Table 3.
Proposed melanoma diagnosis biomarkers and prospective uses.
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| DNA Methylation | 40-CpG classifier | Next generation sequencing | 162 | 89 melanoma, 73 nevi | 250–300 ng of DNA from microdissected slides | Classify uncertain samples as melanoma or nevi | 4 | 0.996 | 96.6/100/ 100/96.2, >90/0.03 | Quantitative | (52) |
| Promoter methylation | 1,505 CpG site microarray, analyzed 12 CpG loci highly predictive of melanoma | 49 | 22 melanoma, 27 nevi | 250 ng of DNA from FFPE tissue | Differentiate nevi and malignant melanoma | NR | 0.89–1.0 | ≤ 100/ ≤ 100/NR/NR | Quantitative | (53) | |
| CpG island hypermethylation in promoter of CLDN11 | 405 | 199 melanoma, 208 nevi | Not reported, extraction from tissue | Differentiate dysplastic nevi and malignant melanoma | NR | 0.806 | 52/94/ /NR/NR, 8.67/0.51 | Quantitative | (54) | ||
| RASSF1A promoter methylation in serum cell-Free DNA | 152 | 84 melanoma, 68 nevi | Serum draw | Differentiate healthy vs. in-situ, invasive, and metastatic melanoma | NR | 0.905 | NR | Quantitative | (55) | ||
| Gene expression | microRNA ratio | Sequencing or qRT-PCR to obtain microRNA Ratio Trained Model score | 179 | 106 melanoma, 73 nevi | Single tissue section | Differentiate nevi and malignant melanoma | 5+ | 0.9 | 81/88/ NR/NR, 6.75/0.22 | Quantitative | (56) |
| RT-PCR | qRT-PCR for SILV | 193 | 47 melanoma, 48 nevi | 3–12 tissue sections | Differentiate dysplastic nevi and malignant melanoma | NR | 0.94 | NR | Quantitative | (57) | |
| Microarray | DNA microarray assay using 14 genes | 120 | 62 melanoma, 58 nevi | 8 μM tissue section, microdissected with laser capture | Differentiate nevi and malignant melanoma | 2–4 | NR | 90/86/NR/ NR*, 6.43/0.10 | Quantitative | (58) | |
| Serum nucleic acid | Circulating miRNA panel | qRT-PCR for six microRNAs in serum | 65 | Serum from 50 uveal melanoma, 5 metastatic uveal melanoma, 10 uveal nevi | Serum draw | Differentiate uveal melanoma from nevi | NR | NR for panel | 93/100*/100/76, 20/0.07 | Quantitative | (59) |
| Protein Expression | Ciliation index | Immunofluorescence for acetylated alpha-Tubulin | 124 | 26 melanoma, 42 nevi | Single tissue section | Classification of Spitzoid tumors as malignant or benign | 3+ | 0.84 | 81/65/NR/NR, 2.31/0.29 | Semi- quantitative | (60) |
| IHC | IHC for 5-hydroxymethyl-cystosine | 190 | 126 melanoma, 45 nevi | Single tissue section | Differentiate nevi from melanoma | 2 | 0.78 | 93/98/NR/NR, 46.5/0.07 | Semi-quantitative | (61) | |
| Multi-IHC semi-quantitative scoring system | IHC scoring of Ki-67, p16, and HMB45 | 308 | 234 melanoma, 74 nevi | Three tissue sections | Differentiate nevi and malignant melanoma | NR | 0.987 | 97.4/97.3/NR/NR, 36.1/0.03 | Semi-quantitative | (62) |
AUC, area under (receiver operating characteristic) curve; FFPE, formalin-fixed paraffin embedded; LR+, positive likelihood radio; LR–, negative likelihood radio; NPV, negative predictive value; NR, not reported; PPV, positive predictive value; S, sensitivity; Sp, specificity; qRT-PCR, quantitative real time polymerase chain reaction.
*
Leave 1-out validation.
‡
All LR values are calculated based on reported sensitivity and specificity.