Development and Validation of a New HPV Genotyping Assay Based on Next-Generation Sequencing

Yi, Xin; Zou, Jing; Xu, Jiajia; Liu, Tao; Liu, Tengfei; Hua, Shuweng; Feng, Xiaobing; Nie, Xifang; Ye, Lili; Yu-fen, Luo; Xu, Lin; Du, Hui; Wu, Ruifang; Yang, Ling; Liu, Ren; Yang, Bin; Wang, Jian; Belinson, Jerome L.

doi:10.1309/ajcp9p2kjsxekcjb

Cited by 54 publications

(37 citation statements)

References 23 publications

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“…Moreover, this assay was optimized to control the cost at <$5.00/case. This assay could be used to detect the presence or absence of one or more 14 HR-HPV types, using the human β-globin gene (HBB) as the internal quality control (Yi et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

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Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening

Chen

et al. 2016

Genet. Mol. Res.

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ABSTRACT. The aim of this study was to evaluate the performance of three new high-risk human papillomavirus (HPV) assays for primary cervical cancer screening, by using self-collected samples, and to identify an HPV assay that could overcome the major obstacles faced during large-scale population-based screening. Two hundred and ten women showing abnormal cervical cytology (and referred for a colposcopy) were recruited in this study. Self-collected samples obtained from all women were tested with the Cobas, Seq, and BioPerfectus Multiplex Real Time HPV assays; simultaneously, clinician-collected samples (from the same women) were tested with the gold-standard Cobas HPV assay. The results of all the assays were consistent. The sensitivity, positive predictive value, and negative predictive value for cervical intraepithelial neoplasia 2+ (CIN2+) and CIN3+ were comparable between the self-collected samples tested with the three new assays and the clinician-collected samples tested with the Cobas HPV assay (P > 0.05). The single-genotype HPV load per sample did not differ significantly between the self-and clinician-collected samples (P = 0.195). In conclusion, the results of this study demonstrated the applicability of the three new HPV assays for primary cervical cancer screening based on self-collection.

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Section: Discussionmentioning

confidence: 99%

“…The SeqHPV assay was used to amplify the approximately 150 bp of the HPV L1 gene using a series of unique primers. The human β-globin (HBB) gene was used as the internal quality control (Yi et al, 2014).…”

Section: Seqhpv Assaymentioning

confidence: 99%

Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening

Chen

et al. 2016

Genet. Mol. Res.

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“…The selfcollected samples were placed on specimen cards contained in the kits that were in turn sent to BGI Clinical Laboratories (BGI Shenzhen, Shenzhen, China), certified by National Health and Family Planning Commission of the People's Republic of China for analysis. They were analyzed using SEQHPV, a new validated high-risk HPV genotyping assay based on next-generation genomic sequencing [25].…”

Section: Home-based Hpv Kit Groupmentioning

confidence: 99%

“…HPV-DNA testing provides a novel and alternative pathway to increasing cervical cancer screening among women who may not readily access a clinic Pap test [21]. It is important to note that that a self-collected sample is equivalent in sensitivity to a direct collected specimen [22][23][24][25]. With this new development, there is a growing need to examine preference, acceptability and reach among women who are less likely to access the clinic-based Pap test.…”

Section: Introductionmentioning

confidence: 99%

Cervical cancer screening with clinic‐based Pap test versus home HPV test among Somali immigrant women in Minnesota: a pilot randomized controlled trial

Sewali

Okuyemi

Askhir³

et al. 2015

Cancer Medicine

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Cervical cancer is more common in the Somali immigrant population than the general population in the United States (US). There are low rates of cervical cancer screening among Somali women. This study compares cervical cancer screening test completion rates for a home human papilloma virus (HPV) test and standard clinic Pap test. Sixty-three Somali immigrant women aged 30–70 years who had not undergone cervical cancer screening within the past 3 years were randomly assigned to a home HPV test group (intervention) or a clinic Pap test group (control). Test completion rates were measured at 3 months. Univariate and multivariate logistic regression models were used to explore factors associated with test completion (intention-to-treat analysis). Participants in the HPV test group were 14 times more likely to complete the test compared to those in the Pap test group (P = 0.0002). Women who reported having friends/family members to talk about cancer screening were approximately three times more likely to complete any screening test than those who did not (P = 0.127) and participants who reported residing in the US longer were more likely to complete a screening test (P = 0.011). Future research should explore the potential of using the home-based HPV test kits as an initial approach to cervical cancer screening. Impact: The use of a self-sampling HPV kit has the potential to increase cervical cancer screening in under-served communities in the US.

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“…HPV typing by NGS is different in that it is not dependent on probes for detection that may cause cross-hybridizations. At least three previous HPV-genotyping assays using NGS have found NGS to be both sensitive and accurate: Arroyo et al and Militello et al both used the PGMY set of primers for the amplification of a 450 bp fragment [18,19], while Yi et al [43] used a series of unique primers for the amplification of a 150 bp fragment of the L1 gene, which is similar in length to the fragments produced by the MGP primers used here.…”

Section: Discussionmentioning

confidence: 99%

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

et al. 2017

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Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay. Furthermore, NGS provided an increased resolution by identifying genetic variants of individual HPV types. The same Modified General Primers (MGP)-amplicon was used in both methods. The NGS method is described in detail to facilitate implementation in the clinical microbiology laboratory and includes suggestions for new standards for detection and calling of types and variants with improved resolution.

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Development and Validation of a New HPV Genotyping Assay Based on Next-Generation Sequencing

Abstract: This population-based study has demonstrated the applicability of a new NGS high-risk HPV assay for primary cervical cancer screening based on self-collection.

Cited by 54 publications

References 23 publications

Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening

Evaluation of novel assays for the detection of human papilloma virus in self-collected samples for cervical cancer screening

Cervical cancer screening with clinic‐based Pap test versus home HPV test among Somali immigrant women in Minnesota: a pilot randomized controlled trial

HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization

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