All genome-wide SNP genotyping for the discovery cohorts was performed using the Illumina HumanHap550 BeadChip at the Center for Applied Genomics at the Children’s Hospital of Philadelphia. Multi-dimensional scaling was performed using PLINK version 1.06 on a subset of SNPs not in linkage disequilibrium to identify subjects of European ancestry, and all control subjects were genetically matched to patients. The first replication case series was genotyped by Illumina Human610 BeadChip, yet two additional replication case series were genotyped by TaqMan. Genotype imputation was performed by MACH (http://www.sph.umich.edu/csg/abecasis/MaCH/) on discovery and replication case series with whole-genome genotypes. Alteration calls in tumour copy number were generated from data of SNP signal intensity by the OverUnder19. Survival analyses used the methods of Kaplan and Meier, with standard errors following the methods of Peto et al.21. For gene expression profiling by Affymetrix U95Av2 microarrays, the expression measures for each probe set was extracted and normalized using robust multi-array average protocols from raw CEL files. Association tests on genotype and expression were performed on log-transformed expression values by linear regression or t-test. For quantitative PCR
