Table 4.
Proposed prognostic, staging, and treatment-monitoring biomarkers.
| Category | Method class | Method specifics | Total study number | Study breakdown | Estimated tissue requirement | Study objective | Number of pathologists confirming cohort | AUC | S/Sp/PPV/NPV (%), LR+/LR-‡ | Qualitative vs. quantitative | Citation |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Prediction of sentinel lymph node biopsy status | |||||||||||
| Castle DecisionDx | 31 GEP | TaqMan qRT-PCR from FFPE tissue | 1421 | By T: 613 T1, 452 T2, 240 T3, 116 T4 | macrodissected FFPE sections | Identify T1–T2 melanomas at low risk for positive SLNB | NR | NR | NR | Quantitative | (70) |
| Skyline | GEP and clinico-pathologic features | TaqMan qRT-PCR from FFPE tissue | 506 | 160 discovery, 360 development, 146 validation | FFPE blocks | Develop and validate a GEP panel to identify positive SLNB | 2+ dermato-pathologists | 0.78 | 89/76/NR/NR, 3.71/0.14 | Quantitative GEP, qualitative clinicopathologic features | (71) |
| 754 | 128 positive SLNB, 626 negative SLNB | FFPE blocks | Identify patients who can forgo SLNB | Initial diagnosis made with 2+ dermato-pathologists. No other review | 0.82 | TIb: 41/82/7/98, 2.28/0.72; TIIa: 80/53/21/95, 1.7/0.24; TIIb: 94/27/21/96, 1.29/0.22; TIIIa: 99/12/33/98, 1.13/0.08; TIIIb: 100/7/45/100, 1.08/ <0.01 | (72) | ||||
| Metastasis identification | |||||||||||
| Circulating Tumor Cells | Flow and fluorescent microscopy | CD146 cell sorting. DAPI+, HMW-MAA+, CD45/CD34– Immuno-fluorescence | 15 | Tumor: 15, 0. Metastasis 6, 9 | Whole blood | Identification of early mets | NR | NR | CTC: 33/100/100/69, >30/0.67; CTC+5-S-cysteinyldopa: 67/100/100/82, >60/0.33 | Semi-quantitative | (73) |
| Serum nucleic acid | Circulating non-coding RNA by qRT-PCR | hsa-miR-1246 miScript assay for RNU2-1f | 122 | 33 training, 16 distant metastasis validation, 16 nevi, 57 healthy control | Serum draw | Use RNU2-1f non-coding RNA serum level to diagnose melanoma mets | NR | 0.9375 (validation) | Regional mets: 69.6/87.2/NR/NR Distant mets: 70.0/87.2/NR/NR | Quantitative | (74) |
| Protein Expression | ELISA | ELISA for S100 and OPN | 106 | 6 squamous cell carcinomas, 76 melanomas, 24 metastatic mela-nomas, 3 normal | Plasma draw | Distinguish metastatic melanoma from local disease with OPN +/– S100 and LDH | NR | OPN and S100: 0.97 | 95.5/85.9/NR/NR, 6.77/0.05 | Quantitative | (75) |
| Prognosis | |||||||||||
| Castle DecisionDx | 31 GEP | TaqMan qRT-PCR from FFPE tissue | 479 | 107 discovery, 268 development, 104 validation | macrodissected FFPE sections | Identification of stage I/II tumors with worse prognosis | NR | 0.93 | 100/78/NR/NR, 4.54/ <0.01 | Quantitative | (76) |
| 217 | All post-SLNB: 58 positive SLN, 159 negative SLN | macrodissected FFPE sections | Prognostic accuracy of GEP and SLNB in predicting RFS, distant mets, and OS | NR | NR | N.R./N.R./50/82 | (77) | ||||
| 205 | By stage: 2 I, 68 IA, 39 IB, 1 II, 40 IIA, 41 IIB, 14 IIC | Biopsy | Compare GEP to AJCC in predicting 5 yr RFS, distant mets, and OS | NR | NR | GEP+AJCC for Recurrence: 90/71/NR/NR, 3.10/0.14; Distant Mets: 88/63/NR/NR., 2.38/0.19; Death: 82/62/NR/NR, 2.16/0.29 | (78) | ||||
| Gene Expression | RT-PCR | qRT-PCR for PAX3d to monitor recurrent in stage II-IV disease | 198 | 111 melanoma, 87 healthy controls | Plasma draw | Identify recurrence in stage II-IV disease with plasma PAX3d mRNA | NR | 0.823 | Stage II–III relapse: 67/75/67/75, 2.68/0.44; Stage IV relapse: 75/93/43/98, 10.7/0.27 | Quantitative | (79) |
| Serum nucleic acid | Circulating tumor DNA | PCR of BRAF and NRAS mutants | 125 | 20 with progression, 9 with pseudo-progression | Plasma draw | Differentiate radiologic pseudo-progression and true progression | NR | NR | 90/100/100/82, >90/0.1 | Quantitative | (80) |
| Monitoring of treatment effect | |||||||||||
| Serum nucleic acid | Circulating tumor DNA | BRAF V600mut ctDNA by qRT-PCR | 36 | 16 before therapy, 20 after therapy | Plasma draw | Monitor patient response to BRAF/MEK inhibition therapy with BRAF V600mut ctDNA | NR | NR | 70/100/NR/NR., >70/0.30 | Quantitative | (81) |
AUC, area under (receiver operating characteristic) curve; CTC, circulating tumor cells; ctDNA, circulating tumor DNA; ELISA, enzyme-linked immunosorbent assay. FFPE, formalin-fixed paraffin embedded; GEP, gene expression panel; LR+, positive likelihood radio; LR–: negative likelihood radio; Mets, metastasis; NPV, negative predictive value; NR, not reported; OS, overall survival; PPV, positive predictive value; RFS, recurrence-free survival; S, sensitivity; qRT-PCR, quantitative real time polymerase chain reaction; SLNB, sentinel lymph node biopsy; Sp, specificity.
‡
All LR values are calculated based on reported sensitivity and specificity.