Table 1.
Most frequently mutated genes accompanied by aUPD or copy number losses in GI cancers
| Cohort | Gene | Cytoband | “1st hit” mutation1 % | “2nd hit” aUPD2 , 3 % (qval) | “2nd hit” CN Loss3 % (qval) |
|---|---|---|---|---|---|
| COAD | APC | 5q22.2 | 74.47 | 22.29 (< 10−9) | 20.57 (< 10−9) |
| TP53 | 17p13.1 | 53.19 | 20 (< 10−9) | 73.6 (< 10−9) | |
| KRAS | 12p12.1 | 39.57 | 15.05 (< 10−9) | 3.23 (0.0061) | |
| FBXW7 | 4q31.3 | 13.62 | 12.5 (0.0098) | 12.5 (0.0772) | |
| SMAD4 | 18q21.2 | 10.64 | 12 (0.00061) | 68 (< 10−9) | |
| SOX9 | 17q24.3 | 10.21 | 16.67 (< 10−9) | 8.33 (0.000087) | |
| READ | APC | 5q22.2 | 80.77 | 34.92 (< 10−9) | 15.87 (< 10−9) |
| TP53 | 17p13.1 | 73.08 | 31.58 (< 10−9) | 57.89 (< 10−9) | |
| KRAS | 12p12.1 | 39.74 | 19.35 (< 10−9) | 3.23 (0.004) | |
| FBXW7 | 4q31.3 | 14.10 | 18.18 (0.0036) | 9.09 (0.031) | |
| NRAS | 1p13.2 | 11.54 | 22.22 (8.4 × 10−6) | 0 | |
| STAD | TP53 | 17p13.1 | 45.00 | 31.48 (< 10−9) | 59.26 (< 10−9) |
| ARID1A | 1p36.11 | 22.50 | 14.81 (0.019) | 3.70 (n.s.) | |
| PIK3CA | 3q26.32 | 11.67 | 21.43 (0.0728) | 0 | |
| APC | 5q22.2 | 7.50 | 22.22 (n.s.) | 44.44 (0.0073) | |
| ESCC | TP53 | 17p13.1 | 71.79 | 53.57 (< 10−9) | 21.43 (< 10−6) |
| NOTCH1 | 9q34.3 | 10.26 | 75 (5.5 × 10−9) | 0 | |
| PTCH1 | 9q22.32 | 10.26 | 100 (< 10−9) | 0 | |
| ZNF750 | 17q25.3 | 7.69 | 66.67 (1.64 × 10−8) | 33.33 (0.000048) | |
| EAC | TP53 | 17p13.1 | 72.22 | 69.23 (< 10−9) | 23.08 (< 10−9) |
| MYH2 | 17p13.1 | 11.11 | 100 (1.41 × 10−8) | 0 |
n.s., not significant.
1
Only genes that reached a 7% threshold of mutation by cohort have been considered.
2
Only genes that reached a 10% threshold of “second hit” driven by an aUPD event have been considered.
3
Genomic events detected in only one sample were not considered for this analysis.