Table 3.
Commonly used primers targeting the L1 region of HPV genome.
| Primer name | Primer sequences | Remarks | References |
|---|---|---|---|
| MY09/11 | Forward (5'-GCMCAGGGWCATAAYAATGG-3') Reverse (5'-CGTCCMARRGGAWACTGATC-3') |
One of the commonly used first generation primers. Target a ∼450-bp fragment which is usually too long for formalin-fixed tissues. The amplified product allows type identification by restriction fragment length polymorphisms, hybridization with type-specific probes or by sequencing. |
143 |
| PGMY09/11 | PGMY11-A (5'-GCA CAG GGA CAT AAC AAT GG-3') PGMY11-B (5'-GCG CAG GGC CAC AAT AAT GG-3') PGMY11-C (5'-GCA CAG GGA CAT AAT AAT GG-3') PGMY11-D (5'-GCC CAG GGC CAC AAC AAT GG-3') PGMY11-E (5'-GCT CAG GGT TTA AAC AAT GG-3') PGMY09-F (5'-CGT CCC AAA GGA AAC TGA TC-3') PGMY09-G (5'-CGA CCT AAA GGA AAC TGA TC-3') PGMY09-H (5'-CGT CCA AAA GGA AAC TGA TC-3') PGMY09-I (5'-GCC AAG GGG AAA CTG ATC-3') PGMY09-J (5'-CGT CCC AAA GGA TAC TGA TC-3') PGMY09-K (5'-CGT CCA AGG GGA TAC TGA TC-3') PGMY09-L (5'-CGA CCT AAA GGG AAT TGA TC-3') PGMY09-M (5'-CGA CCT AGT GGA AAT TGA TC-3') PGMY09-N (5'-CGA CCA AGG GGA TAT TGA TC-3') PGMY09-P (5'-GCC CAA CGG AAA CTG ATC-3') PGMY09-Q (5'-CGA CCC AAG GGA AAC TGG TC-3') PGMY09-R (5'-CGT CCT AAA GGA AAC TGG TC-3') |
An improved version of MY09/MY11 targeting the 144 same 450-bp fragment. Use in the Linear Array HPV Genotyping Test (Roche, Branchburg), where the HPV types are identified by hybridization with type-specific probes. |
144 |
| GP5+/6+ | Forward (5'-TTT GTT ACT GTG GTA GAT ACT AC-3') Reverse (5'-GAA AAA TAA ACT GTA AAT CAT ATT C-3') |
Targets a ∼150-bp fragment suitable for formalin-fixed tissues. Commonly used in large-scale epidemiological studies. Reported to have sub-optimal sensitivity for a variant of HPV 52 commonly found in East Asia due to mutation at the primer binding site. |
145,153 |
| SPF | Forward primer (5'-GCI CAG GGI CAT AAC AAT GG-3') Two reverse primers: (5'-GTI GTA TCI ACA ACA GTA ACA AA-3') and (5'-GTI GTA TCI ACA TCA GTA ACA AA-3') |
Targets a short (∼65-bp) fragment. Good for samples with fragmented DNA such as formalin-fixed tissues. Modifed versions include SPF6 and SPF10 with the addition of more primers. SPF10 primers are used in the INNO-LiPa HPV Genotyping assay, but sequences not disclosed. |
146 |
| L1F/L1R | Forward (5'-CGT AAA CGT TTT CCC TAT TTT TTT-3') Reverse (5'-TAC CCT AAA GAC CCT ATA CTG-3') |
Targets a ∼255-bp fragment, a length that may not be retained in formalin-fixed tissues. | 147 |