Manhattan plot of P values for a genome-wide association with methotrexate clearance. Each chromosome is plotted along the x-axis, whereas the y-axis plots the negative log₁₀ of the P value for the association of each SNP with methotrexate clearance. Higher points on the graph indicate a stronger association with methotrexate clearance. Typed and imputed SNPs are shown in all panels (5.2 million SNPs). Methotrexate clearance is adjusted for age, sex, race, and treatment arm. (A) Association of each SNP with methotrexate clearance in COG patients (n = 1279). (B) Meta-analysis of St Jude (n = 699) and COG patients (n = 1279). (C) Meta-analysis of St Jude and COG patients, after we adjusted for rs4149056.