Figure 1: Meta-analysis results for paediatric BCP-ALL.

(a) Manhattan plot of associations for the discovery GWAS of 1,210 cases and 4,144 controls from four independent studies. The red line denotes the threshold for genome-wide significance. Peaks surpassing this threshold are found at the following: 7p12.2 (IKZF1), 10q21.2 (ARID5B) and 9p21.3 (CDKN2). (b) The top panel is the regional LocusZoom plot of the 9p21.3 locus extending 500 kb on either side of the index SNP, rs77728904 (shown in purple), and including all genotyped and imputed SNPs with MAF >0.01. The bottom panel is zoomed in (indicated by the solid black lines between plots) to include only the CDKN2 locus and surrounding recombination peaks. The r² (visualized by colour) demonstrates that rs77728904 and rs3731217 are in independent linkage blocks between the recombination peaks. r² for all SNPs in both panels is shown relative to rs77728904. (c) Forest plot of OR with 95% confidence intervals (CIs) for rs77728904 in each of the studies comprising the discovery meta-analysis (Disc (Meta)), the full meta-analysis, the replication analysis and the combined analysis. Squares represent the OR; horizontal lines represent the CI; the solid vertical line represents OR=1; the blue dashed vertical line represents the OR in the combined discovery+replication sets.