CNV detection was performed using three algorithms: 1) PennCNV Revision 220, 2) QuantiSNP v1.1, and 3) GNOSIS. PennCNV and QuantiSNP are based on the Hidden Markov Model (HMM). GNOSIS uses a continuous distribution function (CDF) to fit the intensity values from the HapMap data and determine thresholds for significant points in the tails of the distribution that are used to detect copy number changes. Analysis and merging of CNV predictions was performed with CNVision (www.CNVision.org), an in-house script.
