Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders.

paper Cited Public

Authors: O'Brien, Heath E; Hannon, Eilis; Hill, Matthew J; Toste, Carolina C; Robertson, Matthew J; Morgan, Joanne E; McLaughlin, Gemma; Lewis, Cathryn M; Schalkwyk, Leonard C; Hall, Lynsey S; Pardiñas, Antonio F; Owen, Michael J; O'Donovan, Michael C; Mill, Jonathan; Bray, Nicholas J
Year: 2018
Journal: Genome biology
PMID: 30419947
DOI: 10.1186/s13059-018-1567-1
PMCID: PMC6231252

Fig. 1

Genomic characterization of fetal brain cis-eQTL. a Plot of eQTL density (FDR < 0.05) versus distance from transcription start site for all eTranscripts. Expression QTLs mapping to a common 900-kb inversion on chromosome 17q21 were excluded from this analysis due to extensive linkage disequilibrium across the inversion. b Enrichment of eTranscript eQTL within genomic features identified by the ENCODE [8] and Roadmap Epigenomics Consortium [9] projects in six human cell lines. Enrichments are expressed as the natural log of odds ratios, with error bars representing 95% confidence intervals. GM12878 = lymphoblastoid cell line; H1HESC = embryonic stem cell line; HeLa-S3 = cervix adenocarcinoma cell line; HepG2 liver carcinoma cell line; HUVEC = umbilical vein endothelial cells; K562 = myeloid leukemia cell line. Fetal brain eQTL are significantly enriched in regions annotated as TSS, flanking promoter, enhancer, weak enhancer, and CTCF binding sites, but significantly depleted in repressed genomic regions

Fig. 2

Heatmap of m values for fetal brain cis-eQTL (FDR < 0.05) for 974 eGenes across 48 adult tissues assayed by the GTEx Consortium [4]. m values are derived from a Meta-Tissue [68] analysis performed by the GTEx consortium (using v7 data), and estimate the posterior probability that an eQTL is shared between each tissue. GTEx m values are available for 974 gene fetal brain cis-eQTL that are predicted to be shared by at least two adult tissues (m values > 0.9); the five fetal brain cis-eQTL that are eQTL in only one adult tissue (FDR < 0.05) are not included. Greatest sharing of fetal brain eQTL is observed for adult brain regions, where, on average, 79% of the tested fetal brain eQTL are predicted to be shared

Fig. 3

Enrichment of fetal brain transcript eQTL within variants associated with complex post-natal traits. Enrichments were tested at four GWAS P value thresholds (P < 5 × 10− 5, 5 × 10− 6, 5 × 10− 7, and 5 × 10− 8) for each trait. Top panel shows log10 P values at each threshold. The bottom panel shows the natural log of the odds ratio, with 95% confidence intervals, at each threshold. Only traits for which the significance of eQTL enrichment survives correction for multiple tests (P < 0.001; dotted line in upper panel) at one or more GWAS P value threshold are shown. There are no overlaps between fetal brain eQTL and risk variants for bipolar disorder at the P < 5 × 10− 8 threshold

Fig. 4

Association between expression of the Complement C4A gene in fetal brain and genetic risk for schizophrenia. a Effect sizes of SNPs from schizophrenia GWAS [36] plotted against their effect sizes as fetal brain cis-eQTL for C4A. The triangular data point indicates the variant with the lowest P-SMR. Error bars are the standard errors of SNP effects. b Homozygotes for the schizophrenia-associated C-allele of rs9267544 exhibit increased expression of C4A in fetal brain compared with heterozygotes for this SNP. Error bars represent standard errors

#	Section	Preview
40	Methods — eQTL enrichment analyses — Enrichment of fetal brain mQTLs in eQTL	To test for enrichment of genetic variants associated with DNA methylation in the developing brain…
41	Methods — eQTL enrichment analyses — Enrichment of variants associated with brain and non-brain complex traits in eQTLs	GWAS results for attention deficit hyperactivity disorder [31], anorexia nervosa [32], autism…
42	Methods — Testing for pleiotropic association with neuropsychiatric traits	We tested for joint associations between fetal brain eQTL and GWAS signals using…
43	Methods — Testing for pleiotropic association with neuropsychiatric traits	We additionally investigated potential sharing of eQTLs identified by the CommonMind Consortium in…
44	Additional files	Additional file 1:Tables S1-S10. containing sample data, top eQTL for all significant eGenes and…

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Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders.	2018	30419947

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Novel Insight Into the Etiology of Autism Spectrum Disorder Gained by Integrating Expression Data With Genome-wide Association Statistics.	Pain O et al.	—	2019	→
Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders.	O'Brien HE et al.	—	2018	→
Novel Insight into the Aetiology of Autism Spectrum Disorder Gained by Integrating Expression Data with Genome-wide Association Statistics	Pain O et al.	—	2018	—