Table 1. Main features of each dataset included in the analyses.
| Variable | Level | LCE-project datasets | ALL LCE-project datasets N=2575 | TRACERx dataset | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| TCGA LUAD N=515 | TCGA LUSC N=501 | ROUSSEAUX N=293 | SATO N=275 | SCHABATH N=442 | SHEDDEN N=442 | NORO N=107 | ||||
| Type of molecular data | Single-region bulk RNA-sequencing | Multiregion bulk RNA-seq Multiregion WES | ||||||||
| Analyses performed | Cell-types deconvolution, T-cells phenotype characterization, TIDE-score assessment,GSEA of MSigDB and hypoxia signatures | Cell types deconvolution, TCR repertoire, HLA-LOH, clonal and subclonal TMB, antigen presentation machinery alterations | ||||||||
| Gender, N (%) | Male | 238 (46.2) | 371 (74.1) | 250 (85.3) | 148 (53.8) | 202 (45.7) | 223 (50.5) | 96 (89.7) | 1528 (59.3) | 62 (62) |
| female | 277 (53.8) | 130 (25.9) | 43 (14.7) | 127 (46.2) | 240 (54.3) | 219 (49.5) | 11 (10.3) | 1047 (40.7) | 38 (38) | |
| Age(years), N (%) | ≤60 | 157 (30.5) | 108 (21.6) | 130 (44.4) | 91 (33.1) | 70 (15.8) | 147 (33.3) | 29 (27.1) | 732 (28.4) | Median: 68 |
| 61-70 | 174 (33.8) | 195 (38.9) | 96 (32.8) | 91 (33.1) | 152 (34.4) | 164 (37.1) | 62 (57.9) | 934 (36.3) | Range: 34-85 | |
| >70 | 165 (32.0) | 189 (37.7) | 66 (22.5) | 87 (31.6) | 199 (45.0) | 131 (29.6) | 16 (15.0) | 853 (33.1) | ||
| Unknown | 19 (3.7) | 9 (1.8) | 1 (0.3) | 6 (2.2) | 21 (4.8) | 0 | 0 | 56 (2.2) | ||
| Smoking status, | Smoker | 0 | 0 | 0 | 244 (88.7) | 335 (75.8) | 0 | 0 | 579 (22.5) | |
| N(%) | Current Smoker | 119 (23.1) | 133 (26.5) | 0 | 0 | 0 | 32 (7.2) | 54 (50.5) | 338 (13.1) | 40 (40) |
| Former Smoker | 307 (59.6) | 338 (67.5) | 0 | 0 | 0 | 268 (60.6) | 50 (46.7) | 963 (37.4) | 48 (48) | |
| Non-Smoker | 75 (14.6) | 18 (3.6) | 0 | 28 (10.2) | 33 (7.5) | 49 (11.1) | 3 (2.8) | 206 (8.0) | 12 (12) | |
| Unknown | 14 (2.7) | 12 (2.4) | 293 (100.0) | 3 (1.1) | 74 (16.7) | 93 (21.0) | 0 | 489 (19.0) | 0 | |
| Race, N (%) | White | 388 (75.3) | 349 (69.7) | 0 | 244 (88.7) | 399 (90.3) | 294 (66.5) | 0 | 1674 (65.0) | 97 (97) |
| Black | 52 (10.1) | 30 (6.0) | 0 | 16 (5.8) | 13 (2.9) | 12 (2.7) | 0 | 123 (4.8) | 0 | |
| Asian | 8 (1.6) | 9 (1.8) | 0 | 7 (2.5) | 3 (0.7) | 6 (1.4) | 0 | 33 (1.3) | 0 | |
| Other | 1 (0.2) | 0 | 0 | 8 (2.9) | 2 (0.5) | 1 (0.2) | 0 | 12 (0.5) | 3 (3) | |
| Unknown | 66 (12.8) | 113 (22.6) | 293 (100.0) | 0 | 25 (5.7) | 129 (29.2) | 107 (100.0) | 733 (28.5) | 0 | |
| Stage, N (%) | I/II | 402 (78.1) | 409 (81.6) | 226 (77.1) | 182 (66.2) | 334 (75.6) | 371 (83.9) | 107 (100.0) | 2031 (78.9) | 86 (86) |
| III | 84 (16.3) | 84 (16.8) | 53 (18.1) | 86 (31.3) | 63 (14.3) | 68 (15.4) | 0 | 438 (17.0) | 14 (14) | |
| IV | 27 (5.2) | 7 (1.4) | 5 (1.7) | 6 (2.2) | 17 (3.8) | 0 | 0 | 62 (2.4) | 0 | |
| Unknown | 2 (0.4) | 1 (0.2) | 9 (3.1) | 1 (0.4) | 28 (6.3) | 3 (0.7) | 0 | 44 (1.7) | 0 | |
| Subtype, N (%) | Non-Squamous | 515 (100.0) | 0 | 293 (100.0) | 275 (100.0) | 442 (100.0) | 442 (100.0) | 0 | 1967 (76.4) | 68 (68) |
| Squamous | 0 | 501 (100.0) | 0 | 0 | 0 | 0 | 107 (100.0) | 608 (23.6) | 32 (32) | |