Refining the set of ETV6-RUNX1-specific genes by employing gene expression profiles of patients in remission

The chromosomal translocation t(12;21) resulting in the ETV6-RUNX1 fusion gene is the most common genetic abnormality in childhood acute lymphoblastic leukemia (ALL). As the emergence of microarray technology, finding subtype-specific genes becomes one of the main objectives in most ALL studies. However, the list of differentiated genes derived by comparing patients in the subtype versus the others contains many false positives, which are not really subtype-specific. In order to refine the list of subtype-specific genes for ALL with ETV6-RUNX1, this study conducted microarray experiments on patients in both diagnosis and remission status. 36 bone marrow samples (26 diagnosis/9 remission) of acute lymphoblastic leukemia patients were hybridized to Affymetrix HG-U133 plus 2 GeneChips. Please note that the median of the expression value of 'ETV6-RUNX1_D01' sample (around 90) is much smaller than the other samples (around 800-1,070). However, it didn't affect the analysis quality after rank-normalization was applied.