A low density microarray method for the identification of human papillomavirus type 18 variants.
We describe a novel microarray based-method for the screening of oncogenic human papillomavirus 18 (HPV-18) molecular variants. Due to the fact that sequencing methodology may underestimate samples containing more than one variant we designed a specific and sensitive stacking DNA hybridization assay. This technology can be used to discriminate between three possible phylogenetic branches of HPV-18. Probes were attached covalently on glass slides and hybridized with single-stranded DNA targets. Prior to hybridization with the probes, the target strands were pre-annealed with the three auxiliary contiguous oligonucleotides flanking the target sequences. Screening HPV-18 positive cell lines and cervical samples were used to evaluate the performance of this HPV DNA microarray. Our results demonstrate that the HPV-18's variants hybridized specifically to probes, with no detection of unspecific signals. Specific probes successfully reveal detectable point mutations in these variants. The present DNA oligoarray system can be used as a reliable, sensitive and specific method for HPV-18 variant screening. Furthermore, this simple assay allows the use of inexpensive equipment, making it accessible in resource-poor settings.
Laboratory of Molecular Biology, Health Services Studies Centre, University of Veracruz, 147 Carmen Serdan St., Centre, Veracruz-Llave, Veracruz 91700, Mexico. tmeza@uv.mx.
Thuluz
T
Meza-Menchaca
John
J
Williams
Rocío B
RB
Rodríguez-Estrada
Aracely
A
García-Bravo
Ángel
Á
Ramos-Ligonio
Aracely
A
López-Monteon
Rossana C
RC
Zepeda
D004252:DNA Mutational Analysis / Q000295:instrumentation*; D015342:DNA Probes / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D014644:Genetic Variation / Q000235:genetics*; D052161:Human papillomavirus 18 / Q000235:genetics* / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D015342:DNA Probes; D004279:DNA, Viral