Development and evaluation of a PCR and mass spectroscopy (PCR-MS)-based method for quantitative, type-specific detection of human papillomavirus

Development of high-throughput genotyping method of all 18 HR HPV based on the MALDI-TOF MS platform and compared with the Roche Cobas 4800 HPV assay using clinical specimens

Background

To develop a new 18 high-risk human papillomavirus (HR HPV) detection and genotyping assay, which is important to evaluate the risk degree of HR HPV for causing cancers.

Methods

All 18 HR HPV and β-globin relative DNA fragments were synthesized and cloned to a plasmid pUC57 to obtain their recombinant plasmids. Based on the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform, each of the 18 HR HPV genotypes were investigated using their constructed recombinant plasmids. The new 18 HR HPV genotyping assay was tested using 356 clinical specimens and the results were compared to ones detected by the Roche Cobas 4800 HPV assay (Cobas). The discrepant results between two assays were resolved by sequencing and genotyping methods.

Results

The new 18 HR HPV MALDI-TOF MS genotyping assay was developed using HPV recombination plasmids. The sensitivity was 10³ to 10² copies/reaction for the all 18 HR HPV. This new developed HR HPV genotyping test was used to detect the clinical specimens. When the results on clinical samples detected by the new MALDI-TOF MS HPV test were compared with ones detected by the Roche Cobas 4800 HPV assay in terms of 14 HR HPV, the concordance was 80.1% (kappa coefficient, 0.60; 95% confidence interval [CI], 0.52–0.69). The discrepant results were resolved by sequencing and genotyping and suggests that the developed HR HPV assay is more sensitive and specific.

Conclusions

The new developed 18 HR HPV detection method based on MALDI-TOF MS platform is a high-throughput assay for the all 18 HR HPV genotypes and a powerful complement to current detection methods.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-6036-z) contains supplementary material, which is available to authorized users.

Intranodal cystic changes: a potential radiologic signature/biomarker to assess the human papillomavirus status of cases with oropharyngeal malignancies

OBJECTIVE

The aim of this study was to determine if lymph node imaging findings can predict human papillomavirus (HPV) positivity in oropharyngeal squamous cell cancers.

METHODS AND MATERIALS

Pretreatment postcontrast neck computed tomographic scans of 49 patients (male, 35; female, 14; age range, 45-76 years) diagnosed with oropharyngeal malignancies and with available HPV data were retrospectively reviewed. Metastatic lymph nodes were identified based on standardly accepted size and morphological criteria. Various lymph node parameters were studied, including presence of cystic foci in the metastatic lymph nodes, abnormal lymph nodes showing low-attenuation foci, matted lymph nodes, and morphologically normal smaller (<1.5 cm) lymph nodes. These parameters were then independently correlated with the available HPV status of these patients. Finally, an extended criterion, that is, intranodal cystic changes in cases with morphologically normal small (<1.5 cm) lymph nodes, was correlated with HPV status. Sensitivity, specificity, and positive predictive values (PPVs) and negative predictive values (NPVs) were calculated.

RESULTS

Of these 49 cases with oropharyngeal cancers, 27 were HPV positive, and 22 cases were HPV negative. Eight cases (3 HPV positive and 5 HPV negative) did not have metastatic lymph nodes. Of remaining 41 cases with metastatic abnormal lymph nodes, 26 were HPV positive, and 15 were HPV negative. Of these 41 cases with metastatic lymph nodes, 14 had 1 or more lymph nodes with cystic foci. Of these 14 cases, 10 (71.4%) were HPV positive. Resultant sensitivity, specificity, PPV, and NPV of cystic foci for the presence of HPV status were 38.4%, 73.3%, 71.4%, and 40.7%, respectively. Intranodal cystic changes in cases with morphologically normal small (<1.5 cm) lymph nodes were found in 5 cases; all 5 were HPV positive. Resultant accuracy was specificity and PPV of 100%, sensitivity of 19.2% and NPV of 41.6%.

CONCLUSIONS

Intranodal cystic changes seen on the pretreatment postcontrast neck computed tomographic scan of patients with oropharyngeal malignancies are radiologic signatures strongly associated with the HPV status of the patient. The results in this initial study warrant larger prospective studies to determine if this finding may be used in addition to other molecular biomarkers to help identify those patients who may be amenable to the most appropriate treatment options.

Simultaneous detection and identification of enteric viruses by PCR-mass assay

Simultaneous detection of enteric viruses that cause similar symptoms (e.g. hand, foot and mouth disease) is essential to the prevention of outbreaks and control of infections. In this study, a novel PCR-Mass assay combining multiplex polymerase chain reaction (PCR) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was developed and used for simultaneous detection of eight distinct human enteric viruses. Enteric viral isolates and standard viral RNAs were examined to determine the sensitivity and specificity of the PCR-Mass assay. Clinical performance was evaluated with a total of 101 clinical specimens from patients suspected of having hand, foot and mouth disease (HFMD). The results were compared to those of previous analyses using real-time RT-PCR. The identification of specific viruses and clinical specimens shows that the PCR-Mass assay performed as well as or better than standard methods with respect to indicating the presence of multiplex pathogens in a single specimen.

MassARRAY spectrometry is more sensitive than PreTect HPV-Proofer and consensus PCR for type-specific detection of high-risk oncogenic human papillomavirus genotypes in cervical cancer

Type-specific detection of human papillomavirus (HPV) is indicated for better risk stratification and clinical management of women testing positive for HPV and for epidemiologic surveillance. MassARRAY spectrometry (MassARRAY; Sequenom) is a novel method for type-specific detection of 15 high-risk oncogenic HPV types: HPV-16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, -68, and -73. PreTect HPV-Proofer (Proofer; Norchip) is a type-specific assay that detects E6/E7 mRNA from five high-risk oncogenic HPV types: HPV-16, -18, -31, -33, and -45. The performance of these tests for type-specific identification of HPV was assessed with cervical specimens from 192 cases of cervical cancer in comparison with consensus MY09/MY11 PCR followed by nucleotide sequencing (consensus PCR). The overall HPV detection rates were 94.8% (95% confidence interval [CI], 91.7, 97.9), 83.3% (95% CI, 78.1, 88.5), and 86.5% (95% CI, 81.7, 91.3) for MassARRAY, Proofer, and consensus PCR, respectively. All tests were negative in six (3.1%) of the 192 cases. Considering only the specimens that contained at least one of the five types targeted by Proofer, the detection rates were 96.6%, 91.4%, and 86.9% for MassARRAY, Proofer, and consensus PCR, respectively. MassARRAY detected multiple infections in 14.1%, Proofer detected multiple infections in 3.6%, and consensus PCR failed to detect any multiple infections. The agreement was highest at 86.0% (kappa = 0.76) between MassARRAY and Proofer and lowest at 81.8% (kappa = 0.69) between Proofer and consensus PCR. In conclusion, MassARRAY is a highly sensitive and accurate method for type-specific detection of oncogenic HPV in cervical cancer, with Proofer showing impressive performance.

Lack of HPV 16 and 18 detection in serum of colposcopy clinic patients

BACKGROUND

Persistent infection with high-risk human papillomavirus (HPV) types is necessary for the development of high-grade cervical dysplasia and cervical carcinoma. The presence of HPV DNA in the blood of cervical cancer patients has been reported; however, whether HPV DNA is detectable in the blood of patients with pre-invasive cervical disease is unclear.

OBJECTIVES

The objectives of this study were to determine if HPV 16 and HPV 18 DNA could be detected in the serum of colposcopy clinic patients, and if serum HPV detection was associated with grade of cervical disease and HPV cofactors.

STUDY DESIGN

Samples were selected from a biorepository collected from non-pregnant, HIV-negative women ages 18-69 attending colposcopy clinics at two urban public hospitals. Cervical disease status was based on review of colposcopy, biopsy and cytology findings. Serum HPV DNA detection was conducted using a novel PCR and mass spectroscopy-based assay.

RESULTS

Of the 116 adequate serum samples, all (100%) were negative for HPV 16 and HPV 18. Over half (51.7%) of participants had cervical HPV 16 and/or HPV 18 infection. Nearly one-third (31.1%) had high grade, 10.3% had low grade, and 50.9% had no cervical disease. Nearly one-third (28.5%) had ever regularly smoked cigarettes, 70.7% had early onset of sexual intercourse, and 75% had ever used oral contraceptives.

CONCLUSIONS

In this colposcopy clinic population with a range of clinical characteristics and established HPV cofactors, HPV DNA was undetectable in their serum. Our findings suggest that serum HPV DNA detection is not a cervical cancer screening tool.

A comparison of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and surface plasmon resonance for genotyping of high-risk human papillomaviruses

BACKGROUND

Human papillomavirus (HPV) testing coupled with appropriate clinical management is associated with a significant decline in the rate of advanced cervical cancer and associated death.

METHODS

In this present study, we evaluated the performance of 2 new HPV genotyping methods, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and surface plasmon resonance (SPR) in 30 kinds of HPV control materials and in 129 cases of cervical smears including 79 HPV-positive samples screened from 1,600 abnormal clinical samples and 50 cervical cytology samples.

RESULTS

The HPV genotyping accuracy of both MALDI-TOFMS and SPR was 100% for the HPV genotyping of control materials. In the analysis of the 79 HPV-positive samples by MALDI-TOFMS, HPV positivity was 88.6% (70/79). Nine samples were non-high-risk HPV (non-HR-HPV), which were not targets of MALDI-TOFMS. In the analysis of the 50 cervical samples, the agreement of both tests was 84% with a κ value of 0.660. By using consensus results that mean agreement between 2 of 3 methods, the HR-HPV genotyping accuracy was 100% (77/77) by MALDI-TOFMS and 94.8% (73/77) by SPR in the 129 cervical samples. The sensitivity (88.2%; 82/93) and specificity (88.9%; 32/36) of MALDI-TOFMS were similar to those of SPR.

CONCLUSION

These results support that MALDI-TOFMS is a sensitive, specific and feasible method for HR-HPV detection in clinical application, compared with the SPR method.

Simultaneous detection of attomolar pathogen DNAs by Bio-MassCode mass spectrometry

A general method is described to analyze pathogen DNAs in homogenous solution by a novel Bio-MassCode probe, using a small organic (namely disulfide) "reporter mass" that self-assembled in oligonucleotide-modified gold nanoparticles. With conventional MALDI TOF MS, the assay simultaneously detected DNAs for HIV, HBV, HCV, and TP with extraordinarily high sensitivity in the low attomolar (10(-18) M) range without any other amplification.