Selected SCA features for esophageal adenocarcinoma risk prediction models
| Chromosome: (1-Mb segment) of SCA location selected in model | SCA type | HR | Frequency of SCA by patient (T1+T2) in progressors (%)a | Frequency of SCA by patient (T1+T2) in nonprogressors (%)a | Average size contiguous SCA (Mb) spanning selected location in progressorsb (SD) | Average size contiguous SCA (Mb) spanning selected location in nonprogressorsb (SD) |
|---|---|---|---|---|---|---|
| 1: 36–37c | Loss | >30 | 2.5 | 0.6 | 25.5 (31.8) | 14d |
| 2: 226–227 | cnLOH | >30 | 8.6 | 0.0 | 48.7 (46.7) | e |
| 5: 93–94 | cnLOH | 7.9 | 11.9 | 0.6 | 102.7 (41.1) | 132d |
| 6: 1–2 | Gain | 8.2 | 12.7 | 0.6 | 30.1 (26.0) | 32d |
| 6: 5–6 | Gain | 5.9 | 15.2 | 0.6 | 35.3 (22.7) | 32d |
| 6: 29–30 | cnLOH | 5.2 | 14.9 | 3.0 | 24.1 (19.3) | 34.6 (12.3) |
| 6: 146–147 | cnLOH | 8.5 | 6.5 | 0.6 | 91.8 (35.2) | 67.3 (1.2) |
| 7: 77–78 | Loss | 23.1 | 6.3 | 0.0 | 74.0 (43.5) | e |
| 7: 78–79 | cnLOH | >30 | 6.5 | 0.0 | 67.6 (38) | e |
| 8: 138–139 | cnLOH | >30 | 5.9 | 0.0 | 35.8 (40.1) | e |
| 9: 0–1 | Loss | 2.0 | 59.5 | 33.1 | 25.8 (16.1) | 10.2 (12.2) |
| 9: 33–34 | Loss | 4.8 | 38.0 | 12.4 | 27.5 (18.1) | 18.5 (13.8) |
| 9: 65–66 | Loss | 2.6 | 12.7 | 3.6 | 23.9 (27.4) | 5.1 (1.7) |
| 11: 38–39 | cnLOH | 6.9 | 4.6 | 0.6 | 34.9 (17.8) | 50.5 (0.7) |
| 11: 50–51 | cnLOH | 3.8 | 3.3 | 1.2 | 39.2 (17.7) | 28 (32.5) |
| 11: 110–111 | cnLOH | 4.3 | 6.0 | 1.8 | 55.3 (20.4) | 72.3 (11.3) |
| 12: 45–46 | Loss | 4.0 | 11.4 | 2.4 | 39.9 (44.1) | 57.2 (44.2) |
| 13: 42–43 | cnLOH | 18.0 | 17.7 | 0.6 | 81.9 (27.2) | 51d |
| 15: 70–71 | Gain | 14.4 | 40.5 | 1.8 | 58.6 (22.2) | 68 (19.7) |
| 17: 8–9 | Loss | 8.9 | 46.8 | 7.1 | 21.0 (3.5) | 22 (4.2) |
| 17: 9–10 | cnLOH | 8.5 | 24.2 | 2.4 | 20.7 (3.0) | 16 (6.7) |
| 17: 12–13 | cnLOH | 10.8 | 24.2 | 1.8 | 20.4 (4.0) | 22 (1) |
| 17: 37–38 | Gain | 12.3 | 34.2 | 2.4 | 23.2 (22.3) | 20.5 (23.9) |
| 18: 19–20 | Gain | 4.6 | 60.8 | 21.3 | 16.2 (19.9) | 26.5 (26.0) |
| 19: 48–49 | cnLOH | >30 | 5.8 | 0.0 | 25.0 (9.7) | e |
| X: 42–43 | Loss | >30 | 13.9 | 0.0 | 46.5 (19.2) | e |
| Y: 13–14 | Loss | 4.6 | 54.4 | 16.6 | 15.3 (3.0) | 13.2 (5.8) |
| Sum of copy loss events in the 86 regions | ||||||
| Sum of all SCA events in the 86 regions | ||||||
NOTE: Loss = allele-specific copy loss; Gain = allele-specific copy gain.
↵aThe frequency was calculated from all biopsies from both time points within each patient.
↵bThe average of the sizes of SCA in a chromosome arm surrounding the SCA locations used in prediction models.
↵cBoundaries for each 1-Mb segment follow the standard as in chromosome 1: 36–37, which includes the nucleotides on chromosome 1 from 36,000,001 to 37,000,000 base pairs on human genome reference hg19.
↵dOnly one sample with SCA in this region so no variance in average SCA size can be calculated.
↵eNo samples had SCA spanning this region.