Table 1 Formalin-fixed and paraffin embedded (FFPE) specimen processing, cytology specimens and human papillomavirus (HPV) testing methods
From: Detection of HPV DNA in paraffin-embedded cervical samples: a comparison of four genotyping methods
Cytology specimens | HPV genotyping methods/protocol for FFPE specimens | ||||
|---|---|---|---|---|---|
Characteristics | Linear array | Onclarity | Inno-LiPA | Linear array | SPF-LiPA25 |
Deparaffinization | NA | No | Yes | No | No |
DNA extraction | Crude extraction | One-step heat / chemical lysis + FOX™ magnetic particle DNA purification | Xylene, proteinase K, phenol-chloroform extraction, ethanol precipitation | Crude extraction | Crude extraction |
HPV testing | PGMY09/11 Linear Array | The BD Onclarity™HPV Assay | Inno-LiPA | PGMY09/11 Linear Array | SPF10-DEIA, LiPA25(version 1) |
Probes for oncogenic types detectable | 16, 18, 31, 33, 35, 39, 45, 51, 56, 58, 59, 66, 68 and 52/33/35/58 | 16, 18, 31, 45, 51, 52, 33/58, 39/68/35, and 59/ 56/66 | 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68 | 16, 18, 31, 33, 35, 39, 45, 51, 56, 58, 59, 66, 68, and 52/33/35/58 | 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68/73 |
Amplicon length (bp) | 450 | 79-137 | 65 | 450 | 65 |