Table 1.
Tumor Samples Used in the Study
| Discovery |
Training |
Validation | |||
|---|---|---|---|---|---|
| Study phase Cohort | Microarray | qRT-PCR | Full training set | Threshold delineation | Validation set |
| Figure # | Fig. 1ABC | Fig. 1D | Fig. 2AB | Fig. 3ABC | Fig. 4 |
| Samples (new samples) | 104 | 65 (51 new) | 145 (88 new) | 39 (no new) | 63 (all new) |
| Sample type (total N) | |||||
| Mesothelioma (47) | 7 | 22 (15) | 32 (11) | 16 | 14 |
| Epithelioid (29) | 4 | 18 (14) | 21 (3) | 8 | 8 |
| Sarcomatoid (6) | 3 | 3 (0) | 4 (1) | 3 | 2 |
| Biphasic (mixed) (6) | — | 1 (1) | 1 (1) | 1 | 4 |
| Unspecified (6) | — | — | 6 (6) | 4 | — |
| Carcinoma (259) | 97 | 43 (36) | 113 (77) | 23 | 49 |
| Bladder (15) | — | 2 (2) | 14 (13) | 2 | — |
| Breast (26) | 4 | 4 (4) | 9 (9) | 2 | 9* |
| Colon (36) | 17 | 2 (1) | 9 (5) | 2 | 13* |
| Endometrium (12) | 9 | — | — | — | 3* |
| Esophagus (11) | 11 | — | — | — | — |
| Kidney (RCC) (33) | 16 | 4 (2) | 18 (10) | 4 | 5* |
| Kidney (TCC) (1) | — | — | — | — | 1* |
| Liver (HCC) (10) | — | — | 10 (10) | 2 | — |
| Lung (76) | 15 | 25 (25) | 35 (20) | 8 | 16 |
| Ovary (19) | 10 | 4 (1) | 10 (6) | 1 | 2* |
| Pancreas (11) | 6 | 2 (1) | 8 (4) | 2 | — |
| Prostate (3) | 3 | — | — | — | — |
| Stomach (6) | 6 | — | — | — | — |
Table 1 shows the number of tumor samples from different origins or mesotheliomas used in each phase of the study. For the third and fourth columns, the numbers in parentheses indicate the number of new samples that were not used in previous phases. The threshold delineation cohort (fifth column) included only previously used samples, and the validation set (last column) included only new samples. The rows titled Samples, Mesothelioma, and Carcinoma (in bold) indicate the total number of samples used in each of these sets. The samples that were repeated in the threshold delineation cohort were chosen to represent the full range of signals in the full training set (see Results). All other samples that were used in more than one cohort were selected randomly based on the amount of RNA left from the sample. In the first column, the numbers in parentheses indicate the total number of samples of this type.
The validation set included only samples of tumors that were located in the lung and pleura: primary tumors included lung adenocarcinoma and MPM; lung metastases included RCC, TCC, endometrial, breast, and colonic carcinomas; and pleural metastases were from adenocarcinomas of the breast and ovary.