title: Development and clinical evaluation of a highly sensitive DNA microarray for detection and genotyping of human papillomaviruses.
abstract: Human papillomavirus (HPV) has been found in cervical cancer, tonsillar cancer, and certain types of head and neck cancers. We report on a DNA microarray-based method for the simultaneous detection and typing of HPVs. The genotype spectrum discriminated by this HPV DNA microarray includes 15 high-risk HPV genotypes and 12 low-risk HPV genotypes. The HPV DNA microarray showed high degrees of specificity and reproducibility. We evaluated the performance of the HPV DNA microarray by application to three HPV-positive cell lines (HeLa, Caski, and SiHa cells) and two HPV-negative cell lines (C33A and A549 cells). The HPV DNA microarray successfully identified the known types of HPV present in the cell lines. The detection limit of the HPV DNA microarray was at least 100-fold higher than that of PCR. To assess the clinical applicability of the HPV DNA microarray, we performed the HPV genotyping assay with 73 nonmalignant and malignant samples from 39 tonsillar cancer patients. Twenty-five of the 39 (64.1%) malignant samples were positive for HPV, whereas 3 of 34 (8.8%) nonmalignant samples were positive for HPV. This result shows a preferential association of HPV with tonsillar carcinomas. The correlations of the presence of HPV with the grade of differentiation and risk factors were not significant. Our data show that the HPV DNA microarray may be useful for the diagnosis and typing of HPV in large-scale epidemiological studies.
authors.affiliation: Research and Development, GenomicTree, Inc., 461-6 Jonmin-dong Yusong, Taejon 305-811, South Korea.
authors.forename: Tae Jeong
authors.initials: TJ
authors.lastname: Oh
authors.forename: Chang Jin
authors.initials: CJ
authors.lastname: Kim
authors.forename: Suk Kyung
authors.initials: SK
authors.lastname: Woo
authors.forename: Tae Seung
authors.initials: TS
authors.lastname: Kim
authors.forename: Dong Jun
authors.initials: DJ
authors.lastname: Jeong
authors.forename: Myung Soon
authors.initials: MS
authors.lastname: Kim
authors.forename: Sunwoo
authors.initials: S
authors.lastname: Lee
authors.forename: Hyun Sill
authors.initials: HS
authors.lastname: Cho
authors.forename: Sungwhan
authors.initials: S
authors.lastname: An
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000821:virology; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014067:Tonsillar Neoplasms / Q000821:virology