Search PubMed⌕ Search
Home/Archive/PubMed

PubMed · 16564098

Human papillomavirus genotyping using a modified linear array detection protocol.

Matthew P Stevens·Suzanne M Garland·Sepehr N Tabrizi
View original source ↗Export metadata ↓

Abstract

A standardized PCR-based linear array genotyping assay has been developed (Roche Molecular Systems) allowing the concurrent typing of 37 human papillomavirus (HPV) types. A component of this assay, the PCR amplicon detection protocol, requires the use of a shaking water-bath incubator for amplicon/probe hybridization and subsequent stringent washing, which many laboratories may find cumbersome or simply not possess. In this study, the utility of a dry-air incubator in substitution of the recommended shaking water-bath for use in this assay was confirmed. DNA was extracted by AmpliLute method from 150 PreservCyt specimens collected from patients undergoing ablation treatment for histologically confirmed cervical abnormality. The DNA was amplified by PCR and amplicons detected by both standard and modified protocols, varying only by the method of incubation for DNA hybridization and stringent washing. Identical HPV-type profiles were generated in 149/150 (99.3%) of the specimens tested by both protocols, representing a near perfect level of concordance (kappa = 0.98). It was proposed that this modification would markedly simplify the detection process, reduce setup time and eliminate the potential for water spillover, thereby allowing more laboratories to adopt this method subsequent to in-house validation.

Explore related subjects

Cervix UteriDNA, ViralFemaleGenotypeHumansNucleic Acid HybridizationPapillomaviridaePapillomavirus InfectionsPolymerase Chain ReactionJournal Article

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Matthew P Stevens, Suzanne M Garland, Sepehr N Tabrizi. 2006-03-27. Human papillomavirus genotyping using a modified linear array detection protocol.. https://doi.org/10.1016/j.jviromet.2006.02.007

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2006

Labor-associated gene expression in the human uterine fundus, lower segment, and cervix.

BACKGROUND: Preterm labor, failure to progress, and postpartum hemorrhage are the common causes of maternal and neonatal mortality or morbidity. All result from defects in the complex mechanisms controlling labor, which coordinate changes in the uterine fundus, lower segment, and cervix. We aimed to assess labor-associated gene expression profiles in these functionally distinct areas of the human uterus by using microarrays. METHODS AND FINDINGS: Samples of uterine fundus, lower segment, and cervix were obtained from patients at term (mean +/- SD = 39.1 +/- 0.5 wk) prior to the onset of labor (n = 6), or in active phase of labor with spontaneous onset (n = 7). Expression of 12,626 genes was evaluated using microarrays (Human Genome U95A; Affymetrix) and compared between labor and non-labor samples. Genes with the largest labor-associated change and the lowest variability in expression are likely to be fundamental for parturition, so gene expression was ranked accordingly. From 500 genes with the highest rank we identified genes with similar expression profiles using two independent clustering techniques. Sets of genes with a probability of chance grouping by both techniques less than 0.01 represented 71.2%, 81.8%, and 79.8% of the 500 genes in the fundus, lower segment, and cervix, respectively. We identified 14, 14, and 12 those sets of genes in the fundus, lower segment, and cervix, respectively. This enabled networks of co-regulated and co-expressed genes to be discovered. Many genes within the same cluster shared similar functions or had functions pertinent to the process of labor. CONCLUSIONS: Our results provide support for many of the established processes of parturition and also describe novel-to-labor genes not previously associated with this process. The elucidation of these mechanisms likely to be fundamental for controlling labor is an important prerequisite to the development of effective treatments for major obstetric problems--including prematurity, with its long-term consequences to the health of mother and offspring.

Cervix Uteri↗
PubMed2006

Evaluation of HPV 16 PCR detection in self- compared with clinician-collected samples in women referred for colposcopy.

OBJECTIVES: A clinical prospective evaluation study was conducted to evaluate PCR detection of high-risk human papillomavirus (HPV) type 16 in self-sampled vaginal compared with clinician-collected cervical specimens. METHODS: Paired vaginal and cervical specimens were collected from 137 consecutive women referred for colposcopy because of abnormal cervical cytology. In-house and a commercial PCR method for HPV type 16 were used. Self-sampled vaginal HPV 16 detection was compared to histology and physician-collected cervical specimens. RESULTS: Of the 137 patients, 98 had proven abnormal histology and were included in the analysis. Overall, using the cervix HPV detection as reference method, the self-sampled vaginal sample showed sensitivity 91.8%, specificity 96.1% and agreement kappa (kappa) 0.881. Using the histology as reference, all 11 cervical cancer cases were HPV-16-positive in both cervical and vaginal samples, and in 43 high-grade lesions, detection sensitivity in cervix was 72.1% (kappa 0.588) and vagina 67.4% (kappa 0.516). HPV 16 detection did not differ (P=0.27) between clinician-collected cervical and self-sampled vaginal specimens. CONCLUSIONS: The self-collected vaginal sample is highly concordant with the physician-collected cervical sample in HPV 16 detection.

Cervix Uteri↗