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. 2016 Jan;19(1):48-54.
doi: 10.1038/nn.4182. Epub 2015 Nov 30.

Methylation QTLs in the Developing Brain and Their Enrichment in Schizophrenia Risk Loci

Free PMC article

Methylation QTLs in the Developing Brain and Their Enrichment in Schizophrenia Risk Loci

Eilis Hannon et al. Nat Neurosci. .
Free PMC article


We characterized DNA methylation quantitative trait loci (mQTLs) in a large collection (n = 166) of human fetal brain samples spanning 56-166 d post-conception, identifying >16,000 fetal brain mQTLs. Fetal brain mQTLs were primarily cis-acting, enriched in regulatory chromatin domains and transcription factor binding sites, and showed substantial overlap with genetic variants that were also associated with gene expression in the brain. Using tissue from three distinct regions of the adult brain (prefrontal cortex, striatum and cerebellum), we found that most fetal brain mQTLs were developmentally stable, although a subset was characterized by fetal-specific effects. Fetal brain mQTLs were enriched amongst risk loci identified in a recent large-scale genome-wide association study (GWAS) of schizophrenia, a severe psychiatric disorder with a hypothesized neurodevelopmental component. Finally, we found that mQTLs can be used to refine GWAS loci through the identification of discrete sites of variable fetal brain methylation associated with schizophrenia risk variants.

Conflict of interest statement

Competing financial interests

The authors declare no competing financial interests.


Figure 1
Figure 1. mQTLs in the developing human brain are predominantly cis-acting with effect size related to distance, although notable trans-effects are also present
(a) The genomic distribution of Bonferroni significant (P = 3.69 ×10−13) mQTLs in fetal brain, where the position on the x-axis indicates the location of Illumina 450K HumanMethylation array probes and the position on the y-axis indicates the location of informative SNPs. The color of the point corresponds to the difference in DNA methylation per allele compared to the reference allele, with the largest effects plotted in dark red. A clear positive diagonal can be observed demonstrating that the majority of mQTLs in fetal brain are associated with genotype in cis. (b) The relationship between mQTL effect size (DNA methylation change per allele) and distance between the Illumina 450K HumanMethylation array probe and informative SNPs in fetal brain, confirming the predominantly cis nature of mQTLs. A similar relationship is seen between mQTL significance and distance (see Supplementary Fig. 3). (c) Trans-mQTLs in the developing human brain. Shown are all Bonferroni significant (P = 3.69 ×10-13) trans-mQTLs identified in fetal brain samples. The thickness of each line depicts association effect size, with color reflecting the chromosomal location of the mQTL SNP.
Figure 2
Figure 2. Despite a highly-significant overall correlation of individual mQTL effects between fetal brain and adult brain regions, a subset of loci are characterized by fetal-specific mQTLs
(a) Heatmap showing effect sizes in adult brain for all fetal brain mQTLs tested. Using a replication mQTL significance threshold of P < 1.00E-5, the majority (83.46%) of fetal brain mQTLs are present in at least one of the tested adult brain region. Despite the overall strong concordance in the direction of mQTL between fetal and adult brain, there are notable examples of heterogeneity in mQTL effects between fetal and adult brain tissue. Shown are examples of (b) a fetal-specific mQTL between rs10447470 and cg07900658 (heterogeneity P = 7.23E-40) and (c) an mQTL between rs2108854 and cg21577356 showing an opposite direction of effect in fetal brain and cerebellum (heterogeneity P = 8.39E-36).
Figure 3
Figure 3. mQTL mapping can localize putative causal loci associated with disease
Co-localization analyses yielded strong support for variants annotated to the AS3MT gene being associated with both schizophrenia and DNA methylation within a broad genomic region (chr10:104535135-105006335) identified in a recent GWAS analysis of schizophrenia. All potential causal variants (r2 > 0.8 with index variant) present in the imputed mQTL dataset are indicated by vertical blue lines and all DNA methylation probes within each region by vertical red lines. Bonferroni-significant mQTLs are indicated by black lines between the respective variant and DNA methylation probe, where the line width reflects the magnitude of the effect. Additional examples of fetal brain mQTLs in genomic regions showing genome-wide significant association with schizophrenia are available on our website (
Figure 4
Figure 4. Fetal mQTLs in schizophrenia-associated regions have larger effects on DNA methylation during neurodevelopment than the in adult brain
For robustly-associated schizophrenia GWAS variants characterized by human fetal brain mQTLs (Supplementary Table 16), we compared effect sizes between fetal and adult brain. Effect sizes (red to blue) for the corresponding mQTLs in adult brain are significantly lower across all three adult brain regions tested (Wilcoxon rank-sum test: PFC P = 0.0420, STR P = 0.00226, CER P = 0.00998). The heterogeneity P-value for each mQTL is depicted by the green (high heterogeneity) to yellow (low heterogeneity) column. White indicates that the mQTL was not tested in the adult brain samples.

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