Reproducible patterns in genome-wide aCGH and NGS data. (A) Pairwise aCGH analysis results of blood, liver, brain, and testis samples for rat chromosome 16. For all panels, the variability in log2 ratios is displayed (each dot represents the median value over 100 consecutive probes). The top two panels show dye swap aCGH (Nimblegen) results using blood and liver samples from a single animal (Brown Norway strain). The third panel shows the comparison of blood and liver from an animal from a different inbred strain (ACI). The bottom panel shows the aCGH analysis results between brain and testis of that same ACI animal. (B) Comparison of aCGH hybridization signal with NGS depth of coverage analysis results. DNA isolated from the testis and from blood of the same animal was analyzed by aCGH (Nimblegen) and by low-pass next-generation sequencing (6.3-7.2 M reads; 0.075× - 0.086× genome coverage).