Marilyn C. Olson

Clinical validation of the Cervista® HPV HR and 16/18 genotyping tests for use in women with ASC-US cytology

OBJECTIVE High-risk (HR) human papillomavirus (HPV) testing is important in cervical cancer screening for triage to colposcopy. This study evaluated the clinical performance of the Cervista HPV HR and 16/18 genotyping tests for detection of HPV in cervical cytology specimens. METHODS The tests were prospectively evaluated in a multicenter clinical study. DNA was extracted from approximately 4000 residual liquid-based cytology specimens collected during routine liquid-based Papanicolaou tests at standard of care visits and was assessed for the presence of HR HPV and/or HPV types 16 and 18. All women with cytology results of atypical squamous cells of undetermined significance (ASC-US) or greater underwent colposcopic examination and biopsies were collected. Test results were compared with local colposcopy and histology results from a central pathology review panel. RESULTS There were 1347 subjects with complete data sets of cytology, HR HPV, colposcopy, and histology included in the analysis of the HPV HR test. Sensitivity of the HPV HR test for detection of cervical intraepithelial neoplasia (CIN) 2+ among women with ASC-US cytology was 92.8% (95% confidence interval [CI]: 84.1-96.9) and the negative predictive value (NPV) was 99.1% (95% CI: 98.1-99.6). Sensitivity for detection of > or =CIN 3 in women with ASC-US was 100% (95% CI: 85.1-100) and the NPV was 100% (95% CI: 99.4-100). The specificity of the test for detection of > or =CIN 2 and > or =CIN 3 was 44.2% (95% CI: 41.5-46.9) and 43% (95% CI: 40.3-45.7), respectively. The HPV 16/18 genotyping test also performed as expected in women with ASC-US cytology who were positive for HR HPV. CONCLUSION The Cervista HPV HR test can be clinically used for detecting HR HPV types in conjunction with cervical cytology for use in triage of women with ASC-US cytology during routine cervical cancer screening.

An invasive cleavage assay for direct quantitation of specific RNAs

RNA quantitation is becoming increasingly important in basic, pharmaceutical, and clinical research. For example, quantitation of viral RNAs can predict disease progression and therapeutic efficacy. Likewise, gene expression analysis of diseased versus normal, or untreated versus treated, tissue can identify relevant biological responses or assess the effects of pharmacological agents. As the focus of the Human Genome Project moves toward gene expression analysis, the field will require a flexible RNA analysis technology that can quantitatively monitor multiple forms of alternatively transcribed and/or processed RNAs (refs 3,4). We have applied the principles of invasive cleavage and engineered an improved 5′-nuclease to develop an isothermal, fluorescence resonance energy transfer (FRET)–based signal amplification method for detecting RNA in both total RNA and cell lysate samples. This detection format, termed the RNA invasive cleavage assay, obviates the need for target amplification or additional enzymatic signal enhancement. In this report, we describe the assay and present data demonstrating its capabilities for sensitive (<100 copies per reaction), specific (discrimination of 95% homologous sequences, 1 in ≥20,000), and quantitative (1.2-fold changes in RNA levels) detection of unamplified RNA in both single- and biplex-reaction formats.

Invader technology for DNA and RNA analysis: principles and applications.

Concomitant advances made by the Human Genome Project and in the development of nucleic acid screening technologies are driving the expansion of pharmacogenomic research and molecular diagnostics. However, most current technologies are restrictive due to their complexity and/or cost, limiting the potential of personalized medicine. The Invader® assay, which can be used for genotyping as well as for gene expression monitoring without the need for intervening target amplification steps, presents an immediate solution that is accurate, simple to use, scaleable and cost-effective.

Analytical performance of the Investigational Use Only Cervista™ HPV HR test as determined by a multi-center study

BACKGROUND Any HPV test designed to be utilized in cervical cancer screening programs should be highly validated both analytically and clinically. OBJECTIVES The Investigational Use Only (IUO) Cervista HPV HR test is designed to detect 14 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68). The analytical performance of the Cervista HPV HR test was characterized in a multi-center study. RESULTS Analytical sensitivity for the 14 high-risk HPV types that the test is designed to detect ranged from 1,250 copies to 7,500 copies per reaction depending on HPV type. Accuracy compared to PCR with bi-directional sequencing was 91.4% [95% CI: 86.5 95.0%]. The reproducibility, when tested at three different testing centers, resulted in an overall inter-run reproducibility (between day/within site) agreement of 98.8% [1-sided 95% Confidence Lower Limit = 96.9%] and an overall inter-site reproducibility (between site) agreement of 98.7% [1-sided 95% Confidence Lower Limit = 97.9%]. The Cervista HPV HR test showed no cross-reactivity with DNA from seven non-oncogenic HPV types or 17 different infectious agents at up to 10(7) copies per reaction. CONCLUSIONS The analytical performance of the Cervista HPV HR test demonstrates sufficient analytical performance for use in cervical cancer screening. As with any clinical laboratory test, analytical characteristics must be evaluated in light of the clinical performance of this assay.

Analytical performance of Cervista HPV 16/18 genotyping test for cervical cytology samples.

BACKGROUND Human papillomavirus (HPV) types 16 and 18 are the 2 most frequent types associated with cervical cancer. Identifying their presence or absence in cervical samples may assist in triaging women for subsequent management. The Cervista HPV 16/18 genotyping test specifically detects the presence of HPV 16 and 18 in ThinPrep cervical specimens. OBJECTIVES The objective was to establish the analytical performance of the CERVISTA HPV 16/18 genotyping test. STUDY DESIGN These studies were performed in support of a regulatory submission to the US Food and Drug Administration. Here we report the analytical sensitivity (limit of detection), accuracy compared to consensus L1 gene PCR/bi-directional sequencing, precision, reproducibility, and cross-reactivity (specificity) of the genotyping test. RESULTS Analytical sensitivity for detection of HPV 16 and 18 ranged between 625 and 1250 copies/reaction for both types. When compared to PCR/sequencing for women with atypical squamous cells of undetermined significance cytology, the positive percent agreement was 94.1% (95% confidence interval [CI], 89.8-96.7) and the negative percent agreement was 85.7% (95% CI, 82.4-88.4). The test demonstrated high within-laboratory and inter-operator precision. Reproducibility within sites and between 3 testing sites resulted in 100% agreement with expected results (150 positive, 90 negative results). The genotyping test did not exhibit cross-reactivity to DNA from common low-risk HPV types and other microorganisms found in the human female reproductive tract. CONCLUSIONS These analytical performance data support the use of CERVISTA HPV 16/18 genotyping test for the detection and differentiation of HPV 16 and 18 in ThinPrep cervical cytology specimens.

Rate of detection of high-risk HPV with two assays in women ≥ 30 years of age

BACKGROUND High-risk (HR) human papillomavirus (HPV) prevalence rates, as determined by the Cervista(®) HPV HR test, in women aged ≥30 years in a routine screening population have not been studied. OBJECTIVES The primary objective of this study was to estimate HR HPV prevalence in women negative for intraepithelial lesion or malignancy (NILM) cytology using the CERVISTA HPV HR test. The study also compared HR HPV prevalence rates in women aged ≥30 years and NILM cytology using the CERVISTA HPV HR and Hybrid Capture(®) 2 (hc2) tests. STUDY DESIGN A multi-center study was conducted to analyze HR HPV prevalence rates using the CERVISTA HPV HR test from residual ThinPrep(®) specimens. HR HPV positive rates were determined for hc2; percent agreement between the CERVISTA HPV HR and the hc2 tests were reported. RESULTS HR HPV prevalence rates among women with NILM cytology were not statistically different between the CERVISTA HPV HR and hc2 tests (6.92% [98/1417] versus 5.93% [84/1417], respectively; P>0.05). The overall percent agreement between the tests was 95.3% (1351/1417; 95% confidence interval [CI]: 94.1-96.3; κ=0.61, 95% CI: 0.53-0.70). There were no statistically significant differences between tests across age groups or investigational sites. For both tests, there was a statistically significant decrease in HR HPV positive results as age increases (CERVISTA HPV HR, P=0.0009; hc2, P<0.0001). DISCUSSION There is no statistically significant difference between HR HPV prevalence rates obtained with the CERVISTA HPV HR and hc2 tests in women aged ≥30 years with NILM cytology.

Invader Assay for RNA Quantitation

The Invader assay is a homogeneous, isothermal, signal amplification system for the quantitative detection of nucleic acids. The assay can directly detect either DNA or RNA without target amplification or reverse transcription. It is based on the ability of Cleavase enzymes to recognize as a substrate and cleave a specific nucleic acid structure generated through the hybridization of two oligonucleotides to the target sequence. The combination of sequence-specific oligonucleotide hybridization and structure-specific enzymatic cleavage results in a highly specific assay well suited for discriminating closely related gene sequences. This includes detection of single nucleotide polymorphisms directly from genomic DNA as well as highly homologous mRNAs in closely related gene families. Because Cleavase substrate recognition is structure, and not sequence dependent, cleavage and detection can be applied to virtually any DNA or RNA sequence.

Erratum: An invasive cleavage assay for direct quantitation of specific RNAs

Peggy S. Eis, Marilyn C. Olson, Tsetska Takova, Michelle L. Curtis, Sarah M. Olson, Tatiana I. Vener, Hon S. Ip, Kevin L. Vedvik, Christian T. Bartholomay, Hatim T. Allawi, Wu-Po Ma, Jeff G. Hall, Michelle D. Morin, Tom H. Rushmore, Victor I. Lyamichev, and Robert W. Kwiatkowski. Nat. Biotechnol. 19, 673–676 (2001).