A Single Microarray Assay for Simultaneous Diagnosis of t(15;17), t(8;21), Inv(16)/t(16;16), NPM1 Type A/B/D Mutation, CEBPA Double Mutation, and Aberrant Expression of BAALC or EVI1 in AML/APL Patients

In newly diagnosed acute myeloid leukemia (AML) gene expression (RNA) profiling (GEP) (1) on Affymetrix GeneChips identifies homogeneous clusters that correlate with all favorable cytogenetic subtypes t(15;17), t(8;21) and inv(16)/t(16;16) and favourable CEBPA gene double mutants (2). We validated the use of GEP to detect NPM1 type A/B/D with specifically designed probes and validated the prognostic value of qualitative (high vs low) assays for single genes (EVI1 and BAALC).

To develop and validate an in vitro diagnostic (CE-IVD) microarray for use in newly diagnosed AML.

A custom Affymetrix microarray, the AMLprofiler, was produced that contains a combination of generic and specially designed probes. The array was tested following hybridisation of 261 AML training cases. Next, the AMLprofiler was evaluated in an independent cohort of 267 unselected newly diagnosed cases of AML (Erasmus University Medical Center & University Ulm).

During validation in 267 independent cases the AMLprofiler identified 18/17 inv(16), 7/7 t(15;17) and 16/16 t(8;21) AML's and 70/71 NPM1A/B/D cases. There was one false-positive inv(16) namely a t(11;16) translocation concurrent with MYH11 overexpression, suggesting involvement of the 16p13.1 breakpoint as in bona fide inv(16). There was 1 false-negative case of NPM1 type-D, which motivated algorithm retraining and subsequent independent re-validation, resulting in detecting 68/66 NPM1AB/D mutants in 143 Normal Karyotype AML cases. One of the FP cases is a true and relevant but non-A/B/D type mutant. The EVI1 and BAALC cut points were validated in an independent clinical cohort resulting in p < 0.05 in the logrank test for OS between high versus low expressing intermediate cytogenetic risk cases. Finally, reproducibility of the AMLprofiler assay is demonstrated across 5 independent laboratories in four countries.

We report the development of an AML gene expression RNA microarray for diagnostic use that can be applied by physicians in their own laboratories, to detect core binding AML, PML, NPM1 A/B/D mutant, CEBPA double mutant, high EVI1 and low BAALC AML cases for diagnostic use

van Beers:Skyline Diagnostics: Employment, Patents & Royalties. de Best:Skyline Diagnostics: Employment. van Vliet:Skyline Diagnostics: Employment. Brand:Skyline Diagnostics: Employment. Burgmer:Skyline Diagnostics: Employment. de Quartel:Skyline Diagnostics: Employment. Dumee:Skyline Diagnostics: Employment. Provoost:Skyline Diagnostics: Employment. Valk:Skyline Diagnostics: Equity Ownership. van der Spek:Skyline Diagnostics: Equity Ownership. Vietor:Skyline Diagnostics: Employment, Equity Ownership. Lowenberg:Skyline Diagnostics: Equity Ownership.