Figure 3

Selected recurrent genomic alterations in follicular dendritic cell sarcoma. (a–d) Top panels: aggregate of all copy-number calls; x-axis: genomic position; y-axis: percentage of abnormal cases (n=11) with copy-number calls (only). Middle panels: smallest region of overlap (SRO), pan-cancer deletion peaks (Peak), and Cancer Gene Census genes (Genes) are shown (brackets). Bottom panels: copy-number/loss-of-heterozygosity calls within individual cases; ≥2 copy-number alterations are displayed as stacked bars; flanking dotted lines: smallest regions of overlap; arrows: genes of interest. (a) Chromosome 9 view shows 2.0 Mb smallest region of overlap for loss/loss-of-heterozygosity calls across 7 cases, 4 with homozygous deletions (smallest region of overlap: 21,928,114 [1]-21,974,064 [1]; 53 kb, overlapping CDKN2A). Genes CD274 and PDCD1LG2 in 9p24 are shown. (b) Chromosome 11 view shows 15.0 Mb smallest region of overlap for loss/loss-of-heterozygosity calls across 7 cases, 4 with homozygous deletions (smallest region of overlap: 102,166,344 [4]- 102,296,024 [9]; 130 kb, overlapping BIRC3). (c) Chromosome 13 view shows 22.6 Mb smallest region of overlap for loss/loss-of-heterozygosity calls across 10 cases, 2 with homozygous deletions (smallest region of overlap: 48,920,908 [1] - 49,060,447 [1]; 140 kb, overlapping RB1). (d) Chromosome 16: 2 homozygous deletions (smallest region of overlap: 49,852,987 [1] - 51,757,339 [1]; 1.9 Mb, overlapping CYLD).