Table 1.
Comparison of prognostic gene expression studies*
| Protocols for patient selection and tissue handling |
Model validation and presentation of results |
Addressing medical utility |
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| First author, year (reference) | Training sample size | Validation sample size | Platform | Sample size planning | Appropriate patient selection | Description of patient characteristics | Tissue handling | No resubstitution statistics for the training set | Validation results on external data | Complete model specification | Statistically significant for validation in stages IA and IB | Statistically significant for validation in stage II | Statistically significant improvement over standard risk factors |
| Boutros, 2009 (9) | 147 (92 stage I, 38 stage II, 17 stage III) | 589 (409 stage I, 99 stage II, 81 stage III) | RT-qPCR | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| Roepman, 2009 (10) | 103 (72 stage I, 31 stage II) | 69 (45 stage I, 24 stage II) | Microarray | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 |
| Shedden, 2008 (11) | 256 (160 stage I, 49 stage II, 47 stage III) | 186 (119 stage I, 46 stage II, 21 stage III) | Microarray | 1 | 0 | 1 | 0 | 1 | 1 | 0† | 0 | 0 | 0 |
| Sun, 2008 (12) | 86 (ADC: 67 stage I, 19 stage III) 129 (SCC: 73 stage I, 33 stage II, 23 stage III) | 175 (129 stage I, 32 stage II, 14 stage III) | Microarray | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 0 |
| Skrzypski, 2008 (13) | 66 (SCC: 42 stage I, 22 stage II, 2 stage III) | 26 (22 stage I, 4 stage II) | RT-qPCR | 0 | 0 | 1 | 1 | 0 | 1 | 1 | 0 | 0 | 0 |
| Raz, 2008 (14) | 107 (ADC: 70 stage I, 12 stage II, 25 stage III) | No separate validation set | RT-qPCR | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
| Chen, 2007 (15) | 101 (59 stage I or II, 42 stage III) | 146 (109 stage I or II, 37 stage III) | RT-qPCR | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 | 0 | 0 |
| Lau, 2007 (16) | 147 (92 stage I, 38 stage II, 17 stage III) | 216 (143 stage I, 42 stage II, 15 stage III, 16 stage IV) | RT-qPCR | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 |
| Larsen, 2007 (17) | 51 (SCC: 29 stage I, 15 stage II, 7 stage III) | 58 (SCC: 30 stage I, 14 stage II, 14 stage III) | Microarray | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| Larsen, 2007 (18) | 48 (ADC: 46 stage I, 2 stage II) | 95 (ADC: 70 stage I, 17 stage II, 8 stage III) | Microarray | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 0 |
| Guo, 2006 (19) | 86 (ADC: 67 stage I, 19 stage III) | 84 (ADC: 62 stage I, 14 stage II, 8 stage III) | Microarray | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
| Potti, 2006 (20) | 89 (69 stage I, 14 stage II, 6 stage III) | 109 (70 stage I, 22 stage II, 17 stage III) | Microarray | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 1‡ | 0 | 0 |
| Lu, 2006 (21) | 197 (85 stage I, 112 stage IB) | 120 (55 stage IA, 65 stage IB) | Microarray | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 |
| Raponi, 2006 (22) | 129 (SCC: 73 stage I, 33 stage II, 23 stage III) | 36 (SCC: 25 stage I, 9 stage II, 1 stage III, 1 stage IV) | Microarray | 0 | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
| Tomida, 2004 (23) | 50 (23 stage I, 11 stage II, 16 stage III) | 6 (stage information not available) | Microarray | 0 | 0 | 0 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
| Beer, 2002 (24) | 86 (ADC: 67 stage I, 19 stage III) | 84 (ADC: 62 stage I, 14 stage II, 8 stage III) | Microarray | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | 0 |
| Total No. of studies | 1 | 3 | 12 | 9 | 7 | 15 | 3 | 2 | 1 | 0 | |||
*
A score of 1 means that the study complied with the specific evaluation criterion, and a score of 0 means that it did not. ADC = adenocarcinoma; RT-qPCR = real-time quantitative polymerase chain reaction; SCC = squamous cell carcinoma.
†
For method A reported in the article.
‡
Reported only for stage IA.