-related abilities and nonverbal cognition (7-13 years) were assessed in unrelated children from the Avon Longitudinal Study of Parents and Children (ALSPAC, Nindividuals  ≤ 6,092). We investigated the multivariate genetic architecture underlying early-childhood expressive and receptive vocabulary, and each of 14 mid-childhood/early-adolescent language, literacy or cognitive skills with trivariate structural equation (Cholesky) models as captured by genome-wide genetic relationship matrices. The individual path coefficients of the resulting structural models were finally meta-analysed to evaluate evidence for overarching patterns. RESULTS: We observed little support for the emergence of novel genetic sources for language, literacy or cognitive abilities during mid-childhood or early adolescence. Instead, genetic factors of early-childhood vocabulary, especially those unique to receptive skills, were amplified and represented the majority of genetic variance underlying many of these later complex skills (≤99%). The most predictive early genetic factor accounted for 29.4%(SE = 12.9%) to 45.1%(SE = 7.6%) of the phenotypic variation in verbal intelligence and literacy skills, but also for 25.7%(SE = 6.4%) in performance intelligence, while explaining only a fraction of the phenotypic variation in receptive vocabulary (3.9%(SE = 1.8%)). CONCLUSIONS: Genetic factors contributing to many complex skills during mid-childhood and early adolescence, including literacy, verbal cognition and nonverbal cognition, originate developmentally in early-childhood and are captured by receptive vocabulary. This suggests developmental genetic stability and overarching aetiological mechanisms.

School quality ratings are weak predictors of students' achievement and well-being.

BACKGROUND: In England, all state-funded schools are inspected by an independent government agency, the Office for Standards in Education, Children's Services and Skills (Ofsted). Inspections aim to hold schools accountable and to promote the improvement of education, with the results made available to the public. Ofsted reports intend to index school quality, but their influence on students' individual outcomes has not been previously studied. The aim of the current study was to explore the extent to which school quality, as indexed by Ofsted ratings, is associated with students' educational achievement, well-being and school engagement. METHODS: We use an England population-based sample of 4,391 individuals, for whom school performance at age 11 and GCSE grades at age 16 were accessed from the National Pupil Database, and who completed measures of well-being and school engagement at age 16. RESULTS: We found that Ofsted ratings of secondary school quality accounted for 4% of the variance in students' educational achievement at age 16, which was further reduced to 1% of the variance after we accounted for prior school performance at age 11 and family socioeconomic status. Furthermore, Ofsted ratings were weak predictors of school engagement and student well-being, with an average correlation of .03. CONCLUSION: Our findings suggest that differences in school quality, as indexed by Ofsted ratings, have little relation to students' individual outcomes. Accordingly, our results challenge the usefulness of Ofsted ratings as guides for parents and students when choosing secondary schools.

Breadth versus depth: Cumulative risk model and continuous measure prediction of poor language and reading outcomes at 12.

This study examines whether, and how, multiple risks in early childhood are associated with an increased likelihood of a poor language or literacy outcome in early adolescence. Using data from 210 participants in the longitudinal Twins Early Developmental Study, we focus on the following risk factors at age 4: family risk, and poor language, speech, emergent literacy and nonverbal skills. The outcomes of interest at age 12 are language, reading fluency and reading comprehension. We contrast a 'cumulative risk' model, counting the presence or absence of each risk factor (breadth), with a model that also considers the severity of the early deficits (depth). A 'cumulative risk index' correlated modestly but significantly with outcome (r = 0.32-0.40). Odds ratios confirmed that having many risk factors (3-6) confers a higher probability of a poor outcome (OR 7.86-17.71) than having one or two (OR 3.65-7.28). Logistic regression models showed that predictive validity is not improved by including information about the severity of each deficit. Even with rich information on children's risk status at age 4, we can make only a moderately accurate prediction of the likelihood of a language or literacy disorder 8 years later (Area Under the Curve = 0.74-0.84; Positive Predictive Value = 0.33-0.55, Negative Predictive Value = 0.86-0.91). Taken together, and consistent with the idea of 'cumulative risk', these results suggest that the breadth of risk is a core predictor of outcome, and furthermore, that the severity of early deficits does not add significantly to this prediction.

Predicting educational achievement from genomic measures and socioeconomic status.

The two best predictors of children's educational achievement available from birth are parents' socioeconomic status (SES) and, recently, children's inherited DNA differences that can be aggregated in genome-wide polygenic scores (GPS). Here, we chart for the first time the developmental interplay between these two predictors of educational achievement at ages 7, 11, 14 and 16 in a sample of almost 5,000 UK school children. We show that the prediction of educational achievement from both GPS and SES increases steadily throughout the school years. Using latent growth curve models, we find that GPS and SES not only predict educational achievement in the first grade but they also account for systematic changes in achievement across the school years. At the end of compulsory education at age 16, GPS and SES, respectively, predict 14% and 23% of the variance of educational achievement. Analyses of the extremes of GPS and SES highlight their influence and interplay: In children who have high GPS and come from high SES families, 77% go to university, whereas 21% of children with low GPS and from low SES backgrounds attend university. We find that the associations of GPS and SES with educational achievement are primarily additive, suggesting that their joint influence is particularly dramatic for children at the extreme ends of the distribution.

Preschool Verbal and Nonverbal Ability Mediate the Association Between Socioeconomic Status and School Performance.

We compared the extent to which the long-term influence of family socioeconomic status (SES) on children's school performance from age 7 through 16 years was mediated by their preschool verbal and nonverbal ability. In 661 British children, who completed 17 researcher-administered ability tests at age 4.5 years, SES correlated more strongly with verbal than nonverbal ability (.39 vs. .26). Verbal ability mediated about half of the association between SES and school performance at age 7, while nonverbal ability accounted for a third of the link. Only SES, but not verbal or nonverbal ability, was associated with changes in school performance from age 7 to 16. We found that SES-related differences in school performance are only partly transmitted through children's preschool verbal abilities.

Phenotypic and genetic evidence for a unifactorial structure of spatial abilities.

Spatial abilities encompass several skills differentiable from general cognitive ability (g). Importantly, spatial abilities have been shown to be significant predictors of many life outcomes, even after controlling for g. To date, no studies have analyzed the genetic architecture of diverse spatial abilities using a multivariate approach. We developed "gamified" measures of diverse putative spatial abilities. The battery of 10 tests was administered online to 1,367 twin pairs (age 19-21) from the UK-representative Twins Early Development Study (TEDS). We show that spatial abilities constitute a single factor, both phenotypically and genetically, even after controlling for g This spatial ability factor is highly heritable (69%). We draw three conclusions: (i) The high heritability of spatial ability makes it a good target for gene-hunting research; (ii) some genes will be specific to spatial ability, independent of g; and (iii) these genes will be associated with all components of spatial ability.

Teacher assessments during compulsory education are as reliable, stable and heritable as standardized test scores.

BACKGROUND: Children in the UK go through rigorous teacher assessments and standardized exams throughout compulsory (elementary and secondary) education, culminating with the GCSE exams (General Certificate of Secondary Education) at the age of 16 and A-level exams (Advanced Certificate of Secondary Education) at the age of 18. These exams are a major tipping point directing young individuals towards different lifelong trajectories. However, little is known about the associations between teacher assessments and exam performance or how well these two measurement approaches predict educational outcomes at the end of compulsory education and beyond. METHODS: The current investigation used the UK-representative Twins Early Development Study (TEDS) sample of over 5,000 twin pairs studied longitudinally from childhood to young adulthood (age 7-18). We used teacher assessment and exam performance across development to investigate, using genetically sensitive designs, the associations between teacher assessment and standardized exam scores, as well as teacher assessments' prediction of exam scores at ages 16 and 18, and university enrolment. RESULTS: Teacher assessments of achievement are as reliable, stable and heritable (~60%) as test scores at every stage of the educational experience. Teacher and test scores correlate strongly phenotypically (r ~ .70) and genetically (genetic correlation ~.80) both contemporaneously and over time. Earlier exam performance accounts for additional variance in standardized exam results (~10%) at age 16, when controlling for teacher assessments. However, exam performance explains less additional variance in later academic success, ~5% for exam grades at 18, and ~3% for university entry, when controlling for teacher assessments. Teacher assessments also predict additional variance in later exam performance and university enrolment, when controlling for previous exam scores. CONCLUSIONS: Teachers can reliably and validly monitor students' progress, abilities and inclinations. High-stakes exams may shift educational experience away from learning towards exam performance. For these reasons, we suggest that teacher assessments could replace some, or all, high-stakes exams.

Twins Early Development Study: A Genetically Sensitive Investigation into Behavioral and Cognitive Development from Infancy to Emerging Adulthood.

The Twins Early Development Study (TEDS) is a longitudinal twin study that recruited over 16,000 twin-pairs born between 1994 and 1996 in England and Wales through national birth records. More than 10,000 of these families are still engaged in the study. TEDS was and still is a representative sample of the population in England and Wales. Rich cognitive and emotional/behavioral data have been collected from the twins from infancy to emerging adulthood, with data collection at first contact and at ages 2, 3, 4, 7, 8, 9, 10, 12, 14, 16, 18 and 21, enabling longitudinal genetically sensitive analyses. Data have been collected from the twins themselves, from their parents and teachers, and from the UK National Pupil Database. Genotyped DNA data are available for 10,346 individuals (who are unrelated except for 3320 dizygotic co-twins). TEDS data have contributed to over 400 scientific papers involving more than 140 researchers in 50 research institutions. TEDS offers an outstanding resource for investigating cognitive and behavioral development across childhood and early adulthood and actively fosters scientific collaborations.

Children of the Twins Early Development Study (CoTEDS): A Children-of-Twins Study.

The Children of the Twins Early Development Study (CoTEDS) is a new prospective children-of-twins study in the UK, designed to investigate intergenerational associations across child developmental stages. CoTEDS will enable research on genetic and environmental factors that underpin parent-child associations, with a focus on mental health and cognitive-related traits. Through CoTEDS, we will have a new lens to examine the roles that parents play in influencing child development, as well as the genetic and environmental factors that shape parenting behavior and experiences. Recruitment is ongoing from the sample of approximately 20,000 contactable adult twins who have been enrolled in the Twins Early Development Study (TEDS) since infancy. TEDS twins are invited to register all offspring to CoTEDS at birth, with 554 children registered as of May 2019. By recruiting the second generation of TEDS participants, CoTEDS will include information on adult twins and their offspring from infancy. Parent questionnaire-based data collection is now underway for 1- and 2-year-old CoTEDS infants, with further waves of data collection planned. Current data collection includes the following primary constructs: child mental health, temperament, language and cognitive development; parent mental health and social relationships; parenting behaviors and feelings; and other socioecological factors. Measurement tools have been selected with reference to existing genetically informative cohort studies to ensure overlap in phenotypes measured at corresponding stages of development. This built-in study overlap is intended to enable replication and triangulation of future analyses across samples and research designs. Here, we summarize study protocols and measurement procedures and describe future plans.

The Effectiveness of a Large-Scale Language and Preliteracy Intervention: The SPELL Randomized Controlled Trial in Denmark.

The present article reports results of a real-world effectiveness trial conducted in Denmark with six thousand four hundred eighty-three 3- to 6-year-olds designed to improve children's language and preliteracy skills. Children in 144 child cares were assigned to a control condition or one of three planned variations of a 20-week storybook-based intervention: a base intervention and two enhanced versions featuring extended professional development for educators or a home-based program for parents. Pre- to posttest comparisons revealed a significant impact of all three interventions for preliteracy skills (= .21-.27) but not language skills (d = .04-.16), with little differentiation among the three variations. Fidelity, indexed by number of lessons delivered, was a significant predictor of most outcomes. Implications for real-world research and practice are considered.

Self-reported parental vocabulary input frequency for young children.

Vocabulary input frequency influences age of acquisition, and is also an essential control for investigating the influence of other factors. We propose a new method of frequency estimation, self-report. 918 Danish-speaking parents of 12-36-month-old children estimated their frequency of use of 725 words. Self-report was substantially correlated with both language sample based frequencies (0.67) and frequencies of a large written corpus of Danish (0.58). Correlations within vocabulary categories between frequency and age of acquisition, restricted to words occurring in the language samples, were comparable for the two estimates. Overall, self-report based frequency estimates appear to have a promising degree of validity, which reflects their greatest strength, independence of the situation.

The high heritability of educational achievement reflects many genetically influenced traits, not just intelligence.

Because educational achievement at the end of compulsory schooling represents a major tipping point in life, understanding its causes and correlates is important for individual children, their families, and society. Here we identify the general ingredients of educational achievement using a multivariate design that goes beyond intelligence to consider a wide range of predictors, such as self-efficacy, personality, and behavior problems, to assess their independent and joint contributions to educational achievement. We use a genetically sensitive design to address the question of why educational achievement is so highly heritable. We focus on the results of a United Kingdom-wide examination, the General Certificate of Secondary Education (GCSE), which is administered at the end of compulsory education at age 16. GCSE scores were obtained for 13,306 twins at age 16, whom we also assessed contemporaneously on 83 scales that were condensed to nine broad psychological domains, including intelligence, self-efficacy, personality, well-being, and behavior problems. The mean of GCSE core subjects (English, mathematics, science) is more heritable (62%) than the nine predictor domains (35-58%). Each of the domains correlates significantly with GCSE results, and these correlations are largely mediated genetically. The main finding is that, although intelligence accounts for more of the heritability of GCSE than any other single domain, the other domains collectively account for about as much GCSE heritability as intelligence. Together with intelligence, these domains account for 75% of the heritability of GCSE. We conclude that the high heritability of educational achievement reflects many genetically influenced traits, not just intelligence.

Genome-Wide Polygenic Scores Predict Reading Performance Throughout the School Years.

It is now possible to create individual-specific genetic scores, called genome-wide polygenic scores (GPS). We used a GPS for years of education (EduYears) to predict reading performance assessed at UK National Curriculum Key Stages 1 (age 7), 2 (age 12) and 3 (age 14) and on reading tests administered at ages 7 and 12 in a UK sample of 5,825 unrelated individuals. EduYears GPS accounts for up to 5% of the variance in reading performance at age 14. GPS predictions remained significant after accounting for general cognitive ability and family socioeconomic status. Reading performance of children in the lowest and highest 12.5% of the EduYears GPS distribution differed by a mean growth in reading ability of approximately two school years. It seems certain that polygenic scores will be used to predict strengths and weaknesses in education.

Why do spatial abilities predict mathematical performance?

Spatial ability predicts performance in mathematics and eventual expertise in science, technology and engineering. Spatial skills have also been shown to rely on neuronal networks partially shared with mathematics. Understanding the nature of this association can inform educational practices and intervention for mathematical underperformance. Using data on two aspects of spatial ability and three domains of mathematical ability from 4174 pairs of 12-year-old twins, we examined the relative genetic and environmental contributions to variation in spatial ability and to its relationship with different aspects of mathematics. Environmental effects explained most of the variation in spatial ability (~70%) and in mathematical ability (~60%) at this age, and the effects were the same for boys and girls. Genetic factors explained about 60% of the observed relationship between spatial ability and mathematics, with a substantial portion of the relationship explained by common environmental influences (26% and 14% by shared and non-shared environments respectively). These findings call for further research aimed at identifying specific environmental mediators of the spatial-mathematics relationship.

Word reading fluency: role of genome-wide single-nucleotide polymorphisms in developmental stability and correlations with print exposure.

The genetic effects on individual differences in reading development were examined using genome-wide complex trait analysis (GCTA) in a twin sample. In unrelated individuals (one twin per pair, n = 2,942), the GCTA-based heritability of reading fluency was ~20%-29% at ages 7 and 12. GCTA bivariate results showed that the phenotypic stability of reading fluency from 7 to 12 years (r = 0.69) is largely driven by genetic stability (genetic r = 0.69). Genetic effects on print exposure at age 12 were moderate (~26%) and correlated with those influencing reading fluency at 12 (genetic r = 0.89), indicative of a gene-environment correlation. These findings were largely consistent with quantitative genetic twin analyses that used both twins in each pair (n = 1,066-1,409).

Genetic influence on family socioeconomic status and children's intelligence.

Environmental measures used widely in the behavioral sciences show nearly as much genetic influence as behavioral measures, a critical finding for interpreting associations between environmental factors and children's development. This research depends on the twin method that compares monozygotic and dizygotic twins, but key aspects of children's environment such as socioeconomic status (SES) cannot be investigated in twin studies because they are the same for children growing up together in a family. Here, using a new technique applied to DNA from 3000 unrelated children, we show significant genetic influence on family SES, and on its association with children's IQ at ages 7 and 12. In addition to demonstrating the ability to investigate genetic influence on between-family environmental measures, our results emphasize the need to consider genetics in research and policy on family SES and its association with children's IQ.