Discovery of genetic factors for reading ability and dyslexia

The ability to read is critical to access wider learning and achieve qualifications, for accessing employment, and for adult life skills. Approximately one in ten individuals are affected by dyslexia, a learning difficulty which primarily impacts word reading and spelling. Specifically, phonological processing (the ability to decode phonemes) is impaired in dyslexia. Whilst some believe dyslexia represents the extreme end of a continuum of reading ability, others have suggested it is a distinct trait. Variation in reading ability is a highly heritable (possibly 70%) complex trait caused by many genetic variants with a small effect size. However, the genetic architecture of reading ability and dyslexia is largely unknown due to a lack of quantitative genetic studies with sufficient statistical power to detect such small effect sizes. Previously, most genetic studies of reading ability have been conducted using samples of children with dyslexia, which tend to be modest in size. Whilst large samples of genotyped unselected adults have been collected (for example UK Biobank), phenotypic data on reading or language skills is rarely prioritised. The overall aim of this thesis is to discover genetic variants associated with dyslexia and variation in reading skill in order to better understand the aetiology of reading difficulties, which in turn, may inform prediction, identification and intervention strategies in the future. Firstly, I will conduct a genome-wide association (GWA) study of over 50,000 adults with a self-reported dyslexia diagnosis and over 1 million controls to identify associated single nucleotide polymorphisms (SNPs). I will also explore ways to improve power for discovering genetic factors associated with reading ability. To do this, I will first investigate whether unselected adult samples are valid as a means to identify genetic factors associated with reading skill through a candidate gene approach. Secondly, I will investigate whether proxy reading phenotypes are also a means to gain power through large cohorts that have no quantitative measure of reading ability. Such samples may be informative for future GWA meta-analysis of quantitative reading ability. In Chapter 1, I will first introduce reading ability and dyslexia. I will discuss how reading ability is a quantitative trait and how it can be measured before discussing how dyslexia is identified. Then, I will consider how dyslexia may relate to reading ability: whether it represents the extreme end of a continuum of reading or whether it is a distinct trait. I will then introduce the known causes of variation in reading ability and dyslexia, which includes both environmental and genetic factors. Next, I will present the history of genetic studies of reading ability and dyslexia and their limitations. Finally, I will discuss the current state of genetic research into reading ability and introduce the aims of my thesis in detail. Chapter 2 is a publication in Nature Genetics entitled ‘Discovery of 42 genome-wide significant loci associated with dyslexia’ which includes GWA analysis of over 1 million 23andMe, Inc participants reporting on dyslexia diagnosis. I identify 42 independent genome-wide significant loci, 15 of which are in genes previously linked to cognitive ability and/or educational attainment, and 27 of which are novel and may be more specific to dyslexia. Extensive downstream biological analysis is performed alongside genetic correlations with other traits and dyslexia polygenic score prediction of quantitative reading scores. Chapter 3 is a publication in Twin Research and Human Genetics on ‘The association of dyslexia and developmental speech and language disorder candidate genes with reading and language abilities in adults’ which analyses an adult population cohort with quantitative measures of reading and language ability to replicate previous associations of candidate genes and biological pathways with dyslexia. I demonstrate that unselected adult populations are a valid means by which to identify genes which have previously been associated with dyslexia and/or speech and language disorder. Chapter 4 is a research chapter in which I construct a proxy reading phenotype from measures of reading frequency in an unselected adult sample for whom a quantitative measure of reading ability is not available. I find that a dyslexia polygenic score constructed from the dyslexia GWA analysis in Chapter 3 cannot explain variation in the proxy phenotype suggesting that book reading is not a sufficient substitute for reading ability. Finally, in Chapter 5, I integrate and discuss my research findings. I highlight the discovery of 42 variants associated with dyslexia through GWAS, in addition to the discovery of new genes and biological pathways which may form part of the biological basis of dyslexia. Following this, I consider what GWAS tells us about candidate gene findings. I discuss traits which are genetically correlated with dyslexia, including quantitative reading skills and ADHD. I consider the relationship between dyslexia and reading ability, and how genetic studies can help us to understand this better. I also consider the relationship between dyslexia and other developmental disorders, and how genetic studies can help us to understand this better. Lastly, I discuss methods to boost power for GWAS of reading ability

Discovery of 42 genome-wide significant loci associated with dyslexia

Reading and writing are crucial life skills but roughly one in ten children are affected by dyslexia, which can persist into adulthood. Family studies of dyslexia suggest heritability up to 70%, yet few convincing genetic markers have been found. Here we performed a genome-wide association study of 51,800 adults self-reporting a dyslexia diagnosis and 1,087,070 controls and identified 42 independent genome-wide significant loci: 15 in genes linked to cognitive ability/educational attainment, and 27 new and potentially more specific to dyslexia. We validated 23 loci (13 new) in independent cohorts of Chinese and European ancestry. Genetic etiology of dyslexia was similar between sexes, and genetic covariance with many traits was found, including ambidexterity, but not neuroanatomical measures of language-related circuitry. Dyslexia polygenic scores explained up to 6% of variance in reading traits, and might in future contribute to earlier identification and remediation of dyslexia

The association of dyslexia and developmental speech and language disorder candidate genes with reading and language abilities in adults

Reading and language abilities are critical for educational achievement and success in adulthood. Variation in these traits is highly heritable, but the underlying genetic architecture is largely undiscovered. Genetic studies of reading and language skills traditionally focus on children with developmental disorders; however, much larger unselected adult samples are available, increasing power to identify associations with specific genetic variants of small effect size. We introduce an Australian adult population cohort (41.7–73.2 years of age, N = 1505) in which we obtained data using validated measures of several aspects of reading and language abilities. We performed genetic association analysis for a reading and spelling composite score, nonword reading (assessing phonological processing: a core component in learning to read), phonetic spelling, self-reported reading impairment and nonword repetition (a marker of language ability). Given the limited power in a sample of this size (~80% power to find a minimum effect size of 0.005), we focused on analyzing candidate genes that have been associated with dyslexia and developmental speech and language disorders in prior studies. In gene-based tests, FOXP2, a gene implicated in speech/language disorders, was associated with nonword repetition (p < .001), phonetic spelling (p = .002) and the reading and spelling composite score (p < .001). Gene-set analyses of candidate dyslexia and speech/language disorder genes were not significant. These findings contribute to the assessment of genetic associations in reading and language disorders, crucial for understanding their etiology and informing intervention strategies, and validate the approach of using unselected adult samples for gene discovery in language and reading

Early (Days 1–4) post-treatment serum hCG level changes predict single-dose methotrexate treatment success in tubal ectopic pregnancy

Acknowledgements S.C.M. was supported by the South-East Scotland Academic Foundation Programme. Medical Research Council (MRC) Centre grants to the Centre for Reproductive Health (CRH) (G1002033 and MR/N022556/1) are also gratefully acknowledged. Funding This project was supported by funding from the Efficacy and Mechanism Evaluation programme, a Medical Research Council and National Institute for Health Research partnership (grant reference number 14/150/03).Peer reviewedPublisher PD

Author Correction: Discovery of 42 genome-wide significant loci associated with dyslexia

Correction to: Nature Genetics https://doi.org/10.1038/s41588-022-01192-y. Published online 20 October 2022. In the version of this article originally published, a paragraph was omitted in the Methods section, reading “Genomic control. Top SNPs are reported from the more conservative GWAS results adjusted for genomic control (Fig. 1, Extended Data Figs. 1–4, and Supplementary Tables 1, 2, 9 and 10), whereas downstream analyses (including gene-set analysis, enrichment and heritability partitioning, genetic correlations, polygenic prediction, candidate gene replication) are based on GWAS results without genomic control.” The paragraph has now been included in the HTML and PDF versions of the article

Discovery of 42 genome-wide significant loci associated with dyslexia

Funding: EE, GA, BM, BSP, CF and SEF are supported by the Max Planck Society (Germany). The Chinese Reading Study was supported by grants from the National Natural Science Foundation of China Youth Project (Grant No. 61807023), the Youth Fund for Humanities and Social Sciences Research of the Ministry of Education (Grant No. 19YJC190023 and 17XJC190010), and the Natural Science Basic Research Plan in Shaanxi Province of China (Grant No. 2021JQ-309). SP is funded by the Royal Society.Reading and writing are crucial life skills but roughly one in ten children are affected by dyslexia, which can persist into adulthood. Family studies of dyslexia suggest heritability up to 70%, yet few convincing genetic markers have been found. Here we performed a genome-wide association study of 51,800 adults self-reporting a dyslexia diagnosis and 1,087,070 controls and identified 42 independent genome-wide significant loci: 15 in genes linked to cognitive ability/educational attainment, and 27 new and potentially more specific to dyslexia. We validated 23 loci (13 new) in independent cohorts of Chinese and European ancestry. Genetic etiology of dyslexia was similar between sexes, and genetic covariance with many traits was found, including ambidexterity, but not neuroanatomical measures of language-related circuitry. Dyslexia polygenic scores explained up to 6% of variance in reading traits, and might in future contribute to earlier identification and remediation of dyslexia.Publisher PDFPeer reviewe

Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global consistency would imply that traits could serve as valuable proxies for the complex suite of factors that determine growth rate, and, therefore, could underpin a new generation of robust dynamic vegetation models. Alternatively, growth rates may depend more strongly on the local environment or growth–trait relationships may vary along environmental gradients. 3. We tested these alternative hypotheses using data on 27 352 juvenile trees, representing 278 species from 27 sites on all forested continents, and extensive functional trait data, 38% of which were obtained at the same sites at which growth was assessed. Data on potential evapotranspiration (PET), which summarizes the joint ecological effects of temperature and precipitation, were obtained from a global data base. 4. We estimated size-standardized relative height growth rates (SGR) for all species, then related them to functional traits and PET using mixed-effect models for the fastest growing species and for all species together. 5. Both the mean and 95th percentile SGR were more strongly associated with functional traits than with PET. PET was unrelated to SGR at the global scale. SGR increased with increasing SLA and decreased with increasing wood density and seed mass, but these traits explained only 3.1% of the variation in SGR. SGR–trait relationships were consistently weak across families and biogeographic zones, and over a range of tree statures. Thus, the most widely studied functional traits in plant ecology were poor predictors of tree growth over large scales. 6. Synthesis. We conclude that these functional traits alone may be unsuitable for predicting growth of trees over broad scales. Determining the functional traits that predict vital rates under specific environmental conditions may generate more insight than a monolithic global relationship can offer