Table 1. Reference sequences for the twelve oncogenic HPV types and CpG positions.
| HPV type | Reference sequence | CpG position | ||||||
|---|---|---|---|---|---|---|---|---|
| L1 Ia | L1 IIb | L2 | ||||||
| 16 | NCBI: NC_001526.2 | 5601 | 5606 | 5609 | 5616 | 6457 | 4261 | |
| 18 | GenBank: KC470224.1 (L1) EF202151.1 (L2) | 5599 | 5616 | 6433 | 4268 | |||
| 31 | GenBank: J04353.1 | 5518 | 5521 | 5524 | 5530 | 6498 | 4195 | |
| 33 | GenBank: M12732.1 | 5557 | 5560 | 5566 | 5572 | 6409 | 4234 | |
| 35 | GenBank: M74117.1 | 5540 | 5543 | 5546 | 5553 | 6519 | 4208 | |
| 39 | GenBank: KC470245.1 | 5682 | 6513 | 4301 | ||||
| 45 | GenBank: KC470260.1 | 5620 | 5636 | 6463 | 4260 | |||
| 51 | GenBank: GQ487711.1 (L1) KF436879.1 (L2) | 13 | 848 | 4158 | ||||
| 52 | GenBank: HQ537750.1 | 5613 | 5616 | 5622 | 5628 | 6450 | 4290 | |
| 56 | GenBank: EF177179.1 | 5561 | 5567 | 5570 | 5576 | 6475 | 6496 | 4247 |
| 58 | GenBank: GI222386 | 5606 | 5609 | 5615 | 5621 | 6447 | 6458 | 4268 |
| 59 | GenBank: KC470266.1 | 5618 | 6452 | 4255 | ||||
a Some HPV types do not have all the four CpGs found in the HPV16 reference sequence, but only two (HPV18, 45) or one (HPV39, 51, 59)
b Some HPV types (HPV56, 58) have two CpGs close to the CpGs selected in HPV16 sequence. For these types the average between the methylation values of two CpGs can be considered.