Table 2.
Imprinted control genes, expression threshold and analysis by our statistical ASE test on the Illumina array.
| SNP ID | Gene | Chr | Average intensity across all samples | Total number of heterozygous samples (hets) | Hets showing ASE: p < 0.01 & |lfc|>0.585 | Percentage of hets which show ASE |
|---|---|---|---|---|---|---|
| rs2075745 | H19 | 11 | 14.01 | 12 | 12 | 100% |
| rs1860565 | PEG3 | 19 | 13.63 | 9 | 9 | 100% |
| rs1802710 | DLK1 | 14 | 13.57 | 15 | 14 | 93% |
| rs3730171 | GNAS | 20 | 13.54 | 1 | 0 | 0%† |
| rs2839702 | H19 | 11 | 13.48 | 11 | 11 | 100% |
| rs998075 | IGF2R | 6 | 12.78 | 13 | 0 | 0%* |
| rs8100247 | ZNF331 | 19 | 12.61 | 13 | 12 | 92% |
| rs9373409 | PLAGL1 | 6 | 12.48 | 11 | 9 | 82% |
| rs13390 | PHLDA2 | 11 | 12.33 | 2 | 2 | 100% |
| rs10863 | MEST | 7 | 12.32 | 4 | 4 | 100% |
| rs12982082 | ZNF331 | 19 | 12.27 | 12 | 10 | 83% |
| rs13073 | PEG10 | 7 | 12.09 | 11 | 10 | 91% |
| rs8386 | GNAS | 20 | 11.97 | 1 | 0 | 0%† |
| rs1055359 | PEG3 | 19 | 11.8 | 10 | 10 | 100% |
| rs1003483 | IGF2AS | 11 | 11.32 | 8 | 7 | 88% |
| rs854541 | PPP1R9A | 7 | 11.2 | 13 | 0 | 0% |
| rs2285185 | L3MBTL | 20 | 10.97 | 10 | 1 | 10% |
| rs2171492 | CPA4 | 7 | 10.57 | 12 | 0 | 0% |
| rs2071970 | L3MBTL | 20 | 10.51 | 11 | 0 | 0% |
| rs854524 | PPP1R9A | 7 | 10.41 | 10 | 0 | 0% |
| rs8234 | KCNQ1 | 11 | 10.18 | 10 | 0 | 0% |
| rs1049846 | PLAGL1 | 6 | 10.06 | 13 | 3 | 23% |
| rs1800504 | GRB10 | 7 | 9.98 | 14 | 0 | 0% |
| rs3741208 | IGF2AS | 11 | 9.67 | 10 | 0 | 0% |
| rs367035 | SLC22A18 | 11 | 9.09 | 13 | 0 | 0% |
| rs3816800 | ATP10A | 15 | 9.09 | 15 | 0 | 0% |
| rs1570070 | IGF2R | 6 | 9.06 | 0 | 0 | 0% |
| rs1800900 | GNAS | 20 | 8.86 | 9 | 2 | 22% |
| rs2066710 | ATP10A | 15 | 8.8 | 16 | 0 | 0% |
Imprinted genes tested on the array are listed alongside the exonic SNP used and the intensity obtained for the cDNA (average log2 fluorescence for the 23 placentas). The fore last column shows the number of heterozygous samples that are significant for ASE (p < 0.01) and that have a good probe hybridisation signal on the array (absolute log-fold change (lfc) >0.58). Examination of the last column (percentage of heterozygous placentas which exhibit statistically significant ASE) shows the difference for reliable detection of imprinting above or below the 11.25 average intensity threshold. *IGF2R is known to be biallelically expressed in human term placenta. †The two heterozygous GNAS placentas showed biallelic expression.