Fig. 2

Genome-wide association findings for AUC for patient-rated toxicity xerostomia in HNC patients. 2A. Manhattan plot: The X-axis shows the location in the genome. The Y-axis shows − log10 P-values for the association of each of the tested SNPs with the outcome. The red line shows the threshold for genome-wide significance (P < 5 × 10–8), and the blue line shows the suggestive threshold (P < 1 × 10–5). 2B. Quantile–quantile (QQ) plot comparing the distribution of observed P-values (test statistics) from discovery study to the distribution of expected P-value based on the theoretical probability distribution, inflation of plot to upper part suggest inflation of test statistics due to the possibility of population substructure or type 1 error (small sample size bias). The Y-axis shows observed − log10 P-values, and the X-axis shows the expected − log10 P-values. Each SNP is plotted as a dark blue dot, and the red line indicates a null hypothesis of no true association. Deviation from the expected P-value distribution is evident only in the tail area, with a lambda of 1.001, suggesting that population stratification was adequately controlled. 2C. Locuszoom plot of the associated region on chromosome 5. The blue circle (query variant) points to the top SNP (rs35542). Points representing nearby SNPs are color-coded according to linkage disequilibrium r2 value as indicated in the legends. The X-axis shows the genomic coordinates chromosome 5. The Y1 axis shows − log10 P-values for each of the SNPs in the genome. The Y2 axis shows the combined recombination rate which is estimated from the international HapMap project