Computational protocol: Simultaneous copy number gains of NUPR1 and ERBB2 predicting poor prognosis in early-stage breast cancer

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Protocol publication

[…] For array-CGH analysis, 30K whole-genome human oligoarrays (Human OneArrayTM; Phalanx Biotech, Palo Alto, CA) were used. Oligoarray-CGH was performed as described elsewhere []. In brief, 1 μg of genomic DNA from tumor tissue was labeled with Cy3-dCTP. The reference DNA was labeled with Cy5-dCTP (GeneChem, Daejon, Korea). Dye-labeled DNA was purified with BioPrime spin columns (Invitrogen, Carlsbad, CA) and precipitated with 100 μg of human Cot-1 DNA (ConnectaGen, Seoul, Korea). The labeled DNA pellet was dissolved in 50 μl of DIG hybridization buffer (Roche, Mannheim, Germany), to which 600 μg of yeast t-RNA (Invitrogen) was added. The labeled DNA solution was applied on the array and incubated for 48 hours at 37°C in a MAUI hybridization machine (BioMicro, Salt Lake City, UT). After washing the slides, arrays were scanned using a GenePix 4000B scanner (Axon Instruments, Sunnyvale, CA) and feature extraction was performed using GenePix Pro 6.0. Normalization and re-alignment of raw array CGH data were performed using the web-based array CGH analysis interface, ArrayCyGHt []. A print-tip Loess normalization method was used and each probe was mapped according to its genomic location in the UCSC genome browser (Human NCBI36/hg18). In total, 24,107 probes were processed out of initial 26,616 probes. Array-CGH data for all 48 cancers are available through GEO (accession no GSE37839). […]

Pipeline specifications

Software tools GenePix Pro, arrayCyGHt
Application aCGH data analysis
Organisms Homo sapiens
Diseases Breast Neoplasms