Table 3. CDKN2A analysis results.
| CDKN2A | CDKN2A | CDKN2A | CDKN2A | |
| Case | IHC | MSP1 | MSP2 | Copy Number Status |
| CH1 | + | NP | NP | 1 |
| CH2 | − | U | F | 0 |
| CH3 | − | NP | NP | 2 |
| CH5 | − | NP | NP | 1 |
| CH6 | + | NP | NP | 1 |
| CH7 | NP | U | U | 0 |
| CH8 | NP | NP | NP | 2 |
| CH9 | − | NP | NP | 1 |
| CH14 | − | U | U | 0 |
| CH30 | − | U | U | 1 |
| CH33 | − | M | M | 2 |
| CH34 | − | U | U | 0 |
| CH35 | + | U | U | 1 |
| CH36 | − | U | F | 0 |
| CH37 | − | U | U | 0 |
| CH39 | − | U | U | 0 |
| P527 | − | U | U | 1 |
| P554 | − | U | U | 1 |
| P937 | − | U | U | 1 |
| P984 | − | M | U | 1 |
| P1033 | − | U | U | 1 |
Immunohistochemistry (IHC) was performed using standard protocol on formalin-fixed paraffin-embedded tumor specimen to assess for expression of CDKN2A (9p21.3). Methylation specific PCR was performed on bisulfite treated DNA using two primers sets (MSP1 and MSP2) targeted to the promoter region of CDKN2A. CDKN2A copy number status for each case is summarized from the array CGH results. Italicized and bolded are two cases (CH3 and CH33) showing loss of CDKN2A while maintaining normal CDKN2A copy number status. NP = not performed. F = Technical failure. U = Unmethylated. M = Methylated. CDKN2A copy number status based on array CGH: 0 = Homozygous deletion, 1 = Hemizygous deletion, 2 = Copy number neutral.