Computational protocol: Microsatellite instability and mutations in BRAF and KRAS are significant predictors of disseminated disease in colon cancer

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Protocol publication

[…] Array experiments were performed according to the standard protocols for AffymetrixGeneChip® Mapping SNP 6.0 arrays (AffymetrixCytogenetics Copy Number Assay User Guide (P/N 702607 Rev2.), Affymetrix Inc., Santa Clara, CA). Briefly, 500 ng total genomicDNA was digested with a restriction enzyme (Nsp, Sty), ligated to an appropriate adapter for the enzyme, and subjected to PCR amplification using a single primer. After digestionwith DNase I, the PCR products were labeled with a biotinylatednucleotide analogue using terminal deoxynucleotidyltransferaseand hybridized to the microarray. Hybridized probes were captured by streptavidin-phycoerythrin conjugates using the Fluidics Station 450 and the arrays were finally scanned using the GeneChip® Scanner 3000 7G. Normalization and segmentation of genomic data was performed using BioDiscovery Nexus Copy Number 6.0 and the SNP Rank Segmentation algorithm [,] with default settings. Genome-wide average DNA copy number (ploidy) and the proportion of the genome with allelic imbalance were determined using Tumour Aberration Prediction Suite (TAPS) []. Average DNA copy number was calculated as the mean copy number of all genomic segments, weighted on segment length. Near diploid tumours were defined to have average copy number <2.5 and aneuploid tumours to have average copy number ≥2.5. SNP array data is available at GEO with accession number: (GSE62875). […]

Pipeline specifications

Software tools DNA copy, TAPS
Application aCGH data analysis
Organisms Homo sapiens
Diseases Colonic Neoplasms, Neoplasms, Genetic Diseases, Inborn