Genome-Wide Human SNP Array 6.0, CNV analysis
Overview
Affymetrix Genome-Wide Human SNP Array 6.0 is a powerful tool for a variety of cytogenetic applications that features over 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 demonstrates industry-leading performance and represents more genetic variation on a single array than any other product, providing maximum panel power and the highest physical coverage of the genome.
This course aims to introduce you the steps followed for analysis of SNP 6.0 array data, specifically focused on deriving somatic copy-number alterations (SCNAs). The course discusses on CBS algorithm, tangent normalization method followed by running different tools for getting copy number information. The course ends with discussion on how TCGA used SNP 6.0 to obtain CNV data, their data processing steps. Course content
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