However, the RLB assays are relatively laborious, are limited to a maximum of about 40 samples per assay, and depend on visual read-out of the hybridization signal. To overcome these drawbacks, HPV genotyping using Luminex® suspension array technology has
been developed (11–14). The Luminex®-based genotyping coupled with GP5+/6+ PCR allowed sensitive GPCR Compound Library and specific genotyping of 27 mucosal HPV types in a 96-well plate format with a digital read-out (13). Moreover, a modified version of GP5+/6+ PCR was successfully introduced into the Luminex®-based assay, and showed improved sensitivity (15). A VeraCode-ASPE method was first developed for the detection of SNP in the human genome (16) and has
been applied to multiplex SNP genotyping on the Illumina BeadXpress® platform (17, 18). The ASPE primer is composed of two check details distinct regions: the 5′ region that contains the capture sequence, which is used in a subsequent hybridization reaction, and the 3′ region that contains the genomic target region with a SNP nucleotide at the extreme 3′ end. For SNP genotyping, the ASPE primer that matches the SNP nucleotide to the genome is extended by the primer extension reaction and is thus labeled with biotinylated nucleotides. After the primer extension, the products are mixed with VeraCode beads, so that the capture sequence on the primer hybridizes to its complementary sequence attached to the VeraCode beads. Labeling is then carried out with a streptavidin-fluorophore conjugate, followed by scanning and detection of the fluorescent signal using an Illumina
BeadXpress® reader (Illumina Inc., San Diego, CA, USA). In this work, the VeraCode-ASPE method on the Illumina BeadXpress® platform was evaluated for its suitability as a method to detect and genotype HPV-DNA (Fig. 1). The HPV-DNA amplified by PGMY-PCR was selected as a target for the VeraCode-ASPE genotyping, as PGMY-PCR 2-hydroxyphytanoyl-CoA lyase has been validated as a sensitive and specific means for HPV-DNA amplification (19, 20). HPV-type-specific ASPE primers were designed to target the PCR amplicons of 16 HPV types (HPV6, 11, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) in the 3′ region (Table 1), and with type-specific capture sequences in the 5′ region. The Tm values of the HPV-type-specific sequences, the lengths of which ranged from 19 to 28 bases, were adjusted to be between 54°C and 66°C using Primer3Plus software (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi) thus allowing similar annealing profiles. HPV-DNA, which was provided by the HPV laboratory network in the WHO as a quality-assured authentic panel for validation of HPV genotyping, was used to assess the sensitivity and specificity of the VeraCode-ASPE HPV genotyping.