Comprehensive Profiling of CN-AML Patients

Gene expression and methylation data have been previously published (accession number GSE1159 [27 (link)], GSE9476 [28 (link)], GSE6891 [53 (link)] and GSE12417 [54 (link)] for expression, The Cancer Genome Atlas (TCGA) [50 (link)] for methylation). Briefly, gene expression data were obtained using Affymetrix Human Genome 133 plus 2.0 and U133A Gene Chips. All the designs and quality control for microarray experiment were according to the standard Affymetrix protocols. Expression data for microRNA were from TCGA obtained using whole-genome high-throughput sequencing, which provided 79 CN-AML patients [50 (link)]. In addition, genome-wide methylation levels in these patients were determined using Illumina 450K chips [50 (link)]. Patients with RUNX1 expression values above the median of all patients were classified as having RUNX1^high, and the others were considered to have RUNX1^low. Levels of ERG, BAALC, LEF1, MN1, WT1, DNMT3B, TCF4, MIR155HG, ITPR2 and MAPKBP1 expression were also determined from the microarray data.