Table 3.
Copy numbers of allele and loss of heterozygosity (LOH) for the genes using the allele-specific copy number (ASCN) analysis
| Gene symbol | The copy number of A allele | The copy number of B allele | Proportion (%) | Description | Log2 FC |
|---|---|---|---|---|---|
| TGFB3 | 1.7 | 0.3 | 70 | Copy neutral LOH in 70% | −0.96 |
| SPHK1 | 0.3 | 1.7 | 70 | Copy neutral LOH in 70% | 0.6825 |
| NTS | 0.5 | 1.5 | 50 | Copy neutral LOH in 50% | −0.7975 |
| CXCL10 | 1.5 | 0.5 | 50 | Copy neutral LOH in 50% | 0.66 |
| F2RL1 | 0.5 | 1.5 | 50 | Copy neutral LOH in 50% | −1.375 |
| TGFBI | 0.6 | 1.4 | 40 | Loss of one allele in 40% | −1.23 |
| COL3A1 | 1.4 | 0.6 | 40 | Loss of one allele in 50% | −1.12 |
| LUM | 1.2 | 0.8 | 20 | Loss of one allele in 20% | −0.665 |
| IGF2 | 0.8 | 1.2 | 20 | Loss of one allele in 20% | 1.07125 |
| GNG2 | 0.9 | 1.1 | 10 | Imbalance in 10% | −1.3775 |
| COL14A1 | 1.1 | 0.9 | 10 | Imbalance in 10% | −1.8125 |
| WNT2 | 1.1 | 1 | 5 | Imbalance in 5% | −1.1275 |
| MGP | 1 | 1 | 0 | Expected balance | −2.3075 |
| BMP4 | 1 | 1 | 0 | Expected balance | −1.115 |
| PPARG | 1 | 1 | 0 | Expected balance | −1.1 |
| TLR4 | 1 | 1 | 0 | Expected balance | 1.09 |
Gene symbol the name of one gene, proportion the percentage of copy number of A allele minus copy number of B allele, Description the frequency of LOH, FC fold change