Technical data

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Patient inclusion criteria

Age at diagnosis 18 years or older, cytopathologically confirmed diagnosis of AML (including APL and MDS) or RAEB according to the WHO 2008 classification, primary, secondary or relapse, no prior allogeneic or autologous stem cell transplant, no Myeloproliferative Syndrome (MPS)

Sample

1 ml bone marrow, no stabilizers required or allowed, collection in generic heparin or EDTA anticoagulant collection tubes. 

Time constraints and QC

Blast cell enrichment (Ficoll) and RNA isolation process should start within 48 hours after collection. Array QC based on Minimum Percent Present Call, and Minimum linearity of hybridization controls.

Markers reported

In total 9 markers are determined: t(8;21) (RUNX1-RUNXT1 fusion) detected by 31 proprietary gene expression levels, t(15;17) (PML-RARA fusion) detected by 27 proprietary gene expression levels, inv(16)/t(16;16) (CBFB-MYH11 fusion) detected by 19 proprietary gene expression levels, (CCAAT/enhancer Binding Protein Alpha) CEBPA double mutants detected with 55 proprietary gene expression levels.

NPM1 (Nucleophosmin 1) three top prevalent mutant types (A, B and D) insertions in exon 12 at position 956-959

High expression of EVI1 (Ectotropic Viral Integration Site 1) and high expression of BAALC (Brain and Acute Leukemia, Cytoplasmic), MN1 (Menigioma (disrupted in balanced translocation) 1) and ERG (Ets Related Gene) 

Assay system

GeneChip 3000Dx v.2 Instrumentation System running Skyline’s dedicated AMLprofiler assay software module (ASM) “AMLprofiler v 1.0”. The instrument platform has received 510(k) clearance from the FDA for use as an in-vitro diagnostics Instrument for Clinical Multiplex Testing under 510(k) K042279 and K080995.

Data analysis and reporting

The AMLprofiler assay is performed using Skyline’s dedicated AMLprofiler assay software module (ASM) “AMLprofiler v 1.0”. The ASM enables the Affymetrix system to process the array, and ensures the expression data (CEL file) is generated and transferred to the server. CEL-file data generated by Affymetrix workstations are automatically transferred for analysis using the Skyline software through a secure FTP transfer protocol and processed by the algorithm to determine genotyping and AML classification. The results are returned the Affymetrix system on which the analysis has been performed over a secure internet connection.

 

Dr. Molewaterplein 50, Suite Ee-1540, 3015 GE Rotterdam. The Netherlands, Europe. Phone: +31 (0)10 70 43 491. Fax: +31 (0)10 70 44 161. E-mail: bioinformatics@erasmusmc.nl