Low-density addressable array for the detection and typing of the human papillomavirus

We have developed a low-density DNA array for the detection and typing of human papillomavirus (HPV) DNA. The gene chemistry strategy involves using a combination of the polymerase chain reaction (PCR) with the consensus oligonucleotide primers MY09/MY11 followed by a ligase detection reaction (LDR). Fluorochrome-labeled HPV-specific primers are joined to a common primer modified with a unique anchoring sequence called a zip code on its 3' end. The result is a series of 60-70 base pair and single-stranded ligation products that are then hybridized to their respective zip code complements affixed to glass slide based arrays. Nine separate zip codes were assigned, one for each HPV type (6,11,16,18, 31, 33, 35, and 53) and one for a beta-globin internal control marker. Two additional zip-codes were reserved for a pair of consensus HPV LDR products: the cLDR1 and cLDR2 primers hybridize to a conserved sequence within the HPV L1 open reading frame internal to the MY09/MY11 fragment. These consensus primers were shown to detect over 40 different HPV types. The purpose of this study was to evaluate the analytic performance of this low-density microarray based assay for HPV, as well as to introduce our simplified read-out instrumentation, shown here to be a low cost and highly efficient way to detect and genotype HPV for clinical testing.