TCGA AML microarray data and LSC17 score calculation

Microarray data of 183 AML patients within the TCGA LAML data set³⁸ were obtained from the TCGA data portal. Raw Affymetrix CEL files (generated on the HG-U133 Plus 2.0 array) were processed with the R package gcrma. The LSC17 score was calculated for each patient as described³⁹ as a linear combination of Affymetrix probesets belonging to the LSC17 signature with the provided coefficents for each probeset. The median of all LSC17 scores was determined and patients were assigned a LSC17-high status if they had a LSC17 score above the median or LSC17 low if their LSC17 score was below the median. For analysis of overlaps between the ncRNA signatures and LSC17 scores, only patients who had Microarray and mapped RNA-seq data available were included (162 patients). The survival between the different groups was compared using Kaplan–Meier Plots and standard log-rank tests.