We also adapted our OB-HMM method to perform analysis on multiple samples simultaneously. If regions of copy number variation are common across individuals (perhaps due to a shared disease phenotype), the use of the data jointly allows for borrowing of strength and improved detection of copy number variants. For example, a 5 SNP CNV which is typically undetectable by QuantiSNP at stringent false positive rates can be located accurately if the same CNV region is aberrant in 1000 individuals (Figure 3).
