RefDB—10-fold cross-validation (4429 samples) | Metastatic FFPE sample set (real-time PCR vs RefDB—105 samples) | |||||||||||
Sensitivity | Specificity | Sensitivity | Specificity | |||||||||
Tumour superclass | Ratio | Positive % agreement | 95% CI | Ratio | Negative % agreement | 95% Cl | Ratio | Positive % agreement | 95% Cl | Ratio | Negative % agreement | 95% Cl |
Adrenal | 64/68 | 94.12 | 85.62 to 98.37 | 4357/4361 | 99.91 | 99.77 to 99.98 | 0/4 | 0.00 | 0.00 to 0.00 | 97/101 | 96.04 | 90.17 to 98.91 |
Breast | 104/142 | 73.24 | 65.17 to 80.32 | 4249/4287 | 99.11 | 98.79 to 99.37 | 12/12 | 100.00 | 73.53 to 100.00 | 93/93 | 100.00 | 96.52 to 100.00 |
Gastro-oesophageal | 61/78 | 78.21 | 67.41 to 86.76 | 4334/4351 | 99.61 | 99.37 to 99.77 | 11/14 | 78.57 | 49.20 to 95.34 | 88/91 | 96.70 | 90.67 to 99.31 |
Germ cell non-seminomatous | 121/133 | 90.98 | 84.77 to 95.25 | 4284/4296 | 99.72 | 99.51 to 99.86 | – | – | – | – | – | – |
Germ cell seminomatous | 34/42 | 80.95 | 65.88 to 91.40 | 4382/4387 | 99.89 | 99.73 to 99.96 | – | – | – | – | – | – |
Gatrointestinal stromal tumour | 53/54 | 98.15 | 90.11 to 99.95 | 4374/4375 | 99.98 | 99.87 to 100.00 | 0/1 | 0.00 | 0.00 to 0.00 | 103/104 | 99.04 | 94.76 to 99.98 |
Head and neck (salivary gland) | 14/22 | 63.64 | 40.66 to 82.80 | 4399/4407 | 99.82 | 99.64 to 99.92 | 0/1 | 0.00 | 0.00 to 0.00 | 103/104 | 99.04 | 94.76 to 99.98 |
Intestine (colorectal adenocarcinoma) | 210/212 | 99.06 | 96.63 to 99.89 | 4215/4217 | 99.95 | 99.83 to 99.99 | 13/13 | 100.00 | 75.29 to 100.00 | 92/92 | 100.00 | 96.07 to 100.00 |
Kidney | 346/360 | 96.11 | 93.56 to 97.86 | 4055/4069 | 99.66 | 99.42 to 99.81 | 3/4 | 75.00 | 19.41 to 99.37 | 100/101 | 99.01 | 94.61 to 99.98 |
Liver | 120/139 | 86.33 | 79.48 to 91.57 | 4271/4290 | 99.56 | 99.31 to 99.73 | 1/1 | 100.00 | 2.50 to 100.00 | 104/104 | 100.00 | 96.52 to 100.00 |
Lung adenocarcinoma/large cell carcinoma | 302/327 | 92.35 | 88.92 to 94.99 | 4077/4102 | 99.39 | 99.10 to 99.61 | – | – | – | – | – | – |
Lung small cell carcinoma | 27/54 | 50.00 | 36.08 to 63.92 | 4348/4375 | 99.38 | 99.10 to 99.59 | – | – | – | – | – | – |
Lymphoma | 136/151 | 90.07 | 84.15 to 94.33 | 4263/4278 | 99.65 | 99.42 to 99.80 | 2/2 | 100.00 | 15.81 to 100.00 | 103/103 | 100.00 | 96.48 to 100.00 |
Melanoma | 71/85 | 83.53 | 73.91 to 90.69 | 4330/4344 | 99.68 | 99.46 to 99.82 | 12/12 | 100.00 | 73.53 to 100.00 | 93/93 | 100.00 | 96.11 to 100.00 |
Mesothelioma | 90/102 | 88.24 | 80.35 to 93.77 | 4315/4327 | 99.72 | 99.52 to 99.86 | – | – | – | – | – | – |
Neuroendocrine | 326/334 | 97.60 | 95.34 to 98.96 | 4087/4095 | 99.80 | 99.62 to 99.92 | 1/2 | 50.00 | 1.26 to 98.74 | 102/103 | 99.03 | 94.71 to 99.98 |
Ovary | 519/626 | 82.91 | 79.73 to 85.77 | 3696/3803 | 97.19 | 96.61 to 97.69 | 4/4 | 100.00 | 39.76 to 100.00 | 101/101 | 100.00 | 96.41 to 100.00 |
Pancreas | 79/107 | 73.83 | 64.45 to 81.85 | 4294/4322 | 99.35 | 99.07 to 99.57 | 0/2 | 0.00 | 0.00 to 0.00 | 101/103 | 98.06 | 93.16 to 99.76 |
Prostate | 112/119 | 94.12 | 88.26 to 97.60 | 4303/4310 | 99.84 | 99.67 to 99.93 | 1/1 | 100.00 | 2.50 to 100.00 | 104/104 | 100.00 | 96.52 to 100.00 |
Sarcoma | 105/130 | 80.77 | 72.93 to 87.15 | 4274/4299 | 99.42 | 99.14 to 99.62 | 8/10 | 80.00 | 44.39 to 97.48 | 93/95 | 97.89 | 92.60 to 99.74 |
Squamous cell carcinomas | 422/460 | 91.74 | 88.84 to 94.09 | 3931/3969 | 99.04 | 98.69 to 99.32 | 13/14 | 92.86 | 66.13 to 99.82 | 90/91 | 98.90 | 94.03 to 99.97 |
Thymus | 34/36 | 94.44 | 81.34 to 99.32 | 4391/4393 | 99.95 | 99.84 to 99.99 | – | – | – | – | – | – |
Thyroid | 205/230 | 89.13 | 84.37 to 92.84 | 4174/4199 | 99.40 | 99.12 to 99.61 | 4/5 | 80.00 | 28.36 to 99.49 | 99/100 | 99.00 | 94.55 to 99.98 |
Urinary (bladder) | 130/144 | 90.28 | 84.23 to 94.58 | 4271/4285 | 99.67 | 99.45 to 99.82 | – | – | – | – | – | – |
Uterus | 147/274 | 53.65 | 47.55 to 59.67 | 4028/4155 | 96.94 | 96.37 to 97.45 | 3/3 | 100.00 | 29.24 to 100.00 | 102/102 | 100.00 | 96.45 to 100.00 |
Overall | 3835/4429 | 86.59 | 85.55 to 87.58 | NA | 99.43 | 99.18 to 99.60 | 88/105 | 83.81 | 75.35 to 90.28 | NA | 99.04 | 94.73 to 99.87 |
Sensitivity and specificity of the gene-expression classifier on the RefDB itself by 10-fold cross-validation and on the metastatic FFPE samples from the validation set. See also at online supplementary tables S3, S4, S5 and S6.
FFPE, formalin-fixed, paraffin-embedded; NA, not available; RefDB, Reference Database.