title: Detection of CEBPA double mutants in acute myeloid leukemia using a custom gene expression array.
abstract: Double (bi-allelic) mutations in the gene encoding the CCAAT/enhancer-binding protein-alpha (CEBPA) transcription factor have a favorable prognostic impact in acute myeloid leukemia (AML). Double mutations in CEBPA can be detected using various techniques, but it is a notoriously difficult gene to sequence due to its high GC-content. Here we developed a two-step gene expression classifier for accurate and standardized detection of CEBPA double mutations. The key feature of the two-step classifier is that it explicitly removes cases with low CEBPA expression, thereby excluding CEBPA hypermethylated cases that have similar gene expression profiles as a CEBPA double mutant, which would result in false-positive predictions. In the second step, we have developed a 55 gene signature to identity the true CEBPA double-mutation cases. This two-step classifier was tested on a cohort of 505 unselected AML cases, including 26 CEBPA double mutants, 12 CEBPA single mutants, and seven CEBPA promoter hypermethylated cases, on which its performance was estimated by a double-loop cross-validation protocol. The two-step classifier achieves a sensitivity of 96.2% (95% confidence interval [CI] 81.1 to 99.3) and specificity of 100.0% (95% CI 99.2 to 100.0). There are no false-positive detections. This two-step CEBPA double-mutation classifier has been incorporated on a microarray platform that can simultaneously detect other relevant molecular biomarkers, which allows for a standardized comprehensive diagnostic assay. In conclusion, gene expression profiling provides a reliable method for CEBPA double-mutation detection in patients with AML for clinical use.
authors.affiliation: Skyline Diagnostics BV, Rotterdam, The Netherlands.
authors.forename: Martin H
authors.initials: MH
authors.lastname: van Vliet
authors.forename: Pia
authors.initials: P
authors.lastname: Burgmer
authors.forename: Linda
authors.initials: L
authors.lastname: de Quartel
authors.forename: Jaap P L
authors.initials: JP
authors.lastname: Brand
authors.forename: Leonie C M
authors.initials: LC
authors.lastname: de Best
authors.forename: Henk
authors.initials: H
authors.lastname: Viëtor
authors.forename: Bob
authors.initials: B
authors.lastname: Löwenberg
authors.forename: Peter J M
authors.initials: PJ
authors.lastname: Valk
authors.forename: Erik H
authors.initials: EH
authors.lastname: van Beers
mesh_terms: D022763:CCAAT-Enhancer-Binding Protein-alpha / Q000378:metabolism; D022762:CCAAT-Enhancer-Binding Proteins / Q000235:genetics*; D019175:DNA Methylation; D020869:Gene Expression Profiling; D015973:Gene Expression Regulation, Leukemic / Q000235:genetics; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000175:diagnosis* / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011379:Prognosis
chemical_list: D022763:CCAAT-Enhancer-Binding Protein-alpha; D022762:CCAAT-Enhancer-Binding Proteins; C515848:CEBPA protein, human; D009363:Neoplasm Proteins