Evaluation of HPV Genotyping Assays for Archival Clinical Samples
Open accessAbstract
Human papillomavirus (HPV) testing and genotyping of FFPE tissue samples is important in epidemiological investigations. Here, we compare four different HPV genotyping methods for use in FFPE clinical samples. Comparative testing was performed on 99 samples with a clinical suspicion of HPV. Specimens were analyzed with Anyplex II HPV28 detecting 28 genotypes using real-time PCR and melting curve analysis, CLART HPV2 detecting 35 genotypes using PCR and microarray detection, and MGP5+/6+ consensus primer system together with pyrosequencing. Results were compared to a real-time PCR reference protocol detecting 14 genotypes. In total, 68% of the samples were positive for an HPV genotype using the reference protocol and MGP5+/6+ primer system. Anyplex II HPV28 analysis and CLART HPV2 had 82% and 72% positive samples, respectively. All four methods showed good agreement when comparing the 14 genotypes included in the reference protocol. When evaluating all genotypes, the Anyplex II HPV28 assay and the CLART assay changed the status of the sample (individually or together) from negative with respect to the reference protocol to positive for either a Group 1 (n = 4) or Group 2 (n = 6) genotype. We conclude from this study that for an extended genotyping approach with a high sensitivity for FFPE specimens, both the Anyplex II HPV28 and CLART HPV2 assays are suitable alternatives despite minor intra-assay differences.
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In several studies that compared HPV genotyping methodologies, AnyplexTM II HPV28 demonstrated good agreement with other HPV assays, including LA.
“In several studies that compared HPV genotyping methodologies, Anyplex™ II HPV28 demonstrated good agreement with other HPV assays, including LA.”
From Comparative evaluation of HPV genotyping: A study on the performance concordance between Anyplex II HPV28 detection and Linear Array genotyping tests in nationwide studies in Brazil (2024) · cites this paper as [29]
The Discussion (page not supplied) says all four methods showed good agreement for the specified HPV genotypes, and the Detection of Genotypes Specified by Reference Protocol section reports 97% agreement for Anyplex II HPV28 against the reference protocol. But this study did not compare Anyplex directly with LA (Roche Linear Array); it mentions LA only as an assay against which primers had previously been validated. The cited paper is also one study, not evidence by itself for 'several studies.' (LLM, conf=0.88)
Experimental — accuracy not yet measuredAnyplexTM II HPV28's good agreement with other HPV assays is likely due to its highly sensitive multiplexed detection approach.
“This is likely due to its highly sensitive multiplexed detection approach [8, 28–30].”
From Comparative evaluation of HPV genotyping: A study on the performance concordance between Anyplex II HPV28 detection and Linear Array genotyping tests in nationwide studies in Brazil (2024) · cites this paper as [29]
The paper reports good agreement for Anyplex II HPV28 in the Discussion and describes its technology as allowing a “very sensitive multiplexed detection approach” in the assay description. It does not explicitly attribute the agreement to that approach; the proposed causal link is an inference. (LLM, conf=0.79)
Experimental — accuracy not yet measured
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- Authors
- Lillsunde Larsson, G., Carlsson, J., Karlsson, M. G., & Helenius, G.
- Affiliations
- Örebro University (SE)
- Venue
- The Journal of Molecular Diagnostics
- Publisher
- Elsevier BV
- Published
- 2015-05
- Volume
- 17
- Issue
- 3
- Pages
- 293-301
- ISSN
- 1525-1578 (ISSN-L)
- OpenAlex
- W2064571822
- Cited by
- 49
- References
- 18
- Citations by year
- 2026: 3 · 2025: 4 · 2024: 6 · 2023: 7 · 2022: 2 · 2021: 5 · 2019: 5 · 2018: 6 · 2017: 3 · 2016: 6 · 2015: 2
- FWCI
- 4.45
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Journal of Molecular Diagnostics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Örebro University Hospital
- Topics
- Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
- Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
- Health Sciences › Medicine › Oncology › HER2/EGFR in Cancer Research
- Keywords
- human papillomavirus, HPV genotyping, formalin-fixed paraffin-embedded tissue, pyrosequencing, microarray detection, real-time PCR, assay comparison, diagnostic sensitivity
- MeSH terms
- Base Sequence, DNA, Viral, Female, Genotype, Humans, DNA Primers, Papillomaviridae, Papillomavirus Infections, Genotyping Techniques, Real-Time Polymerase Chain Reaction
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