Table 1.
Primer and probe sequences
| Gene | Detection | Oligonucleotide | Sequence 5′ to 3′ | Amplicon length (bp) | Annealing temperature (°C) |
|---|---|---|---|---|---|
| ITGA4 | Promotor methylation | Forward | TAGTTCGTTGGCGTCGGATAC | 90 | 60 |
| Reverse | TACCCCAAAATTACACGAAATACG | ||||
| Probe | GGGGCGTTTTTTTTCGTTGGTTAATCG | ||||
| MSC | Promotor methylation | Forward | GGTTGGTTTTTAGTTATATCGTTTATTTGC | 89 | 62 |
| Reverse | TACCAAATTCACTAAATACACGTAACCG | ||||
| Probe | CGATCCTCCTACAACAA (MGB*) | ||||
| EYA4 | Promotor methylation | Forward | TTTTTTTTAAGGTAGCGATAATTTTAC | 104 | 60 |
| Reverse | CAAATACGAAACTACCGACAACG | ||||
| Probe | ACGCACGCTCCGAC (MGB*) | ||||
| GRIA4 | Promotor methylation | Forward | TGTTTATCGGAGCGTTTTAGTTTTTC | 120 | 60 |
| Reverse | AATCGATCCCTCTACGAACCG | ||||
| Probe | CGTTTCGGAGTTAGTTTGGTGTTAGGTTTTTTTTTTT | ||||
| ACTB | Bisulphite conversion | Forward | AACCAATAAAACCTACTCCTCCCTTAA | 133 | 62 |
| Reverse | TGGTGATGGAGGAGGTTTAGTAAGT | ||||
| Probe | ACCACCACCCAACACACAATAACAAACACA | ||||
| TP53 | R273C VAF | Forward | CTCTGTGCGCCGGTCTCT | 62 | 56 |
| Reverse | TGGGACGGAACAGCTTTGA | ||||
| Probe-WT | AGGCACAAACACGCAC | ||||
| Probe-Mut | AGGCACAAACACACA |
CpG dinucleotides are bold and underlined
*MGB minor groove binder, bp base pairs