A Genome-Wide Association Study Identifies Genetic Variants Associated with Mathematics Ability

Multi-polygenic score prediction of mathematics, reading, and language abilities independent of general cognitive ability

Specific cognitive abilities (SCA) correlate genetically about 0.50, which underpins general cognitive ability (g), but it also means that there is considerable genetic specificity. If g is not controlled, then genomic prediction of specific cognitive abilities is not truly specific because they are all perfused with g. Here, we investigated the heritability of mathematics, reading, and language ability independent of g (SCA.g) using twins and DNA, and the extent to which multiple genome-wide polygenic scores (multi-PGS) can jointly predict these SCA.g as compared to SCA uncorrected for g. We created SCA and SCA.g composites from a battery of 14 cognitive tests administered at age 12 to 5,000 twin pairs in the Twins Early Development Study (TEDS). Univariate twin analyses yielded an average heritability estimate of 40% for SCA.g, compared to 53% for uncorrected SCA. Using genome-wide SNP genotypes, average SNP-based heritabilities were 26% for SCA.g and 35% for SCA. We then created multi-PGS from at least 50 PGS to predict each SCA and SCA.g using elastic net penalised regression models. Multi-PGS predicted 4.4% of the variance of SCA.g on average, compared to 11.1% for SCA uncorrected for g. The twin, SNP and PGS heritability estimates for SCA.g provide further evidence that the heritabilities of SCA are not merely a reflection of g. Although the relative reduction in heritability from SCA to SCA.g was greater for PGS heritability than for twin or SNP heritability, this decrease is likely due to the paucity of PGS for SCA. We hope that these results encourage researchers to conduct genome-wide association studies of SCA, and especially SCA.g, that can be used to predict PGS profiles of SCA strengths and weaknesses independent of g.

Human dermal fibroblast-derived secretory proteins for regulating nerve restoration: A bioinformatic approach

BACKGROUND

Human dermal fibroblasts secrete diverse proteins that regulate wound repair and tissue regeneration.

METHODS

In this study, dermal fibroblast-conditioned medium (DFCM) proteins potentially regulating nerve restoration were bioinformatically selected among the 337 protein lists identified by quantitative liquid chromatography-tandem mass spectrometry. Using these proteins, protein-protein interaction network analysis was conducted. In addition, the roles of DFCM proteins were reviewed according to their protein classifications.

RESULTS

Gene Ontology protein classification categorized these 57 DFCM proteins into various classes, including protein-binding activity modulator (N = 11), cytoskeletal protein (N = 8), extracellular matrix protein (N = 6), metabolite interconversion enzyme (N = 5), chaperone (N = 4), scaffold/adapter protein (N = 4), calcium-binding protein (N = 3), cell adhesion molecule (N = 2), intercellular signal molecule (N = 2), protein modifying enzyme (N = 2), transfer/carrier protein (N = 2), membrane traffic protein (N = 1), translational protein (N = 1), and unclassified proteins (N = 6). Further protein-protein interaction network analysis of 57 proteins revealed significant interactions among the proteins that varied according to the settings of confidence score.

CONCLUSIONS

Our bioinformatic analysis demonstrated that DFCM contains many secretory proteins that form significant protein-protein interaction networks crucial for regulating nerve restoration. These findings underscore DFCM proteins' critical roles in various nerve restoration stages during the wound repair process.

A genome-wide association study identified new variants associated with mathematical abilities in Chinese children

Mathematical ability is moderately heritable, and it is a complex trait which can be evaluated in several different categories. A few genetic studies have been published on general mathematical ability. However, no genetic study focused on specific mathematical ability categories. In this study, we separately performed genome-wide association studies on 11 mathematical ability categories in 1146 students from Chinese elementary schools. We identified seven genome-wide significant single nucleotide polymorphisms (SNPs) with strong linkage disequilibrium among each other (all r²  > 0.8) associated with mathematical reasoning ability (top SNP: rs34034296, p = 2.01 × 10^-8 , nearest gene: CUB and Sushi multiple domains 3, CSMD3). We replicated one SNP (rs133885) from 585 SNPs previously reported to be associated with general mathematical ability associated with division ability in our data (p = 1.053 × 10^-5 ). In the gene- and gene-set enrichment analysis by MAGMA, we found three significant enrichments of associations with three mathematical ability categories for three genes (LINGO2, OAS1 and HECTD1). We also observed four significant enrichments of associations with four mathematical ability categories for three gene sets. Our results suggest new candidate genetic loci for the genetics of mathematical ability.

Quantity as a Fish Views It: Behavior and Neurobiology

An ability to estimate quantities, such as the number of conspecifics or the size of a predator, has been reported in vertebrates. Fish, in particular zebrafish, may be instrumental in advancing the understanding of magnitude cognition. We review here the behavioral studies that have described the ecological relevance of quantity estimation in fish and the current status of the research aimed at investigating the neurobiological bases of these abilities. By combining behavioral methods with molecular genetics and calcium imaging, the involvement of the retina and the optic tectum has been documented for the estimation of continuous quantities in the larval and adult zebrafish brain, and the contributions of the thalamus and the dorsal-central pallium for discrete magnitude estimation in the adult zebrafish brain. Evidence for basic circuitry can now be complemented and extended to research that make use of transgenic lines to deepen our understanding of quantity cognition at genetic and molecular levels.

Genome wide association study of frost tolerance in wheat

Winter wheat growing areas in the Northern hemisphere are regularly exposed to heavy frost. Due to the negative impact on yield, the identification of genetic factors controlling frost tolerance (FroT) and development of tools for breeding is of prime importance. Here, we detected QTL associated with FroT by genome wide association studies (GWAS) using a diverse panel of 276 winter wheat genotypes that was phenotyped at five locations in Germany and Russia in three years. The panel was genotyped using the 90 K iSelect array and SNPs in FroT candidate genes. In total, 17,566 SNPs were used for GWAS resulting in the identification of 53 markers significantly associated (LOD ≥ 4) to FroT, corresponding to 23 QTL regions located on 11 chromosomes (1A, 1B, 2A, 2B, 2D, 3A, 3D, 4A, 5A, 5B and 7D). The strongest QTL effect confirmed the importance of chromosome 5A for FroT. In addition, to our best knowledge, eight FroT QTLs were discovered for the first time in this study comprising one QTL on chromosomes 3A, 3D, 4A, 7D and two on chromosomes 1B and 2D. Identification of novel FroT candidate genes will help to better understand the FroT mechanism in wheat and to develop more effective combating strategies.

Molecular signature of extracellular matrix pathology in schizophrenia

Growing evidence points to a critical involvement of the extracellular matrix (ECM) in the pathophysiology of schizophrenia (SZ). Decreases of perineuronal nets (PNNs) and altered expression of chondroitin sulphate proteoglycans (CSPGs) in glial cells have been identified in several brain regions. GWAS data have identified several SZ vulnerability variants of genes encoding for ECM molecules. Given the potential relevance of ECM functions to the pathophysiology of this disorder, it is necessary to understand the extent of ECM changes across brain regions, their region- and sex-specificity and which ECM components contribute to these changes. We tested the hypothesis that the expression of genes encoding for ECM molecules may be broadly disrupted in SZ across several cortical and subcortical brain regions and include key ECM components as well as factors such as ECM posttranslational modifications and regulator factors. Gene expression profiling of 14 neocortical brain regions, caudate, putamen and hippocampus from control subjects (n = 14/region) and subjects with SZ (n = 16/region) was conducted using Affymetrix microarray analysis. Analysis across brain regions revealed widespread dysregulation of ECM gene expression in cortical and subcortical brain regions in SZ, impacting several ECM functional key components. SRGN, CD44, ADAMTS1, ADAM10, BCAN, NCAN and SEMA4G showed some of the most robust changes. Region-, sex- and age-specific gene expression patterns and correlation with cognitive scores were also detected. Taken together, these findings contribute to emerging evidence for large-scale ECM dysregulation in SZ and point to molecular pathways involved in PNN decreases, glial cell dysfunction and cognitive impairment in SZ.

The Polygenic Nature and Complex Genetic Architecture of Specific Learning Disorder

Specific Learning Disorder (SLD) is a multifactorial, neurodevelopmental disorder which may involve persistent difficulties in reading (dyslexia), written expression and/or mathematics. Dyslexia is characterized by difficulties with speed and accuracy of word reading, deficient decoding abilities, and poor spelling. Several studies from different, but complementary, scientific disciplines have investigated possible causal/risk factors for SLD. Biological, neurological, hereditary, cognitive, linguistic-phonological, developmental and environmental factors have been incriminated. Despite worldwide agreement that SLD is highly heritable, its exact biological basis remains elusive. We herein present: (a) an update of studies that have shaped our current knowledge on the disorder’s genetic architecture; (b) a discussion on whether this genetic architecture is ‘unique’ to SLD or, alternatively, whether there is an underlying common genetic background with other neurodevelopmental disorders; and, (c) a brief discussion on whether we are at a position of generating meaningful correlations between genetic findings and anatomical data from neuroimaging studies or specific molecular/cellular pathways. We conclude with open research questions that could drive future research directions.

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 = 5983), maths (N = 6017) and science (N = 6089) 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 = 3197-5895). One genome-wide significant single nucleotide polymorphism (rs952964, p = 4.86 × 10-8) and four gene-level associations with science attainment (MEF2C, BRINP1, S100A1 and S100A13) were identified. Rs952964 remained 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.

Neurobiological origins of individual differences in mathematical ability

Mathematical ability is heritable and related to several genes expressing proteins in the brain. It is unknown, however, which intermediate neural phenotypes could explain how these genes relate to mathematical ability. Here, we examined genetic effects on cerebral cortical volume of 3-6-year-old children without mathematical training to predict mathematical ability in school at 7-9 years of age. To this end, we followed an exploration sample (n = 101) and an independent replication sample (n = 77). We found that ROBO1, a gene known to regulate prenatal growth of cerebral cortical layers, is associated with the volume of the right parietal cortex, a key region for quantity representation. Individual volume differences in this region predicted up to a fifth of the behavioral variance in mathematical ability. Our findings indicate that a fundamental genetic component of the quantity processing system is rooted in the early development of the parietal cortex.

Are specific learning disorders truly specific, and are they disorders?

Specific learning disorders, such as dyslexia and dyscalculia, are frequently studied to inform our understanding of cognitive development, genetic mechanisms and brain function. In this Opinion Paper, we discuss limitations of this research approach, including the use of arbitrary criteria to select groups of children, heterogeneity within groups and overlap between domains of learning. By drawing on evidence from cognitive science, neuroscience and genetics, we propose an alternative, dimensional framework. We argue that we need to overcome the problems associated with a categorical approach by taking into account interacting factors at multiple levels of analysis that are associated with overlapping rather than entirely distinct domains of learning. We conclude that this research strategy will allow for a richer understanding of learning and development.

Common genetic variants have associations with human cortical brain regions and risk of schizophrenia

Schizophrenia is a highly heritable mental disorder and is reported to be associated with measurements in cortical regions of the human brain. In this study, we considered genome-wide association studies to uncover genetic effects on cortical regions and prodromal symptoms of schizophrenia. Specifically, area, thickness, and volume of 66 cortical regions derived from magnetic resonance imaging scans of 1,445 children and adolescents from the Philadelphia Neurodevelopmental Cohort were studied. Two common variants were identified as being associated with two prefrontal cortical regions (one significant variant rs11601331 on chromosome 11p11 for right rostral middle frontal gyral area, p = 1.97 × 10 ^-8 ; one suggestive variant rs2345981 on chromosome 6q11 for left frontal pole gyral volume, p = 2.07 × 10 ^-7 ), where the significance of rs11601331 was independently replicated on the Pediatric Imaging, Neurocognition, and Genetics study of size 1,239 (p = 9.19 × 10 ^-3 ). Moreover, genetic effects on schizophrenia were investigated based on a sample of 8,719 subjects. The two identified variants rs11601331 and rs2345981 showed significant association with the longest prodromal symptoms duration (p = 0.048 and p = 0.027, respectively).

Understanding the effects of education through the lens of biology

Early educational interventions aim to close gaps in achievement levels between children. However, early interventions do not eliminate individual differences in populations and the effects of early interventions often fade-out over time, despite changes of the mean of the population immediately following the intervention. Here, we discuss biological factors that help to better understand why early educational interventions do not eliminate achievement gaps. Children experience and respond to educational interventions differently. These stable individual differences are a consequence of biological mechanisms that support the interplay between genetic predispositions and the embedding of experience into our biology. Accordingly, we argue that it is not plausible to conceptualize the goals of educational interventions as both a shifting of the mean and a narrowing of the distribution of a particular measure of educational attainment assumed to be of utmost importance (such as a standardized test score). Instead of aiming to equalize the performance of students, the key goal of educational interventions should be to maximize potential at the individual level and consider a kaleidoscope of educational outcomes across which individuals vary. Additionally, in place of employing short-term interventions in the hope of achieving long-term gains, educational interventions need to be sustained throughout development and their long-term, rather than short-term, efficacy be evaluated. In summary, this paper highlights how biological research is valuable for driving a re-evaluation of how educational success across development can be conceptualized and thus what policy implications may be drawn.

Cognitive genomics: Searching for the genetic roots of neuropsychological functioning

OBJECTIVE

Human cognition has long been known to be under substantial genetic control. With the complete mapping of the human genome, genome-wide association studies for many complex traits have proliferated; however, the highly polygenic nature of intelligence has made the identification of the precise genes that influence both global and specific cognitive abilities more difficult than anticipated.

METHOD

Here, we review the latest developments in the genomics of cognition, including a discussion of methodological advances in the genetic analysis of complex traits, and shared genetic contributions to cognitive abilities and neuropsychiatric disorders.

RESULTS

A wealth of twin and family studies have provided compelling evidence for a strong heritable component of both global and specific cognitive abilities, and for the existence of "generalist genes" responsible for a large portion of the variance in diverse cognitive abilities. Increasingly sophisticated analytic tools and ever-larger sample sizes are now facilitating the identification of specific genetic and molecular underpinnings of cognitive abilities, leading to optimism regarding possibilities for novel treatments for illnesses related to cognitive function.

CONCLUSIONS

We conclude with a set of future directions for the field, which will further accelerate discoveries regarding the biological pathways relevant to cognitive abilities. These, in turn, may be further interrogated in order to link biological mechanisms to behavior. (PsycINFO Database Record

The implications for education of an innate numerosity-processing mechanism

One specific cause of low numeracy is a deficit in a mechanism for representing and processing numerosities that humans inherited and which is putatively shared with many other species. This deficit is evident at each of the four levels of explanation in the 'causal modelling' framework of Morton and Frith (Morton and Frith 1995 In Manual of developmental psychopathology, vol. 1 (eds D Cichetti, D Cohen), pp. 357-390). Very low numeracy can occur in cognitively able individuals with normal access to good education: it is linked to an easily measured deficit in basic numerosity processing; it has a distinctive neural signature; and twin studies suggest specific heritability, though the relevant genes have not yet been identified. Unfortunately, educators and policymakers seem largely unaware of this cause, but appropriate interventions could alleviate the suffering and handicap of those with low numeracy, and would be a major benefit to society.This article is part of a discussion meeting issue 'The origins of numerical abilities'.