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Get an integrated analysis of copy number and sequence variation using data from The Cancer Genome Atlas (TCGA), and learn how CNV, allelic events, and seq. variations can aid in the discovery process in cancer studies.
Get a general overview of the basic principles of array CGH including how arrays measure copy number, signal intensities, probe mapping, experiment/reference sample ratios, etc.
Learn a few different ways to re-center (median, mode, median probe intensity of known diploid regions) and in what scenarios (e.g. aCGH arrays, SNP arrays) to use a specific re-centering method.
This video will cover some basic principles of log ratios, how to identify regions of LOH, and some calling algorithms including HMM. Also, learn about the effect of mosaic loss or copy neutral LOH on the BAF profile.
This video covers the FASST2 CNV calling algorithm, including how it works and pros and cons of the algorithm