Table 1.

Selected SCA features for esophageal adenocarcinoma risk prediction models

Chromosome: (1-Mb segment) of SCA location selected in modelSCA typeHRFrequency of SCA by patient (T1+T2) in progressors (%)aFrequency of SCA by patient (T1+T2) in nonprogressors (%)aAverage size contiguous SCA (Mb) spanning selected location in progressorsb (SD)Average size contiguous SCA (Mb) spanning selected location in nonprogressorsb (SD)
1: 36–37cLoss>302.50.625.5 (31.8)14d
2: 226–227cnLOH>308.60.048.7 (46.7)e
5: 93–94cnLOH7.911.90.6102.7 (41.1)132d
6: 1–2Gain8.212.70.630.1 (26.0)32d
6: 5–6Gain5.915.20.635.3 (22.7)32d
6: 29–30cnLOH5.214.93.024.1 (19.3)34.6 (12.3)
6: 146–147cnLOH8.56.50.691.8 (35.2)67.3 (1.2)
7: 77–78Loss23.16.30.074.0 (43.5)e
7: 78–79cnLOH>306.50.067.6 (38)e
8: 138–139cnLOH>305.90.035.8 (40.1)e
9: 0–1Loss2.059.533.125.8 (16.1)10.2 (12.2)
9: 33–34Loss4.838.012.427.5 (18.1)18.5 (13.8)
9: 65–66Loss2.612.73.623.9 (27.4)5.1 (1.7)
11: 38–39cnLOH6.94.60.634.9 (17.8)50.5 (0.7)
11: 50–51cnLOH3.83.31.239.2 (17.7)28 (32.5)
11: 110–111cnLOH4.36.01.855.3 (20.4)72.3 (11.3)
12: 45–46Loss4.011.42.439.9 (44.1)57.2 (44.2)
13: 42–43cnLOH18.017.70.681.9 (27.2)51d
15: 70–71Gain14.440.51.858.6 (22.2)68 (19.7)
17: 8–9Loss8.946.87.121.0 (3.5)22 (4.2)
17: 9–10cnLOH8.524.22.420.7 (3.0)16 (6.7)
17: 12–13cnLOH10.824.21.820.4 (4.0)22 (1)
17: 37–38Gain12.334.22.423.2 (22.3)20.5 (23.9)
18: 19–20Gain4.660.821.316.2 (19.9)26.5 (26.0)
19: 48–49cnLOH>305.80.025.0 (9.7)e
X: 42–43Loss>3013.90.046.5 (19.2)e
Y: 13–14Loss4.654.416.615.3 (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.