Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV ...genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
•Molecular assays reliably detect norovirus from stool and vomit.•Fast turnaround and simplicity of Xpert Norovirus suit it to near patient testing.•The BD-MAX System is useful for high-throughput ...norovirus testing.•xTAG GPP had lower norovirus sensitivity/specificity compared to other platforms.
Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available.
Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples.
163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms.
In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus.
The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.
Background
The incidence of anal cancer is increasing globally. Evidence‐based improvement in early detection and management of this morbid cancer is thus required. In other cancers associated with ...Human Papillomavirus (HPV), viral status and dynamics, including viral load (VL) has been shown to influence clinical outcome. Our aim was to determine the influence of HPV status and HPV16 VL on the clinical outcomes of anal cancer patients.
Methods
A total of 185 anal cancer lesions were genotyped for HPV. Of the HPV16 positive component, VL was determined using a digital droplet PCR assay. The association of qualitative HPV status and VL (low (<12.3), medium (12.3–57) and high (>57 copies/cell)) on overall survival and hazard of death was assessed.
Results
Of the 185 cases, 164 (88.6%) samples were HPV positive. HPV16 was detected in 154/185 samples (83.2%). HPV positive status was associated with improved overall survival in the univariate analysis hazard ratio (HR) of 0.44, 0.23–0.82, p = 0.01. When adjusted by age, sex, stage and response to treatment, the association of positive HPV status with improved survival remained (HR 0.24 0.11–0.55 p < 0.001). High VL was associated with improved overall survival in the univariate analysis with a HR of 0.28 (0.11–0.71, p = 0.007). When adjusted only by age and sex, high VL was associated with better overall survival (HR 0.27, 0.11–0.68 p = 0.006).
Conclusions
HPV status appears to be independently associated with improved outcomes in anal cancer patients. Moreover, HPV viral load quantification may be informative for further risk stratification and warrants further investigation.
While human papillomavirus (HPV) status has been linked to clinical outcome in oropharyngeal cancer, there are sparse data on how viral presence and dynamics affect the trajectory of anal cancer. This work suggests HPV positive status is independently associated with improved outcomes in anal cancer patients and that viral load measurement shows potential for further risk stratification. Given the rise in anal cancer, identification of biomarkers that can delineate discrete prognostic groups are welcome.
The incidence of anal cancer is rising worldwide. As identified in cervical cancer management, an improvement in the early detection and management of anal pre-cancer is essential. In other cancers ...associated with human papillomavirus (HPV), HPV 16 sub-lineages have been shown to be associated with disease status and prognosis. However, in anal cancer, they have been under-explored. A total of 119 HPV 16-positive anal cancer lesions diagnosed between 2009 and 2018 in Scotland and 134 HPV 16-positive residual rectal swabs from asymptomatic men collected in 2016/7 were whole genome sequenced. The association of HPV 16 sub-lineages with underlying disease status (cancer vs. asymptomatic) and overall survival in anal cancer samples was assessed (comparing A1 vs non-A1 sub-lineages). A1 was the dominant sub-lineage present in the anal cancer (76.5%) and the asymptomatic (76.1%) cohorts. A2 was the second most dominant sub-lineage in both groups (16.8% and 17.2%, respectively). We did not observe significant associations of sub-lineage with demographics, clinical variables or survival (A1 vs. non-A1 sub-lineages (HR 0.83, 0.28-2.46
= 0.743)). HPV 16 sub-lineages do to not appear to cluster with disease vs asymptomatic carriage or be independently associated with outcomes in anal cancer patients. Further international studies on anal HPV sub-lineage mapping will help to determine whether this is a consistent observation.
Several
nucleic acid amplification tests (NAATs) with high sensitivity exist. However, the specificity of
NAATs may be suboptimal, particularly for extragenital biospecimens. Consequently, ...confirmation with a second NAAT is common, although this represents a burden on resources. Furthermore, the rationale for confirmation is contentious. The objective of this work was to assess
confirmation in over 13,000
screen-positive samples representing various biospecimens and three separate screening assays, the Abbott RealTime CT/NG (Abbott Molecular, Inc., Des Plaines, IL), the Cobas CT/NG test (Roche Molecular Systems Inc., Alameda, CA), and the BD ProbeTec ET CT/GC amplified DNA assay (BD Diagnostics, Sparks, MD). Factors predictive of confirmation were determined via logistic regression involving sex, year, whether the sample was formally validated, and sample site. Level of confirmation varied according to screening assay (96.2%, 86.0%, and 73.9% for the Abbott, Roche, and BD tests, respectively) in sample types formally included according to the manufacturers' instructions (i.e., validated). Sex did not affect confirmation for 2/3 assays, and the likelihood of confirmation of samples not formally included in manufacturer instructions (i.e., nonvalidated) was 89.1%, 82.1%, and 59.2% for the Abbott, Roche, and BD tests, respectively. Rectal swabs, which are nonvalidated samples, confirmed in 91.5%, 90.1%, and 87.4% of samples initially tested with the respective assays. The requirement to confirm
in validated samples is not required for all NAATs, although initial assay-specific evaluation is justified given observed variability. Rectal samples represent robust biospecimens for
NAAT testing and may not require confirmation when screened with the assays described.
Highlights • There is an increasing demand for HPV annotation of FFPE material. • The performance of the Xpert® HPV assay, was assessed for FFPE material. • FFPE material is amenable to HPV detection ...by the Xpert assay.
Background The Xpert registered HPV Assay (Cepheid registered , Sunnyvale, USA) is a rapid, cartridge-based HPV test validated for use on cervical cytology samples. However, there is an increasing ...demand for HPV annotation of formalin fixed paraffin embedded (FFPE) material. Objectives The aim of this study was to determine the suitability of the Xpert HPV assay for the detection of nucleic acid (NA) derived from FFPE samples. Study design A total of 88, 10 mu m sections derived from FFPE tissue blocks were assessed, 74 originated from oropharyngeal squamous cell carcinomas (OPSCC) and 14 from a range of other sites. All had previously been tested with a sensitive Luminex registered based assay with a component also tested with p16 immunohistochemistry (IHC). NA was extracted from samples using the easyMag registered platform and after dilution was added directly to the Xpert cartridge. Agreement between assays was assessed. Results Overall agreement between the assays was 92%; with a Kappa for HR-HPV detection of 0.833 (95% CI 0.725-0.953). In the 50 samples that had been annotated for p16 status overall agreement between the Xpert assay and the p16 IHC was 90%. Conclusions These data indicate that FFPE material is amenable to HPV detection by the Xpert assay. To our knowledge, this is the first study to interrogate the use of the Xpert registered HPV assay for this application.
PDF
