Table 1 Clinicopathological patient characteristics of the gastric cancer test cohort consisting of nine men (mean age 68 years; range 50–85 years)
From: Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine
Case | Case #1 | Case #2 | Case #3 | Case #4 | Case #5 | Case #6 | Case #7 | Case #8 | Case #9 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Localization | Cardia | Cardia | Antrum/Corpus | Antrum | Fundus | Cardia | Cardia | Cardia | Antrum | |||||||||
Neoadjuvant treatment | Yes | Yes | No | No | No | No | Yes | No | Yes | |||||||||
Laurén phenotype | Intestinal | Mixed | Mixed | Mixed | Diffuse | Intestinal | Intestinal | Mixed | Diffuse | |||||||||
Tumor size [cm] | 3.8 | 4.4 | 12.9 | 4.0 | 4.8 | 4.1 | 6.7 | 6.2 | 3.7 | |||||||||
Epstein-Barr virus status | Negative | Negative | Negative | Negative | Negative | Negative | Negative | Negative | Negative | |||||||||
Microsatellite status | MSS | MSS | MSS | MSS | MSS | MSI | MSS | MSS | MSS | |||||||||
HER2 status | Negative | Negative | Positive | Positive | Negative | Negative | Negative | Negative | Negative | |||||||||
pT category | ypT3 | ypT3 | pT3 | pT3 | pT3 | pT3 | ypT3 | pT2 | ypT3 | |||||||||
pN category | ypN1 (1/29) | ypN1 (2/51) | pN3a (13/17) | pN2 (3/19) | pN3b (28/46) | pN0Â (0/19) | ypN0Â (0/12) | pN0 (0/25) | ypN2 (4/22) | |||||||||
pM category | X | X | X | X | X | X | X | X | X | |||||||||
Grading | n.a. | n.a. | G3 | G3 | G3 | G2 | n.a. | n.a. | n.a. | |||||||||
Number of tumor samples sequenced | 4 | 3 | 6 | 5 | 10 | 5 | 4 | 6 | 5 | |||||||||
Non-synonymous mutations (total valid) | 184 | 373 | 714 | 348 | 425 | 3111 | 181 | 369 | 242 | |||||||||
Copy number variations (number of genes) | 6 | 22 | 65 | 11 | 98 | 3 | 5 | 1 | 0 | |||||||||
Tumor sample | Number/percentage of non-synonymous mutations present only in a single sample | |||||||||||||||||
 1 sample | 71 | (38.6%) | 159 | (42.6%) | 350 | (49.0%) | 133 | (38.2%) | 211 | (49.6%) | 1262 | (40.6%) | 112 | (61.9%) | 235 | (63.7%) | 140 | (57.8%) |
|  | Number/percentage of same non-synonymous mutations present in ≥ 2 samples | |||||||||||||||||
 2 samples | 25 | (13.6%) | 59 | (15.8%) | 78 | (10.9%) | 15 | (4.3%) | 29 | (6.8%) | 360 | (11.6%) | 24 | (13.3%) | 25 | (6.8%) | 30 | (12.4%) |
 3 samples | 58 | (31.5%) | 155 | (41.6%) | 31 | (4.3%) | 11 | (3.2%) | 27 | (6.4%) | 180 | (5.8%) | 18 | (9.9%) | 9 | (2.4%) | 23 | (9.5%) |
 4 samples | 30 | (16.3%) |  |  | 8 | (1.1%) | 26 | (7.5%) | 17 | (4.0%) | 148 | (4.8%) | 27 | (14.9%) | 14 | (3.8%) | 28 | (11.6%) |
 5 samples |  |  |  |  | 25 | (3.5%) | 163 | (46.8%) | 13 | (3.1%) | 1161 | (37.3%) |  |  | 17 | (4.6%) | 21 | (8.7%) |
 6 samples |  |  |  |  | 222 | (31.1%) |  |  | 18 | (4.2%) |  |  |  |  | 69 | (18.7%) |  |  |
 7 samples |  |  |  |  |  |  |  |  | 24 | (5.6%) |  |  |  |  |  |  |  |  |
 8 samples |  |  |  |  |  |  |  |  | 15 | (3.5%) |  |  |  |  |  |  |  |  |
 9 samples |  |  |  |  |  |  |  |  | 25 | (5.9%) |  |  |  |  |  |  |  |  |
 10 samples |  |  |  |  |  |  |  |  | 46 | (10.8%) |  |  |  |  |  |  |  |  |
Per patient | Clonality | |||||||||||||||||
 Clonal (non-synonymous) | 2 | (2.0%) | 80 | (50.0%) | 62 | (23.9%) | 1 | (0.9%) | 1 | (1.3%) | 0 | (0%) | 0 | (0%) | 0 | (0%) | 0 | (0%) |
 Subclonal (non-synonymous) | 98 | (98.0%) | 80 | (50.0%) | 197 | (76.1%) | 110 | (98.2%) | 76 | (98.7%) | 1083 | (100%) | 48 | (100%) | 81 | (100%) | 106 | (100%) |
 Not assessable (non-synonymous) | 0 | (0%) | 0 | (0%) | 0 | (0%) | 1 | (0.9%) | 0 | (0%) | 0 | (0%) | 0 | (0%) | 0 | (0%) | 0 | (0%) |
Total (non-synonymous) | 100 | Â | 160 | Â | 259 | Â | 112 | Â | 77 | Â | 1083 | Â | 48 | Â | 81 | Â | 106 | Â |
Clonal (synonymous) | 1 | (6.0%) | 32 | (15.9%) | 26 | (10.1%) | 2 | (1.3%) | 1 | (5.7%) | 0 | (0%) | 1 | (0.4%) | 0 | (0%) | 0 | (0%) |
Subclonal (synonymous) | 159 | (94.0%) | 168 | (83.6%) | 231 | (89.9%) | 157 | (98.7%) | 174 | (99.4%) | 825 | (97.6%) | 229 | (99.6%) | 168 | (100%) | 257 | (99.6%) |
Not assessable (synonymous) | 0 | (0%) | 1 | (4.9%) | 0 | (0%) | 0 | (0%) | 0 | (0%) | 2 | (2.4%) | 0 | (0%) | 0 | (0%) | 1 | (0.4%) |
Total (synonymous) | 160 | Â | 201 | Â | 257 | Â | 159 | Â | 175 | Â | 827 | Â | 230 | Â | 168 | Â | 258 | Â |