Specimens were obtained from patients, with appropriate consent from institutional review boards. Using a co-isolation protocol, DNA and RNA were purified. In total, 446 patients were assayed on at least one molecular profiling platform, which platforms included: (1) RNA sequencing; (2) DNA methylation arrays; (3) miRNA sequencing; (4) Affymetrix SNP arrays; (5) exome sequencing; and (6) reverse phase protein arrays. As described above and in the Supplemental Methods, both single platform analyses and integrated cross-platform analyses were performed.