Clonal and subclonal CNVs highlight the spatial variation. (A) Hidden Markov Model (HMM)-based CNVs prediction depicting the state of CNVs (complete loss, loss of 1 copy, neutral, gain of 1 copy, gain of 2 copies, and gain of >2 copies) in regions across all 22 chromosomes. Each row represents a patient and each column represents a chromosome. The samples were ordered according to the number of CNV predicted with the patient with the highest number at the top. (B) The total number of predicted CNVs in each patient, color-coded, as in panel A. (C-D) Per spot mean residual expression values of all detected genes across a chromosome or chromosome arm in the ST sample of PT10B (C) and PT03 (D), respectively. The gain in the CNVs is represented in red and the loss is represented in blue. (E) The total number of predicted CNVs for each spot of PT10B. (F) The total number of predicted CNVs for each spot for PT03. (G) H&E staining of the punch biopsy from PT03. (H) Black and white images of punch biopsy of PT03 used for ST. Spots belonging to cluster 8 (normal skin) are highlighted. (I) HMM-based CNVs prediction of the ST Leiden clustering of the sample obtained from PT03, in which each row represents a cluster identified.