Differential Gene Expression Analysis of iAMP21 Pediatric ALL

Gene expression microarrays (Affymetrix U133 Plus 2) from a previously described population-based paediatric ALL cohort were used (25 (link), 26 (link)). In short, expression data was normalized using vsnrma (27 (link)), and batch effects were removed using the empirical Bayes method (28 (link)). Differential gene expression between 12 iAMP21 and 143 B-other cases was determined using Limma with false discovery rate (FDR) multiple testing correction (29 ). Gene expression data are available at GEO under accession number GSE87070 (see Supplementary Table S1 for used samples). As a validation cohort, RNA sequencing gene expression data from the Pediatric Cancer (PeCan) database (https://pecan.stjude.cloud/) were used. Gene expression in fragments per kilobase per million mapped reads (FPKM) of selected genes was extracted. BCP-ALL samples annotated as BCR-ABL1, ETV6-RUNX1, TCF3-PBX1, high hyperdiploidy, low hypodiploidy, and infant ALL were excluded from analysis, resulting in a validation cohort of 17 iAMP21 samples and 174 B-other samples. Differential gene expression of target genes was determined using the Mann Whitney U test with Bonferroni multiple testing correction.