Table 1 Description of genes with frequent biallelic loss in ESCC1
Gene no. | Gene name | Cytoband | No. cases with biallelic loss | No. SNPs with biallelic loss2 | No. SNPs in gene | Fraction of SNPs in gene with biallelic loss |
|---|---|---|---|---|---|---|
on 2q | ||||||
1 | SPAG16 | 2q34 | 8 | 7 | 164 | 0.04 |
on 3p | ||||||
2 | CADM2 | 3p12.1 | 9 | 6 | 44 | 0.14 |
3 | CNTN3 | 3p12.3 | 11 | 9 | 56 | 0.16 |
4 | ROBO1 | 3p12.3 | 9 | 6 | 60 | 0.10 |
5 | ROBO2 | 3p12.3 | 11 | 18 | 93 | 0.19 |
6 | EIF4E3 | 3p13 | 9 | 6 | 16 | 0.38 |
7 | ADAMTS9 | 3p14.1 | 10 | 10 | 52 | 0.19 |
8 | FAM19A1 | 3p14.1 | 11 | 15 | 128 | 0.12 |
9 | FOXP1 | 3p14.1 | 12 | 10 | 104 | 0.10 |
10 | MAGI1 | 3p14.1 | 10 | 12 | 192 | 0.06 |
11 | PRICKLE2 | 3p14.1 | 9 | 7 | 56 | 0.13 |
12 | SUCLG2 | 3p14.1 | 10 | 13 | 66 | 0.20 |
13 | CADPS | 3p14.2 | 10 | 11 | 137 | 0.08 |
14 | FHIT | 3p14.2 | 12 | 31 | 345 | 0.09 |
15 | PTPRG | 3p14.2 | 10 | 28 | 199 | 0.14 |
16 | CACNA2D3 | 3p14.2-p21.1 | 11 | 22 | 246 | 0.09 |
17 | ERC2 | 3p14.3 | 9 | 8 | 211 | 0.04 |
18 | PBRM1 | 3p21.1 | 7 | 8 | 19 | 0.42 |
19 | CACNA2D2 | 3p21.31 | 10 | 9 | 17 | 0.53 |
20 | DOCK3 | 3p21.31 | 7 | 8 | 57 | 0.14 |
21 | MYRIP | 3p22.1 | 9 | 8 | 66 | 0.12 |
22 | TRAK1 | 3p22.1 | 9 | 9 | 39 | 0.23 |
23 | DLEC1 | 3p22.2 | 10 | 5 | 12 | 0.42 |
24 | ITGA9 | 3p22.2 | 11 | 14 | 101 | 0.14 |
25 | SLC22A14 | 3p22.2 | 8 | 7 | 11 | 0.64 |
26 | GPD1L | 3p22.3 | 9 | 5 | 14 | 0.36 |
27 | OSBPL10 | 3p23 | 9 | 6 | 63 | 0.10 |
28 | LRRC3B | 3p24.1 | 7 | 5 | 12 | 0.42 |
29 | RBMS3 | 3p24.1 | 12 | 10 | 166 | 0.06 |
30 | RARB | 3p24.2 | 8 | 5 | 42 | 0.12 |
31 | THRB | 3p24.2 | 9 | 9 | 84 | 0.11 |
32 | RFTN1 | 3p24.3 | 11 | 13 | 54 | 0.24 |
33 | UBE2E2 | 3p24.3 | 10 | 9 | 55 | 0.16 |
34 | ZNF385D | 3p24.3 | 12 | 21 | 108 | 0.19 |
35 | SLC6A6 | 3p25.1 | 8 | 5 | 14 | 0.36 |
36 | ATP2B2 | 3p25.3 | 9 | 10 | 108 | 0.09 |
37 | SRGAP3 | 3p25.3 | 9 | 12 | 97 | 0.12 |
38 | GRM7 | 3p26.1 | 11 | 38 | 276 | 0.14 |
39 | LMCD1 | 3p26.1 | 9 | 5 | 36 | 0.14 |
40 | ITPR1 | 3p26.2 | 11 | 16 | 121 | 0.13 |
41 | CHL1 | 3p26.3 | 7 | 6 | 78 | 0.08 |
42 | CNTN4 | 3p26.3 | 10 | 11 | 163 | 0.07 |
43 | CNTN6 | 3p26.3 | 8 | 6 | 111 | 0.05 |
on 4p & 4q | ||||||
44 | PCDH7 | 4p15.1 | 11 | 6 | 58 | 0.10 |
45 | KCNIP4 | 4p15.31 | 10 | 22 | 338 | 0.07 |
46 | LDB2 | 4p15.32 | 7 | 5 | 103 | 0.05 |
47 | EVC | 4p16.1 | 8 | 5 | 41 | 0.12 |
48 | EVC2 | 4p16.1 | 6 | 5 | 45 | 0.12 |
49 | SORCS2 | 4p16.1 | 6 | 5 | 115 | 0.04 |
50 | WDR1 | 4p16.1 | 7 | 5 | 12 | 0.42 |
51 | FSTL5 | 4q32.2 | 11 | 10 | 126 | 0.08 |
52 | GALNT17 | 4q34.1 | 7 | 6 | 187 | 0.03 |
on 5q | ||||||
53 | RGS7BP | 5q12.3 | 8 | 5 | 37 | 0.14 |
54 | IQGAP2 | 5q13.3 | 8 | 8 | 87 | 0.09 |
55 | SV2C | 5q13.3 | 7 | 5 | 67 | 0.07 |
56 | GPR98 | 5q14.3 | 5 | 6 | 95 | 0.06 |
57 | MCTP1 | 5q15 | 6 | 5 | 98 | 0.05 |
58 | PPP2R2B | 5q32 | 7 | 8 | 114 | 0.07 |
59 | CYFIP2 | 5q33.3 | 7 | 6 | 41 | 0.15 |
60 | DOCK2 | 5q35.1 | 6 | 6 | 166 | 0.04 |
61 | SLIT3 | 5q35.1 | 7 | 5 | 221 | 0.02 |
62 | COL23A1 | 5q35.3 | 9 | 8 | 68 | 0.12 |
on 8p | ||||||
63 | CSMD1 | 8p23.2 | 7 | 4 | 153 | 0.03 |
on 9p | ||||||
64 | LNGCO2 | 9p21.1 | 9 | 6 | 140 | 0.04 |
65 | CDKN2A/2B | 9p21.1 | 8 | 3 | 6 | 0.50 |
66 | KIAA1797 | 9p21.3 | 5 | 5 | 57 | 0.09 |
67 | MTAP | 9p21.3 | 8 | 4 | 17 | 0.24 |
68 | ADAMTSL1 | 9p22.1 | 9 | 7 | 108 | 0.06 |
69 | C9orf138 | 9p22.1 | 7 | 5 | 37 | 0.14 |
70 | BNC2 | 9p22.2-p22.3 | 8 | 7 | 99 | 0.07 |
71 | JMJD2C | 9p24.1 | 9 | 6 | 151 | 0.04 |
72 | PTPRD | 9p24.1 | 9 | 17 | 199 | 0.09 |
73 | UHRF2 | 9P24.1 | 5 | 6 | 19 | 0.32 |
74 | GLIS3 | 9p24.2 | 7 | 5 | 155 | 0.03 |
75 | ANKRD15 | 9P24.3 | 6 | 7 | 103 | 0.07 |
76 | DOCK8 | 9p24.3 | 7 | 5 | 65 | 0.08 |
77 | SMARCA2 | 9p24.3 | 6 | 5 | 63 | 0.08 |