HPV Direct Flow CHIP: A new human papillomavirus genotyping method based on direct PCR from crude-cell extracts

Abstract

HPV Direct Flow CHIP is a newly developed test for identifying 18 high-risk and 18 low-risk human papillomavirus (HPV) genotypes. It is based on direct PCR from crude-cell extracts, automatic flow-through hybridization, and colorimetric detection. The aim of this study was to evaluate the performance of HPV Direct Flow CHIP in the analysis of 947 samples from routine cervical screening or the follow-up of abnormal Pap smears. The specimens were dry swab samples, liquid-based cytology samples, or formalin-fixed paraffin-embedded tissues. The genotype distribution was in agreement with known epidemiological data for the Spanish population. Three different subgroups of the samples were also tested by Linear Array (LA) HPV Genotyping Test (n=108), CLART HPV2 (n=82), or Digene Hybrid Capture 2 (HC2) HPV DNA Test (n=101). HPV positivity was 73.6% by HPV Direct Flow CHIP versus 67% by LA, 65.9% by HPV Direct Flow CHIP versus 59.8% by CLART, and 62.4% by HPV Direct Flow CHIP versus 42.6% by HC2. HPV Direct Flow CHIP showed a positive agreement of 88.6% with LA (k=0.798), 87.3% with CLART (k=0.818), and 68.2% with HC2 (k=0.618). In conclusion, HPV Direct Flow CHIP results were comparable with those of the other methods tested. Although further investigation is needed to compare the performance of this new test with a gold-standard reference method, these preliminary findings evidence the potential value of HPV Direct Flow CHIP in HPV vaccinology and epidemiology studies.

Clinical Validation of AdvanSure GenoBlot Assay as Primary Screening and Test of Cure for Human Papillomavirus Infection

“…The overall positive rates and the concordance rate of the two assays were comparable to those of previous reports [4][5][6][7][8][9][10][11]. The positive rates of individual genotypes were relatively higher in GenoBlot than in HPVDNAChip, with exceptions for genotypes 51 and 56, for which HPVDNAChip showed higher positive rates than GenoBlot.…”

“…In current practice, there are three major contexts in which tests for high risk (HR) genotypes of HPV are relevant: 1) primary screening of cervical cancer and precancerous lesions; 2) triage of low-grade disease; and 3) test of cure after treatment [2,3]. A significant number of studies have been reported for the primary cervical high risk lesion screen and triage; however, little has been reported in terms of the evaluation of test of cure [2][3][4][5][6][7][8][9][10][11].…”

Distribution of Human Papillomavirus Genotypes among Women in Mashhad, Iran

“…Based on their association with different grades of lesions, HPV that can induce carcinogenesis has been classified as high risk or oncogenic, while low-risk HPVs are those which cause genital warts and collaborate with high-risk HPVs. The HPV Direct Flow CHIP is intended for the simultaneous screening and genotyping of 18 high-risk genotypes (HPV16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, and 82) and 4 low-risk genotypes (HPV6, 11, 42, and 44/45) by PCR, followed by reverse dot-blot hybridization that is based on DNA flow technology (semi-automated hybriSpot 12 TM and automated hybriSpot 24 TM ) [16] . Finally, descriptive statistics were used to determine the distribution of HPV.…”

“…The average global prevalence of HPV infection has been reported to be almost 10% (in the range of 1.4-25.6%). This group of viruses consists of low-risk HPVs that do not cause cancer but can cause skin warts (genotypes 6, 11, 42, and 44), and high-risk HPVs that cause cancer (genotypes 16,18,26,31,33,35,39,45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82). Neoplastic and cervical cancer may occur due to exposure to high-risk HPV infection.…”

Detection and Genotyping of Human Papillomavirus DNA in Formalin-Fixed Paraffin-Embedded Specimens with the HPV Direct Flow CHIP System

“…The performance of HPV Direct Flow CHIP in cytological samples was found to be highly similar to that of the Linear Array Genotyping Test (Roche Molecular Systems, Alameda, CA, USA), Hybrid Capture 2 (Digene Corp., Gaithersburg, MD, USA), and CLART HPV2 (Genomica, Tres Cantos, Madrid, Spain) commercial assays, by Direct PCR (using crude cell extracts) [7]. In addition, a high agreement was observed among the results of HPV Direct Flow CHIP, Linear Array Genotyping Test, and Direct Sequencing when purified DNA was used as amplification template (submitted for publication).…”