A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines.
paper
Cited
Public
- Authors
- Liang, Liming; Morar, Nilesh; Dixon, Anna L; Lathrop, G Mark; Abecasis, Goncalo R; Moffatt, Miriam F; Cookson, William O C
- Year
- 2013
- Journal
- Genome research
- PMID
- 23345460
- DOI
- 10.1101/gr.142521.112
- PMCID
- PMC3613588
Gene expression levels can be an important link DNA between variation and phenotypic manifestations. Our previous map of global gene expression, based on ~400K single nucleotide polymorphisms (SNPs) and 50K transcripts in 400 sib pairs from the MRCA family panel, has been widely used to interpret the results of genome-wide association studies (GWASs). Here, we more than double the size of our initial data set with expression data on 550 additional individuals from the MRCE family panel using the Illumina whole-genome expression array. We have used new statistical methods for dimension reduction to account for nongenetic effects in estimates of expression levels, and we have also included SNPs imputed from the 1000 Genomes Project. Our methods reduced false-discovery rates and increased the number of expression quantitative trait loci (eQTLs) mapped either locally or at a distance (i.e., in cis or trans) from 1534 in the MRCA data set to 4452 (with <5% FDR). Imputation of 1000 Genomes SNPs further increased the number of eQTLs to 7302. Using the same methods and imputed SNPs in the newly acquired MRCE data set, we identified eQTLs for 9000 genes. The combined results identify strong local and distant effects for transcripts from 14,177 genes. Our eQTL database based on these results is freely available to help define the function of disease-associated variants.
Empirical estimate of false discovery rate. (noPC) Using original expression value; (PC) adjusting nongenetic effect using the top 69 principal components; (1000G) imputation using SNPs from the 1000 Genomes project; (HapMap) imputation using HapMap2 SNPs; (300K) using autosomal SNPs from the Illumina 300K panel.
Replication rate by distance from the eQTL to the transcript. (Red lines) Replication of eQTL. (A) Local effect; (B) distant syntenic effect (>1 Mb but gene and SNP on the same chromosome); and (C) distant effect (on a different chromosome). The analysis is based on autosomal SNPs from the Illumina 300K panel.
Imputation accuracy by minor allele frequency (MAF; MRCA panel). (A) Correlation (R2) between 1000G imputed allele dosage derived from Illumina 300K arrays and true allele counts measured by Illumina 100K arrays, plotted by MAF. (B) Histogram of correlation with true allele counts by MAF in sample (upper panels) and minor allele counts in the 1000G reference haplotype. Note that there are no data in the bottom left panel following removal of singletons from the reference haplotype.
Comparison of number of local eQTLs identified by directly genotyped SNPs, imputed HapMap2 SNPs, and imputed SNPs from the 1000 Genomes Project. (A) Results from Affymetrix expression data in the MRCA panel. (B) Results from Illumina expression data in the MRCE panel. (Blue bars) Original unadjusted expression; (red bars) expression values adjusted by the top principal components.
Proportion of significant transcripts by overall heritability. (A) Unadjusted expression data and SNPs from the Illumina 300K panel in the MRCA subjects. (B) PC-adjusted expression data and the imputation of 1000G SNPs in the MRCA subjects. (C) Unadjusted expression data and SNPs from the Illumina 300K panel in the MRCE subjects. (D) PC-adjusted expression data and the imputation of 1000G SNPs in the MRCE subjects. The number of transcripts in each heritability category is given at the bottom of each bar.
cis eQTL of the gene TIMM22. A map of association of SNPs to transcript abundance of the TIMM22 gene exemplifies the progressive increase in information for the experimental genotypes (A), experimental plus HapMap imputed SNPs (B), and experimental, HapMap imputed and 1000G imputed SNPs (C). The gray vertical bar at the gene TIMM22 indicates the position of the Affymetrix probe
| Name | Type |
|---|---|
| 1000 Genomes Project | cohort |
| 1000 Genomes SNP imputation local | cohort |
| 1000G imputation local | drug |
| 1000G SNPs local | variant |
| Affymetrix | drug |
| Affymetrix expression data set (MRCA) local | cohort |
| Affymetrix HG-U133 Plus 2.0 chips local | drug |
| Affymetrix U133 Plus2 local | cohort |
| alternative gene local | gene |
| asthma | phenotype |
| Atopic dermatitis | phenotype |
| autoimmune disease-associated SNPs local | variant |
| basal cell skin carcinoma local | phenotype |
| body mass index | phenotype |
| brain tissue | anatomy |
| CEPH | cohort |
| CEU | cohort |
| childhood asthma local | phenotype |
| complex traits | phenotype |
| Crohn's disease | phenotype |
| disease | phenotype |
| disease susceptibility loci local | phenotype |
| distant eQTL | cohort |
| Epstein-Barr virus | drug |
| eQTLGen Consortium | cohort |
| eSNP | variant |
| familial clustering local | phenotype |
| gene | gene |
| gene expression | phenotype |
| gene expression traits | phenotype |
| genes | gene |
| Graves' disease | phenotype |
| GWAS | cohort |
| H2 0.3-0.4 local | phenotype |
| H2 0.6-0.7 local | phenotype |
| HapMap | cohort |
| HapMap3 | cohort |
| HapMap CEU samples local | cohort |
| HapMap reference local | cohort |
| height | phenotype |
| Illumina | drug |
| Illumina 100K local | drug |
| Illumina 300K local | drug |
| Illumina expression data set (MRCE) local | cohort |
| Illumina Human 6 BeadChips local | drug |
| Illumina Human6 V1 local | cohort |
| Illumina HumanHap300 Beadchip | drug |
| Illumina Sentrix Human-1 Genotyping BeadChip local | drug |
| Illumina Sentrix HumanHap300 Genotyping BeadChip local | drug |
| ILMN100K local | cohort |
| ILMN100K local | drug |
| imputation | drug |
| LCL | gene |
| LCL eQTL database local | cohort |
| local eQTL | cohort |
| local eQTLs local | phenotype |
| low-coverage next-generation sequencing local | drug |
| MaCH program local | drug |
| microarray-based genotyping local | drug |
| MRCA local | cohort |
| MRCA data set local | cohort |
| MRCA sample local | cohort |
| MRCE local | cohort |
| MRCE data set local | cohort |
| MRCE panel local | cohort |
| mRNA transcript levels local | phenotype |
| narrow-sense heritability | phenotype |
| neuropsychiatric trait local | phenotype |
| Northern and Western European ancestry | cohort |
| osteoporosis-related traits local | phenotype |
| pancreatic cancer | phenotype |
| PC local | cohort |
| PC-adjusted analysis local | drug |
| PC_adjustment local | drug |
| principal components | drug |
| psychiatric association local | phenotype |
| psychological trait local | phenotype |
| rare variant | cohort |
| SNP | cohort |
| SNPs with MAF >5% local | variant |
| suspected gene local | gene |
| TIMM22 local | gene |
| transcript local | phenotype |
| type 1 diabetes | phenotype |
| waistβhip ratio local | phenotype |
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| Identification of a new locus at 16q12 associated with time to asthma onset. | Sarnowski C et al. | β | 2016 | β |
| Population-specific genome-wide mapping of expression quantitative trait loci in the colon of Han Chinese. | Guo CC et al. | β | 2016 | β |
| The importance of p53 pathway genetics in inherited and somatic cancer genomes. | Stracquadanio G et al. | β | 2016 | β |
| The study of the relation of DNA repair pathway genes SNPs and the sensitivity to radiotherapy and chemotherapy of NSCLC. | Wang C et al. | β | 2016 | β |
| A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults. | Bouzigon E et al. | β | 2015 | β |
| A common variant in the CLDN7/ELP5 locus predicts adiponectin change with lifestyle intervention and improved fitness in obese individuals with diabetes. | Belalcazar LM et al. | β | 2015 | β |
| A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease. | Nikpay M et al. | β | 2015 | β |
| A genetic variant of MDM4 influences regulation by multiple microRNAs in prostate cancer. | Stegeman S et al. | β | 2015 | β |
| An integrated network of microRNA and gene expression in ovarian cancer. | Quitadamo A et al. | β | 2015 | β |
| A novel common variant in DCST2 is associated with length in early life and height in adulthood. | van der Valk RJ et al. | β | 2015 | β |
| Cross-population joint analysis of eQTLs: fine mapping and functional annotation. | Wen X et al. | β | 2015 | β |
| Enhanced meta-analysis and replication studies identify five new psoriasis susceptibility loci. | Tsoi LC et al. | β | 2015 | β |
| eQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues. | Huang J et al. | β | 2015 | β |
| Expression quantitative trait loci (eQTL) mapping in Puerto Rican children. | Chen W et al. | β | 2015 | β |
| FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk. | Nikolova YS et al. | β | 2015 | β |
| Gene expression in transformed lymphocytes reveals variation in endomembrane and HLA pathways modifying cystic fibrosis pulmonary phenotypes. | O'Neal WK et al. | β | 2015 | β |
| Genomic approaches for understanding the genetics of complex disease. | Lowe WL et al. | β | 2015 | β |
| iGWAS: Integrative Genome-Wide Association Studies of Genetic and Genomic Data for Disease Susceptibility Using Mediation Analysis. | Huang YT et al. | β | 2015 | β |
| Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. | Li YR et al. | β | 2015 | β |
| PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6. | Oparina NY et al. | β | 2015 | β |
| Recent positive selection has acted on genes encoding proteins with more interactions within the whole human interactome. | Luisi P et al. | β | 2015 | β |
| What Does Genetics Tell Us About Age-Related Macular Degeneration? | Grassmann F et al. | β | 2015 | β |
| An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. | Forni D et al. | β | 2014 | β |
| Association between Expression Quantitative Trait Loci and Metabolic Traits in Two Korean Populations. | Hong KW et al. | β | 2014 | β |
| Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. | Battle A et al. | β | 2014 | β |
| Common mechanisms underlying refractive error identified in functional analysis of gene lists from genome-wide association study results in 2 European British cohorts. | Hysi PG et al. | β | 2014 | β |
| Determining causality and consequence of expression quantitative trait loci. | Battle A et al. | β | 2014 | β |
| Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. | Ganesh SK et al. | β | 2014 | β |
| Evidence for the role of EPHX2 gene variants in anorexia nervosa. | Scott-Van Zeeland AA et al. | β | 2014 | β |
| Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. | van der Valk RJ et al. | β | 2014 | β |
| Future clinical implications emerging from recent genome-wide expression studies in asthma. | BΓ©rubΓ© JC et al. | β | 2014 | β |
| Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. | Tragante V et al. | β | 2014 | β |
| Genetics of gene expression in immunity to infection. | Fairfax BP et al. | β | 2014 | β |
| Genetic variant in SWI/SNF complexes influences hepatocellular carcinoma risk: a new clue for the contribution of chromatin remodeling in carcinogenesis. | Zhong R et al. | β | 2014 | β |
| Genome-wide association study of metabolic syndrome in koreans. | Jeong SW et al. | β | 2014 | β |
| Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. | Liang L et al. | β | 2014 | β |
| Identification and validation of genetic variants that influence transcription factor and cell signaling protein levels. | Hause RJ et al. | β | 2014 | β |
| Integrative modeling of multiple genomic data from different types of genetic association studies. | Huang YT | β | 2014 | β |
| Linking polymorphic p53 response elements with gene expression in airway epithelial cells of smokers and cancer risk. | Wang X et al. | β | 2014 | β |
| Meta-eQTL: a tool set for flexible eQTL meta-analysis. | Di Narzo AF et al. | β | 2014 | β |
| Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. | Perry JR et al. | β | 2014 | β |
| Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. | Postmus I et al. | β | 2014 | β |
| RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses. | Ma B et al. | β | 2014 | β |
| Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. | Zhang X et al. | β | 2014 | β |
| Trans-ethnic meta-analysis of white blood cell phenotypes. | Keller MF et al. | β | 2014 | β |
| A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis. | Weidinger S et al. | β | 2013 | β |
| A tool for RNA sequencing sample identity check. | Huang J et al. | β | 2013 | β |
| Genetics of human gene expression. | Stranger BE et al. | β | 2013 | β |
| Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population. | Zhong R et al. | β | 2013 | β |
| Genome-wide and candidate gene association studies of placental abruption. | Workalemahu T et al. | β | 2013 | β |
| GSTCD and INTS12 regulation and expression in the human lung. | Obeidat M et al. | β | 2013 | β |
| rs2072135, a low-penetrance variant for chronic lymphocytic leukaemia? | Sava GP et al. | β | 2013 | β |
| SNPs located at CpG sites modulate genome-epigenome interaction. | Zhi D et al. | β | 2013 | β |
| Using eQTL weights to improve power for genome-wide association studies: a genetic study of childhood asthma. | Li L et al. | β | 2013 | β |