Adopting discrete states (loss, copy neutral, gain) as model features (see the “Methods” section), which was favored to disregard variable tumor fractions, downweighs the presence of amplifications, indicated by, for example, patient 32: a 7p11.2 (EGFR) amplification, indicative for NSCLC, is clearly present (Additional file 4), yet the overall signal (wrongly) pushed classification towards SCLC [14]. Here, EGFR is linked to neoplasm.