Table 2 Methylation specific PCR primer sequences
From: Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers
Gene | Nucleotide sequence | PCR product size, base pair (bp) |
|---|---|---|
Methylation-independent primer sequences (nested) | ||
 RASSF1α | Forward: 5′-GGAGGGAAGGAAGGGTAAGG-3′ | 260 |
Reverse: 5′-CAACTCAATAAACTCAAACTCCC-3′ | ||
 p16INK4a | Forward: 5′-GAGGAAGAAAGAGGAGGGGTTG-3′ | 274 |
Reverse: 5′-ACAAACCCTCTACCCACCTAAATC-3′ | ||
Methylated allele-specific primer sequences | ||
 RASSF1α | Forward: 5′-GGGGGTTTTGCGAGAGCGC-3′ | 203 |
Reverse: 5′-CCCGATTAAACCCGTACTTCG-3′ | ||
 p16INK4a | Forward: 5′-GAGGGTGGGGCGGATCGC-3′ | 143 |
Reverse: 5′-GACCCCGAACCGCGACCG-3′ | ||
 TIMP3 | Forward: 5′-GCGTCGGAGGTTAAGGTTGTT-3′ | 116 |
Reverse: 5′-CTCTCCAAAATTACCGTACGCG-3′ | ||
 PCQAP 5′ | Forward: 5′-GTTTTGTGATTGAGGYGGCGGC -3′ | 167 |
Reverse: 5′-AAAAATCCCACAATCCAACCC -3′ | ||
 PCQAP 3′ | Forward: 5′-GATATGGGTGGTGGGAGTTGGG -3′ | 172 |
Reverse: 5′- AATCAGACCCTAACCTCGCCCG -3′ | ||
Unmethylated allele-specific primer sequences | ||
 RASSF1α | Forward: 5′-GGTTTTGTGAGAGTGTGTTTAG-3′ | 172 |
Reverse: 5′-ACACTAACAAACACAAACCAAAC-3′ | ||
 p16INK4a | Forward: 5′-TTATTAGAGGGTGGGGTGGATTGT-3′ | 145 |
Reverse: 5′-CAACCCCAAACCACAACCATAA-3′ | ||
 TIMP3 | Forward: 5′-TGTGTTGGAGGTTAAGGTTGTTTT-3′ | 122 |
Reverse: 5′-ACTCTCCAAAATTACCATACACACC-3′ | ||
 PCQAP 5′ | Forward: 5′-GTTTTGTGATTGAGGYGGTGGT -3′ | 167 |
Reverse: 5′-AAAAATCCCACAATCCAACCC -3′ | ||
 PCQAP 3′ | Forward: 5′- TGATTAATTTAGATTGGGTTTAGAGAA -3′ | 158 |
Reverse: 5′- CCAACTCCAAATCCCCTCTCTAT -3′ | ||