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Fig. 3 | Genome Biology

Fig. 3

From: Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity

Fig. 3

Using the interaction model to identify cancer eQTL profiles from TCGA breast bulk tumor gene expression data. a Quantile-quantile plot of P values for cis-eQTL associations in TCGA breast cancer samples, recovered using a conventional eQTL analysis of bulk tumor gene expression data (green), when eQTLs are attributed to cancer using the interaction model (blue), and when tumor purity estimates in the interaction model are randomly permuted (orange). Observed P values (y-axis) are plotted against the uniform distribution of P values (x-axis). b Strip chart showing the association of rs6458012 and the expression MDGA1 in TCGA breast cancer tumors, with the association identified by the conventional model shown as a red line. c Plot deconstructing the association between rs6458012 and MDGA1. Points are effect sizes and whiskers represent 95% confidence intervals. The association from the conventional model applied to TCGA breast cancer bulk tumors is shown in green (corresponding to b). Shown in black are the effect sizes and confidence intervals for the association of rs6458012 and MDGA1 when TCGA breast samples are divided into five equally sized bins, based on each sample’s estimated proportion of cancer cells. The estimated effect size decreases as the proportion of cancer cells decreases. The extrapolated effect size in cancer cells, estimated by the interaction model, is shown in red; this association is not statistically significant, illustrated by the 95% confidence interval overlapping the gray dashed line, which represents an effect size of 0. This suggests the association recovered by the conventional model did not arise in cancer cells. d Strip chart showing the association of rs6458012 and expression of MDGA1 in fibroblasts from GTEx. These are associated (P = 6.3 × 10− 13) with the same directionality as identified in TCGA breast tumors (b). e Strip chart showing the association of rs6458012 and expression of MDGA1 in LCLs from GTEx. These are associated (P = 1.4 × 10− 10) with the same directionality as identified in TCGA breast tumors (b)

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