Table 4

Copy number changes in formalin-fixed, paraffin-embedded (FFPE) and cavitronic ultrasonic surgical aspiration (CUSA) specimen DNA
Tumors Genes with normalized CN ratios ≥ 2.0 (gains in copy number) Genes with normalized CN ratios < 0.75 (losses in copy number)
Total FFPE CUSA Only FFPE Only CUSA Total FFPE CUSA Only FFPE Only CUSA
GBM1 18 17 7 11 1 16 12 6 10 4
GBM2 10 10 5 5 0 21 17 9 12 4
GBM3 13 13 7 6 0 21 18 8 13 3
GBM4 10 8 8 2 2 15 13 7 8 2
LCM1 7 7 5 2 0 15 12 11 4 3
LCM2 15 13 5 10 2 32 22 18 14 10
EP1 7 7 3 4 0 16 15 6 10 1
Totals 80 75 40 40 5 136 109 65 71 27

GBM1-4 had increased CN ratios for 22 genes (AURKA, BCL2A1, BCL6, BIRC1,2,4, BRAF, CDK4,6, CYP27B1, EGFR, ERBB4, ESR1, EVI1, GNAS, GSTP1, MDM2, NRAS, PDGFRA, PIK3CA, RNF139, & SERPINB9) and decreased CN ratios for 35 (AKT1, BCAR3, BCAS1, BCL2, BCL2L13, BCLG, BIRC5, BRMS1, CCND1, CCNE1, CDK4, CENPF, EMS, FGF4, FGFR1, FLJ20517, GSTP1, IGF1R, IGFBP2, IRS2, JAK2, MDM4, MYBL2, MYC, MYCL1, MYCN, NFKBIE, NTRK1, PDGFRB, PIK3C2B, PTK2, PTP4A3, PTPN1, TERT, &TOM1L2). LCM1-2 had increased CN ratios for 16 genes that overlapped with those for GBM1-4 plus CCNE1, MET, PPM1D, and PSMB4, and decreased CN ratios were found for thirty six genes that overlapped with those listed for GBM1-4 plus BCL2L1, BIRC3, CYP27B1, MMP7, NTRK2, NTRK3, PDGFRA, RELA, & SERPINB2. EP1 had increased CN ratios for genes among those for GBM1-4 and decreased CN ratios for those for GBM1-4 or LCM1-2 plus CCND3, HMGA1, & MOS.

Truong et al.

Truong et al. Diagnostic Pathology 2012 7:66   doi:10.1186/1746-1596-7-66

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