Table 3.
Reproducibility of the gene-expression classifier
| First classification | Second classification | Third classification | ||||||
| Sample # (ref. diagnosis —gender) | TLDA card lot | TLDA card # | Tumour superclass | Probability (%) | Tumour superclass | Probability (%) | Tumour superclass | Probability (%) |
| Sample #19 (liver —male) |
1 | 1 | Liver* | 29.6 | Prostate | 29.2 | Gastro-oesophageal | 25.0 |
| 2 | 2 | Liver* | 48.2 | Lung—AC/LCC | 18.5 | Gastro-oesophageal | 17.1 | |
| 3 | Liver* | 36.4 | Gastro-oesophageal | 25.7 | Prostate | 21.7 | ||
| Prostate | 36.9 | Liver* | 27.6 | Gastro-oesophageal | 19.3 | |||
| 3 | 4 | Liver* | 39.5 | Gastro-oesophageal | 23.5 | Lung—AC/LCC | 20.8 | |
| 6 | Liver* | 47.4 | Gastro-oesophageal | 19.8 | Lung—AC/LCC | 16.7 | ||
| Liver* | 40.4 | Prostate | 26.4 | Gastro-oesophageal | 17.0 | |||
| Liver* | 45.4 | Gastro-oesophageal | 19.9 | Prostate | 18.5 | |||
| Liver* | 36.4 | Lung—AC/LCC | 29.4 | Gastro-oesophageal | 18.0 | |||
| Sample #52 (ovary—female) | 1 | 1 | Ovary* | 49.0 | Uterus | 26.2 | Kidney | 8.6 |
| 2 | 2 | Ovary* | 47.6 | Uterus | 24.6 | Squamous CC | 11.6 | |
| 3 | Ovary* | 45.3 | Uterus | 28.9 | Squamous CC | 9.7 | ||
| Ovary* | 40.4 | Uterus | 23.1 | Melanoma | 20.2 | |||
| 3 | 4 | Ovary* | 47.2 | Uterus | 31.8 | Squamous CC | 4.8 | |
| 7 | Ovary* | 45.3 | Uterus | 24.6 | Urinary (bladder) | 13.9 | ||
| Ovary* | 51.1 | Uterus | 21.9 | Melanoma | 10.8 | |||
| Ovary* | 48.9 | Uterus | 25.3 | Sarcoma | 9.7 | |||
| Ovary* | 51.2 | Uterus | 25.3 | Sarcoma | 7.3 | |||
| Sample #58 (thyroid—male) | 1 | 1 | Thyroid* | 53.4 | Thymus | 18.3 | Lymphoma | 12.2 |
| 2 | 2 | Thyroid* | 52.6 | Melanoma | 16.0 | Gastro-oesophageal | 15.2 | |
| 3 | 4 | Thyroid* | 66.7 | Squamous CC/thymus | 8.6 | Lung—AC/LCC | 8.4 | |
| 5 | Thyroid* | 59.9 | Thymus | 13.6 | Lymphoma | 10.3 | ||
| Thyroid* | 45.3 | Gastro-oesophageal | 21.8 | Kidney | 16.8 | |||
| 8 | Thyroid* | 61.1 | Gastro-oesophageal | 11.5 | Thymus | 11.3 | ||
| Thyroid* | 60.8 | Thymus | 14.2 | Lymphoma | 8.7 | |||
| Thyroid* | 44.8 | Gastro-oesophageal | 20.8 | Melanoma | 18.3 | |||
| Thyroid* | 51.3 | Gastro-oesophageal | 18.6 | Squamous CC | 14.0 | |||
| Sample #56 (kidney—female) | 1 | 1 | Kidney* | 43.1 | Ovary | 21.7 | Uterus | 19.0 |
| 2 | 2 | Ovary | 40.7 | Uterus | 24.0 | Kidney* | 19.1 | |
| 3 | 4 | Kidney* | 35.9 | Uterus | 24.3 | Ovary | 23.6 | |
| 5 | Kidney* | 45.3 | Ovary | 20.5 | Uterus | 17.9 | ||
| Kidney* | 52.5 | Uterus | 15.8 | Ovary | 15.5 | |||
| 9 | Kidney* | 47.8 | Ovary | 18.7 | Squamous CC | 17.3 | ||
| Squamous CC | 28.7 | Ovary | 28.4 | Kidney*/breast | 26.7 | |||
| Squamous CC | 41.4 | Ovary | 21.8 | Urinary (bladder) | 20.6 | |||
| Ovary | 36.9 | Kidney* | 23.9 | Squamous CC | 22.9 | |||
*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.