Table 3

Reproducibility of the gene-expression classifier 

First classificationSecond classificationThird classification
Sample # (ref. diagnosis —gender)TLDA card lotTLDA card #Tumour superclassProbability (%)Tumour superclassProbability (%)Tumour superclassProbability (%)
Sample #19
(liver —male)
11Liver*29.6Prostate29.2Gastro-oesophageal25.0
22Liver*48.2Lung—AC/LCC18.5Gastro-oesophageal17.1
3Liver*36.4Gastro-oesophageal25.7Prostate21.7
Prostate36.9Liver*27.6Gastro-oesophageal19.3
34Liver*39.5Gastro-oesophageal23.5Lung—AC/LCC20.8
6Liver*47.4Gastro-oesophageal19.8Lung—AC/LCC16.7
Liver*40.4Prostate26.4Gastro-oesophageal17.0
Liver*45.4Gastro-oesophageal19.9Prostate18.5
Liver*36.4Lung—AC/LCC29.4Gastro-oesophageal18.0
Sample #52 (ovary—female)11Ovary*49.0Uterus26.2Kidney8.6
22Ovary*47.6Uterus24.6Squamous CC11.6
3Ovary*45.3Uterus28.9Squamous CC9.7
Ovary*40.4Uterus23.1Melanoma20.2
34Ovary*47.2Uterus31.8Squamous CC4.8
7Ovary*45.3Uterus24.6Urinary (bladder)13.9
Ovary*51.1Uterus21.9Melanoma10.8
Ovary*48.9Uterus25.3Sarcoma9.7
Ovary*51.2Uterus25.3Sarcoma7.3
Sample #58 (thyroid—male)11Thyroid*53.4Thymus18.3Lymphoma12.2
22Thyroid*52.6Melanoma16.0Gastro-oesophageal15.2
34Thyroid*66.7Squamous CC/thymus8.6Lung—AC/LCC8.4
5Thyroid*59.9Thymus13.6Lymphoma10.3
Thyroid*45.3Gastro-oesophageal21.8Kidney16.8
8Thyroid*61.1Gastro-oesophageal11.5Thymus11.3
Thyroid*60.8Thymus14.2Lymphoma8.7
Thyroid*44.8Gastro-oesophageal20.8Melanoma18.3
Thyroid*51.3Gastro-oesophageal18.6Squamous CC14.0
Sample #56 (kidney—female)11Kidney*43.1Ovary21.7Uterus19.0
22Ovary40.7Uterus24.0Kidney*19.1
34Kidney*35.9Uterus24.3Ovary23.6
5Kidney*45.3Ovary20.5Uterus17.9
Kidney*52.5Uterus15.8Ovary15.5
9Kidney*47.8Ovary18.7Squamous CC17.3
Squamous CC28.7Ovary28.4Kidney*/breast26.7
Squamous CC41.4Ovary21.8Urinary (bladder)20.6
Ovary36.9Kidney*23.9Squamous CC22.9
  • *Indicates the correct classifications. See also online supplementary table S6.

  • AC, adenocarcinoma; CC, cell carcinoma; LCC, large cell carcinoma;  TLDA card lot, different lots of low-density array cards customisation provided by the manufacturer.