Table 2:
SNPs showing evidence of ASI after replication
| SNP ID | Tagged Gene (Locus) |
Alleles | Sample Set | Allele 1 Imbalance* |
Allele 2 Imbalance† |
Total Imbalance§ |
P-value‡ | Adjusted P-value∞ |
Potential Role in Cancer |
|---|---|---|---|---|---|---|---|---|---|
| rs1919935 |
SNX10 (SCC13) |
CT | Discovery | 18/67 (27%) | 6/67 (9%) | 24/67 (36%) | 0.01431 | Endosome trafficking of EGFR and PDGFR | |
| Validation | 22/109 (20%) | 4/109 (4%) | 26/109 (24%) | 0.00042 | |||||
| Combined | 40/176 (23%) | 10/176 (6%) | 50/176 (28%) | 0.00002 | 0.00228 | ||||
| rs2699814 |
SNX10 (SCC13) |
TA | Discovery | 5/89 (6%) | 19/89 (21%) | 24/89 (27%) | 0.00427 | Endosome trafficking of EGFR and PDGFR | |
| Validation | 6/136 (4%) | 16/136 (12%) | 22/136 (16%) | 0.03301 | |||||
| Combined | 11/225 (5%) | 35/225 (16%) | 46/225 (20%) | 0.00040 | 0.04143 | ||||
| rs6958331 |
LANCL2 (SCC13) |
CT | Discovery | 17/63 (27%) | 7/63 (11%) | 24/63 (38%) | 0.04123 | Positive regulator of Akt | |
| Validation | 14/93 (15%) | 2/93 (2%) | 16/93 (17%) | 0.00270 | |||||
| Combined | 31/156 (20%) | 9/156 (6%) | 40/156 (26%) | 0.00050 | 0.05193 | ||||
| rs6891155 |
CEP120 (SCC5) |
GA | Discovery | 26/98 (27%) | 11/98 (11%) | 37/98 (38%) | 0.01366 | Centriole assembly | |
| Validation | 26/153 (17%) | 12/153 (8%) | 38/153 (25%) | 0.02314 | |||||
| Combined | 52/251 (21%) | 23/251 (9%) | 75/251 (30%) | 0.00081 | 0.08365 | ||||
| rs4835907 |
GRAMD3 (SCC5) |
TA | Discovery | 8/89 (9%) | 21/89 (24%) | 29/89 (33%) | 0.01578 | Membrane-coupled processes | |
| Validation | 10/118 (8%) | 23/118 (19%) | 33/118 (28%) | 0.02364 | |||||
| Combined | 18/207 (9%) | 44/207 (21%) | 62/207 (30%) | 0.00096 | 0.09888 |
*
Relative loss of allele 1 compared to allele 2
†
Relative loss of allele 2 compared to allele 1
§
Total number of tumors with imbalance/total heterozygous samples (% of heterozygotes showing imbalance)
‡
Chi-squared statistical test, df = 1
∞
Bonferroni corrected p-value