Table 1.
Clinical characteristics of breast cancer patients with copy number imbalances
| Characteristic | Discovery dataset (n = 960)
|
Validation dataset (n = 335)
|
||||
|---|---|---|---|---|---|---|
| No n (%)* |
Bone n (%)* |
Non-bone n (%)* |
No n (%)* |
Bone n (%)* |
Non-bone n (%)* |
|
| n | 757 | 74 | 129 | 259 | 26 | 50 |
| Median time to first metastasis, y | — | 4.6 | 4.7 | — | 3.5 | 2.8 |
| Median follow-up time, y | 10.3 | — | — | 9.8 | — | — |
| Age at primary diagnosis, y | ||||||
| Mean (SD) | 55 (13) | 51 (12) | 51 (12) | 62 (14) | 62 (15) | 59 (16) |
| ≤50 | 295 (38.9) | 36 (48.7) | 68 (52.7) | 62 (23.9) | 7 (26.9) | 17 (34.0) |
| >50 | 462 (61.1) | 38 (51.3) | 61 (47.3) | 197 (76.1) | 19 (73.1) | 33 (66.0) |
| Race/ethnicity & | ||||||
| White | 561 (74.1) | 54 (72.9) | 93 (72.1) | — | — | — |
| Black | 95 (12.6) | 11 (14.9) | 17 (13.2) | — | — | — |
| Hispanic | 97 (12.8) | 7 (9.5) | 17 (13.2) | — | — | — |
| Unknown | 4 (0.5) | 2 (2.7) | 2 (1.5) | — | — | — |
| Tumor subtype # | ||||||
| Luminal A | 271 (35.8) | 21 (28.4) | 24 (18.6) | 72 (27.8) | 7 (26.9) | 11 (22.0) |
| Luminal B | 172 (22.7) | 27 (36.5) | 26 (20.2) | 16 (6.2) | 2 (7.7) | 5 (10.0) |
| HER2+ | 112 (14.8) | 14 (18.9) | 31 (24.0) | 26 (10.0) | 2 (7.7) | 5 (10.0) |
| TNBC | 138 (18.2) | 4 (5.4) | 40 (31.0) | 16 (6.2) | 1 (3.9) | 6 (12.0) |
| Normal | — | — | — | 16 (6.2) | 2 (7.7) | 3 (6.0) |
| Unknown | 64 (8.5) | 8 (10.8) | — | 113 (43.6) | 12 (46.1) | 20 (40.0) |
| Stage | ||||||
| I | 278 (36.7) | 12 (16.2) | 14 (10.9) | 56 (21.6) | — | 6 (12.0) |
| II | 479 (63.3) | 62 (83.8) | 115 (89.2) | 76 (29.4) | 10 (38.5) | 16 (32.0) |
| III | — | — | — | 21 (8.1) | 10 (38.5) | 14 (28.0) |
| Unknown | — | — | — | 106 (40.9) | 6 (23.0) | 14 (28.0) |
| Nuclear grade† | ||||||
| I–II | 454 (60.0) | 46 (62.2) | 66 (51.2) | 169 (65.2) | 20 (76.9) | 38 (76.0) |
| III | 255 (33.7) | 19 (25.7) | 56 (43.4) | 59 (22.8) | 6 (23.1) | 11 (22.0) |
| Unknown | 48 (6.3) | 9 (12.1) | 7 (5.4) | 31 (12.0) | — | 1 (2.0) |
| Tumor size | ||||||
| < 2 cm | 477 (63.0) | 30 (40.5) | 56 (43.4) | 126 (48.7) | 6 (23.1) | 18 (36.0) |
| ≥2 cm | 257 (34.0) | 38 (51.4) | 68 (52.7) | 95 (36.7) | 17 (65.4) | 26 (52.0) |
| Infiltrating skin/thoracic wall | — | — | — | 2 (0.8) | 2 (7.7) | 1 (2.0) |
| Carcinoma in situ | — | — | — | 27 (10.4) | — | 1 (2.0) |
| Unknown | 23 (3.0) | 6 (8.1) | 5 (3.9) | 9 (3.4) | 1 (3.8) | 4 (8.0) |
| Lymph node status | ||||||
| Positive | 267 (35.3) | 40 (54.1) | 71 (55.0) | 67 (25.9) | 17 (65.4) | 26 (52.0) |
| Negative | 476 (62.9) | 30 (40.5) | 55 (42.6) | 163 (62.9) | 7 (26.9) | 19 (38.0) |
| Unknown | 14 (1.8) | 4 (5.4) | 3 (2.4) | 29 (11.2) | 2 (7.7) | 5 (10.0) |
| Radiation therapy | ||||||
| Yes | 321 (42.4) | 35 (47.3) | 51 (39.5) | 109 (42.1) | 13 (50.0) | 20 (40.0) |
| No | 418 (55.2) | 36 (48.7) | 75 (58.2) | 112 (43.2) | 12 (46.2) | 24 (48.0) |
| Unknown | 18 (2.4) | 3 (4.1) | 3 (2.3) | 38 (14.7) | 1(3.8) | 6 (12.0) |
| Chemotherapy | ||||||
| Yes | 319 (42.2) | 38 (51.3) | 76 (61.9) | 44 (17.0) | 4 (15.4) | 8 (16.0) |
| No | 397 (52.4) | 31 (41.9) | 47 (36.4) | 209 (80.7) | 21 (80.8) | 41 (82.0) |
| Unknown | 41 (5.4) | 5 (6.8) | 6 (4.7) | 6 (2.3) | 1 (3.8) | 1 (2.0) |
| Endocrine therapy | ||||||
| Yes | 353 (46.6) | 28 (37.8) | 37 (28.7) | 79 (30.5) | 12 (46.2) | 16 (32.0) |
| No | 386 (51.0) | 43 (58.1) | 88 (68.2) | 173 (66.8) | 13 (50.0) | 33 (66.0) |
| Unknown | 18 (2.4) | 3 (4.1) | 4 (3.1) | 7 (2.7) | 1 (3.8) | 1 (2.0) |
Abbreviations: SD, standard deviation; HER2, human epidermal growth factor receptor 2; TNBC, triple-negative breast cancer.
*
Numbers do not add up because of missing data.
&
Nearly all of the validation dataset samples are Caucasian; however, some might come from Pakistan or other places.
#
Tumor subtype was determined using ER, PR, Ki67, and HER2 as defined in Materials and Methods.
†
Nuclear grade was determined by the modified Black’s method.