Table 2

Algorithm performance 

RefDB—10-fold cross-validation (4429 samples)Metastatic FFPE sample set (real-time PCR vs RefDB—105 samples)
SensitivitySpecificitySensitivitySpecificity
Tumour superclassRatioPositive % agreement 95% CIRatioNegative % agreement95% ClRatioPositive % agreement95% ClRatioNegative % agreement95% Cl
Adrenal64/6894.1285.62 to 98.374357/436199.9199.77 to 99.980/40.000.00 to 0.0097/10196.0490.17 to 98.91
Breast104/14273.2465.17 to 80.324249/428799.1198.79 to 99.3712/12100.0073.53 to 100.0093/93100.0096.52 to 100.00
Gastro-oesophageal61/7878.2167.41 to 86.764334/435199.6199.37 to 99.7711/1478.5749.20 to 95.3488/9196.7090.67 to 99.31
Germ cell non-seminomatous121/13390.9884.77 to 95.254284/429699.7299.51 to 99.86
Germ cell seminomatous34/4280.9565.88 to 91.404382/438799.8999.73 to 99.96
Gatrointestinal stromal tumour53/5498.1590.11 to 99.954374/437599.9899.87 to 100.000/10.000.00 to 0.00103/10499.0494.76 to 99.98
Head and neck (salivary gland)14/2263.6440.66 to 82.804399/440799.8299.64 to 99.920/10.000.00 to 0.00103/10499.0494.76 to 99.98
Intestine (colorectal adenocarcinoma)210/21299.0696.63 to 99.894215/421799.9599.83 to 99.9913/13100.0075.29 to 100.0092/92100.0096.07 to 100.00
Kidney346/36096.1193.56 to 97.864055/406999.6699.42 to 99.813/475.0019.41 to 99.37100/10199.0194.61 to 99.98
Liver120/13986.3379.48 to 91.574271/429099.5699.31 to 99.731/1100.002.50 to 100.00104/104100.0096.52 to 100.00
Lung adenocarcinoma/large cell carcinoma302/32792.3588.92 to 94.994077/410299.3999.10 to 99.61
Lung small cell carcinoma27/5450.0036.08 to 63.924348/437599.3899.10 to 99.59
Lymphoma136/15190.0784.15 to 94.334263/427899.6599.42 to 99.802/2100.0015.81 to 100.00103/103100.0096.48 to 100.00
Melanoma71/8583.5373.91 to 90.694330/434499.6899.46 to 99.8212/12100.0073.53 to 100.0093/93100.0096.11 to 100.00
Mesothelioma90/10288.2480.35 to 93.774315/432799.7299.52 to 99.86
Neuroendocrine326/33497.6095.34 to 98.964087/409599.8099.62 to 99.921/250.001.26 to 98.74102/10399.0394.71 to 99.98
Ovary519/62682.9179.73 to 85.773696/380397.1996.61 to 97.694/4100.0039.76 to 100.00101/101100.0096.41 to 100.00
Pancreas79/10773.8364.45 to 81.854294/432299.3599.07 to 99.570/20.000.00 to 0.00101/10398.0693.16 to 99.76
Prostate112/11994.1288.26 to 97.604303/431099.8499.67 to 99.931/1100.002.50 to 100.00104/104100.0096.52 to 100.00
Sarcoma105/13080.7772.93 to 87.154274/429999.4299.14 to 99.628/1080.0044.39 to 97.4893/9597.8992.60 to 99.74
Squamous cell carcinomas422/46091.7488.84 to 94.093931/396999.0498.69 to 99.3213/1492.8666.13 to 99.8290/9198.9094.03 to 99.97
Thymus34/3694.4481.34 to 99.324391/439399.9599.84 to 99.99
Thyroid205/23089.1384.37 to 92.844174/419999.4099.12 to 99.614/580.0028.36 to 99.4999/10099.0094.55 to 99.98
Urinary (bladder)130/14490.2884.23 to 94.584271/428599.6799.45 to 99.82
Uterus147/27453.6547.55 to 59.674028/415596.9496.37 to 97.453/3100.0029.24 to 100.00102/102100.0096.45 to 100.00
Overall3835/442986.5985.55 to 87.58NA99.4399.18 to 99.6088/10583.8175.35 to 90.28NA99.0494.73 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.