Table 1 Literature curated 37 AI peak loci
From: Contribution of allelic imbalance to colorectal cancer
Gene | Location | AI type | Protein coding genes in peak | CRCs with AI | MSS CRCs with SNV or indel at target gene | Annotation |
---|---|---|---|---|---|---|
TP53 | 17p | Loss | 2 | 1076 (63%) | 148 (63%) | S.E |
SMAD4 | 18q | Loss | 5 | 1054 (61%) | 27 (11%) | STE |
HNF4A | 20q | Gain | 5 | 804 (47%) | 3 (1%) | STE |
APC | 5q | Loss | 1 | 764 (45%) | 179 (76%) | STE |
KLF5 | 13q | Gain | 1 | 709 (42%) | 5 (2%) | STE |
USP12 | 13q | Gain | 0 | 694 (41%) | 0 (0%) | .TE |
RUNX3 | 1p | Loss | 2 | 678 (40%) | 3 (1%) | … |
TLR3 | 4q | Loss | 4 | 642 (38%) | 7 (2%) | ..E |
SOX9 | 17q | Loss | 0 | 621 (36%) | 11 (4%) | STE |
MYC | 8q | Gain | 1 | 585 (34%) | 1 (0%) | STE |
BMPR1A | 10q | Loss | 4 | 581 (34%) | 3 (1%) | ..E |
PTEN | 10q | Loss | 5 | 581 (34%) | 9 (4%) | STE |
FGFR3 | 4p | Loss | 3 | 551 (32%) | 1 (0%) | S.E |
TCF7L2 | 10q | Loss | 1 | 548 (32%) | 21 (8%) | STE |
PARK2 | 6q | Loss | 1 | 545 (33%) | 8 (3%) | ST. |
NCOR2 | 12q | Loss | 1 | 495 (29%) | 5 (2%) | S.E |
GPRC5A | 12p | Loss | 3 | 495 (29%) | 0 (0%) | STE |
SMARCA2 | 9p | Loss | 0 | 440 (26%) | 5 (2%) | .TE |
CDKN2B | 9p | Loss | 0 | 437 (26%) | 0 (0%) | ST. |
RHOB | 2p | Loss | 1 | 433 (26%) | 0 (0%) | ..E |
ACVR2A | 2q | Loss | 3 | 430 (25%) | 7 (3%) | S.E |
MLK4 | 1q | Loss | 2 | 428 (25%) | 0 (0%) | S.E |
G0S2 | 1q | Loss | 9 | 408 (24%) | 0 (0%) | S.. |
CTCF | 16q | Loss | 13 | 387 (23%) | 3 (1%) | S.E |
FGFR1 | 8p | Gain | 2 | 254 (15%) | 6 (2%) | S.. |
CCND2 | 12p | Gain | 1 | 186 (11%) | 0 (0%) | STE |
KRAS | 12p | Gain | 4 | 179 (11%) | 121 (51%) | ..E |
IGF2 | 11p | Gain | 4 | 126 (7%) | 0 (0%) | STE |
BPTF | 17q | Gain | 5 | 110 (6%) | 9 (3%) | STE |
NOTCH1 | 9q | Gain | 4 | 101 (6%) | 4 (1%) | ..E |
ERBB2 | 17q | Gain | 14 | 99 (6%) | 10 (4%) | STE |
SATB2 | 2q | Gain | 1 | 83 (5%) | 4 (2%) | .TE |
PDGFRB, CDX1 | 5q | Gain | 6 | 69 (4%) | 5 (2%) | …, ..E |
ITGB1 | 10p | Gain | 3 | 56 (3%) | 0 (0%) | S.E |
FOXA1 | 14q | Gain | 4 | 48 (3%) | 1 (0%) | S.E |
TNFAIP2 | 14q | Gain | 11 | 36 (2%) | 1 (0%) | … |
DGCR8 | 22q | Gain | 11 | 32 (2%) | 0 (0%) | ..E |