Large-scale GWAS reveals genetic architecture of brain white matter microstructure and genetic overlap with cognitive and mental health traits (n = 17,706)

Abstract

Individual variations of white matter (WM) tracts are known to be associated with various cognitive and neuropsychiatric traits. Diffusion tensor imaging (DTI) and genome-wide single-nucleotide polymorphism (SNP) data from 17,706 UK Biobank participants offer the opportunity to identify novel genetic variants of WM tracts and explore the genetic overlap with other brain-related complex traits. We analyzed the genetic architecture of 110 tract-based DTI parameters, carried out genome-wide association studies (GWAS), and performed post-GWAS analyses, including association lookups, gene-based association analysis, functional gene mapping, and genetic correlation estimation. We found that DTI parameters are substantially heritable for all WM tracts (mean heritability 48.7%). We observed a highly polygenic architecture of genetic influence across the genome (p value = 1.67 × 10^-05) as well as the enrichment of genetic effects for active SNPs annotated by central nervous system cells (p value = 8.95 × 10^-12). GWAS identified 213 independent significant SNPs associated with 90 DTI parameters (696 SNP-level and 205 locus-level associations; p value < 4.5 × 10^-10, adjusted for testing multiple phenotypes). Gene-based association study prioritized 112 significant genes, most of which are novel. More importantly, association lookups found that many of the novel SNPs and genes of DTI parameters have previously been implicated with cognitive and mental health traits. In conclusion, the present study identifies many new genetic variants at SNP, locus and gene levels for integrity of brain WM tracts and provides the overview of pleiotropy with cognitive and mental health traits.

Figure 1.

SNP heritability estimates grouped by white matter tract functions. The white matter tracts are clustered into four communities including complex fibers (C1), associative fibers (C2), commissural fibers (C3), and projection fibers (C4) according to the Connectopedia Knowledge Database, http://www.fmritools.com/kdb/white-matter/

Figure 2.

Distribution of SNP heritability estimates of the 21 white matter tracts in brain.

Figure 3.

Heritability estimated by SNPs in each chromosome or in functionally annotated SNP categories.

Figure 4.

Number of independent significant SNPs discovered for each DTI parameter at different GWAS significance levels. Outer layer: p-value <5*10⁻⁸; middle layer: p-value <5*10⁻⁹; and inner layer: p-value <4.5*10⁻¹⁰.

Figure 5.

Genes identified in gene-based association analysis of DTI parameters that have been implicated with traits of neuroticism, neurodegenerative diseases, neuropsychiatric disorders, education, cognitive, and reaction time in previous GWAS.