Formalin-fixed, paraffin-embedded (FFPE) skin specimens were obtained from a cohort of eight patients with cutaneous squamous cell carcinoma (cSCC). For each patient, tissue blocks contained histologically distinct regions corresponding to (i) healthy skin, (ii) actinic keratosis (AK) and/or in situ cSCC, and (iii) advanced invasive cSCC. Hematoxylin and eosin–stained sections were reviewed by a board-certified dermatopathologist to confirm diagnoses and to guide region selection. The three regions of interest (healthy, AK/in situ cSCC, and advanced cSCC) were macro-dissected separately from 5-µm FFPE unstained sections using annotated reference slides. Care was taken to minimize cross-contamination between regions. Sections were then subjected to lysis and Proteinase K treatment for 20min at 56°C. After protein inactivation, DNase digestion was performed at 37°C for 30 min and the quantitative nuclease protection assay was run using the HTG EdgeSeq Processors. Adapters and sample tags were finally added in a PCR amplification. The resulting libraries were sequenced using on an Illumina NextSeq 2000 (Flow cell P2 - 100 cycles).