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Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: gene expression

ABSTRACT: In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. Trait-associated SNPs located in putative regulatory regions likely exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. To this end, left ventricular mycardium samples from non-diseased human donor hearts were hybridized to Illumina HumanOmniExpress BeadChips for genotyping (n = 129) and Illumina Human HT12 Version 4 BeadChips (n = 129) for transcription profiling. To assess the gene expression levels of 129 human donor hearts from the study, genome-wide transcription profiling was carried out using Illumina Human HT12 Version 4 Beadchips interrogating over 47,000 unique transcripts (total of 47323 probes including controls).

ORGANISM(S): Homo sapiens

SUBMITTER: Michiel Adriaens

PROVIDER: E-GEOD-55231 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: genotyping

Project description:In recent years genome-wide association studies (GWAS) have uncovered numerous chromosomal loci associated with various electrocardiographic traits and cardiac arrhythmia predisposition. A considerable fraction of these loci lie within inter-genic regions. Trait-associated SNPs located in putative regulatory regions likely exert their effect by modulating gene expression. Hence, the key to unraveling the molecular mechanisms underlying cardiac traits is to interrogate variants for association with differential transcript abundance by expression quantitative trait locus (eQTL) analysis. In this study we conducted an eQTL analysis of human heart. To this end, left ventricular mycardium samples from non-diseased human donor hearts were hybridized to Illumina HumanOmniExpress BeadChips for genotyping (n = 129) and Illumina Human HT12 Version 4 BeadChips (n = 129) for transcription profiling. To assess the genotypes of 129 human donor hearts from the study, genome-wide SNP genotyping was carried out using Illumina HumanOmniExpress Beadchips interrogating 733,202 genetic markers.

2014-05-21 | E-GEOD-55230 | biostudies-arrayexpress

Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: gene expression

2014-05-21 | GSE55231 | GEO

Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart: genotyping

2014-05-21 | GSE55230 | GEO

Characterization of expression quantitative trait loci in extensively phenotyped pedigrees from Colombia and Costa Rica

Project description:The observation that variants regulating gene expression (expression quantitative trait loci, eQTL) are at a high frequency among SNPs associated with complex traits has made the genome-wide characterization of gene expression an important tool in genetic mapping studies of such traits. As part of a study to identify genetic loci contributing to bipolar disorder and a wide range of BP-related quantitative traits in members of 26 pedigrees from Costa Rica and Colombia, we measured gene expression in lymphoblastoid cell lines derived from 786 pedigree members. The study design enabled us to comprehensively reconstruct the genetic regulatory network in these families, provide estimates of heritability, identify eQTL, evaluate missing heritability for the eQTL, and quantify the number of different alleles contributing to any given locus. Lymphoblastoid cell lines (LCLs) were established by in vitro infection of peripheral blood mononuclear cells with Epstein Barr virus, and RNA was extracted from these cell lines and its expression quantified using Illumina Human HT-12 v4.0 Expression BeadChips. Expression values were background corrected, quantile normalized, log2 transformed, and corrected for major known batch effects. The outcome of these procedures is what we refer to as â??probe expressionâ?? for all subsequent analyses. After quality control filters, the 34,030 probes included in the final set were uniquely aligned to hg19, contained no common SNPs (as defined in dbSNP 137 or 138), queried 24,385 unique genes, and their expression was detected in at least one individual. For a detailed description of the processing steps used at each site and the RNA quantification, normalization, and quality control procedures, see the supplementary note. Please note that charateristics FID, IID and DiagnosisBP1 represents family ID, individual ID and BP1 diagnosis (0= no BP1, 2= BP1), respectively.

2016-07-01 | E-GEOD-82042 | biostudies-arrayexpress

Characterization of expression quantitative trait loci in extensively phenotyped pedigrees from Colombia and Costa Rica

2016-07-01 | GSE82042 | GEO

Genome-wide expression analysis of mouse chromosome 2 in gonadal fat and liver tissues reveals a complex architecture of obesity

Project description:Transcript abundance in adipose and liver tissues was used to map expression quantitative trait loci (eQTL) underlying fat accretion, weight gain and liver weight. Gonadal fat and liver tissues were used from 48 individuals F2 selected from a cohort (1,200 mice) originated from a cross between M16i and MB2 mice. A complex polygenic architecture within the MB2 locus was observed which was comprised of several locally regulated eQTL (cis-eQTL) with significant correlations to obesity traits.

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Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

Project description:Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Using a genome-wide association study based on a fixed linear model, we identified 7,192 cis-eQTL corresponding to 2,098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6,400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9,815 significant ASE-SNPs in 2,253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3).This study provides valuable information on the genetics of gene expression in porcine skeletal muscle. The characterized cis-genes and ASE genes, combined with the correlations between gene expression level and meat quality traits will be useful to prioritize candidate genes in further studies.

2019-06-24 | GSE124315 | GEO

Genome-wide expression analysis of mouse chromosome 2 in gonadal fat and liver tissues reveals a complex architecture of obesity

2010-09-15 | E-GEOD-20724 | biostudies-arrayexpress

Systems biology with high-throughput sequencing revealed genetic mechanisms underlying the Metabolic Syndrome in the Lyon Hypertensive Rat

Project description:The metabolic syndrome (MetS) is a collection of co-occurring complex disorders including obesity, hypertension, dyslipidemia, and insulin resistance. The Lyon Hypertensive (LH) and Lyon Normotensive (LN) rats are models of MetS sensitivity and resistance, respectively. To identify genetic determinants and mechanisms underlying MetS, 169 rats from an F2 intercross between LH and LN were studied. Multi-dimensional data were obtained including genotypes of 1536 SNPs, 23 physiological traits including blood pressure, plasma lipid and leptin levels, and body weight/adiposity, and more than 150 billion nucleotides of RNA-seq reads from the livers of 36 F2 individuals, 6 LH and 6 LN individuals. We identified 17 pQTLs (physiological quantitative trait loci) and 1200 eQTLs (gene expression quantitative trait loci). Systems biology methods were applied to identify 18 candidate MetS genes, including genes (Prcp and Aqp11) previously shown to be MetS-related. We found an eQTL hotspot on RNO17, which was also located within pQTLs for MetS-related traits. The genes regulated by this eQTL hotspot were mainly in two co-expression network modules (a mitochondria related module and a gene regulation related module) and were predicted to causally affect many MetS-related traits. Multiple evidences strongly and consistently support RGD1562963, a gene regulated in cis by this eQTL hotspot and possibly related to RNA stability, as the eQTL driver gene directly affected by genetic variation between LH and LN rats; the expression of this gene is also correlated with MetS-related traits. Our study sheds light on the intricate pathogenesis of MetS and proved that systems biology with high-throughput sequencing is a powerful method to study the etiology of complicated diseases. RNA-Seq of the liver of 6 LH (Lyon Hypertensive) rats and 6 LN (Lyon Normotensive) rats and 36 F2 rats.

2014-10-31 | E-GEOD-50027 | biostudies-arrayexpress

Genome-wide pQTL analysis of protein expression regulatory networks in the human liver

Project description:Background: Previous expression quantitative trait loci (eQTL) studies have identified thousands of genetic variants to be associated with gene expression at the mRNA level in the human liver. However, protein expression often correlates poorly with mRNA levels. Thus, protein quantitative trait loci (pQTL) study is required to identify genetics variants that regulate protein expression in human livers. Results: We conducted a genome-wide pQTL study in 287 normal human liver samples and identified 900 local-pQTL variants and 4,026 distant-pQTL variants. We further discovered 53 genome hotspots of pQTL variants. Transcriptional region mapping analysis showed that 1,133 pQTL variants are in transcriptional regulatory regions. Genomic region enrichment analysis of the identified pQTL variants revealed 804 potential regulatory interactions among 595 regulators (e.g. non-coding RNAs) and 394 proteins. Moreover, pQTL variants and trait-variant integration analysis uncovered several novel mechanisms underlying the relationships between protein expression and liver diseases, such as alcohol dependence. Notably, over 2,000 of the identified pQTL variants have not been reported in previous eQTL studies, suggesting extensive involvement of genetic polymorphisms in post-transcriptional regulation of protein expression in human livers. Conclusions: We have partially established protein expression regulation networks in human livers and generated a wealth of pQTL data that could serve as a valuable resource for the scientific community.

2020-07-21 | PXD019169 | Pride

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