Comparison of the Third Wave Invader human papillomavirus (HPV) assay and the digene HPV hybrid capture 2 assay for detection of high-risk HPV DNA

Molecular diagnostics of infectious disease: Detection and characterization of microbial agents in cytology samples

BACKGROUND

Cytology samples are widely used to diagnose various infectious diseases by detection and identification of causative infectious agents, including bacteria, fungi, and viruses. The role of cytopathology in infectious disease has expanded tremendously in the past decades with the advances in molecular techniques. Molecular diagnostic methods, compared to conventional methods, have shown improved patient outcome, reduction in cost, and shortened hospital stay times. The aim of this article is to review molecular testing in cytology samples for diagnosis of infectious diseases.

METHODS

The literature search for molecular testing in common cytology samples for diagnosis of infectious diseases was performed. The findings of the studies were summarized. The common cytology samples included in this article were gynecologic specimens, cerebrospinal fluid, bronchoalveolar lavage, and urine samples.

CONCLUSIONS

There are a number of molecular diagnostic tests that are available to be used in common cytology samples to detect infectious agents. Each test has its own advantages and limitations. It is our hope that upon reading this review article, the readers will have better understanding of molecular diagnostic testing of infectious diseases utilizing commonly sampled cytology specimens in daily practice.

Prognostic and clinicopathological value of ZIC1 in patients with cervical squamous cell carcinoma

The aim of the present study was to analyze the differences in zinc finger of the cerebellum 1 (ZIC1) expression between cervical cancer tissue, precancer tissue and normal cervical tissue to determine its clinicopathological and prognostic value in cervical squamous cell carcinoma (CSCC). Reverse transcription-quantitative PCR was used to determine the mRNA expression levels of ZIC1 in 569 fresh-frozen biopsy tissues, and immunohistochemistry was performed to detect ZIC1 protein expression in 80 CSCC tissues and 320 cervical intraepithelial neoplasia (CIN) grade III samples. The association of ZIC1 expression with the clinicopathological characteristics of CSCC was then analyzed using Cox regression analysis, and Kaplan-Meier curves were used to analyze the prognostic value. The level of ZIC1 mRNA expression in CSCC was significantly lower compared with normal cervical tissues and CIN I–III tissues (P<0.001). There was a negative correlation between ZIC1 immunoreactivity score (IRS) in CSCC tissue and adjacent noncancerous tissue (R=−0.279; P=0.012); the mean IRS of ZIC1 in CSCC tissue was 5.36±3.48, which was significantly lower compared with the corresponding adjacent noncancerous tissues (11.31±5.68; P<0.001) and CIN III samples (10.42±1.54; P<0.001). In addition, expression of ZIC1 was negatively associated with International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.027) and lymph node metastasis (P<0.001). In Cox regression analysis, ZIC1 expression [hazard ratio (HR), 0.61; 95% confidence interval (CI), 0.40–0.92; P=0.018), FIGO staging (HR, 3.55; 95% CI, 2.35–5.37; P<0.001) and lymph node metastasis (HR, 2.50; 95% CI, 1.62–3.86; P<0.001) were three independent prognostic factors of overall survival. Furthermore, ZIC1 expression was also associated with disease-free survival (P=0.003). These results suggest that ZIC1 expression in CSCC may be lower than in normal cervical tissues or CIN tissues, and high expression of ZIC1 may be negatively associated with FIGO stage and lymph node metastasis. Therefore, ZIC1 may be a promising biomarker for the prognosis of CSCC.

Amplification chemistries in clinical virology

Molecular diagnostic methods have evolved and matured considerably over the last several decades and are constantly being evaluated and adopted by clinical laboratories for the identification of infectious pathogens. Advancement in other technologies such as fluorescence, electronics, instrumentation, automation, and sensors have made the overall diagnostic process more accurate, sensitive, and rapid. Nucleic acid based detection procedures, which rely on the fundamental principles of DNA replication have emerged as a popular and standard diagnostic method, and several commercial assays are currently available based on different nucleic acid amplification techniques. This review focuses on the major amplification chemistries that are used for developing commercial assays and discusses their application in the clinical virology laboratory.

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

The precision prevention and therapy of HPV-related cervical cancer: new concepts and clinical implications

Cervical cancer is the third most common cancer in women worldwide, with concepts and knowledge about its prevention and treatment evolving rapidly. Human papillomavirus (HPV) has been identified as a major factor that leads to cervical cancer, although HPV infection alone cannot cause the disease. In fact, HPV-driven cancer is a small probability event because most infections are transient and could be cleared spontaneously by host immune system. With persistent HPV infection, decades are required for progression to cervical cancer. Therefore, this long time window provides golden opportunity for clinical intervention, and the fundament here is to elucidate the carcinogenic pattern and applicable targets during HPV-host interaction. In this review, we discuss the key factors that contribute to the persistence of HPV and cervical carcinogenesis, emerging new concepts and technologies for cancer interventions, and more urgently, how these concepts and technologies might lead to clinical precision medicine which could provide prediction, prevention, and early treatment for patients.

The new frontier of diagnostics: Molecular assays and their role in infection prevention and control

Recent advances in technology over the last decade have propelled the microbiology laboratory into a pivotal role in infection prevention and control. The rapid adaptation of molecular technologies to the field of clinical microbiology now greatly influences infectious disease management and significantly impacts infection control practices. This review discusses recent developments in molecular techniques in the diagnosis of infectious diseases. It describes the basic concepts of molecular assays, discusses their advantages and limitations, and characterizes currently available commercial assays with respect to cost, interpretive requirements, and clinical utility.

Human Papillomavirus Laboratory Testing: the Changing Paradigm

High-risk human papillomaviruses (HPVs) cause essentially all cervical cancers, most anal and oropharyngeal cancers, and some vaginal, vulvar, and penile cancers. Improved understanding of the pathogenesis of infection and the availability of newer tests are changing the approach to screening and diagnosis. Molecular tests to detect DNA from the most common high-risk HPVs are FDA approved for use in conjunction with cytology in cervical cancer screening programs. More-specific tests that detect RNA from high-risk HPV types are now also available. The use of molecular tests as the primary screening tests is being adopted in some areas. Genotyping to identify HPV16 and -18 has a recommended role in triaging patients for colposcopy who are high-risk HPV positive but have normal cytology. There are currently no recommended screening methods for anal, vulvar, vaginal, penile, or oropharyngeal HPV infections. HPV testing has limited utility in patients at high risk for anal cancer, but p16 immunohistochemistry is recommended to clarify lesions in tissue biopsy specimens that show moderate dysplasia or precancer mimics. HPV testing is recommended for oropharyngeal squamous cell tumors as a prognostic indicator. Ongoing research will help to improve the content of future guidelines for screening and diagnostic testing.

A population-based observational study comparing Cervista and Hybrid Capture 2 methods: improved relative specificity of the Cervista assay by increasing its cut-off

BACKGROUND

High-risk human papillomavirus (HR HPV) testing has been shown to be a valuable tool in cervical cancer screening for the detection of cervical pre-cancer and cancer.

METHODS

We report a purely observational study evaluating HR HPV prevalences in residual liquid-based cytology (LBC) samples using both the Cervista™ HPV HR Test and the Digene Hybrid Capture 2 High-Risk HPV DNA Test (HC2) in a sample of 1,741 women aged ≥30 years of a German routine screening population of 13,372 women. Test characteristics were calculated and a novel method for measuring test performances was applied by calculating ratios of sensitivity or specificity.

RESULTS

The overall agreement of both tests for detection of HR HPV was excellent (κ = 0.8). Relative sensitivities for the detection of histologically confirmed severe cervical intraepithelial dysplasia (CIN3+) were similar for both HPV-tests, which was confirmed by the ratio analysis. However, discrepancy analysis between the Cervista HPV HR test and HC2 revealed a high false positive rate of the Cervista HPV HR test in the cytology normal category.

CONCLUSIONS

Performance of the Cervista HPV test in cervical specimens with abnormal cytology is comparable to HC2 as both tests were highly sensitive and specific for the detection of high grade cervical disease. We also demonstrate evidence that modification of the cut-off values drastically reduces the false positive rate in the cytology normal category without affecting the detection of CIN3+, which ultimately improved specificity of the Cervista HPV HR assay.

Clinical validation of the Cervista HPV HR test according to the international guidelines for human papillomavirus test requirements for cervical cancer screening

This study demonstrates that both the clinical sensitivity and specificity of the Cervista HPV HR test for high-risk human papillomavirus (HPV) detection are not inferior to those of the Hybrid Capture 2 (HC2) test. The intra- and interlaboratory reproducibilities of Cervista were 92.0% (kappa, 0.83) and 90.4% (kappa, 0.80), respectively. The Cervista HPV HR test fulfills all the international HPV test requirements for cervical primary screening purposes.

Comparing the Cervista HPV HR test and Hybrid Capture 2 assay in a Dutch screening population: improved specificity of the Cervista HPV HR test by changing the cut-off

The diagnostic performance of the widely-used Cervista HPV HR test was compared to the Hybrid Capture 2 (HC2) test in a Dutch population-based cervical cancer screening program. In 900 scrapings of women with normal cytomorphology, specificity was 90% (95%CI: 87.84–91.87) for the Cervista HPV HR test and 96% (95%CI: 94.76–97.37) for the HC2 test with 93% agreement between both tests (κ = 0.5, p<0.001). The sensitivity for CIN2+ using 65 scrapings of women with histological-confirmed CIN2+ was 91% (95%CI: 80.97–96.51) for the Cervista HPV HR test and 92% (95%CI: 82.94–97.43) for the HC2 test with 95% agreement between both tests (κ = 0.7, p<0.001). Fifty-seven of 60 HC2 negative/Cervista positive cases tested HPV-negative with PCR-based HPV assays; of these cases 56% were defined as Cervista triple-positive with FOZ values in all 3 mixes higher than the second cut-off of 1.93 (as set by manufacturer). By setting this cut-off at 5.0, specificity improved significantly without affecting sensitivity. External validation of this new cut-off at 5.0 in triple-positive scrapings of women selected from the SHENCCASTII database revealed that 22/24 histological normal cases now tested HPV-negative in the Cervista HPV HR test, while CIN2+ lesions remained HPV-positive. The intra-laboratory reproducibility of the Cervista HPV HR test (n = 510) showed a concordance of 92% and 93% for cut-off 1.93 and 5.0 (κ = 0.83 and κ = 0.84, p<0.001) and inter-laboratory agreement of the Cervista HPV HR test was 90% and 93% for cut-off 1.93 and 5.0 (κ = 0.80 and κ = 0.85, p<0.001). In conclusion, the specificity of the Cervista HPV HR test could be improved significantly by increasing the second cut-off from 1.93 to 5.0, without affecting the sensitivity of the test in a population-based screening setting.

"Equivocal" high-risk HPV DNA tests performed on ThinPrep specimens after ASC-US diagnoses are associated with an increased incidence of CIN3: a cytologic/histologic review of 315 cases

OBJECTIVE

The Hybrid Capture II high-risk HPV test (HC II hrHPVT) improves early detection of cervical neoplasia in Pap tests. However, weakly positive HC II results may be reported as indeterminate or "equivocal," for which there is little clinical guidance. This study is designed to evaluate the clinical outcome of equivocal HC II hrHPVTs and concurrent atypical squamous cells of undetermined significance (ASC-US) on ThinPrep Pap specimens through correlation with 2-year follow-up cervical biopsies.

MATERIALS AND METHODS

Over a 5-year period, ThinPrep Pap tests diagnosed as ASC-US were grouped according to their hrHPVT results (i.e., positive, negative, or equivocal) and correlated with histologic follow-up. All equivocal and representative positive and negative hrHPVTs were included. Biopsies showing high-grade dysplasia were reviewed by two pathologists.

RESULTS

Of 9,012 ASCUS Pap tests, 945 had corresponding hrHPVTs and follow-up cervical biopsies. High-grade squamous intraepithelial lesion (HSIL-cervical intraepithelial neoplasia grades 2/3, CIN2/3) was identified in 20.3% (14/69) of biopsies after equivocal hrHPVTs (CIN2-5.8%, CIN3-14.5% (p=.0261); 16.7% (25/150) after positive hrHPVT (CIN2-12%, CIN3-4.7%); and 5.4% (5/93) of biopsies after negative hrHPVT (CIN2-4.3%, CIN3-1.1%).

CONCLUSION

ASC-US in association with equivocal and positive HC II results respectively shows similar incidences of CIN2/3 on 2-year follow-up cervical biopsy. Additionally, a significant proportion of CIN3 biopsies are in the equivocal HC II cohort. As clinical decision making would be impacted by this finding, laboratories should consider evaluating the clinical performance of their HC II assay via correlation with subsequent cervical biopsies.

Review of the clinical and biologic aspects of human papillomavirus-positive squamous cell carcinomas of the head and neck

Human papillomavirus (HPV), a known etiology of a subset of head-and-neck squamous cell carcinomas (HNCs), causes numerous alterations in normal cellular functions. This article reviews the biology, detection, and treatment of HPV-positive HNC. The role of HPV oncoproteins in tumor development, the natural history of HPV infection, and risk factors for and prevention of transmission of oral HPV are considered. Commonly used methods for detecting HPV infection, including limitations of these methods, are discussed to aid the practicing clinician in using these tests in their clinical practice. Clinical characteristics of HPV-positive HNC, including potential explanations for the improved outcomes seen in patients with HPV-positive HNC, are assessed. Ongoing clinical trials specific for patients with HPV-positive HNC are described, and areas in need of additional research are summarized. Until the results of ongoing trials are known, treatment of HPV-positive HNC should not differ in clinical practice from treatment of similar non-HPV related cancers.

High-Risk Human Papillomavirus DNA Detected in Primary Squamous Cell Carcinoma of Urinary Bladder

Context.—We reported previously that more than one-third (37%) of primary bladder squamous cell carcinomas (SCCs) demonstrate diffuse p16 immunoreactivity independent of gender. This observation made us question whether p16 overexpression in bladder carcinoma is due to human papillomavirus (HPV)–dependent mechanisms.

Objectives.—To determine whether the presence of high-risk HPV (HR-HPV) DNA could be detected in these tumor cells.

Design.—Fourteen cases of primary bladder SCC, which were positive for p16 by immunohistochemistry, were probed for the detection of HR-HPV by in situ hybridization and the signal amplification Invader assay. Samples positive for detection of HR-HPV by Invader assay were amplified by using HR-HPV type-specific primers, and amplification products were DNA sequenced.

Results.—Detection of HR-HPV by the in situ hybridization method was negative in all cases (0 of 14). However, in 3 of 14 cases (21.4%), the presence of HR-HPV DNA was detected with the Cervista HPV HR Invader assay, which was followed by identification of genotype. All positive cases were confirmed by using HR-HPV type-specific amplification followed by DNA sequencing. Identified HR-HPV genotypes included HPV 16 (2 cases) and HPV 35 (1 case).

Conclusions.—High-risk HPV DNA is detectable in a subset of primary bladder SCCs. Based on the well-documented carcinogenic potential of HR-HPV, there is a necessity for additional studies to investigate the role of HR-HPV in bladder carcinogenesis.

Comparative study of the cervista and hybrid capture 2 methods in detecting high-risk human papillomavirus in cervical lesions

High-risk human papillomavirus (HR HPV) testing is important for the follow-up of patients with cytological abnormalities. This study was undertaken to compare the clinical value of the Cervista and hybrid capture 2 (HC2) tests for detection of HR HPV in cervical lesions. Overall 439 cervical specimens with abnormal cytology and 22 normal cervical specimens were subjected to the Cervista and HC2 tests. HPV positivity and its predictive value for high-grade cervical lesions were assessed. The Cervista and HC2 tests showed comparable HR HPV detection rates in women with all cytological and histological diagnoses, with a positive and negative percent agreement of 90.8% and 64.5%, respectively. The two methods had a same sensitivity of 90% in detecting CIN II or greater cervical lesions, while the specificity for the Cervista test and HC2 assay was 47% and 43%, respectively. The positive rate for the Cervista assay probe set A9 increased with the histological severity, ranging from 25.0% in normal specimens to 69.5% in high-grade lesions. In conclusion, the clinical performance for the Cervista test is as excellent as the HC2 test in detecting HR HPV and predicting high-grade cervical lesions.

Type-specific detection of 30 oncogenic human papillomaviruses by genotyping both E6 and L1 genes

Human papillomavirus (HPV) is the principal cause of invasive cervical cancer and benign genital lesions. There are currently 30 HPV types linked to cervical cancer. HPV infection also leads to other types of cancer. We developed a 61-plex analysis of these 30 HPV types by examining two genes, E6 and L1, using MassARRAY matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (PCR-MS). Two hundred samples from homosexual males (HM) were screened by PCR-MS and MY09/MY11 primer set-mediated PCR (MY-PCR) followed by sequencing. One hundred thirty-five formalin-fixed, paraffin-embedded (FFPE) cervical cancer samples were also analyzed by PCR-MS, and results were compared to those of the commercially available GenoArray (GA) assay. One or more HPV types were identified in 64.5% (129/200) of the samples from HM. Comprising all 30 HPV types, PCR-MS detected 51.9% (67/129) of samples with multiple HPV types, whereas MY-PCR detected only one single HPV type in these samples. All PCR-MS results were confirmed by MY-PCR. In the cervical cancer samples, PCR-MS and GA detected 97% (131/135) and 90.4% (122/135) of HPV-positive samples, respectively. PCR-MS and GA results were fully concordant for 122 positive and 4 negative samples. The sequencing results for the 9 samples that tested negative by GA were completely concordant with the positive PCR-MS results. Multiple HPV types were identified in 25.2% (34/135) and 55.6% (75/135) of the cervical cancer samples by GA and PCR-MS, respectively, and results were confirmed by sequencing. The new assay allows the genotyping of >1,000 samples per day. It provides a good alternative to current methods, especially for large-scale investigations of multiple HPV infections and degraded FFPE samples.

Comparison of the Abbott RealTime High-Risk Human Papillomavirus (HPV), Roche Cobas HPV, and Hybrid Capture 2 assays to direct sequencing and genotyping of HPV DNA

Infection with high-risk (HR) human papillomavirus (HPV) genotypes is an important risk factor for cervical cancers. We evaluated the clinical performances of two new real-time PCR assays for detecting HR HPVs compared to that of the Hybrid Capture 2 test (HC2). A total of 356 cervical swab specimens, which had been examined for cervical cytology, were assayed by Abbott RealTime HR and Roche Cobas HPV as well as HC2. Sensitivities and specificities of these assays were determined based on the criteria that concordant results among the three assays were regarded as true-positive or -negative and that the results of genotyping and sequencing were considered true findings when the HPV assays presented discrepant results. The overall concordance rate among the results for the three assays was 82.6%, and RealTime HR and Cobas HPV assays agreed with HC2 in 86.1% and 89.9% of cases, respectively. The two real-time PCR assays agreed with each other for 89.6% of the samples, and the concordance rate between them was equal to or greater than 98.0% for detecting HPV type 16 or 18. HC2 demonstrated a sensitivity of 96.6% with a specificity of 89.1% for detecting HR HPVs, while RealTime HR presented a sensitivity of 78.3% with a specificity of 99.2%. The sensitivity and specificity of Cobas HPV for detecting HR HPVs were 91.7% and 97.0%. The new real-time PCR assays exhibited lower sensitivities for detecting HR HPVs than that of HC2. Nevertheless, the newly introduced assays have an advantage of simultaneously identifying HPV types 16 and 18 from clinical samples.

Effect of glacial acetic acid treatment of liquid-based cytology collections on performance of Cervista HPV HR for detection of high-risk human papillomavirus

Inadequate cervical cytological analysis can be facilitated by glacial acetic acid (GAA) treatment of primary liquid-based collections to remove mucus, erythrocytes, inflammatory cells, and cellular debris. In the context of a commercial human papillomavirus (HPV) hybridization assay performed on 465 tandem specimens with and without GAA treatment, we show that GAA treatment significantly reduces genomic DNA content (P < 0.0001) and creates an increased potential for indeterminate and false-negative results. In the context of cytological workflow, laboratories should consider providing a specimen aliquot for HPV DNA detection prior to GAA treatment.

Comparison of the Seeplex HPV4A ACE and the Cervista HPV assays for the detection of HPV in hybrid capture 2 positive media

Objective

To validate the efficacy of Seeplex HPV4A ACE for the detection of high-risk (HR) human papillomavirus (HPV) and HPV 16 and/or HPV 18 genotypes as compared to the PCR method and the Cervista HPV assays in cervical swab samples.

Methods

Besides liquid-based cytology, additional 97 cervical swab samples were collected for HPV genotyping by HPV4A ACE, Cervista HPV assays, and PCR method. To check the statistical differences, we also conducted the paired proportion test, Cohen's κ statistic, and a receiver operating characteristic curve.

Results

Seeplex HPV4A ACE and the Cervista HPV HR showed substantial agreement with PCR for detection of HR HPVs (88.3%, κ=0.767 and 81.7%, κ=0.636, respectively). Seeplex HPV4A ACE also showed substantial agreement with the Cervista HPV 16/18 test (89.5%, κ=0.628). Additionally, the sensitivity and specificity of Seeplex HPV4A ACE and Cervista HPV HR were 91.4% vs. 84.5% and 73.4%, vs. 72.7%, respectively, when those higher than low-grade squamous intraepithelial lesions were regarded as abnormalities. HPV genotyping for HPV 16/18 detected cervical intraepithelial neoplasias (CINs) better than HR HPV tests (66.7% vs. 24.6% by HPV4A ACE, 52.6% vs. 25.9% by Cervista HPV assays in CIN II or more, relatively).

Conclusion

Seeplex HPV4A ACE is an effective method as the PCR and the Cervista HPV assays for the detection of HR HPVs and for genotyping of HPV 16 and 18.

A new PCR-based mass spectrometry system for high-risk HPV, part I: methods

Infection with high-risk (HR) human papillomaviruses (HPVs) has been confirmed as the necessary cause of cervical cancer. There are many studies that have established and confirmed the relationship of specific HPV types and the risk of invasive cervical cancer. We have developed a novel genotyping method for detecting 14 HR-HPV genotypes simultaneously with MassARRAY (Sequenom, San Diego, CA) technique based on the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). All 14 HPVs showed high specificities and high sensitivities in the plasmid test; lower detection limits for each genotype were from 10 to 100 copies. Furthermore, the MS system has high-throughput capacities, capable of processing, with type-specific output, 4,500 samples in 24 hours. The MS HPV assay is a sensitive and useful tool for HPV genotyping. It has the potential to be suitable for large-scale epidemiologic studies and routine diagnostic clinical applications owing to its high-throughput capacity, high sensitivity, and low cost per case.

Cervista HR and HPV 16/18 assays vs hybrid capture 2 assay: outcome comparison in women with negative cervical cytology

Sensitive and specific assays for human papillomavirus (HPV) are essential for patient management. In this study, we directly compared the efficacy of the Hybrid Capture 2 (HC2; Qiagen, Valencia, CA) and Cervista assays (Hologic, Madison, WI). Consecutive cervical cytology specimens (n = 601) were tested using HC2, Cervista HR, and Cervista HPV 16/18 with analysis of only cytology-negative cases (n = 533). Results indicated no significant difference (P = .458) in prevalence rates between HC2 (7.5%) and Cervista HR (8.5%). The Cervista 16/18 prevalence was 1.6%. The negative percentage of agreement was 95.1% (468/492) vs a 70% (28/40) positive percentage of agreement. No false-negative results were detected by the Cervista internal DNA control. Our data show 29 discordant positive results (12 HC2 and 17 Cervista HR), suggesting some women with negative cytology may be triaged for unnecessary follow-up with either assay. For clinical screening, Cervista HR and HC2 are comparable and, by extension, should provide excellent negative predictive value for histologically relevant disease.

Clinical laboratory evaluation of Invader® chemistry and hybrid capture for detection of high-risk human papillomavirus in liquid-based cytology specimens

A laboratory-developed test for high-risk human papillomavirus (HPV) that utilizes the Invader technology (Hologic, Madison, WI, USA) was compared to hybrid capture (Digene, Gaithersburg, MD, USA). A total of 342 ThinPrep specimens were de-identified following cytology screening (10 high-grade squamous intraepithelial lesions, 14 low-grade squamous intraepithelial lesions, 199 atypical squamous cells of undetermined significance, 119 normal). DNA was manually extracted prior to interrogation with Invader. Hybrid capture/Invader discrepancies were subject to HPV sequencing. One sample (0.3%) was indeterminate by Invader due to low genomic DNA content. Concordance of 341 available tandem hybrid capture/Invader results occurred at a rate of 91.5%. Differences in HPV detection rate between the 2 assays were not statistically significant (P = 0.17). A propensity for false-positive hybrid capture result was confirmed by HPV sequencing in 83% of instances. Manual DNA extraction efficacy did not statistically differ between cytologic classifications (P ≥ 0.19). Invader detection of high-risk HPV is comparably sensitive and more specific than hybrid capture, providing an alternative for molecular HPV detection.

MassARRAY spectrometry is more sensitive than PreTect HPV-Proofer and consensus PCR for type-specific detection of high-risk oncogenic human papillomavirus genotypes in cervical cancer

Type-specific detection of human papillomavirus (HPV) is indicated for better risk stratification and clinical management of women testing positive for HPV and for epidemiologic surveillance. MassARRAY spectrometry (MassARRAY; Sequenom) is a novel method for type-specific detection of 15 high-risk oncogenic HPV types: HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73. PreTect HPV-Proofer (Proofer; Norchip) is a type-specific assay that detects E6/E7 mRNA from five high-risk oncogenic HPV types: HPV-16, -18, -31, -33, and -45. The performance of these tests for type-specific identification of HPV was assessed with cervical specimens from 192 cases of cervical cancer in comparison with consensus MY09/MY11 PCR followed by nucleotide sequencing (consensus PCR). The overall HPV detection rates were 94.8% (95% confidence interval [CI], 91.7, 97.9), 83.3% (95% CI, 78.1, 88.5), and 86.5% (95% CI, 81.7, 91.3) for MassARRAY, Proofer, and consensus PCR, respectively. All tests were negative in six (3.1%) of the 192 cases. Considering only the specimens that contained at least one of the five types targeted by Proofer, the detection rates were 96.6%, 91.4%, and 86.9% for MassARRAY, Proofer, and consensus PCR, respectively. MassARRAY detected multiple infections in 14.1%, Proofer detected multiple infections in 3.6%, and consensus PCR failed to detect any multiple infections. The agreement was highest at 86.0% (kappa = 0.76) between MassARRAY and Proofer and lowest at 81.8% (kappa = 0.69) between Proofer and consensus PCR. In conclusion, MassARRAY is a highly sensitive and accurate method for type-specific detection of oncogenic HPV in cervical cancer, with Proofer showing impressive performance.

A quantum dots and superparamagnetic nanoparticle-based method for the detection of HPV DNA

BACKGROUND

The recent advance in nanomaterial research field prompts the development of diagnostics of infectious diseases greatly. Many nanomaterials have been developed and applied to molecular diagnostics in labs. At present, the diagnostic test of human papillomavirus (HPV) relies exclusively on molecular test. Hereon, we report a rapid and facile quantum dots (QDs) and superparamagnetic nanoparticle-based hybridization assay for the detection of (HPV) 16 infections which combines the merits of superparamagnetic nanoparticles and QDs and wholly differs from a conventional hybridization assay at that the reaction occurs at homogeneous solution, and total time for detection is no more than 1 h.

METHODS

The probes were labeled with superparamagnetic nanoparticles and QDs. Sixty cervical swab samples were used to perform a hybridization assay with these probes, and the results were compared with type-specific polymerase chain reaction (PCR) method.

RESULTS

The statistic analysis suggests that there is no significant difference between these two methods. Furthermore, this method is much quicker and easier than the type-specific PCR method.

CONCLUSION

This study has successfully validated the clinical performance of our hybridization assay. The advantages in the time of detection and ease of process endow this method with great potential in clinical usage, especially mass epidemiological screening.

Testing for human papillomavirus in cervical cancer screening: a review of indications and methodology

High-risk human papillomavirus (hrHPV) testing has become an integral component of cervical cancer screening, given that persistent infection with hrHPV was recognized as a significant risk factor for most precancers and cancers of the cervix. Particularly, testing for hrHPV types (in conjunction with cervical cytology) has been approved for primary screening in women over 30 years of age and for cost-effective triaging of equivocal cervical cytology results. HPV was a small double-stranded DNA virus that cannot be cultured in vitro; so, different types of tests have been developed to detect its presence. Various molecular techniques were available for detecting the presence and/or quantity of hrHPV. In this review, the testing options for hrHPV and its surrogates, with an emphasis on those approved by the US Food and Drug Administration (FDA), were detailed. Cancer (Cancer Cytopathol) 2011;. © 2011 American Cancer Society.

Clinical experience with the Cervista HPV HR assay: correlation of cytology and HPV status from 56,501 specimens

Testing for high-risk (HR) human papillomavirus (HPV) is a key component of current recommendations for cervical cancer screening. Herein is described our clinical experience using Cervista HPV HR, a testing platform recently approved by the US Food and Drug Administration for clinical use. Using data from a high-volume commercial laboratory, a retrospective analysis of cytologic and Cervista HPV HR test results from 56,501 samples was performed, and an indirect comparison was made with previous experience with 53,008 samples tested using the Hybrid Capture 2 platform. Of samples analyzed using Cervista HPV HR, 1.5% were of insufficient volume for testing and 1.1% yielded an insufficient signal from the internal control to be reported. In samples with a cytological interpretation of atypical squamous cells of undetermined significance, 48.5% (95% confidence interval [CI], 47.5 to 49.5) tested positive using Cervista HPV HR, compared with 59.4% (95% CI, 58.3 to 60.5) of samples using Hybrid Capture 2. Of samples from women aged 30 years or older with a negative cytological interpretation, 5.8% (95% CI, 5.6 to 6.1) tested positive using Cervista HPV HR, compared with 5.5% (95% CI, 5.3 to 5.7) of samples using Hybrid Capture 2. When stratified by five-year age groups between 30 and 65 years, positivity rates for high-risk human papillomavirus were similar in the Cervista HPV HR and Hybrid Capture 2 populations, and were consistent with expectations established by the literature.

Clinical performance of the PreTect HPV-Proofer E6/E7 mRNA assay in comparison with that of the Hybrid Capture 2 test for identification of women at risk of cervical cancer

Human papillomavirus (HPV) DNA testing has a higher clinical sensitivity than cytology for the detection of high-grade cervical intraepithelial neoplasia or worse (CIN 2+). However, an improvement in specificity would be desirable. As malignant transformation is induced by HPV E6/E7 oncogenes, detection of E6/E7 oncogene activity may improve specificity and be more predictive of cervical cancer risk. The PreTect HPV-Proofer assay (Proofer; Norchip) detects E6/E7 mRNA transcripts from HPV types 16, 18, 31, 33, and 45 with simultaneous genotype-specific identification. The clinical performance of this assay was assessed in a cross-sectional study of women referred for colposcopy in comparison with the Hybrid Capture 2 (HC2; Qiagen) test, which detects DNA of 13 high-risk oncogenic HPV types collectively. Cervical specimens were collected in PreservCyt, and cytology was performed using the ThinPrep method (Hologic). The samples were processed for HPV detection with Proofer and HC2 and genotyping with the Linear Array method (Roche Molecular Systems). Histology-confirmed CIN 2+ served as the disease endpoint to assess the clinical performance of the tests. A total of 1,551 women were studied, and of these, 402 (25.9%) were diagnosed with CIN 2+ on histology. The Proofer assay showed a sensitivity of 78.1% (95% confidence interval [CI], 74.1 to 82.1) versus 95.8% (95% CI, 93.8 to 97.8) for HC2 (P < 0.05) and a specificity of 75.5% (95% CI, 73.0 to 78.0) versus 39.6% (95% CI, 36.8 to 42.4), respectively (P < 0.05). The lower sensitivity and higher specificity of Proofer for detection of CIN 2+ can be attributed to the fact that this test detects the expression of E6/E7 genes beyond a threshold from a limited number of oncogenic HPV types. In conclusion, Proofer is more specific than HC2 in identifying women with CIN 2+ but has a lower sensitivity.

Comparison of methods trial for high-risk HPV

In efforts to improve service, we compared the performance of four methods of HPV detection: Invader HPV (Hologic), Hybrid Capture 2 (Qiagen), Inform HPV detection (Ventana), and standard PCR.Using blinded/de-identified cervical samples in Preservcyt (Hologic), we compared Ventana's Inform HPV Test, against Hologic's HPV Invader and PCR. In a separate evaluation, we compared Inform versus Invader versus hc2. Ventana employs in situ hybridization; Hologic's technology uses three specifically designed oligonucleotides and a fluorescent signal for detection. Qiagen's hc2 method incorporates enzyme-linked antibody detection of RNA-DNA hybrids. PCR testing was provided by Access Genetics (Minneapolis, MN). The United States Food and Drug Administration recently approved the Third Wave/Hologic Invader HPV high-risk test (rebranded as Cervista HPV HR Test).In this small study, involving a few hundred tests, Third Wave, Qiagen, and PCR tests were comparable. Kappa statistics comparing Third Wave to PCR and Third Wave to Qiagen were 0.88 and 0.74, respectively. Ventana's method did not correlate well with any of the other methods with Kappa's ranging from a low of 0.25 versus Qiagen to 0.31 versus PCR. Kappa statistics measure correlation and not accuracy of measurement.Although we felt that the specificity of our original HPV method, Ventana Inform was satisfactory and lowered our subsequent colposcopy rate, worries about its lower sensitivity caused us to look at other techniques. Other methods, PCR, hc2, and Invader, appeared comparable with one another in our series. We chose to implement the Third Wave test in our laboratory.

A comparative review of laboratory-developed tests utilizing Invader HPV analyte-specific reagents for the detection of high-risk human papillomavirus

BACKGROUND

Testing for human papillomavirus (HPV) has emerged as an important component of cervical cancer screening and disease management. Analytic performance (sensitivity, specificity, positive predictive value, negative predictive value, accuracy) and clinical relevance are important criteria by which any new test must be reviewed.

OBJECTIVE

This paper compares laboratory-developed tests, utilizing Invader analyte-specific reagents (ASRs) for the detection of oncogenic HPV DNA, to the Digene Hybrid Capture 2 test (HC2). In addition to accurately identifying the presence or absence of HPV, genotyping has emerged as an important consideration for risk stratification and patient management. This paper reviews all current relevant Invader HPV literature to explain how these results shape our current understanding of the topic.

History of the use of HPV testing in cervical screening and in the management of abnormal cervical screening results

Twenty years have passed since the first studies using human papillomavirus (HPV) testing began in clinical settings. At that time controversy regarding the role of HPV in cervical carcinogenesis still divided the scientific world. Epidemiological and natural history studies on HPV and cervical cancer in the ensuing two decades secured the necessary role of high-risk (carcinogenic) HPV in the genesis of cervical cancer, providing the rationale for testing for its cause. Subsequently, cross sectional studies and large randomized trials have provided clinical validation for high-risk HPV testing in triage of atypical squamous cells of undetermined significance (ASC-US), in postcolposcopy management of women referred for ASC-US, atypical squamous cells "cannot rule out high grade" (ASC-H), atypical glandular cells "not otherwise specified" (AGC NOS) and low grade squamous intraepithelial lesion (LSIL) and not found to have cervical intraepithelial neoplasia (CIN) 2+ or adenocarcinoma in situ (AIS) at initial colposcopy, in post-treatment of CIN 2+ surveillance, and in cotesting with the Papanicolaou (Pap) test of women age 30 and over. This is the story of the road traveled that brought the clinical use of HPV testing from its genesis only a few years after Dr. zur Hausen's discovery to its present eminent role in both primary cervical cancer screening and abnormal Pap management.

Clinical performance of the APTIMA HPV Assay for the detection of high-risk HPV and high-grade cervical lesions

BACKGROUND

Human papillomavirus (HPV) DNA testing is widely used in conjunction with Papanicolaou (Pap) testing in cervical cancer screening programs to improve the detection of high-grade lesions. While HPV DNA test sensitivity is good, an improvement in specificity is desired. Detection of HPV mRNA may improve specificity. The APTIMA HPV Assay detects the mRNA of 14 high-risk HPV types in liquid-based cytology specimens.

OBJECTIVE

To evaluate APTIMA HPV Assay performance for detection of high-risk HPV and high-grade cervical intraepithelial neoplasia (CIN) compared to Qiagen's Hybrid Capture 2 HPV DNA (HC2) test.

STUDY DESIGN

Liquid Pap specimens were collected from 800 women referred to colposcopy and tested with the APTIMA HPV Assay and the HC2 test. Complete results were available for 753 subjects. A subset of samples (n = 393) were typed using Roche's Linear Array HPV Genotyping Test.

RESULTS

Sensitivity and specificity for detection of high-risk HPV were >92% and 99% for the APTIMA HPV Assay and 93% and 82% for the HC2 test. Clinical sensitivity and specificity were 91% and >55% for detection of CIN 2+, and 98% and 53% for detection of CIN 3+ for the APTIMA HPV Assay; values for the HC2 test were 95% and 47% for CIN 2+, and 99% and 44% for CIN 3+.

CONCLUSIONS

The APTIMA HPV Assay is sensitive and very specific for detection of high-risk HPV. The APTIMA HPV Assay had similar clinical sensitivity for disease detection but higher clinical specificity than the HC2 test, which may improve patient management and reduce the cost of care.

Development and evaluation of a PCR and mass spectroscopy (PCR-MS)-based method for quantitative, type-specific detection of human papillomavirus

Knowledge of the central role of high-risk human papillomavirus (HPV) in cervical carcinogenesis, coupled with an emerging need to monitor the efficacy of newly introduced HPV vaccines, warrant development and evaluation of type-specific, quantitative HPV detection methods. In the present study, a prototype PCR and mass spectroscopy (PCR-MS)-based method to detect and quantitate 13 high-risk HPV types is compared to the Hybrid Capture 2 High-Risk HPV DNA test (HC2; Digene Corp., Gaithersburg, MD) in 199 cervical scraping samples and to DNA sequencing in 77 cervical tumor samples. High-risk HPV types were detected in 76/77 (98.7%) cervical tumor samples by PCR-MS. Degenerate and type-specific sequencing confirmed the types detected by PCR-MS. In 199 cervical scraping samples, all 13 HPV types were detected by PCR-MS. Eighteen (14.5%) of 124 cervical scraping samples that were positive for high-risk HPV by HC2 were negative by PCR-MS. In all these cases, degenerate DNA sequencing failed to detect any of the 13 high-risk HPV types. Nearly half (46.7%) of the 75 cervical scraping samples that were negative for high-risk HPV by the HC2 assay were positive by PCR-MS. Type-specific sequencing in a subset of these samples confirmed the HPV type detected by PCR-MS. Quantitative PCR-MS results demonstrated that 11/75 (14.7%) samples contained as much HPV copies/cell as HC2-positive samples. These findings suggest that this prototype PCR-MS assay performs at least as well as HC2 for HPV detection, while offering the additional, unique advantages of type-specific identification and quantitation. Further validation work is underway to define clinically meaningful HPV detection thresholds and to evaluate the potential clinical application of future generations of the PCR-MS assay.

Molecular diagnostics of infectious diseases

PURPOSE OF REVIEW

The purpose of this article is to review the molecular methods commonly used in medical microbiology as well as to update the clinician as to newer molecular technologies that show promise in the identification of microorganisms as well as evaluation of the presence of virulence factors and antibiotic resistance determinants.

RECENT FINDINGS

Numerous molecular assays have been developed recently using a variety of technologies. Direct hybridization techniques have allowed analysis of blood culture bottles for organisms such as methicillin-resistant Staphylococcus aureus. Target amplification methods allow postamplification analysis using a variety of technologies depending on the clinical needs for the assay. Postamplification analysis includes methods such as Sanger sequencing, pyrosequencing, reverse hybridization, and Luminex analysis, which are becoming more widely utilized. In the future, whole genome sequencing, mass spectrometry, and microarray analysis may provide a wealth of information that can be used to specifically tailor the treatment of infectious diseases.

SUMMARY

The implications of current trends in molecular infectious diseases are moving towards high-throughput, simple, array-type technologies that will provide a wealth of data regarding types of organisms present in a sample and the virulence factors/resistance determinants that influence the severity of disease. As a result of these developments, infectious diseases will be more accurately and effectively treated.