This tutorial will illustrate:
Copy number analysis asks whether there are regions of the genome with altered abundance. Of particular interest are any genes within those regions and how might a change in gene abundance alter phenotype. Partek Genomics Suite software allows these questions to be answered by analyzing a variety of commercially available assays for copy number analysis. SNP-genotyping arrays with closely spaced genomic markers (Affymetrix and Illumina), and comparative genomic hybridization (CGH) arrays (Agilent, NimbleGen, or custom spotted arrays) to detect amplified or deleted regions within and share across samples can be imported into Partek Genomics Suite and analyzed.
When performing copy number analysis, it is important to remember the inherent limitation of copy number region analysis - the inability to detect copy-neutral events, i.e. copy neutral loss of heterozygosity (LOH) or copy-neutral allelic imbalance. This issue can be addressed by supplementing copy number analysis with SNP genotyping data. Partek Genomics Suite supports both LOH and allele-specific copy number (AsCN) analysis with dedicated workflows. To view tutorials on LOH and AsCN analysis, select the respective links.
The example data set consists of 20 paired samples from an ovarian cancer study in which a fresh-frozen tumor sample and peripheral blood sample were obtained from 10 female patients (Ramakrishna et al. 2010). All 20 samples were analyzed using the Affymetrix Genome Wide Human SNP Array 6.0. To download the data set, select this link - CNV Tutorial Data Set. The data set is a spreadsheet generated from the import of SNP6 CEL files and annotated with attributes for each sample. The experimental goal is to identify copy number variation between paired tumor and normal samples.
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