Analyzing Tissue-Specific eQTLs in GTEx and TCGA

Publicly available data generated by the Genotype-Tissue Expression Project (GTEx)20 (link) and The Cancer Genome Atlas (TCGA) were accessed to examine tissue-specific eQTLs. For GTEx, expression and genotype data were generated from 70 normal uteri from post-mortem biopsies, using an Affymetrix Expression array and Illumina Omni 5M SNP array. GTEx provided processed results, evaluating association between genotype and expression data. The expression levels are represented as a rank normalized score. TCGA genotype and copy number variation (CNV) data were derived from Affymetrix 6.0 SNP arrays. Expression data were from RNAseq arrays (Illumina HiSeq and Illumina GA) for 458 endometrial cancer tissues and 30 adjacent normal endometrial tissues. Association analyses for TCGA datasets were performed as follows. Genes within 500kb flanking our SNPs of interest were selected for analysis. Since there may be significant variation in tumour tissue copy number, somatic CNVs were taken into account by regressing gene expression to average copy number spanning the gene. Residual unexplained variance in gene expression was then regressed on the genotype of the lead SNP at each locus, using genotyped or imputed data. Statistical comparisons were subject to Bonferroni correction for number of tests (number of sample sets, and number of genes assessed).

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Cheng T.H., Thompson D.J., O’Mara T.A., Painter J.N., Glubb D.M., Flach S., Lewis A., French J.D., Freeman-Mills L., Church D., Gorman M., Martin L., Hodgson S., Webb P.M., Attia J., Holliday E.G., McEvoy M., Scott R.J., Henders A.K., Martin N.G., Montgomery G.W., Nyholt D.R., Ahmed S., Healey C.S., Shah M., Dennis J., Fasching P.A., Beckmann M.W., Hein A., Ekici A.B., Hall P., Czene K., Darabi H., Li J., Dörk T., Dürst M., Hillemanns P., Runnebaum I., Amant F., Schrauwen S., Zhao H., Lambrechts D., Depreeuw J., Dowdy S.C., Goode E.L., Fridley B.L., Winham S.J., Njølstad T.S., Salvesen H.B., Trovik J., Werner H.M., Ashton K., Otton G., Proietto T., Liu T., Mints M., Tham E., Consortium C., Jun Li M., Yip S.H., Wang J., Bolla M.K., Michailidou K., Wang Q., Tyrer J.P., Dunlop M., Houlston R., Palles C., Hopper J.L., Peto J., Swerdlow A.J., Burwinkel B., Brenner H., Meindl A., Brauch H., Lindblom A., Chang-Claude J., Couch F.J., Giles G.G., Kristensen V.N., Cox A., Cunningham J.M., Pharoah P.D., Dunning A.M., Edwards S.L., Easton D.F., Tomlinson I, & Spurdle A.B. (2016). Five endometrial cancer risk loci identified through genome-wide association analysis. Nature genetics, 48(6), 667-674.

Publication 2016

Omni 5M SNP array 6.0 SNP arrays

Biopsies Cancer Copy number variation Endometrial Endometrial cancer Gene variance Genes Genome Post mortem Somatic Tissue Tissue specific Tumour Uteri

Corresponding Organization :

Other organizations : Wellcome Centre for Human Genetics, University of Oxford, University of Cambridge, QIMR Berghofer Medical Research Institute, St George's, University of London, John Hunter Hospital, Hunter Medical Research Institute, University of Newcastle Australia, Cancer Research UK Cambridge Center, University of California, Los Angeles, Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Karolinska Institutet, Medizinische Hochschule Hannover, Friedrich Schiller University Jena, Jena University Hospital, KU Leuven, Mayo Clinic, Mayo Clinic in Florida, University of Kansas Medical Center, University of Bergen, Karolinska University Hospital, Chinese University of Hong Kong, University of Hong Kong, University of Edinburgh, Institute of Cancer Research, University of Melbourne, London School of Hygiene & Tropical Medicine, German Cancer Research Center, Technical University of Munich, Norwegian Cancer Society, University of Sheffield

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Variable analysis

independent variables

Genotype of the lead SNP at each locus

dependent variables

Gene expression levels
Copy number variation (CNV)

control variables

Average copy number spanning the gene
70 normal uteri from post-mortem biopsies
458 endometrial cancer tissues and 30 adjacent normal endometrial tissues

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