Table 2.
Chronic lymphocytic leukemia: REMARK-like profile of the analysis performed on the dataset
| a) Patients, treatment and variables | ||||
|---|---|---|---|---|
| Study and marker | Remarks | |||
| Marker | OS = 8-probe-set gene-expression signature | |||
| Further variables | v1 = age, v2 = sex, v3 = FISH, v4 = IGVH | |||
| Reference | Herold et al. (2011) | |||
| Source of the data | GEO (reference: GSE22762) | |||
| Patients | n | Remarks | ||
| Assessed for eligibility | 151 | Disease: chronic lymphocytic leukemia | ||
| Patient source: Department of Internal Medicine III, University of Munich (2001 - 2005) | ||||
| Training set | Excluded | 0 | ||
| Included | 151 | Criteria: sample availability | ||
| Gene expression profiling: 44 Affymetrix HG-U133 A&B microarrays, 107 Affymetrix HG-U133 plus 2.0 microarrays | ||||
| With outcome events | 41 | Overall survival | ||
| Assessed for eligibility | 149 | Disease: chronic lymphocytic leukemia | ||
| Patient source: Department of Internal Medicine III, University of Munich (2005 - 2007) | ||||
| Validation set | Excluded | 18 | Due to missing clinical information | |
| Included | 131 | Criteria: sample availability | ||
| Gene expression profiling: 149 qRT-PCR (only selected genes) | ||||
| With outcome events | 40 | Overall survival | ||
| Relevant differences between training and validation sets | ||||
| Data source | Same institution, different time (see above) | |||
| Measurement of gene expressions | Affymetrix HG-U133 vs. TaqMan LDA (see text) | |||
| Survival rate | Lower in the validation set (see Figure 4) | |||
| b) Statistical analyses of survival outcomes | ||||
| Analysis | n | e | Variables considered | Results/remarks |
| F: preliminary analysis (separately on training and validation sets) | ||||
| F1: univariate | 151 | 41 | v1 to v4 | Kaplan-Meier curves (Figure 3) |
| 131 | 40 | |||
| G: Multivariate testing of the omics score in the validation data (only validation set involved) | ||||
| G1: significance | 131 | 40 | OS, v1 to v4 | Multivariate Cox model (Table 5) |
| H: Comparison of the predictive accuracy of clinical and combined models through cross-validation in the validation data (only validation set involved) | ||||
| H1: Overall prediction | 131 | 40 | OS, v1 to v4 | Prediction error curves based on cross-validation (Figure 11) |
| Integrated Brier score based on cross-validation (text) | ||||