2013
DOI: 10.1101/gr.142521.112
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A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines

Abstract: 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… Show more

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Cited by 140 publications
(167 citation statements)
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“…We obtained summary statistics from GWAS on CAD 8 and large artery stroke 9 for SNPs ±50kb from the 5' and 3' gene borders of the 659 studied murine genes (Supplemental Material). We used these as input for a gene-based analysis using VEGAS which assigned an empirical p-value (after permutations) to each of the 659 genes based on the p-value of the SNPs in and ±50 kb around the genes of interest 10 .…”
Section: Validation Within Gwas Of Cad and Lasmentioning
confidence: 99%
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“…We obtained summary statistics from GWAS on CAD 8 and large artery stroke 9 for SNPs ±50kb from the 5' and 3' gene borders of the 659 studied murine genes (Supplemental Material). We used these as input for a gene-based analysis using VEGAS which assigned an empirical p-value (after permutations) to each of the 659 genes based on the p-value of the SNPs in and ±50 kb around the genes of interest 10 .…”
Section: Validation Within Gwas Of Cad and Lasmentioning
confidence: 99%
“…Therefore, we identified eQTLs through two approaches. First, we queried three online resources (table SVI) for eQTLs in lymphoblastoid cells 7,8 , monocytes 9 , subcutaneous adipose tissue 7 , and skin tissue 7 . Secondly, we performed eQTL analyses in 7 tissue types that could be relevant for disease development in the STAGE study 10 .…”
Section: Eqtl Of Human Orthologues Of Selected Murine Genesmentioning
confidence: 99%
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“…We used the significant association of random SNP/CpG site pairs as an upper bound of false discoveries, a strategy used in expression QTL analysis. 12 While that approach overestimates the true false discovery rate (FDR) due to ignoring any potential true trans-meQTLs, it is easier to compute and preserve all family structure and covariates. Using 130 million pairs, we estimated that the nominal P value of 10 −9 as equivalent to the FDR of 0.000 004, and the nominal P value of 10 −200 as FDR < 7.7 × 10 −9 (no random pairs with P < 10 −200 ).…”
mentioning
confidence: 99%
“…The three components critical to validating eQTL results include i) a SNP marker; ii) the gene expression levels, as measured by a probe or sequence information; and iii) a measure of the statistical association between the two in a study population, such as the P-value. The eQTL browser provides an approach to query the eQTL database [52].…”
Section: Expression Quantitative Trait Loci Analysis Of the Neurogenesmentioning
confidence: 99%