Figure 1.

SMARCB1-deficient carcinoma involving scalp of an 18-year-old female. The tumor cells infiltrate dermis in the form of nests and cords intersected by variably thick, dense collagenous stroma and is associated with lymphoid aggregates at the tumor periphery [A, H&E, scanning magnification]. The tumor cells surround adnexal structures and no connection to the overlying epidermis was identified [B, H&E, 200x magnification]. Perineural invasion is seen (arrow). The tumor cells are of intermediate size and show smooth cell borders. No prominent rhabdoid features are seen although in areas, they do have a subtle plasmacytoid appearance. The nuclear/cytoplasmic ratio is high and the nuclei are round with finely dispersed chromatin and one or multiple conspicuous nucleoli [C, H&E, 400x magnification]. A cytologic preparation reveals clusters of cells with indistinct nuclear borders and scant delicate cytoplasm, vesicular chromatin and prominent nucleoli [D, Papanicolaou stain, 600x magnification]. Immunohistochemistry revealed loss of nuclear INI1 expression [E, 400x magnification] and positive staining for claudin-4 [F, 400x magnification], p40 [G, 400x magnification], with patchy CK 5/6 expression throughout the tumor [H, 400x magnification].

A CNA plot of Case 1 shows homozygous deletion of SMARCB1 (green arrow). The Y-axis depicts copy number changes expressed as the log2 transformed tumor/normal ratio by their genomic positions indicated on the x-axis. The blue dots represent individual exons and red dots indicate a ≥2-fold tumor/normal ratio [I]. FACETS analysis shows deletion of both SMARCB1 alleles as indicated by the total integer copy number 0 (black line, y-axis). A red line indicates a minor allele. SMARCB1 genomic position on chromosome 22 is indicated by the vertical green line [H].

Abbreviations: FACETS, Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing; CNA, copy number alterations.