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