Fig. 2

HPV DNA detection by PCR amplification, capillary electrophoresis and dideoxy (Sanger) sequencing. a Gel image and electropherogram of amplicon detection by high-resolution capillary electrophoresis. Representative samples #311, 312, 319, and 330 (HSIL) reveal 1 or 2 amplicons after using consensus primers (GP-E6/E7 F/B) to amplify an E6/E7 segment with an expected fragment size of ~660 bp (range, 619-819 bp). Amplicon size variability reflects sequence differences between HPV genotypes. In general, deep sequencing resolved a greater number of HPV genotypes than capillary electrophoresis per sample. Sample #330 illustrates this with detection of 2 amplicons on electrophoresis, but 8 genotypes by deep sequencing. b Representative sample (#311) with a single HPV infection revealing 1 amplicon (699 bp peak on electropherogram) and clean sequencing chromatogram. Representative sample (#319) with multiple HPV infections revealing 2 amplicons (619 and 656 bp peaks on electropherogram) and “noisy” overlapping peaks on the chromatogram. AM, alignment marker; B, buffer; bp, base pair; M, molecular-weight marker