Table 1 LOH by copy number in ESCC cases by individual case (N = 30)
Case ID | Total no. informative SNPs with LOH | No. informative SNPs with LOH and CN = 1 (fraction) | No. informative SNPs with LOH and CN = 2 (fraction) | No. informative SNPs with LOH and CN = 3 or 4 (fraction) |
|---|---|---|---|---|
*1 | 31,808 | 2,260 (0.07) | 26,801 (0.84) | 2,747 (0.09) |
2 | 368 | 0 (0) | 205 (0.56) | 163 (0.44) |
3 | 377 | 0 (0) | 139 (0.37) | 238 (0.63) |
*4 | 36,175 | 2,093 (0.06) | 27,655 (0.76) | 6,427 (0.18) |
*5 | 24 | 0 (0) | 0 (0) | 24 (1.00) |
*6 | 14,751 | 210 (0.01) | 12,661 (0.86) | 1,880 (0.13) |
*7 | 3,559 | 0 (0) | 2,905 (0.82) | 654 (0.18) |
*8 | 2,408 | 4 (0) | 2,217 (0.92) | 187 (0.08) |
*9 | 593 | 1 (0) | 266 (0.45) | 326 (0.55) |
10 | 17,546 | 1,075 (0.06) | 12,087 (0.69) | 4,384 (0.25) |
11 | 78,159 | 3,678 (0.05) | 67,726 (0.87) | 6,755 (0.09) |
12 | 41 | 0 (0) | 0 (0) | 41 (1.00) |
*13 | 6,113 | 209 (0.03) | 5,154 (0.84) | 750 (0.12) |
14 | 13,498 | 4,084 (0.30) | 9,190 (0.68) | 224 (0.02) |
15 | 3 | 0 (0) | 3 (1.00) | 0 (0) |
16 | 1431 | 0 (0) | 54 (0.04) | 1,377 (0.96) |
17 | 16,934 | 5,732 (0.34) | 10,842 (0.64) | 360 (0.02) |
18 | 2,107 | 0 (0) | 1,553 (0.74) | 554 (0.26) |
*19 | 0 | 0 (0) | 0 (0) | 0 (0) |
*20 | 527 | 0 (0) | 137 (0.26) | 390 (0.74) |
*21 | 19,954 | 62 (0) | 16,332 (0.82) | 3,560 (0.18) |
*22 | 11,180 | 4,410 (0.39) | 6,357 (0.57) | 413 (0.04) |
*23 | 14,523 | 5,939 (0.41) | 5,953 (0.41) | 2,631 (0.18) |
24 | 15,773 | 5,672 (0.36) | 9,354 (0.59) | 747 (0.05) |
*25 | 23,005 | 20 (0) | 17,114 (0.74) | 5,871 (0.26) |
*26 | 37,691 | 21,495 (0.57) | 15,229 (0.40) | 967 (0.03) |
27 | 12,120 | 4,500 (0.37) | 6,299 (0.52) | 1,321 (0.11) |
28 | 494 | 0 (0) | 37 (0.07) | 457 (0.93) |
*29 | 18,222 | 444 (0.02) | 15,400 (0.85) | 2,378 (0.13) |
*30 | 42,499 | 16,432 (0.39) | 25,394 (0.60) | 673 (0.02) |
No. cases with SNP LOH fraction = 0 | 15 | 3 | 2 | |
Range (fraction SNPs with LOH) | 0-0.57 | 0-1.00 | 0-1.00 | |
Median (fraction SNPs with LOH) | 0.00 | 0.60 | 0.13 | |
Global average (fraction SNPs with LOH) | 0.19 | 0.70 | 0.11 | |