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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
  1. Onclarity, The BD Onclarity™ HPV Assay; Inno-LiPA, The Inno-LiPA system; Linear Array, The PGMY09/11 Linear Array, and SPF-LiPA25, The SPF10-DEIA, LiPA25(version 1) NA, not applicable; HPV 52 is positively identified in the linear Array when the presence of HPV 33, 35, and 58 is excluded