Array-comparative genomic hybridization by using DualChip® human cancer 1.1 arrays

Tumors often harbor several genetic aberrations at both RNA and DNA level. Integration of expression data with copy number changes represents a powerful strategy to investigate genes involved in tumorigenesis. Here we describe a fluorescent array-based Comparative Genomic Hybridization protocol to be used on a commercial microarray platform optimized to detect cancer-related gene expression. This method will be valuable to use a single low-density array platform monitoring gene expression and copy number assessment in parallel. Keywords: Comparative genomic hybridization, neuroblastoma Here we describe a fluorescent array-based Comparative Genomic Hybridization (aCGH) protocol to be used on DualChip® (Eppendorf, Hamburg, Germany) arrays, in view of an application of cancer-specific DualChip® platforms for both gene expression profiling and copy number assessment. Since we previously analyzed #501 and #2270 neuroblastoma samples by Agilent Human Genome CGH 44A microarrays (Scaruffi, P. Coco, S., Cifuentes, F., Albino, D., Nair, M., Defferrari, R., Mazzocco, K., and G.P. Tonini. 2007. Identification and characterization of DNA imbalances in neuroblastoma by high-resolution oligonucleotide array comparative genomic hybridization. Cancer Genetics and Cytogenetics. 177(1): 20-29) and all 294 genes contained in DualChip® human cancer 1.1 arrays were present also in Agilent arrays, it has been possible to compare results obtained by the two different platforms. We assumed aCGH performed by Agilent slides as reference method to assess gene gains and losses in neuroblastoma samples. This approach allowed us to select 120 genes printed on DualChip® arrays as invariant genes (ABI2, ADAM9, ANGPT1, AREG, BAK1, BIK, BARD1, BCL2A1, BCL2L2, BMP1, CASP3, CASP8, CDH12, CFLAR, CTNNA1, CD34, CLK1, CGRRF1, COL6A1, CSF1R, CSPG2, CTGF, CXCL9, CCNA2, CCNB1, CCNG1, CCNH, CDKN1A, CDKN1C, CDKN2A, CDKN2B, CDKL1, DSP, E2F3, E2F5, EFNA1, EGF, EGR1, FASTK, FGF1, FGF2, FGFR1, FGR, FN1, GAS1, HGFAC, HMMR, IGF1R, IGFBP2, IK, IFNAR1, IFNGR1, ILK, IRF1, ITGA1, ITGA4, IL10, IL13, IL15, IL1A, IL2, IL3, IL4, IL5, IL6R, IL8, KDR, KISS1, LIF, MIF, MMP11, MMP14, MDH1, MAP2K1, MAP2K5, MAPK10, MAPK14, MCL1, NF2, NID1, NINJ1, NRG1, NTRK1, PGF, PDGFB, PDGFRA, PLAT, PLG, PDCD2, PPBP, PRODH, PTGES, PCDH1, PTK2, PURA, QSCN6, RIPK1, RRM1, ARHGDIA, SFRP2, SOD1, STAT1, TEK, TERT, THBS1, TIAM1, TNC, TANK, TGFA, TGFB2, XRCC6, TGFB3, TGFBR1, TMED10, TPBG, TYRO3, ERBB4, FLT4, FOS, VIL2).