Snp6 array

Cambridge: gDNA and total mRNA were extracted from tissue samples (Qiagen AllPrep), and gDNA from whole blood (Tepnel). All DNAs were assayed on Illumina HumanOmni2.5–8 M bead chip arrays; 16 samples were also assayed on Affymetrix SNP6 arrays (Aros, Denmark). Stockholm gDNA samples were assayed on Affymetrix SNP6 arrays, as previously described (Liu et al., 2012 (link)). All mRNAs were profiled on Illumina HT12 v4 BeadChip arrays.

Segmented DNA copy-number data for tumor and normal samples were obtained using Affymetrix SNP6 arrays by TCGA. We compared log-ratio copy number values between tumor samples and matched normal samples using paired Wilcoxon tests and corrected p-values using Benjamini-Hochberg’s procedure. We required genes to have a mean copy number difference larger than 0.1 between tumors and normal to prevent small effects becoming significant because of a large number of samples. For genes with significant difference in copy-number (FDR < 0.05), we calculated the Spearman correlation between copy-number and gene expression (Fig. S14). A gene was scored as potential tumor suppressor or oncogene if 1) its copy-number value in tumor samples was significantly lower or higher than in normal samples and 2) the copy-number was significantly (FDR < 0.05) positively correlated with gene expression across the tumor samples.

DNA extracted from buffy coat samples were genotyped using Affymetrix Genome-Wide Human SNP 6.0 array following manufacture’s protocol^{56 (link)}. Affymetrix SNP 6 array has independent probes for SNPs (~ 906,600 probes) and CNVs (~ 946,000 probes). Genotyping quality control was assessed using Birdseed V2 algorithm in Affymetrix genotyping console. Sample Contrast Quality Control (CQC) ≥ 1.7 indicates acceptable genotyping quality. All our study samples had a CQC value more than 2.