Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.

Studying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established. We examined 4-hour test-retest reliability and 10 month test-retest stability of individual differences in gene expression in ten 12-year-old children. Blood was collected on four occasions: 10 a.m. and 2 p.m. on Day 1 and 10 months later at 10 a.m. and 2 p.m. Total RNA was hybridized to Affymetrix-U133 plus 2.0 arrays. For each probeset, the correlation across individuals between 10 a.m. and 2 p.m. on Day 1 estimates test-retest reliability. We identified 3,414 variable and abundantly expressed probesets whose 4-hour test-retest reliability exceeded .70, a conventionally accepted level of reliability, which we had 80% power to detect. Of the 3,414 reliable probesets, 1,752 were also significantly reliable 10 months later. We assessed the long-term stability of individual differences in gene expression by correlating the average expression level for each probe-set across the two 4-hour assessments on Day 1 with the average level of each probe-set across the two 4-hour assessments 10 months later. 1,291 (73.7%) of the 1,752 probe-sets that reliably detected individual differences across 4 hours on two occasions, 10 months apart, also stably detected individual differences across 10 months. Heritability, as estimated from the MZ twin intraclass correlations, is twice as high for the 1,752 reliable probesets versus all present probesets on the array (0.68 vs 0.34), and is even higher (0.76) for the 1,291 reliable probesets that are also stable across 10 months. The 1,291 probesets that reliably detect individual differences from a single peripheral blood collection and stably detect individual differences over 10 months are promising targets for research on the causes (e.g., eQTLs) and correlates (e.g., psychopathology) of individual differences in gene expression

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans

The identification of quantitative trait loci (QTLs) of small effect size that underlie complex traits poses a particular challenge for geneticists due to the large sample sizes and large numbers of genetic markers required for genomewide association scans. An efficient solution for screening purposes is to combine single nucleotide polymorphism (SNP) microarrays and DNA pooling (SNP-MaP), an approach that has been shown to be valid, reliable and accurate in deriving relative allele frequency estimates from pooled DNA for groups such as cases and controls for 10K SNP microarrays. However, in order to conduct a genomewide association study many more SNP markers are needed. To this end, we assessed the validity and reliability of the SNP-MaP method using Affymetrix GeneChip(®) Mapping 100K Array set. Interpretable results emerged for 95% of the SNPs (nearly 110 000 SNPs). We found that SNP-MaP allele frequency estimates correlated 0.939 with allele frequencies for 97 605 SNPs that were genotyped individually in an independent population; the correlation was 0.971 for 26 SNPs that were genotyped individually for the 1028 individuals used to construct the DNA pools. We conclude that extending the SNP-MaP method to the Affymetrix GeneChip(®) Mapping 100K Array set provides a useful screen of >100 000 SNP markers for QTL association scans

Genome-wide association study of latent cognitive measures in adolescence: genetic overlap with intelligence and education

Individual differences in executive functions (EF) are heritable and predictive of academic attainment (AA). However, little is known about genetic contributions to EFs or their genetic relationship with AA and intelligence. We conducted genome-wide association analyses for processing speed (PS) and the latent EF measures of working memory (WM) and inhibitory control (IC) in 4,611 adolescents from ALSPAC. Whilst no loci reached genome-wide significance, common genetic variants explained 30% of the variance in WM and 19% in PS. In contrast, we failed to find common genetic contributions to IC. Finally, we examined shared genetic effects between EFs, and general intelligence, AA and ADHD. We identified significant genetic correlations between WM, intelligence and AA. A more specific pattern was observed for PS, with modest genetic overlap with intelligence. Together these findings highlight diversity in the genetic contributions to specific cognitive functions and their genetic relationship with educational and psychiatric outcome

Reading and Generalist Genes

Twin-study research suggests that many (but not all) of the same genes contribute to genetic influence on diverse learning abilities and disabilities, a hypothesis called generalist genes. This generalist genes hypothesis was tested using a set of 10 DNA markers (single nucleotide polymorphisms [SNPs]) found to be associated with early reading ability in a study of 4,258 7-year-old children that screened 100,000 SNPs. Using the same sample, we show that this early reading SNP set also correlates with other aspects of literacy, components of mathematics, and more general cognitive abilities. These results provide support for the generalist genes hypothesis. Although the effect size of the current SNP set is small, such SNP sets could eventually be used to predict genetic risk for learning disabilities as well as to prescribe genetically tailored intervention and prevention programs

Internalising and externalising in early adolescence predict later executive function, not the other way around: a cross-lagged panel analysis

Developmental changes in the brain networks involved in emotion regulation are thought to contribute to vulnerability to mental health problems during adolescence. Executive control is often viewed as allowing top-down regulation of emotional responses. However, while associations between executive control and mental health are commonly observed in both clinical and non-clinical populations, the direction of these associations remains unclear. Low, or immature, cognitive control could limit emotion regulation. Reversely, high emotionality could impede cognitive functioning. The scarcity of longitudinal studies testing for bi-directional effects, particularly in adolescence, has made it difficult to draw conclusions. This study utilised data from 1,445 participants of a longitudinal cohort in a cross-lagged panel design to understand bi-directional longitudinal associations between executive function and emotional behaviours across adolescence. Executive function was assessed using experimental working memory and inhibitory control tasks, emotional behaviours through parental report of internalising and externalising behaviours. Cross-sectional associations were replicated. Controlling for cross-sectional associations, early executive functions were not found to predict later emotional behaviours. Instead, early emotional behaviours predicted later executive function, with the strongest link observed between early externalising and later working memory. These results suggest that emotional well-being may affect the maturation of executive function during adolescence

The specificity of associations between cognition and attainment in English, maths and science during adolescence

Executive functions (EFs) are predictive of early academic attainment. However, there is little research investigating whether academic outcomes are differentially associated with cognitive abilities during adolescence, when EFs are still developing. Using a large population-based sample, three latent components, working memory, inhibitory control, and processing speed, were characterised from ten cognitive tasks. These components were used in structural equation models alongside measures of IQ (vocabulary, matrix reasoning) to assess specific relationships with English, maths and science attainment at 16 years of age while controlling for socio-economic status (SES) and previous attainment at age 11. Cognitive measures and SES contributed to individual differences in change in academic performance across adolescence, and specific associations between cognitive abilities and academic subjects could be observed. These results show that SES and cognitive abilities, in particular working memory, continue to influence academic progress beyond childhood, and that these associations are specific to individual academic subjects

Evidence for specificity of polygenic contributions to attainment in English, maths and science during adolescence

How well one does at school is predictive of a wide range of important cognitive, socioeconomic, and health outcomes. The last few years have shown marked advancement in our understanding of the genetic contributions to, and correlations with, academic attainment. However, there exists a gap in our understanding of the specificity of genetic associations with performance in academic subjects during adolescence, a critical developmental period. To address this, the Avon Longitudinal Study of Parents and Children was used to conduct genome-wide association studies of standardised national English (N = 5,983), maths (N = 6,017) and science (N = 6,089) tests. High SNP-based heritabilities (h2SNP) for all subjects were found (41-53%). Further, h2SNP for maths and science remained after removing shared variance between subjects or IQ (N= 3,197 – 5,895). One genome-wide significant single nucleotide polymorphism (rs952964, p = 4.86 x 10-8) and four gene-level associations with science attainment (MEF2C, BRINP1, S100A1 and S100A13) were identified. Rs952964 remains significant after removing the variance shared between academic subjects. The findings highlight the benefits of using environmentally homogeneous samples for genetic analyses and indicate that finer-grained phenotyping will help build more specific biological models of variance in learning processes and abilities

Genotyping DNA pools on microarrays: Tackling the QTL problem of large samples and large numbers of SNPs

BACKGROUND: Quantitative trait locus (QTL) theory predicts that genetic influence on complex traits involves multiple genes of small effect size. To detect QTL associations of small effect size, large samples and systematic screens of thousands of DNA markers are required. An efficient solution is to genotype case and control DNA pools using SNP microarrays. We demonstrate that this is practical using DNA pools of 100 individuals. RESULTS: Using standard microarray protocols for the Affymetrix GeneChip(® )Mapping 10 K Array Xba 131, we show that relative allele signal (RAS) values provide a quantitative index of allele frequencies in pooled DNA that correlate 0.986 with allele frequencies for 104 SNPs that were genotyped individually for 100 individuals. The sensitivity of the assay was demonstrated empirically in a spiking experiment in which 15% and 20% of one individual's DNA was added to a DNA pool. CONCLUSION: We conclude that this approach, which we call SNP-MaP (SNP microarrays and pooling), is rapid, cost effective and promises to be a valuable initial screening method in the hunt for QTLs

Tissue-specific patterns of allelically-skewed DNA methylation

While DNA methylation is usually thought to be symmetrical across both alleles, there are some notable exceptions. Genomic imprinting and X chromosome inactivation are two well-studied sources of allele-specific methylation (ASM), but recent research has indicated a more complex pattern in which genotypic variation can be associated with allelically-skewed DNA methylation in cis. Given the known heterogeneity of DNA methylation across tissues and cell types we explored inter- and intra-individual variation in ASM across several regions of the human brain and whole blood from multiple individuals. Consistent with previous studies, we find widespread ASM with >4% of the ~220,000 loci interrogated showing evidence of allelically-skewed DNA methylation. We identify ASM flanking known imprinted regions, and show that ASM sites are enriched in DNase I hypersensitivity sites and often located in an extended genomic context of intermediate DNA methylation. We also detect examples of genotype-driven ASM, some of which are also tissue-specific. These findings contribute to our understanding about the nature of differential DNA methylation across tissues and have important implications for genetic studies of complex disease. As a resource to the community, ASM patterns across each of the tissues studied are available in a searchable online database: http://epigenetics.essex.ac.uk/ASMBrainBlood

Association of Polygenic Liability for Autism with face-sensitive cortical responses from infancy

This cohort study investigates whether N290 latency to faces vs nonfaces is associated with autism polygenic scores and cross-disorder polygenic scores in infants with and without a family history of autism