Gene expression signature of CEBPA^bi AML reclassifies atypical CEBPA^bi AML. (A) Primary structure of CEBPA and positions of mutations in CEBPA^bi samples. (B) Comparative analyses of differentially expressed genes in a typical CEBPA^bi AML subgroup. Diamonds correspond to the 95 most differentially expressed genes listed in supplemental Table 4. Genes with low expression in both groups, defined by a mean (log10 [(RPKM + 0.0001) × 10 000]) <4 (corresponding approximately to 1 RPKM) were not included in this analysis. (C) PCA performed on the entire cohort (n = 415) using the 95-gene signature that characterizes typical CEBPA^bi AML (orange dots). Atypical CEBPA^bi samples (light blue dots) that cluster with typical CEBPA^bi AML (defined by the dashed line) are grouped under GEP+ CEBPA^bi AML, whereas others are termed GEP− CEBPA^bi AML. (D) Classification of CEBPA^bi AML based on CEBPA mutations and gene expression. (E) Representation of CEBPA mutations in atypical GEP+ or GEP− CEBPA^bi AML. (F) HOXA9 expression in GEP+ and GEP− CEBPA^bi AML samples. (G) Gene expression of CEBPA (left) and CSF3R (right) in the entire 415 AML sample cohort. C-ter, C-terminal; CEBPAmono, monoallelic CEBPA mutation; IF, inframe; Mid, middle; MS, missense; NS, nonsense; N-ter, N-terminal; PC, principal component.