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
0	Background	Results from genome-wide association studies (GWAS) have established an important role for common…
1	Background	Genetic influences on gene regulation that are active during human prenatal brain development…
2	Background	In the present study, we carried out deep RNA sequencing and genome-wide genotyping on a large…
3	Results	We performed strand-specific, whole transcriptome sequencing of total RNA derived from brain tissue…
4	Results — Characterization of cis-eQTL in the human fetal brain	We identified cis-eQTL (defined as variants within 1 Mb of the transcription start site [TSS] of the…
5	Results — Characterization of cis-eQTL in the human fetal brain	enhancers, weak enhancers, and CTCF binding sites, but significantly depleted in repressed regions…
6	Results — eQTL at a common inversion polymorphism on chromosome 17q21	Twenty-one of the cis-eQTL eGenes identified in fetal brain are located within a region of…
7	Results — eQTL at a common inversion polymorphism on chromosome 17q21	on the H1 or H2 haplotypes.Table 1Fetal brain eGenes located at a common inversion polymorphism on…
8	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Tissue-sharing and evidence for fetal-specific eQTL	We next explored the extent to which cis-eQTL identified in the fetal brain are shared among 48…
9	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Tissue-sharing and evidence for fetal-specific eQTL	an average of 79% of the tested fetal brain eQTL were predicted to be shared, and lowest for whole…
10	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Regional and developmental expression of fetal eGenes in the human brain	We used RNA sequencing data from dissected regions of the human pre- and post-natal brain, available…
11	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Enrichment of fetal brain cis-eQTL within genetic variants associated with neuropsychiatric traits	Genetic effects on gene expression operating in the human fetal brain could influence a variety of…
12	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Enrichment of fetal brain cis-eQTL within genetic variants associated with neuropsychiatric traits	8), using a method that accounts for allele frequency, linkage disequilibrium, and local gene…
13	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	Given evidence for a potential role of fetal brain eQTL in neuropsychiatric traits, we next applied…
14	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	3.76 × 10− 5; eTranscripts, P-SMR < 1.54 × 10− 5). In addition, we only report associations…
15	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	We identified 6 eGenes and 14 eTranscripts for which fetal brain expression was associated with…
16	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	association with schizophrenia (P-SMR = 6.3 × 10− 8) was in the expression of C4A, encoding…
17	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	We observed association between variants influencing the personality trait of neuroticism and the…
18	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	Reduced expression of one transcript, annotated to the RPL31P12 gene (encoding Ribosomal Protein L31…
19	Results — eQTL at a common inversion polymorphism on chromosome 17q21 — Identification of gene expression changes in fetal brain associated with neuropsychiatric traits	We additionally explored whether eQTLs identified in the adult human brain (dorsolateral prefrontal…

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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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Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders.	Hernandez LM et al.	—	2021	→
A Genetics Perspective on the Role of the (Neuro)Immune System in Schizophrenia.	Birnbaum R et al.	—	2020	→
An association study between methamphetamine use disorder with psychosis and polymorphisms in MiRNA.	Sun Q et al.	—	2020	→
A transcriptome-wide association study implicates specific pre- and post-synaptic abnormalities in schizophrenia.	Hall LS et al.	—	2020	→
Combinatorial and statistical prediction of gene expression from haplotype sequence.	Alpay BA et al.	—	2020	→
Functional genomics links genetic origins to pathophysiology in neurodegenerative and neuropsychiatric disease.	Wamsley B et al.	—	2020	→
Further confirmation of netrin 1 receptor (DCC) as a depression risk gene via integrations of multi-omics data.	Li HJ et al.	—	2020	→
Genes regulated by BCL11B during T-cell development are enriched for de novo mutations found in schizophrenia patients.	Fahey L et al.	—	2020	→
Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration.	Revez JA et al.	—	2020	→
Integrative analyses prioritize GNL3 as a risk gene for bipolar disorder.	Meng Q et al.	—	2020	→
Integrative Genomics for the Interpretation of Genetic Loci Implicated in Neurodevelopmental Disorders.	Walker RL	—	2020	→
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions.	Sieberts SK et al.	—	2020	→
Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk.	Huang QQ et al.	—	2020	→
Perspective: Quality Versus Quantity; Is It Important to Assess the Role of Enhancers in Complex Disease from an In Vivo Perspective?	McEwan AR et al.	—	2020	→
Refining Attention-Deficit/Hyperactivity Disorder and Autism Spectrum Disorder Genetic Loci by Integrating Summary Data From Genome-wide Association, Gene Expression, and DNA Methylation Studies.	Hammerschlag AR et al.	—	2020	→
Regional Variation of Splicing QTLs in Human Brain.	Zhang Y et al.	—	2020	→
Regulatory landscape in brain development and disease.	Spiess K et al.	—	2020	→
Resources for functional genomic studies of health and development in nonhuman primates.	Jasinska AJ	—	2020	→
The genetic architecture of the human cerebral cortex.	Grasby KL et al.	—	2020	→
The genetics of bipolar disorder.	Gordovez FJA et al.	—	2020	→
Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex.	Werling DM et al.	—	2020	→
Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms.	Walker RL et al.	—	2019	→
Identification of the primate-specific gene BTN3A2 as an additional schizophrenia risk gene in the MHC loci.	Wu Y et al.	—	2019	→
No Effect of Genome-Wide Significant Schizophrenia Risk Variation at the <i>DRD2</i> Locus on the Allelic Expression of <i>DRD2</i> in Postmortem Striatum.	Toste CC et al.	—	2019	→
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	—