Table 3A.
Comparison of qPCR validation in gastric and colorectal cancers.
| RTR |
TCGA |
|||||
|---|---|---|---|---|---|---|
| Tumor | Adjacent normal | Cases | Tumor | Adjacent normal | Cases | |
| Gastric (N = 21) | Gastric (N = 85) | |||||
| Helicobacter pylori | positive | positive | 1 | positive | positive | 4 |
| positive | negative | 1 | positive | negative | 3 | |
| RTR: P-value = 1 | negative | positive | 1 | negative | positive | 19 |
| TCGA: P-value = 0.001 | negative | negative | 18 | negative | negative | 59 |
| Fusobacterium nucleatum | positive | positive | 2 | positive | positive | 0 |
| positive | negative | 1 | positive | negative | 8 | |
| RTR: P-value = 1 | negative | positive | 0 | negative | positive | 0 |
| TCGA: P-value = 0.01 | negative | negative | 18 | negative | negative | 77 |
| Selenomonas sputigena (+) | positive | positive | 0 | positive | positive | 3 |
| positive | negative | 2 | positive | negative | 12 | |
| RTR: P-value = 0.479 | negative | positive | 0 | negative | positive | 5 |
| TCGA: P-value = 0.146 | negative | negative | 19 | negative | negative | 65 |
| Colorectal (N = 63) | Colorectal (N = 106) | |||||
| Bacteroides vulgatus | positive | positive | 3 | positive | positive | 62 |
| positive | negative | 3 | positive | negative | 6 | |
| RTR: P-value = 1 | negative | positive | 2 | negative | positive | 18 |
| TCGA: P-value = 0.025 | negative | negative | 55 | negative | negative | 20 |
| Fusobacterium nucleatum | positive | positive | 1 | positive | positive | 5 |
| positive | negative | 10 | positive | negative | 15 | |
| RTR: P-value = 0.043 | negative | positive | 2 | negative | positive | 4 |
| TCGA: P-value = 0.021 | negative | negative | 50 | negative | negative | 82 |
Bacteria presence counts for each taxa examined in tumor and adjacent normal gastric and colorectal cances in TCGA cohorts versus Hawaii RTR. Selenomonas sputigena and Fusobacterium nucleatum were found to co-occur in Hawaii RTR gastric cases in similar patterns to those observed in TCGA gastric cancer cohort. Percent positivity in White vs non-White for Fusobacterium nucleatum was similar in TCGA and Hawaii RTR (17% vs 18% of respectively), whereas percent positivity for Bacteroides vulgatus was strikingly different (64% vs 5% respectively). Possible explanation for differences observed could be due to other population characteristics (Table 3B), FFPE sample degradation and sample size. N = paired cases; P values were from McNemar’s test. Null hypothesis: there is no difference between tumor and adjacent normal due to specific microbial presence.