Comparison between two human papillomavirus genotyping assays targeting the L1 or E6/E7 region in cervical cancer biopsies

Agreement between L1 and E6/E7-based assays for detection of high-risk HPV in cervical, oropharyngeal and penile cancers

AIMS

Human papillomavirus (HPV) molecular testing targets either the late gene L1 or early genes E6 and/or E7. Loss of L1 during integration is suggested to compromise sensitivity in samples associated with cancer, however, clear evidence for this is lacking. Our aim is to address this by performing a head-to-head comparison between assays targeting L1 vs E6/E7, using a series of high-grade and invasive disease samples within different biological matrices and anatomical sites.

METHODS

We obtained 298 samples comprising of liquid-based cytology and biopsies of cervical cancer and cervical intraepithelial neoplasia grade 3, in addition to biopsies of penile and oropharyngeal cancers. Two commercially available HPV primary screening assays and two assays with extended genotyping were applied to the sample set targeting L1 (Abbott RealTime HR HPV Assay and Optiplex HPV Genotyping Test) and E6/E7 genes (Xpert HPV Test and EuroArray HPV Test).

RESULTS

Agreement for high-risk HPV (hrHPV) for all samples types between the screening assays is over 88% and over 96% for the two genotyping assays. For HPV 16 agreement is over 90% for both screening and genotyping assays. Kappa statistics show good to very good agreement between the screening and genotyping assays for hrHPV and HPV 16.

CONCLUSIONS

Analysis of the valid results from our data indicates that L1 and E6/E7 targeting assays show similar performance for detection of hrHPV in high grade cervical lesions and cancers of cervix, penis and oropharynx.

Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years

Background

Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time.

Methods

We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp).

Results

Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6–35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1–2.2) for viral DNA.

Conclusions

We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01529-9.

A real-time PCR approach based on SPF10 primers and the INNO-LiPA HPV genotyping extra assay for the detection and typing of human papillomavirus

A highly sensitive SPF10 real-time PCR was developed to achieve simultaneous amplification and detection of the human papillomavirus (HPV) target. That way, LiPA analysis of the HPV-negative samples can be avoided, reducing workload and cost. Here, we describe in detail a SYBR Green I-based real-time PCR assay based on SPF10 primers using the LightCycler(®) 480 system to generate and detect HPV amplicons, which are compatible with the LiPA assay.

Comparison of SPF10 real-time PCR and conventional PCR in combination with the INNO-LiPA HPV Genotyping Extra assay for the detection and typing of human papillomavirus in cervical samples

The novel SPF10 real-time PCR assay allows the simultaneous amplification and detection of the HPV target. That way, LiPA analysis of the HPV-negative samples can be avoided, reducing workload and cost. This study aims to evaluate the performance of the SPF10 real-time PCR in combination with the LiPA assay for HPV detection and typing in cervical samples. Thirty-nine cervical samples were subjected to the SPF10 conventional PCR in combination with the LiPA assay. Subsequently, the SPF10 real-time PCR was performed to enable the comparison between the SPF10 conventional and the real-time PCR results. In case of discrepancy, the samples were subjected to the CLART HPV2 assay. As a result, 27 out of 39 samples were identified as HPV-positive by the SPF10 real-time PCR and were genotyped further by the LiPA assay. Twenty samples (74.1%) showed an absolute agreement between the conventional and real-time SPF10 PCR (concordant), three (11.1%) displayed additional or fewer types (compatible), two (7.4%) did not show any similarity between both assays (discordant) and the remaining two (7.4%) were LiPA-negative. The two assays showed an excellent strength of agreement for individual (κ=0.932) and multiple genotype detection (κ=0.834). In conclusion, the two SPF10 PCR methods are comparable. Therefore, the SPF10 real-time PCR with subsequent LiPA could be used for the detection and genotyping of HPV in cervical samples.

Rapid and easy identification of capsular serotypes of Streptococcus pneumoniae by use of fragment analysis by automated fluorescence-based capillary electrophoresis

The purpose of this study was to develop a high-throughput method for the identification of pneumococcal capsular types. Multiplex PCR combined with fragment analysis and automated fluorescent capillary electrophoresis (FAF-mPCR) was utilized. FAF-mPCR was composed of only 3 PCRs for the specific detection of serotypes 1, 2, 3, 4, 5, 6A/6B, 6C, 7F/7A, 7C/(7B/40), 8, 9V/9A, 9N/9L, 10A, 10F/(10C/33C), 11A/11D/11F, 12F/(12A/44/46), 13, 14, 15A/15F, 15B/15C, 16F, 17F, 18/(18A/18B/18C/18F), 19A, 19F, 20, 21, 22F/22A, 23A, 23B, 23F, 24/(24A/24B/24F), 31, 33F/(33A/37), 34, 35A/(35C/42), 35B, 35F/47F, 38/25F, and 39. In order to evaluate the assay, all invasive pneumococcal isolates (n = 394) characterized at Hospital Sant Joan de Déu, Barcelona, Spain, from July 2010 to July 2011 were included in this study. The Wallace coefficient was used to evaluate the overall agreement between two typing methods (Quellung reaction versus FAF-mPCR). A high concordance with Quellung was found: 97.2% (383/394) of samples. The Wallace coefficient was 0.981 (range, 0.965 to 0.997). Only 11 results were discordant with the Quellung reaction. However, latex reaction and Quellung results of the second reference laboratory agreed with FAF-mPCR for 9 of these 11 strains (82%). Therefore, we considered that only 2 of 394 strains (0.5%) were not properly characterized by the new assay. The automation of the process allowed the typing of 30 isolates in a few hours with a lower cost than that of the Quellung reaction. These results indicate that FAF-mPCR is a good method to determine the capsular serotype of Streptococcus pneumoniae.