Fig. 2

PCR amplification of HPV DNA by three consensus primer sets and HPV genotyping by amplicon sequencing. a Representative gel image of PCR amplicon detection by high-resolution capillary gel electrophoresis. Representative samples #285 (LSIL) and #179 (HSIL) reveal MY09/11, FAP59/64, and GP-E6/E7 F/B amplicons with expected yield of ~450-, 480- (or 260-bp fragment), and 660-bp fragments, respectively. b Parallel PCR testing for HPV by three primer sets. Venn diagrams show intersecting and complementary sets of cytological samples (N) detected of HPV DNA by MY-, FAP-, and E6/E7 primer sets according to cytological diagnoses, i.e., NILM, LSIL, and HSIL. The net positivity of simultaneous testing for HPV (union of the circles) in NILM, LSIL, and HSIL are 31/100 (31 %), 95/100 (95 %), and 71/77 (92 %), respectively. c HPV genotype distribution of 191 cytology samples with PCR-detected HPV DNA according to cytological diagnoses: NILM, LSIL, and HSIL. The increase in carcinogenic HPV genotypes was coincident with cytological grade (Spearman’s ρ = 0.658, p < 0.001). Samples positive for the 260-bp fragment that aligned closest to HPV-58 were assigned as “alpha-9” species because of the non-specific short sequence length. *p < 0.05 by the chi-square test. Abbreviations: AM alignment marker, B buffer, bp base pair, HSIL high-grade squamous intraepithelial lesion, IARC International Agency for Research on Cancer, LSIL low-grade squamous intraepithelial lesion, M molecular weight ladder, NILM negative for intraepithelial lesion or malignancy