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

  1. If the number of protein coding genes in a smoothened peak area was zero, the two flanking genes were considered as candidate targets. Gene names are in bold if they have not been previously reported as high-resolution (identified area containing 10 or fewer genes) AI target in CRC. Type of gross change at the target is indicated as “Loss” or “Gain”. The number of tumors with AI, including the homozygous losses at PTEN and SMAD4, are shown for 1699 CRCs. The number of tumors with somatic nonsynonymous SNVs and indels in the presumed AI target gene is given for the subset of 234 MSS tumors that underwent WGS. Peaks are annotated by re-discovery in the two lower-resolution datasets, 230 Danish colorectal cancers (S) and TCGA COADREAD (n = 573) (T), and significant expression change (FDR < 10%) (E). Citations in Supplementary Data 2