Unsupervised hierarchical clustering of 48 rectal cancers analyzed by HMM. Clones are shown in chromosomal order from 1ptel to 22qtel (red, gain; green, loss; yellow spots, high level gain). Tumor regression grade (TRG) classification: responders (TRG3-4) yellow; non responders (TRG0-2) black. Extreme response classes are reported in the upper line: TRG4 yellow and TRG0-1 black. ypT status: ypT0-1green; ypT2 orange and ypT3 red. ypN status: ypN0 green, ypN1 red and ypNx white.