Multi-region SBCapSeq analysis of dual histology keratinocyte-derived skin masses containing distinct cuKA and cuSCC histological regions.

Two individual mice displayed lesions with both cuKA and cuSCC histologies suggestive of clonal evolution of cuSCC differentiation within cuKA masses. Aperio slide scans of H&E stained FFPE specimens and the adjacent flash frozen tissue for specimen 1 (A-B) and specimen 2 (C-D) prior to sectioning for genomic DNA isolation. Yellow dotted lines demarcate the distinct lesions within each section that were sampled for sequencing SB insertions. Hierarchical two-dimensional clustering (Hamming distance with the Ward method) of recurrent genic SBCapSeq insertion data for specimen 1 (E) and specimen 2 (F) demonstrates trunk (common to all samples) and sub-clonal, lesion-specific SB insertions (S4 Data). Genomic DNA was isolated from adjacent serial sections and included a “bulk” reference consisting of a cross-section of entire mass, and three or four regions dissected from histologically distinct regions.