File S1 - Nanostring-Based Multigene Assay to Predict Recurrence for Gastric Cancer Patients after Surgery

1. Patient characteristics of study cohorts at each step (Table S1). a. Table S1. Patients characteristics. 2. Clinical and pathological characteristics of cases examined at each phase. 3. Detailed description of the discovery step using WG-DASL assay (step 1). a. Figure S1. QA of WG-DASL data. b. Table S2. Comparison of FISH and IHC results for HER2 status in gastric cancer in Step 1. c. Table S3. List of probes that are differentially expressed between HER2-positive and HER2- negative patient groups in Step 1. d. Table S4. List of all probes with univariate p-values<0.01 in Step 1. e. Figure S2. Gradient Lasso algorithm. f. Table S5. List of 26 probes included in the prediction model fitted by the whole data set (n = 432). g. Table S6. Multivariate Cox regression analysis results in gene discovery set (n = 432). 4. Design of focused gene expression assay using nCounter platform. a. Table S7. List of reference genes for nCounter assay. b. Figure S3. Correlation between hazard ratios of prognostic genes based on quantile normalization and self-normalization using WG-DASL assay. 5. nCounter assay and quality control. 6. Selection of cut-off for Gastric Cancer Prognostic Score (GCPS(Figure S4, S5, & S6). a. Figure S4. DFS according to each quartiles of GCPS-g1. b. Figure S5. Cut-point analysis for GCPS-g1. c. Figure S6. DFS according to optimized cut-point of GCPS-g1. 6. Distribution of GCPS between discovery set and validation set. a. Figure S7. Distribution of GCPS-g1 within the discovery and validation set. b. Figure S8. GCPS: intestinal vs diffuse type. 7. Testing of clinical utility of GCPS-g2 in patients treated with surgery only. a. Figure S9. DFS of stage II patients treated with chemoradiotherapy based on quartile of GCPS-g2. b. Figure S10. DFS of stage II patients treated with surgery alone based on quartile of GCPS-g2. c. Figure S11. Expression of adverse prognostic genes included in Gastric Cancer Prognostic Score according to tissue compartments (tumor versus stroma). Normalized expression levels are shown. d. Table S8. List of nCounter probes included in GCPS-g2. 8. Gastric cancer validation study protocol. a. Figure S12. Gastric cancer validation study protocol.
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