| Comparative genomic hybridization (CGH) |
Accurate quantification of DNA copy number variations over a wide dynamic range with detection of single-copy deletions and duplications FFPE |
[54] |
| Analyses of allelic imbalance (AI) |
Detects the presence of deletions or gains of specific alleles |
[55] |
|
Uses PCR amplification of microsatellite polymorphic markers followed by gel electrophoresis |
|
|
Performed on DNA from formalin-fixed paraffin-embedded tissues (FFPE) tissues |
|
| Multiplex ligation-dependent probe amplification (MLPA) |
Measures the copy number of up to 45 nucleic acid sequences in one single reaction |
[56] |
|
Performed on DNA extracted from routinely processed |
|
| Fluorescence in situ hybridization (FISH) |
Utilizes a fluorescent probe or group of probes to search for preselected genomic abnormalities in tumors |
[57] |
| Immunohistochemical markers |
|
|
| S100A6 |
Part of the family of S100 proteins |
[58] |
| PCNA |
A 36-kDa protein that is a cofactor of DNA polymerase d (expressed in all phases of cell cycle proliferation) |
[59, 60] |
|
Proliferation marker |
|
| Ki-67 |
Proliferation marker |
[61, 62] |
| FLIP |
Immune modulatory marker |
[63] |
| CD40 |
Immune modulatory marker-B-cell marker; also a tumor suppressor |
[64] |
| CD26 |
Immune modulatory marker, an adenosine deaminase receptor |
[65] |
| Cancer/testis antigens |
Immune modulatory marker |
[66] |
|
Proteins that are aberrantly expressed in many types of malignancies |
|
| Skp2 |
Cell cycle-related/anti-apoptosis markers |
[67] |
|
F-box protein which aids the formation of a more massive protein complex that degrades p27 |
|
| Retinoblastoma protein (RB) |
Cell cycle-related/anti-apoptosis markers |
[68, 69] |
| P53 |
Cell cycle-related/anti-apoptosis markers |
[69, 70] |
| P21 |
Cell cycle-related/anti-apoptosis markers |
[6, 70] |
| P16 |
Cell cycle-related/anti-apoptosis markers |
[61, 72, 73] |
| HDM2 |
Cell cycle-related/anti-apoptosis markers |
[74] |
|
90-kDa zinc finger protein that binds to p53 transcription activation domain inhibiting its function and targeting it for degradation by proteasomes |
|
| GADD |
Cell cycle-related/anti-apoptosis markers |
[75] |
|
Control transcription factors associated with cell cycle arrest, apoptosis, and cellular differentiation |
|
| Cyclin D3 |
Cell cycle-related/anti-apoptosis markers |
[71] |
| Cyclin B |
Cell cycle-related/anti-apoptosis markers |
[70, 71] |
| Cyclin A |
Cell cycle-related/anti-apoptosis markers |
[70, 71] |
| Cdk2 |
Cell cycle-related/anti-apoptosis markers |
[76] |
| Bcl-2 |
Cell cycle-related/anti-apoptosis markers |
[77] |
| Trk-A |
Signaling molecule |
[78] |
|
Nerve growth factor receptor tyrosine kinase involved in activation of major oncogenic signaling pathways in melanoma, including the Ras/MAPK and phosphatidylinositol-3 kinase pathways |
|
| PTEN |
Signaling molecule |
[71, 79] |
