Workflow of the CNV detection method. A. Median Read Depth (MRD) is calculated for each sample, as a measure of sample coverage (NA18523 shown). B. The gene affinity is estimated for each gene as the slope of the least-square-error linear fit between MRD and RD for that gene (TRIM33 shown). C. Example of observed (magenta) and expected (green) read depth for three samples and four genes. The observed read depths were roughly half of the expected values for genes TRIM33 and NRAS, in sample NA18523, and detected as deletions.