A behavioural genomic analysis of DNA markers associated with general cognitive ability in 7-year-olds

Celebrating a Century of Research in Behavioral Genetics

A century after the first twin and adoption studies of behavior in the 1920s, this review looks back on the journey and celebrates milestones in behavioral genetic research. After a whistle-stop tour of early quantitative genetic research and the parallel journey of molecular genetics, the travelogue focuses on the last fifty years. Just as quantitative genetic discoveries were beginning to slow down in the 1990s, molecular genetics made it possible to assess DNA variation directly. From a rocky start with candidate gene association research, by 2005 the technological advance of DNA microarrays enabled genome-wide association studies, which have successfully identified some of the DNA variants that contribute to the ubiquitous heritability of behavioral traits. The ability to aggregate the effects of thousands of DNA variants in polygenic scores has created a DNA revolution in the behavioral sciences by making it possible to use DNA to predict individual differences in behavior from early in life.

Polygenic scores: Are they a public health hazard?

I argue here that polygenic scores are a public health hazard because the underlying methodology, genome wide association, from which they are derived, incorrectly assumes that the information encoded in the genomic DNA sequence is causal in terms of the cellular phenotype. This is not so when the cell is viewed from the perspective of a) fundamental physics, b) the protein chemistry that characterises the cellular cytoplasm and c) the fundamental requirement for evolution to yield unlimited species diversity.

Differences in exam performance between pupils attending selective and non-selective schools mirror the genetic differences between them

On average, students attending selective schools outperform their non-selective counterparts in national exams. These differences are often attributed to value added by the school, as well as factors schools use to select pupils, including ability, achievement and, in cases where schools charge tuition fees or are located in affluent areas, socioeconomic status. However, the possible role of DNA differences between students of different schools types has not yet been considered. We used a UK-representative sample of 4814 genotyped students to investigate exam performance at age 16 and genetic differences between students in three school types: state-funded, non-selective schools ('non-selective'), state-funded, selective schools ('grammar') and private schools, which are selective ('private'). We created a genome-wide polygenic score (GPS) derived from a genome-wide association study of years of education (EduYears). We found substantial mean genetic differences between students of different school types: students in non-selective schools had lower EduYears GPS compared to those in grammar (d = 0.41) and private schools (d = 0.37). Three times as many students in the top EduYears GPS decile went to a selective school compared to the bottom decile. These results were mirrored in the exam differences between school types. However, once we controlled for factors involved in pupil selection, there were no significant genetic differences between school types, and the variance in exam scores at age 16 explained by school type dropped from 7% to <1%. These results show that genetic and exam differences between school types are primarily due to the heritable characteristics involved in pupil admission.

The paradox of intelligence: Heritability and malleability coexist in hidden gene-environment interplay

Intelligence can have an extremely high heritability, but also be malleable; a paradox that has been the source of continuous controversy. Here we attempt to clarify the issue, and advance a frequently overlooked solution to the paradox: Intelligence is a trait with unusual properties that create a large reservoir of hidden gene-environment (GE) networks, allowing for the contribution of high genetic and environmental influences on individual differences in IQ. GE interplay is difficult to specify with current methods, and is underestimated in standard metrics of heritability (thus inflating estimates of "genetic" effects). We describe empirical evidence for GE interplay in intelligence, with malleability existing on top of heritability. The evidence covers cognitive gains consequent to adoption/immigration, changes in IQ's heritability across life span and socioeconomic status, gains in IQ over time consequent to societal development (the Flynn effect), the slowdown of age-related cognitive decline, and the gains in intelligence from early education. The GE solution has novel implications for enduring problems, including our inability to identify intelligence-related genes (also known as IQ's "missing heritability"), and the loss of initial benefits from early intervention programs (such as "Head Start"). The GE solution can be a powerful guide to future research, and may also aid policies to overcome barriers to the development of intelligence, particularly in impoverished and underprivileged populations. (PsycINFO Database Record

Predicting educational achievement from DNA

A genome-wide polygenic score (GPS), derived from a 2013 genome-wide association study (N=127,000), explained 2% of the variance in total years of education (EduYears). In a follow-up study (N=329,000), a new EduYears GPS explains up to 4%. Here, we tested the association between this latest EduYears GPS and educational achievement scores at ages 7, 12 and 16 in an independent sample of 5825 UK individuals. We found that EduYears GPS explained greater amounts of variance in educational achievement over time, up to 9% at age 16, accounting for 15% of the heritable variance. This is the strongest GPS prediction to date for quantitative behavioral traits. Individuals in the highest and lowest GPS septiles differed by a whole school grade at age 16. Furthermore, EduYears GPS was associated with general cognitive ability (~3.5%) and family socioeconomic status (~7%). There was no evidence of an interaction between EduYears GPS and family socioeconomic status on educational achievement or on general cognitive ability. These results are a harbinger of future widespread use of GPS to predict genetic risk and resilience in the social and behavioral sciences.

Exploring whether genetic differences between siblings explain sibling differences in criminal justice outcomes

Research has revealed that despite many similarities, siblings raised within the same household have also been found to be markedly different from one another. Behavioral differences between siblings have been primarily attributed to differential exposure to a wide variety of environmental influences. The potential role that between-sibling genetic differences play in the development of behavioral differences has been overlooked in the extant literature. The current study examines the association between differences in three dopaminergic polymorphisms (DAT1, DRD2, and DRD4) and differences in arrest, incarceration, and multiple arrests between siblings. Between-sibling difference scores were estimated for each examined polymorphism and each criminal justice outcome measure (along with all controls). Ordinary least squares (OLS) regression models were estimated to examine the potential association between genetic differences between siblings and differences in experiences within the criminal justice system. Models were estimated for the full sample and then for the same-sex male and female subsamples separately. The results provide preliminary evidence that between-sibling differences in some of the examined dopaminergic polymorphisms are associated with differences in contact with the criminal justice system. Findings are discussed in more detail and suggestions for future research are also provided.

The future of genomics for developmentalists

The momentum of genomic science will carry it far into the future and into the heart of research on typical and atypical behavioral development. The purpose of this paper is to focus on a few implications and applications of these advances for understanding behavioral development. Quantitative genetics is genomic and will chart the course for molecular genomic research now that these two worlds of genetics are merging in the search for many genes of small effect. Although current attempts to identify specific genes have had limited success, known as the missing heritability problem, whole-genome sequencing will improve this situation by identifying all DNA sequence variations, including rare variants. Because the heritability of complex traits is caused by many DNA variants of small effect in the population, polygenic scores that are composites of hundreds or thousands of DNA variants will be used by developmentalists to predict children's genetic risk and resilience. The most far-reaching advance will be the widespread availability of whole-genome sequence for children, which means that developmentalists would no longer need to obtain DNA or to genotype children in order to use genomic information in research or in the clinic.

Commentary: missing heritability, polygenic scores, and gene-environment correlation

This special issue amply fulfils its aim of moving the study of gene × environment (GE) interplay forward constructively and creatively, exploiting contributions from diverse disciplines. Rather than discussing the many interesting findings and methods in this special issue, I will comment on two cross-cutting issues - one about genes and the other about the environment - that came to mind as I read these articles.

Twins Early Development Study (TEDS): a genetically sensitive investigation of cognitive and behavioral development from childhood to young adulthood

The Twins Early Development Study (TEDS) is a large longitudinal sample of twins born in England and Wales between 1994 and 1996. The focus of TEDS has been on cognitive and behavioral development, including difficulties in the context of normal development. TEDS began when multiple births were identified from birth records and the families were invited to take part in the study; 16,810 pairs of twins were originally enrolled in TEDS. More than 10,000 of these twin pairs remain enrolled in the study to date. DNA has been collected for more than 7,000 pairs, and genome-wide genotyping data for two million DNA markers are available for 3,500 individuals. The TEDS families have taken part in studies when the twins were aged 2, 3, 4, 7, 8, 9, 10, 12, 14, and 16 years of age. Data collection is currently underway to assess the adult destinations of the twins as they move from school to university and the workplace. Between January 2012 and December 2014, all of the TEDS twins will turn 18, and the study will transition to an adult sample. TEDS represents an outstanding resource for investigating the developmental effects of genes and environments on complex quantitative traits from childhood to young adulthood and beyond.

Child development and molecular genetics: 14 years later

Fourteen years ago, the first article on molecular genetics was published in this journal: Child Development, Molecular Genetics, andWhat to Do With Genes Once They Are Found (R. Plomin & M. Rutter, 1998). The goal of the article was to outline what developmentalists can do with genes once they are found. These new directions for developmental research are still relevant today. The problem lies with the phrase “once they are found”: It has been much more difficult than expected to identify genes responsible for the heritability of complex traits and common disorders, the so-called missing heritability problem. The present article considers reasons for the missing heritability problem and possible solutions.

Gene-environment interaction and the intergenerational transmission of parenting: testing the differential-susceptibility hypothesis

The current study evaluated the differential-susceptibility hypothesis in explaining the intergenerational transmission of parenting, using data from the National Longitudinal Study of Adolescent Health (Add Health). Exposure to maternal parenting was measured prospectively when respondents were adolescents and parental stress was measured when they were parents themselves, some 14 years later, on average. Cumulative-genetic plasticity was measured by dominantly coding the presence of putative plasticity alleles from four genes: the 10R allele of DAT1, the A1 allele of DRD2, the 7R allele of DRD4, and the short allele of 5HTTLPR. Results showed that the more plasticity alleles individuals carried (range 0-4), the more that parenting experienced in adolescence predicted future parenting experience. Those respondents with the most plasticity alleles not only experienced the highest levels of parental stress when exposed to negative maternal parenting in adolescence but the lowest levels when exposed to positive maternal parenting in adolescence. These results indicate that differential susceptibility is operative in the case of the intergenerational transmission of parenting, which could explain why estimates of such transmission have proven so modest in studies which fail to consider GXE interactions.

A latent variable partial least squares path modeling approach to regional association and polygenic effect with applications to a human obesity study

Genetic association studies are now routinely used to identify single nucleotide polymorphisms (SNPs) linked with human diseases or traits through single SNP-single trait tests. Here we introduced partial least squares path modeling (PLSPM) for association between single or multiple SNPs and a latent trait that can involve single or multiple correlated measurement(s). Furthermore, the framework naturally provides estimators of polygenic effect by appropriately weighting trait-attributing alleles. We conducted computer simulations to assess the performance via multiple SNPs and human obesity-related traits as measured by body mass index (BMI), waist and hip circumferences. Our results showed that the associate statistics had type I error rates close to nominal level and were powerful for a range of effect and sample sizes. When applied to 12 candidate regions in data (N = 2,417) from the European Prospective Investigation of Cancer (EPIC)-Norfolk study, a region in FTO was found to have stronger association (rs7204609∼rs9939881 at the first intron P = 4.29×10(-7)) than single SNP analysis (all with P>10(-4)) and a latent quantitative phenotype was obtained using a subset sample of EPIC-Norfolk (N = 12,559). We believe our method is appropriate for assessment of regional association and polygenic effect on a single or multiple traits.

Twins' Early Development Study (TEDS): A Multivariate, Longitudinal Genetic Investigation of Language, Cognition and Behavior Problems from Childhood Through Adolescence

The Twins' Early Development Study (TEDS) is a large-scale longitudinal study of twins from early childhood through adolescence. Since its conception, TEDS has had as its focus the study of problematic development within the context of normal variation, mainly in the development of language, cognitive and academic abilities and behavior problems from multivariate quantitative and molecular genetic perspectives. TEDS twins have been assessed at 2, 3, 4, 7, 9, 10 and (currently) 12 years of age, and DNA collected from more than 12,000 children. Identified from birth records of twins born in the United Kingdom between 1994 and 1996, more than 15,000 pairs of twins originally enrolled in TEDS, and well over 13,000 pairs — representative of the UK population — remain involved in the study to date. Similar to many other twin and adoption studies, TEDS data indicate that both genetic and environmental influences are important in nearly all areas of behavioral development. Multivariate genetic analyses allow researchers to go beyond this basic nature–nurture question, and TEDS results suggest that, especially in the area of learning abilities and disabilities, genes are generalists and environments are specialists. That is, genes largely contribute to similarity in performance within and between learning abilities and disabilities and across age, whereas the environment contributes to differences in performance. Quantitative genetic findings such as these chart the course for molecular genetic research. The TEDS dataset is proving valuable in genome-wide association research that tries to identify some of the many genes responsible for the ubiquitous heritability of behavior.

SNP sets and reading ability: testing confirmation of a 10-SNP set in a population sample

A set of 10 SNPs associated with reading ability in 7-year-olds was reported based on initial pooled analyses of 100K SNP chip data, with follow-up testing stages using pooling and individual testing. Here we examine this association in an adolescent population sample of Australian twins and siblings (N = 1177) aged 12 to 25 years. One (rs1842129) of the 10 SNPs approached significance (P = .05) but no support was found for the remaining 9 SNPs or the SNP set itself. Results indicate that these SNPs are not associated with reading ability in an Australian population. The results are interpreted as supporting use of much larger SNP sets in common disorders where effects are small.

Dopaminergic polymorphisms and educational achievement: results from a longitudinal sample of Americans

Although educational attainment has been found to be moderately heritable, research has yet to explore candidate genes for it. Drawing on data from the National Longitudinal Study of Adolescent Health, in the current study, we examined the association between polymorphisms in three dopaminergic genes (DAT1, DRD2, and DRD4), a dopamine index, and educational attainment. Statistically significant effects were found for DAT1, DRD2, DRD4, and the dopamine index for highest level of education. This study is the first to our knowledge that links measured genes to educational attainment.

Cumulative-genetic plasticity, parenting and adolescent self-regulation

BACKGROUND

The capacity to control or regulate one's emotions, cognitions and behavior is central to competent functioning, with limitations in these abilities associated with developmental problems. Parenting appears to influence such self-regulation. Here the differential-susceptibility hypothesis is tested that the more putative 'plasticity alleles' adolescents carry, the more positively and negatively influenced they will be by, respectively, supportive and unsupportive parenting.

METHODS

One thousand, five hundred and eighty-six (1586) adolescents (n = 754 males; n = 832 females) enrolled in the American Add Health project were scored in terms of how many of 5 putative 'plasticity alleles' they carried - the 10R allele of DAT1, the A1 allele of DRD2, the 7R allele of DRD4, the short allele of 5HTTLPR, and the 2R/3R alleles of MAOA. Then the effect of the resultant index (ranging from 0 to 5) of cumulative-genetic plasticity in moderating effects of parenting on adolescent self-regulation was evaluated.

RESULTS

Consistent with differential susceptibility, the more plasticity alleles males (but not females) carried, the more and less self-regulation they manifested under, respectively, supportive and unsupportive parenting conditions.

CONCLUSION

Adolescent males appear to vary for genetic reasons in their susceptibility to parenting vis-à-vis self-regulation, perhaps due to epistatic and/or epigenetic processes. G×E research may benefit from compositing candidate genes. To afford comparative evaluation of differential-susceptibility vs. diathesis-stress models of environmental action, future G×E work should focus on positive as well as negative environmental conditions and developmental outcomes.

Gene-environment interaction in the etiology of mathematical ability using SNP sets

Mathematics ability and disability is as heritable as other cognitive abilities and disabilities, however its genetic etiology has received relatively little attention. In our recent genome-wide association study of mathematical ability in 10-year-old children, 10 SNP associations were nominated from scans of pooled DNA and validated in an individually genotyped sample. In this paper, we use a 'SNP set' composite of these 10 SNPs to investigate gene-environment (GE) interaction, examining whether the association between the 10-SNP set and mathematical ability differs as a function of ten environmental measures in the home and school in a sample of 1888 children with complete data. We found two significant GE interactions for environmental measures in the home and the school both in the direction of the diathesis-stress type of GE interaction: The 10-SNP set was more strongly associated with mathematical ability in chaotic homes and when parents are negative.

Quantitative genetics in the era of molecular genetics: learning abilities and disabilities as an example

OBJECTIVE

To consider recent findings from quantitative genetic research in the context of molecular genetic research, especially genome-wide association studies. We focus on findings that go beyond merely estimating heritability. We use learning abilities and disabilities as examples.

METHOD

Recent twin research in the area of learning abilities and disabilities was reviewed.

RESULTS

Three findings from quantitative genetic research stand out for their far-reaching implications for child and adolescent psychiatry. First, common disorders such as learning difficulties are the quantitative extreme of the same genetic factors responsible for genetic influence throughout the normal distribution (the Common Disorders are Quantitative Traits Hypothesis). Second, the same set of genes is largely responsible for genetic influence across diverse learning and cognitive abilities and disabilities (the Generalist Genes Hypothesis). Third, experiences are just as influenced genetically as are behaviors and genetic factors mediate associations between widely used measures of the environment and behavioural outcomes (the Nature of Nurture Hypothesis).

CONCLUSIONS

Quantitative genetics can go far beyond the rudimentary "how much" question about nature versus nurture, and can continue to provide important findings in the era of molecular genetics.

Generalist genes analysis of DNA markers associated with mathematical ability and disability reveals shared influence across ages and abilities

BACKGROUND

The Generalist Genes Hypothesis is based upon quantitative genetic findings which indicate that many of the same genes influence diverse cognitive abilities and disabilities across age. In a recent genome-wide association study of mathematical ability in 10-year-old children, 43 SNP associations were nominated from scans of pooled DNA, 10 of which were validated in an individually genotyped sample. The 4927 children in this genotyped sample have also been studied at 7, 9 and 12 years of age on measures of mathematical ability, as well as on other cognitive and learning abilities.

RESULTS

Using these data we have explored the Generalist Genes Hypothesis by assessing the association of the available measures of ability at age 10 and other ages with two composite 'SNP-set' scores, formed from the full set of 43 nominated SNPs and the sub-set of 10 SNPs that were previously found to be associated with mathematical ability at age 10. Both SNP sets yielded significant associations with mathematical ability at ages 7, 9 and 12, as well as with reading and general cognitive ability at age 10.

CONCLUSIONS

Although effect sizes are small, our results correspond with those of quantitative genetic research in supporting the Generalist Genes Hypothesis. SNP sets identified on the basis of their associations with mathematical ability at age 10 show associations with mathematical ability at earlier and later ages and show associations of similar magnitude with reading and general cognitive ability. With small effect sizes expected in such complex traits, future studies may be able to capitalise on power by searching for 'generalist genes' using longitudinal and multivariate approaches.

Association between the A1 allele of the DRD2 gene and reduced verbal abilities in adolescence and early adulthood

Behavioral genetic research has consistently revealed that genetic factors explain at least one half of the variance in measures of cognitive skills. However, the specific DNA markers involved in the etiology of cognitive abilities have remained elusive. The current study examined the association between the TaqI polymorphism in the dopamine D2 receptor gene (DRD2) and verbal skills. Analysis of data drawn from the National Longitudinal Study of Adolescent Health (Add Health) revealed that the A1 allele was associated with group membership in high-, average-, and low-verbal skills groups for Caucasians. The results suggest that DRD2 may be related to domain specific cognitive abilities, such as verbal skills.

Preschool speech, language skills, and reading at 7, 9, and 10 years: etiology of the relationship

PURPOSE

To examine the etiology of the relationship between preschool speech and language, and later reading skills.

METHOD

One thousand six hundred seventy-two children from the Twins Early Development Study (B. R. Oliver & R. Plomin, 2007) were given a comprehensive speech and language assessment at 4(1/2) years. Reading was assessed at 7, 9, and 10 years. Twin analyses were applied to the data to assess the contributions of genetic and environmental factors to the longitudinal relationships between speech and reading, and language and reading.

RESULTS

Phenotypically, there is a moderate and stable relationship between 4(1/2)-year speech and language scores and reading at 7, 9, and 10 years. Etiologically, at the individual-differences level, both genetic and shared environmental factors contribute to the links between language skills and reading. By contrast, genetic factors account for most of the relationship between early speech and later reading. At the extremes, there appears to be an even stronger role for genetic factors in accounting for the prediction from early speech and language impairments to later reading outcome.

CONCLUSION

Both genetic and environmental factors contribute to the relationship between early language skills and reading, whereas genetic factors play a dominant role in the relationship between early speech and reading.

A three-stage genome-wide association study of general cognitive ability: hunting the small effects

Childhood general cognitive ability (g) is important for a wide range of outcomes in later life, from school achievement to occupational success and life expectancy. Large-scale association studies will be essential in the quest to identify variants that make up the substantial genetic component implicated by quantitative genetic studies. We conducted a three-stage genome-wide association study for general cognitive ability using over 350,000 single nucleotide polymorphisms (SNPs) in the quantitative extremes of a population sample of 7,900 7-year-old children from the UK Twins Early Development Study. Using two DNA pooling stages to enrich true positives, each of around 1,000 children selected from the extremes of the distribution, and a third individual genotyping stage of over 3,000 children to test for quantitative associations across the normal range, we aimed to home in on genes of small effect. Genome-wide results suggested that our approach was successful in enriching true associations and 28 SNPs were taken forward to individual genotyping in an unselected population sample. However, although we found an enrichment of low P values and identified nine SNPs nominally associated with g (P < 0.05) that show interesting characteristics for follow-up, further replication will be necessary to meet rigorous standards of association. These replications may take advantage of SNP sets to overcome limitations of statistical power. Despite our large sample size and three-stage design, the genes associated with childhood g remain tantalizingly beyond our current reach, providing further evidence for the small effect sizes of individual loci. Larger samples, denser arrays and multiple replications will be necessary in the hunt for the genetic variants that influence human cognitive ability.

The genetic and environmental etiology of high math performance in 10-year-old twins

The genetic and environmental etiology of high math performance (at or above the 85%tile) was examined in a population-based sample of 10-year-old twins (nMZ = 1,279, nDZ = 2,305). Math skills were assessed using a web-based battery of math performance tapping skills related to the UK National Math Curriculum. Probandwise concordance rates and liability threshold models indicated that genetic and shared environmental influences were significant, and that these estimates were generally similar to those obtained across the normal range of ability and did not vary significantly by gender. These results suggest that the genetic and environmental influences at the high end of ability are likely to be continuous with those that affect the entire range of math performance across all children irrespective of gender.

Attention-deficit hyperactivity disorder (ADHD) and birth order

Birth order is considered one of the most influential environmental factors in child development, affecting cognitive abilities and behavioral traits. This study investigates the effect of birth order in relation to attention-deficit hyperactivity disorder (ADHD), the most common neuro-behavioral disorder of childhood. The study describes birth order of 598 children aged 6 to 18 years diagnosed due to attention-deficit hyperactivity disorder. The cohort contains relatively large size families because 47.1% of the participants were born in families of more than 4 children. The results show no statistically significant differences in birth order of children among all families. We conclude that the chances of first, middle, or later born children, as well as single children, to suffer from attention-deficit hyperactivity disorder are almost equal. This study provides evidence that birth order has no effect in relation to attention-deficit hyperactivity disorder.

The future of genetics in psychology and psychiatry: microarrays, genome-wide association, and non-coding RNA

BACKGROUND

Much of what we thought we knew about genetics needs to be modified in light of recent discoveries. What are the implications of these advances for identifying genes responsible for the high heritability of many behavioural disorders and dimensions in childhood?

METHODS

Although quantitative genetics such as twin studies will continue to yield important findings, nothing will advance the field as much as identifying the specific genes responsible for heritability. Advances in molecular genetics have been driven by technology, especially DNA microarrays the size of a postage stamp that can genotype a million DNA markers simultaneously. DNA microarrays have led to a dramatic shift in research towards genome-wide association (GWA) studies. The ultimate goal of GWA is to sequence each individual's entire genome, which has begun to happen.

RESULTS

GWA studies suggest that for most complex traits and common disorders genetic effects are much smaller than previously considered: The largest effects account for only 1% of the variance of quantitative traits. This finding implies that hundreds of genes are responsible for the heritability of behavioural problems in childhood, and that it will be difficult to identify reliably these genes of small effect. Another discovery with far-reaching implications for future genetic research is the importance of non-coding RNA (DNA transcribed into RNA but not translated into amino acid sequences), which redefines what the word gene means. Non-coding RNA underlines the need for a genome-wide approach that is not limited to the 2% of DNA responsible for specifying the amino acid sequences of proteins.

CONCLUSIONS

The only safe prediction is that the fast pace of genetic discoveries will continue and will increasingly affect research in child psychology and psychiatry. DNA microarrays will make it possible to use hundreds of genes to predict genetic risk and to use these sets of genes in top-down behavioural genomic research that explores developmental change and continuity, multivariate heterogeneity and co-morbidity, and gene-environment interaction and correlation. A crucial question is whether the prediction of genetic risk will be sufficiently robust to translate into genetically based diagnoses, personalized treatments, and prevention programmes.

Testing replication of a 5-SNP set for general cognitive ability in six population samples

A 5-single nucleotide polymorphism (SNP) set has been associated with general cognitive ability in 5000 7-year-old children from the Twins Early Development Study (TEDS). Four of these SNPs were identified through a 10 K microarray analysis and one was identified through a targeted analysis of brain-expressed genes. The present study tested this association with general cognitive ability in six population samples of varying size and age from Australia, the UK (Scotland and England) and the Netherlands. Results from the largest sample (N=1310) approached significance (P=0.06) in the direction of the original finding, but results from the other samples (N=205-758) were mixed. A meta-analysis of the results--allowing for effect size heterogeneity between samples--yielded a non-significant correlation (r=-0.01, P=0.57), indicating that this SNP set was not associated with general cognitive ability in the populations studied.

The nature of nurture: a genomewide association scan for family chaos

Widely used measures of the environment, especially the family environment of children, show genetic influence in dozens of twin and adoption studies. This phenomenon is known as gene-environment correlation in which genetically driven influences of individuals affect their environments. We conducted the first genome-wide association (GWA) analysis of an environmental measure. We used a measure called CHAOS which assesses 'environmental confusion' in the home, a measure that is more strongly associated with cognitive development in childhood than any other environmental measure. CHAOS was assessed by parental report when the children were 3 years and again when the children were 4 years; a composite CHAOS measure was constructed across the 2 years. We screened 490,041 autosomal single-nucleotide polymorphisms (SNPs) in a two-stage design in which children in low chaos families (N = 469) versus high chaos families (N = 369) from 3,000 families of 4-year-old twins were screened in Stage 1 using pooled DNA. In Stage 2, following SNP quality control procedures, 41 nominated SNPs were tested for association with family chaos by individual genotyping an independent representative sample of 3,529. Despite having 99% power to detect associations that account for more than 0.5% of the variance, none of the 41 nominated SNPs met conservative criteria for replication. Similar to GWA analyses of other complex traits, it is likely that most of the heritable variation in environmental measures such as family chaos is due to many genes of very small effect size.

Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays

General cognitive ability (g), which refers to what cognitive abilities have in common, is an important target for molecular genetic research because multivariate quantitative genetic analyses have shown that the same set of genes affects diverse cognitive abilities as well as learning disabilities. In this first autosomal genome-wide association scan of g, we used a two-stage quantitative trait locus (QTL) design with pooled DNA to screen more than 500 000 single nucleotide polymorphisms (SNPs) on microarrays, selecting from a sample of 7000 7-year-old children. In stage 1, we screened for allele frequency differences between groups pooled for low and high g. In stage 2, 47 SNPs nominated in stage 1 were tested by individually genotyping an independent sample of 3195 individuals, representative of the entire distribution of g scores in the full 7000 7-year-old children. Six SNPs yielded significant associations across the normal distribution of g, although only one SNP remained significant after a false discovery rate of 0.05 was imposed. However, none of these SNPs accounted for more than 0.4% of the variance of g, despite 95% power to detect associations of that size. It is likely that QTL effect sizes, even for highly heritable traits such as cognitive abilities and disabilities, are much smaller than previously assumed. Nonetheless, an aggregated ‘SNP set’ of the six SNPs correlated 0.11 (P < 0.00000003) with g. This shows that future SNP sets that will incorporate many more SNPs could be useful for predicting genetic risk and for investigating functional systems of effects from genes to brain to behavior.

Generalist genes and the Internet generation: etiology of learning abilities by web testing at age 10

A key translational issue for neuroscience is to understand how genes affect individual differences in brain function. Although it is reasonable to suppose that genetic effects on specific learning abilities, such as reading and mathematics, as well as general cognitive ability (g), will overlap very little, the counterintuitive finding emerging from multivariate genetic studies is that the same genes affect these diverse learning abilities: a Generalist Genes hypothesis. To conclusively test this hypothesis, we exploited the widespread access to inexpensive and fast Internet connections in the UK to assess 2541 pairs of 10-year-old twins for reading, mathematics and g, using a web-based test battery. Heritabilities were 0.38 for reading, 0.49 for mathematics and 0.44 for g. Multivariate genetic analysis showed substantial genetic correlations between learning abilities: 0.57 between reading and mathematics, 0.61 between reading and g, and 0.75 between mathematics and g, providing strong support for the Generalist Genes hypothesis. If genetic effects on cognition are so general, the effects of these genes on the brain are also likely to be general. In this way, generalist genes may prove invaluable in integrating top-down and bottom-up approaches to the systems biology of the brain.

Follow-up of twins: health, behaviour, speech, language outcomes and implications for parents

The introduction of assisted reproduction has resulted in a growing number of multiple births. These infants and their parents experience increased, and sometimes unique, medical and psychological risks when compared to singletons. Rates of maternal morbidity, fetal and infant mortality are increased in multiple pregnancies. Twins have a death rate four times higher than singletons and this figure is six times higher for triplets. The main reason is preterm and very preterm birth in multiples, resulting in low and very low birth weight children. Perinatal mortality and morbidity are also more elevated in monozygotic (MZ) twins as compared to dizygotic (DZ) twins. In addition to an increased risk of mortality, multiples have higher rates of morbidity, specifically cerebral palsy and mental subnormality. Language and speech delays are more pronounced in multiples, as are cognitive delays, motor development, behavioural problems and difficulties in parent-child interactions. Depression among parents of multiples is reported to be higher than those of singletons. This paper aims to critically appraise the literature regarding the aforementioned topics, including a comparison between the outcomes for iatrogenic and spontaneously conceived twins and to suggest areas for further research.

Generalist genes and cognitive neuroscience

Multivariate genetic research suggests that a single set of genes affects most cognitive abilities and disabilities. This finding already has far-reaching implications for cognitive neuroscience, and will become even more revealing when this - presumably large - set of generalist genes is identified. Similar to other complex disorders and dimensions, molecular genetic research on cognitive abilities and disabilities is adopting genome-wide association strategies. These strategies involve very large samples to detect DNA associations of small effect size using microarrays that simultaneously assess hundreds of thousands of DNA markers. When this set of generalist genes is identified, it can be used to provide solid footholds in the climb towards a systems-level understanding of how genetically driven brain processes work together to affect diverse cognitive abilities and disabilities.

Quantitative trait loci for IQ and other complex traits: single-nucleotide polymorphism genotyping using pooled DNA and microarrays

Similar to other complex traits, it is likely that many DNA polymorphisms of small effect size [quantitative trait loci (QTLs)] are responsible for the high heritability of intelligence, in addition to many rare monogenic disorders known to contribute to lowered intelligence. We review the current status of approaches to identify QTLs associations for intelligence employing genome-wide strategies using pooled DNA from many individuals and evaluate the innovative approach of microarray analysis to genotype DNA pools for large numbers of single nucleotide polymorphisms.

SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children

Mild mental impairment (MMI) represents the low extreme of the quantitative trait of general intelligence and is highly heritable. Quantitative trait loci (QTLs) conferring susceptibility to MMI, as for most complex traits, are likely to be of small effect size. Using a novel approach we call SNP-MaP (SNP Microarrays and Pooling), we have identified four loci associated with MMI. These four loci have been replicated in two SNP-MaP studies and verified by individual genotyping. The two SNP-MaP studies conducted were a case versus control comparison (n = 515 and n = 1028, respectively) and a low versus high general intelligence extremes group comparison (n = 503 and n = 505, respectively). Each of the four groups consisted of five independent 'subpools', with each subpool assayed on a separate microarray. Twelve loci showing the largest significant differences in both SNP-MaP studies were individually genotyped on 6154 children. Of the four loci positively associated with MMI, the minor allele of each conferred the greater risk for MMI. Two of the loci are close to known genes and may be in linkage disequilibrium with them. One of the loci is between the candidate genes KLF7 and CREB1, but given possible long-range effects on expression and the unknown importance of untranslated elements such as micro-RNAs, all four loci deserve attention as candidates. Although each SNP accounts for a small amount of variance, their effects are additive and they can be combined in a 'SNP set' that can be used as a genetic risk index for MMI in behavioral genomic analyses.