TABLE 1.
Summary of ddPCR Data, CMA Data, and Lesion Classification for All Samples
| ID | CDKN2A: LIPI ddPCR Output | CDKN2A: SLAIN2 ddPCR Output | CDKN2A: AGO1 ddPCR Output | CDKN2A: THNSL2 ddPCR Output | CDKN2A: RPPH1 ddPCR Output | Mean ddPCR Output | CDKN2A Loss (ddPCR) | CDKN2A Loss (CMA) | Lesion Classification | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||||||
| 1 | 1.75 | 1.76 | 2.03 | 2.12 | 2.35 | 2.3 | 2.23 | 2.22 | 1.9 | 1.88 | 2.05 | No | No | Borderline lesion |
| 2 | 2.01 | 2.05 | 1.81 | 1.91 | 2.2 | 2.29 | 2.45 | 2.46 | 2.12 | 2.05 | 2.14 | No | No | Benign nevus |
| 3 | 2.15 | 2.14 | 2.13 | 2.12 | 2.59 | 2.59 | 2.49 | 2.45 | - | - | 2.33 | No | No | Benign nevus |
| 4 | 2.3 | 2.23 | 2.22 | 2.18 | 2.31 | 2.36 | 2.23 | 2.33 | 1.88 | 1.87 | 2.19 | No | No | Borderline lesion |
| 5 | 2.4 | 2.29 | 2.42 | 2.39 | 2.17 | 2.21 | 2.21 | 2.18 | 2.01 | 1.99 | 2.23 | No | No | Primary melanoma |
| 6 | 2.06 | 1.94 | 1.82 | 1.87 | 2.28 | 2.29 | 1.96 | 2.03 | 1.76 | 1.74 | 1.98 | No | No | Borderline lesion |
| 7 | 1.82 | 1.8 | 1.8 | 1.96 | 2.49 | - | 2.32 | 2.64 | 1.93 | 1.89 | 2.07 | No | No | Borderline lesion |
| 8 | 3.07 | 3.29 | 1.38 | 1.48 | 2.05 | 2.2 | 1.11 | 1.16 | 0.62 | 0.61 | 1.70 | Yes (monoallelic) | No | Borderline lesion |
| 9 | 3.41 | 3.16 | 1.6 | 1.57 | 2.3 | 2.17 | 1.25 | 1.28 | 0.61 | 0.7 | 1.81 | No | No | Borderline lesion |
| 10 | - | - | - | - | 2.07 | - | 1.65 | 1.99 | 1.44 | 1.6 | 1.75 | No | No | Benign nevus |
| 11 | - | - | - | - | 1.83 | 2.23 | 2.2 | 1.77 | 2.13 | 2.03 | No | No | Borderline lesion | |
| 12 | 1.88 | 1.9 | 1.82 | 1.9 | 2.13 | 2.08 | 2.13 | 2.15 | 1.92 | 1.98 | 1.99 | No | No | Benign nevus |
| 13 | 2.47 | 2.64 | 2.33 | 2.24 | 2.37 | 2.38 | 2.47 | 2.42 | 1.91 | 1.89 | 2.31 | No | No | Borderline lesion |
| 14 | - | - | - | - | 2.25 | - | 2.15 | 2.16 | 1.78 | 1.75 | 2.02 | No | No | Borderline lesion |
| 15 | - | - | - | - | 2.35 | 2.22 | 2.29 | 2.07 | 1.55 | 1.5 | 2.00 | No | No | Borderline lesion |
| 16 | - | - | - | - | 2.34 | 2.46 | 2.41 | 2.49 | 1.8 | 1.67 | 2.20 | No | No | Benign nevus |
| 17 | - | - | - | - | 2.26 | 2.36 | 2.07 | 2.09 | 1.68 | 1.73 | 2.03 | No | No | Benign nevus |
| 18 | 2.49 | 2.43 | 1.98 | 1.97 | 2.07 | 1.97 | 1.84 | 1.85 | 1.69 | 1.77 | 2.01 | No | No | Borderline lesion |
| 19 | 1.98 | 2.01 | 1.89 | 1.85 | 2.16 | 2.17 | 1.81 | 1.82 | 1.85 | 1.87 | 1.94 | No | No | Benign nevus |
| 20 | 1.94 | 2.03 | 1.96 | 2.02 | 2.36 | 2.38 | 2.13 | 2.23 | 1.79 | 1.75 | 2.06 | No | No | Benign nevus |
| 21 | 1.7 | 1.61 | 2.12 | 2.02 | 2.45 | 2.42 | 2.42 | 2.63 | 1.83 | 1.88 | 2.11 | No | No | Borderline lesion |
| 22 | 1.74 | 1.85 | 1.74 | 1.74 | 2.45 | 2.57 | 2.06 | 2.04 | 1.52 | 1.60 | 1.93 | No | Yes (monoallelic) | Primary melanoma |
| 23 | 1.38 | 1.35 | 1.48 | 1.41 | 1.89 | 1.96 | 1.76 | 1.73 | 1.36 | 1.45 | 1.58 | Yes (monoallelic) | Yes (monoallelic) | Borderline lesion |
| 24 | 1.94 | 1.99 | 1.91 | 1.82 | 1.93 | 2.06 | 1.89 | 1.98 | 1.85 | 1.84 | 1.92 | No | Yes (monoallelic) | Primary melanoma |
| 25 | - | - | - | - | 2.22 | 2.11 | 1.40 | 1.38 | 1.01 | 1.04 | 1.53 | Yes (monoallelic) | Yes (monoallelic) | Borderline lesion |
| 26 | 0.88 | 0.89 | 1.48 | 1.51 | 1.79 | 1.57 | 1.37 | 1.44 | 1.73 | 1.79 | 1.44 | Yes (monoallelic) | Yes (monoallelic) | Borderline lesion |
| 27 | 1.19 | 1.19 | 0.46 | 0.48 | 0.43 | 0.44 | 0.39 | 0.39 | 0.42 | 0.42 | 0.58 | Yes (biallelic) | Yes (biallelic) | Metastatic melanoma |
| 28 | 1.26 | 1.26 | 1.12 | 1.09 | 1.03 | 1.03 | 1.15 | 1.15 | 1.03 | 0.98 | 1.11 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 29 | 1.85 | 2.04 | 1.36 | 1.36 | 1.57 | 1.51 | 1.47 | 1.45 | 1.42 | 1.43 | 1.55 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 30 | 1.30 | 1.26 | 1.59 | 1.62 | 1.65 | 1.62 | 1.81 | 1.75 | 1.47 | 1.42 | 1.55 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 31 | 1.21 | 1.22 | 1.50 | 1.54 | 1.56 | 1.49 | 1.58 | 1.59 | 1.30 | 1.23 | 1.42 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 32 | 1.38 | 1.41 | 1.29 | 1.70 | 1.76 | 1.74 | 1.73 | 1.66 | 1.34 | 1.35 | 1.54 | Yes (monoallelic) | Yes (monoallelic) | Borderline lesion |
| 33 | 1.48 | 1.41 | 1.39 | 1.41 | 1.38 | 1.33 | 1.30 | 1.30 | 2.15 | 2.11 | 1.53 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 34 | 2.43 | 2.40 | 1.34 | 1.27 | 1.92 | 1.71 | 1.49 | 1.48 | 1.32 | 1.36 | 1.67 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 35 | 2.57 | 2.69 | 1.36 | 1.27 | 1.67 | 1.82 | 1.29 | 1.32 | 1.28 | 1.21 | 1.65 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 36 | 0.32 | 0.32 | 0.31 | 0.31 | 0.44 | 0.48 | 0.38 | 0.38 | 0.40 | 0.43 | 0.38 | Yes (biallelic) | Yes (biallelic) | Metastatic melanoma |
| 37 | 0.59 | 0.58 | 0.49 | 0.48 | 0.80 | 0.76 | 0.55 | 0.55 | 0.66 | 0.67 | 0.61 | Yes (biallelic) | Yes (biallelic) | Metastatic melanoma |
| 38 | 0.62 | 0.64 | 0.59 | 0.60 | 0.86 | 0.86 | 0.67 | 0.67 | 0.56 | 0.62 | 0.67 | Yes (biallelic) | Yes (biallelic) | Metastatic melanoma |
| 39 | 1.62 | 1.62 | 1.42 | 1.39 | 1.71 | 1.74 | 1.56 | 1.59 | 1.53 | 1.51 | 1.57 | Yes (monoallelic) | Yes (monoallelic) | Metastatic melanoma |
| 40 | 1.32 | 1.44 | 1.32 | 1.31 | 1.36 | 1.40 | 1.36 | 1.38 | 1.18 | 1.17 | 1.32 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 41 | 1.62 | 1.59 | 1.10 | 0.99 | 1.14 | 1.05 | 1.18 | 1.16 | 1.21 | 1.19 | 1.22 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 42 | 0.74 | 0.65 | 0.46 | 0.42 | 0.46 | 0.49 | 0.41 | 0.37 | 0.38 | 0.39 | 0.48 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 43 | 0.32 | 0.31 | 0.37 | 0.39 | 0.36 | 0.37 | 0.34 | 0.33 | 0.39 | 0.38 | 0.36 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 44 | 0.47 | 0.45 | 0.82 | 0.79 | 0.79 | 0.83 | 0.60 | 0.61 | 1.00 | 0.95 | 0.73 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 45 | 2.70 | 2.50 | 1.18 | 1.09 | 1.55 | 1.71 | 0.85 | 0.65 | 0.67 | 0.65 | 1.36 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 46 | 1.69 | 1.85 | 1.58 | 1.49 | 2.20 | 2.07 | 1.65 | 1.58 | 1.51 | 1.57 | 1.72 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 47 | 2.61 | 2.55 | 1.93 | 1.86 | 1.78 | 1.80 | 1.79 | 1.80 | 1.63 | 1.60 | 1.94 | No | Yes (monoallelic) | Primary melanoma |
| 48 | 1.17 | 1.23 | 0.77 | 0.72 | 0.8 | 0.78 | 0.73 | 0.66 | 0.88 | 0.96 | 0.87 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 49 | 2.24 | 2.72 | 2.33 | 2.31 | 1.44 | 1.51 | 1.71 | 1.66 | 1.96 | 1.93 | 1.98 | No | Yes (monoallelic) | Primary melanoma |
| 50 | 1.53 | 1.39 | 1.44 | 1.34 | 1.49 | 1.4 | 1.43 | 1.41 | 1.42 | 1.34 | 1.42 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 51 | 0.776 | 0.798 | 0.901 | 0.88 | 0.97 | 0.98 | 0.95 | 0.98 | 1.07 | 1.04 | 0.93 | Yes (biallelic) | Yes (monoallelic) | Primary melanoma |
| 52 | 0.388 | 0.35 | 0.332 | 0.34 | 0.411 | 0.405 | 0.351 | 0.344 | 0.376 | 0.379 | 0.37 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 53 | 0.836 | 0.902 | 1.47 | 1.55 | 1.02 | 0.991 | 1.26 | 1.25 | 1.71 | 1.67 | 1.27 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 54 | 1.45 | 1.49 | 1.56 | 1.57 | 1.68 | 1.64 | 1.51 | 1.44 | 1.51 | 1.47 | 1.532 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 55 | 0.639 | 0.647 | 0.611 | 0.616 | 0.84 | 0.83 | 0.65 | 0.658 | 0.694 | 0.717 | 0.6902 | Yes (biallelic) | Yes (biallelic) | Primary melanoma |
| 56 | 1.45 | 1.49 | 1.79 | 1.8 | 1.77 | 1.74 | 1.68 | 1.66 | 1.65 | 1.67 | 1.67 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
| 57 | 1.68 | 1.64 | 1.5 | 1.4 | 1.12 | 1.16 | 1.14 | 1.14 | 1.24 | 1.3 | 1.33 | Yes (monoallelic) | Yes (monoallelic) | Primary melanoma |
Note: indicates that the ddPCR run was not performed due to limited amounts of tissue. Cases for which ddPCR and CMA had discordant results are bolded. Each data point represents the CDKN2A copy number output generated from a single ddPCR run. The following mean ddPCR cutoff values were used to generate the “CDKN2A Loss (ddPCR)” column, per receiver operator characteristic (ROC) curve analysis.
Mean ddPCR >1.73 = no. of CDKN2A loss.
1.11 <mean ddPCR ≤1.73 = monoallelic CDKN2A loss.
Mean ddPCR ≤1.11 = biallelic CDKN2A loss.