A genome-wide association study on radiation induced fibrosis in breast cancer patients

Figures

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  Fig. 1. Patient selection. The diagram in red represents the DBCG-HYPO cohort, the blue represents the DBCG-PBI cohort, and the green box represents the combined cohorts with available germ-line genotype data. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

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  Fig. 2. Manhattan plot of GWAS results after relatedness pruning (π^<0.2) and removal of PCA outliers falling outside a four-dimensional ellipsoide 5x standard deviations from the mean. With adjustment for 11 covariates (including PC 1–10 from a second PCA). X-axis shows genomic position of SNPs and y-axis is −log10 of the logistic regression P-value. The horizontal red line indicates a P-value of 5x10-8 used as cut-off for genome-wide significance, while the horizontal grey line indicates a P-value of 7x10-8. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

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  Fig. 3. Quantile-quantile-plot (Q_Q plot) of −log10 of the expected P-values under the null hypothesis of no association versus −log10 of the observed P-values from the GWAS, with genomic inflation factor λ and the genomic inflation factor rescaled to a sample size of 1000 λ1000 using the following formular: λ1000=1+λ-1∙1000/Ne, where Ne is the effective sample size: Ne=4/1/Ncases+1/Nctrls. NP is the number of plottet P-values. Red diagonal line indicates -log1oPexpected=-log1oPobserved, dashed grey lines indicated 95% confidence interval of expected P-values. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)