Neuroblastoma Study Background Information
The neuroblastoma (NB) data set (endpoints J, K, L, and M) was contributed by the Children's Hospital of the University of Cologne, Germany. Tumor samples were checked by a pathologist prior to RNA isolation; only samples with =60% tumor content were utilized and total RNA was isolated from ~50mg of snap-frozen neuroblastoma tissue obtained before chemotherapeutic treatment. First, 502 pre-existing 11K Agilent dye-flipped, dual-color replicate profiles for 251 patients were provided. Of these, profiles of 246 neuroblastoma samples passed an independent MAQC-II quality assessment by majority decision and formed the MAQC-II training data set. Subsequently, 514 dyeflipped dual-color 11K replicate profiles for 256 independent neuroblastoma tumor samples were generated and profiles for 253 samples were selected to form the MAQC-II validation set. Of note, for one patient of the validation set, two different tumor samples were analyzed utilizing both versions of the 2x11K microarray (see below). All dual-color gene-expression of the MAQC-II training set were generated using a customized 2x11K neuroblastoma-related microarray. Furthermore, 20 patients of the MAQC-II validation set were also profiled utilizing this microarray. Dual-color profiles of the remaining patients of the MAQC-II validation set were performed using a slightly revised version of the 2x11K microarray. This version V2.0 of the array comprised 200 novel oligonucleotide probes whereas 100 oligonucleotide probes of the original design were removed due to consistent low expression values (near background) observed in the training set profiles. These minor modifications of the microarray design resulted in a total of 9,986 probes present on both versions of the 2x11K microarray. The experimental protocol did not differ between both sets and gene-expression profiles were performed as described. Furthermore, single-color geneexpression profiles were generated for 478/499 neuroblastoma samples of the MAQC-II dual-color training and validation sets (training set 244/246; validation set 234/253). For the remaining 21 samples no single-color data were available, due to either shortage of tumor material of these patients (n=15), poor experimental quality of the generated single-color profiles (n=5), or correlation of one single-color profile to two different dual-color profiles for the one patient profiled with both versions of the 2x11K microarrays (n=1). Single-color gene-expression profiles were generated using customized 4x44K oligonucleotide microarrays produced by Agilent Technologies (Palo Alto, CA, USA). These 4x44K microarrays included all probes represented by Agilent's Whole Human Genome Oligo Microarray and all probes of the version V2.0 of the 2x11K customized microarray that were not present in the former probe set. Labeling and hybridization was performed following the manufacturer's protocol as described.
MAQC-II Project
Neuroblastoma Study
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