Comparison of Analytical and Clinical Performance of HPV 9G DNA Chip, PANArray HPV Genotyping Chip, and Hybrid-Capture II Assay in Cervicovaginal Swabs

Abstract

Background:Human papillomavirus (HPV) infection can be detected by using several molecular methods, including Hybrid-Capture II (HC2) assay and variable HPV DNA chip tests, although each method has different sensitivities and specificities.Methods:We performed HPV 9G DNA Chip (9G) and PANArray HPV Genotyping Chip (PANArray) tests on 118 cervicovaginal swabs and compared the results with HC2, cytology, histology, and direct sequencing results.ResultsThe overall and high-risk HPV (HR-HPV) positivity rates were 62.7% and 44.9% using 9G, and 61.0% and 30.5% using PANArray, respectively. The positivity rates for HR-HPV with these two chips were significantly lower than 55.1% when HC2 was used. The sensitivity of overall HPV positivity in detecting histologically confirmed low-grade cervical squamous intraepithelial lesions or higher was 88.7% for all three tests. The specificity was 58.5% for 9G and 61.5% for PANArray, which was significantly lower than the 72.3% for HC2. With the HR-HPV+ genotype threshold, the sensitivity decreased to 75.5% for 9G and 52.8% for PANArray, which was significantly lower than the 88.7% for HC2. Comparison of the two chips showed concordant results in 55.1% of the samples, compatible results in 16.9%, and discordant results in 28.0%, exhibiting poor agreement in detecting certain HPV genotypes. Compared with direct sequencing, 9G yielded no discordant results, whereas PANArray yielded 31 discordant results (26.7%).ConclusionsCompared with HC2, the HPV genotyping tests showed lower sensitivity in histologic correlation. When the two chips were compared, the 9G was more sensitive and accurate for detecting HR-HPV than the PANArray.

Analytic performance of PANArray HPV and HPV 9G DNA chip tests for genotyping of high-risk human papillomavirus in cervical ThinPrep PreservCyt samples

“…PANArray HPV was developed in Korea in 2009 [9]. Although a few previous studies have compared the clinical efficacy of PANArray HPV to other HPV detecting assays, the evaluation was performed with respect to the relationship with histologic and cytological diagnoses [14, 21]. However, the authors did not compare diagnostic accuracies of the tests for assaying this specific HPV genotype [14, 21].…”

“…Although a few previous studies have compared the clinical efficacy of PANArray HPV to other HPV detecting assays, the evaluation was performed with respect to the relationship with histologic and cytological diagnoses [14, 21]. However, the authors did not compare diagnostic accuracies of the tests for assaying this specific HPV genotype [14, 21]. Therefore, we focused on highly prevalent HR-HPV genotypes worldwide (HPV-16 and HPV-18) and in East Asia (HPV-58) and purely compared analytic performance of HPV tests using DNA or PNA using result of direct sequencing as reference.…”

“…PCR products were electrophoresed and DNA of samples with a positive band was purified. In samples with discrepant results between HPV 9G DNA and PANArray HPV assays or those with multiple infections by these 2 tests, type specific primers [14] were applied again to obtain specific PCR products. We used type specific primers [14], being able to define 19 HPVs which were commonly detected by both HPV 9G DNA and PANArray HPV tests (S1 Table).…”

“…In samples with discrepant results between HPV 9G DNA and PANArray HPV assays or those with multiple infections by these 2 tests, type specific primers [14] were applied again to obtain specific PCR products. We used type specific primers [14], being able to define 19 HPVs which were commonly detected by both HPV 9G DNA and PANArray HPV tests (S1 Table). Five types of HR-HPVs (including HPV-26, -53, -69, -70, and -73) and 8 LR-HPVs (including HPV-32, -43, -44, -54, -55, -62, -81, and -83) were excluded from the analysis because they could only be detected by PANArray HPV.…”

Stromal p16 Overexpression in Gastric-type Mucinous Carcinoma of the Uterine Cervix

“…HPV genotype assay. Polymerase chain reaction (PCR)-based microarray analysis for HPV genotyping was performed using a commercially available HPV 9G DNA chip (BMT HPV 9G DNA Chip; Biometrix Technology, Chuncheon, Republic of Korea) (31,32). The 9G microarray detected the presence of 14 high-risk (types 16,18,31,33,35,39,45,51,52,56,58,59, 66, and 68) and five low-risk (types 6, 11, 34, 40, and 42) HPV types; the analyses were performed according to the manufacturer's recommendations (33)(34)(35)(36).…”