Genome-wide association study reveals new insights into the heritability and genetic correlates of developmental dyslexia

Abstract

Developmental dyslexia (DD) is a learning disorder affecting the ability to read, with a heritability of 40-60%. A notable part of this heritability remains unexplained, and large genetic studies are warranted to identify new susceptibility genes and clarify the genetic bases of dyslexia. We carried out a genome-wide association study (GWAS) on 2274 dyslexia cases and 6272 controls, testing associations at the single variant, gene, and pathway level, and estimating heritability using single-nucleotide polymorphism (SNP) data. We also calculated polygenic scores (PGSs) based on large-scale GWAS data for different neuropsychiatric disorders and cortical brain measures, educational attainment, and fluid intelligence, testing them for association with dyslexia status in our sample. We observed statistically significant (p < 2.8 × 10^-6) enrichment of associations at the gene level, for LOC388780 (20p13; uncharacterized gene), and for VEPH1 (3q25), a gene implicated in brain development. We estimated an SNP-based heritability of 20-25% for DD, and observed significant associations of dyslexia risk with PGSs for attention deficit hyperactivity disorder (at p_T = 0.05 in the training GWAS: OR = 1.23[1.16; 1.30] per standard deviation increase; p = 8 × 10^-13), bipolar disorder (1.53[1.44; 1.63]; p = 1 × 10^-43), schizophrenia (1.36[1.28; 1.45]; p = 4 × 10^-22), psychiatric cross-disorder susceptibility (1.23[1.16; 1.30]; p = 3 × 10^-12), cortical thickness of the transverse temporal gyrus (0.90[0.86; 0.96]; p = 5 × 10^-4), educational attainment (0.86[0.82; 0.91]; p = 2 × 10^-7), and intelligence (0.72[0.68; 0.76]; p = 9 × 10^-29). This study suggests an important contribution of common genetic variants to dyslexia risk, and novel genomic overlaps with psychiatric conditions like bipolar disorder, schizophrenia, and cross-disorder susceptibility. Moreover, it revealed the presence of shared genetic foundations with a neural correlate previously implicated in dyslexia by neuroimaging evidence.

Fig. 1. Manhattan plot of the GWAS pooled analysis.

The blue and red line represent the genome-wide (α = 5 × 10⁻⁸) and suggestive significance (α = 1 × 10⁻⁵) threshold.

Fig. 2. Details of the genome-wide top hit rs6035856.

a Local association and b forest plot of the genome-wide top variant (rs6035856). The forest plot shows the odds ratio (OR) and 95% confidence intervals (CI) on the x-axis, by dataset and for the pooled analysis. Detailed OR statistics can be found in Table S2b. Note to forest plot: the sibling-based dataset ENall1 was analyzed genome-wide through linear mixed modelling (in FastLMM) for computational reasons, while its OR, as shown here, was computed via a Wald test in a logistic mixed model (GMMAT), to make it comparable to the other ORs produced through logistic regression (PLINK). Hence, the result of the pooled analysis—which here was performed through the inverse variance-based method—is slightly discrepant from the original genome-wide analysis (see Table 2).