Comparing the performance of 2 human papillomavirus assays for a new use indication: a real-world evidence-based evaluation in the United States.

BACKGROUND: The US Food and Drug Administration supports innovations to facilitate new indications for high-risk human papillomavirus testing. This report describes the retrospective testing of stored specimens and analysis of existing data to efficiently and cost-effectively support a new indication for the Onclarity human papillomavirus assay (Becton, Dickinson and Company, BD Life Sciences - Integrated Diagnostic Solutions, Sparks, MD). The performance of this index test was compared with that of a predicate test, the cobas human papillomavirus assay (Roche Diagnostics, Indianapolis, IN). Both human papillomavirus assays are based on real-time polymerase chain reaction platforms that detect the presence of 14 high-risk human papillomavirus genotypes. The predicate assay reports human papillomavirus types 16 and 18 as individual results and the other 12 human papillomavirus genotypes as 1 pooled result. The index assay reports 9 independent results (human papillomavirus types 16, 18, 31, 33/58, 35/39/68, 45, 51, 52, and 56/59/66). Both the index and predicate assays are approved by the Food and Drug Administration for cervical cancer screening, but at the time that this study was initiated, the index human papillomavirus assay was not approved for use with cervical specimens collected in PreservCyt (Hologic, Inc, San Diego, CA) liquid-based cytology media. OBJECTIVE: The performance of the index human papillomavirus assay was compared with that of the predicate human papillomavirus assay for the detection of cervical intraepithelial neoplasia grades 2 or greater and 3 or greater (≥CIN2 or ≥CIN3) using PreservCyt liquid-based cytology specimens collected from women aged 21 to 65 years. In addition, the ability of the index test's extended genotyping to stratify ≥CIN2 and ≥CIN3 risks, using these specimens, was evaluated. STUDY DESIGN: The New Mexico HPV Pap Registry was used to select an age- and cytology-stratified random sample of 19,879 women undergoing opportunistic cervical screening and follow-up in routine clinical practice across New Mexico. A subset (n = 4820) of PreservCyt specimens was selected from 19,879 women for paired testing by the index and predicate human papillomavirus assays within age and cytology strata and included women with or without cervical biopsy follow-up. Point estimate differences and ratios were calculated for cervical disease detection and positivity rates, respectively, with 95% confidence intervals to determine statistical significance. The cumulative risk of ≥CIN2 or ≥CIN3, with up to 5-year follow-up, was estimated for the index assay using Kaplan-Meier methods. RESULTS: The 5-year cumulative ≥CIN3 detection rates were 5.6% for the index assay and 4.6% for the predicate assay (difference, 1.0%; 95% confidence interval, 0.5%-1.5%). The ≥CIN3 positivity rates within <1 year were 95.3% for the index assay and 94.5% for the predicate assay (ratio, 1.01; 95% confidence interval, 0.98-1.06). The ≥CIN3 cumulative positivity rates for the index and predicate assays were also similar at 5 years. Among cases of ≥CIN3, the positive agreement rates between the index and predicate assays for human papillomavirus types 16 and 18 were 100.0% (95% confidence interval, 95.0%-100.0%) and 90.9% (95% confidence interval, 62.3%-98.4%), respectively. Human papillomavirus type 16 carried the highest ≥CIN2 or ≥CIN3 risk, followed by human papillomavirus types 18/31/33/58/52/45 and human papillomavirus types 35/56/59/51/56/59/66. CONCLUSION: The index and predicate human papillomavirus assays demonstrated equivalent performance, and extended human papillomavirus genotyping, using the index assay, provided effective ≥CIN2 and ≥CIN3 risk stratification, supporting a new indication for use of the index assay with PreservCyt.

Stratification of tumour cell radiation response and metabolic signatures visualization with Raman spectroscopy and explainable convolutional neural network.

Reprogramming of cellular metabolism is a driving factor of tumour progression and radiation therapy resistance. Identifying biochemical signatures associated with tumour radioresistance may assist with the development of targeted treatment strategies to improve clinical outcomes. Raman spectroscopy (RS) can monitor post-irradiation biomolecular changes and signatures of radiation response in tumour cells in a label-free manner. Convolutional Neural Networks (CNN) perform feature extraction directly from data in an end-to-end learning manner, with high classification performance. Furthermore, recently developed CNN explainability techniques help visualize the critical discriminative features captured by the model. In this work, a CNN is developed to characterize tumour response to radiotherapy based on its degree of radioresistance. The model was trained to classify Raman spectra of three human tumour cell lines as radiosensitive (LNCaP) or radioresistant (MCF7, H460) over a range of treatment doses and data collection time points. Additionally, a method based on Gradient-Weighted Class Activation Mapping (Grad-CAM) was used to determine response-specific salient Raman peaks influencing the CNN predictions. The CNN effectively classified the cell spectra, with accuracy, sensitivity, specificity, and F1 score exceeding 99.8%. Grad-CAM heatmaps of H460 and MCF7 cell spectra (radioresistant) exhibited high contributions from Raman bands tentatively assigned to glycogen, amino acids, and nucleic acids. Conversely, heatmaps of LNCaP cells (radiosensitive) revealed activations at lipid and phospholipid bands. Finally, Grad-CAM variable importance scores were derived for glycogen, asparagine, and phosphatidylcholine, and we show that their trends over cell line, dose, and acquisition time agreed with previously established models. Thus, the CNN can accurately detect biomolecular differences in the Raman spectra of tumour cells of varying radiosensitivity without requiring manual feature extraction. Finally, Grad-CAM may help identify metabolic signatures associated with the observed categories, offering the potential for automated clinical tumour radiation response characterization.

Metabolic profiling of murine radiation-induced lung injury with Raman spectroscopy and comparative machine learning.

Radiation-induced lung injury (RILI) is a dose-limiting toxicity for cancer patients receiving thoracic radiotherapy. As such, it is important to characterize metabolic associations with the early and late stages of RILI, namely pneumonitis and pulmonary fibrosis. Recently, Raman spectroscopy has shown utility for the differentiation of pneumonitic and fibrotic tissue states in a mouse model; however, the specific metabolite-disease associations remain relatively unexplored from a Raman perspective. This work harnesses Raman spectroscopy and supervised machine learning to investigate metabolic associations with radiation pneumonitis and pulmonary fibrosis in a mouse model. To this end, Raman spectra were collected from lung tissues of irradiated/non-irradiated C3H/HeJ and C57BL/6J mice and labelled as normal, pneumonitis, or fibrosis, based on histological assessment. Spectra were decomposed into metabolic scores via group and basis restricted non-negative matrix factorization, classified with random forest (GBR-NMF-RF), and metabolites predictive of RILI were identified. To provide comparative context, spectra were decomposed and classified via principal component analysis with random forest (PCA-RF), and full spectra were classified with a convolutional neural network (CNN), as well as logistic regression (LR). Through leave-one-mouse-out cross-validation, we observed that GBR-NMF-RF was comparable to other methods by measure of accuracy and log-loss (p > 0.10 by Mann-Whitney U test), and no methodology was dominant across all classification tasks by measure of area under the receiver operating characteristic curve. Moreover, GBR-NMF-RF results were directly interpretable and identified collagen and specific collagen precursors as top fibrosis predictors, while metabolites with immune and inflammatory functions, such as serine and histidine, were top pneumonitis predictors. Further support for GBR-NMF-RF and the identified metabolite associations with RILI was found as CNN interpretation heatmaps revealed spectral regions consistent with these metabolites.

Effects of perceptions of forest change and intergroup competition on community-based conservation behaviors.

Approximately one quarter of the earth's population directly harvests natural resources to meet their daily needs. These individuals are disproportionately required to alter their behaviors in response to increasing climatic variability and global biodiversity loss. Much of the ever-ambitious global conservation agenda relies on the voluntary uptake of conservation behaviors in such populations. Thus, it is critical to understand how such individuals perceive environmental change and use conservation practices as a tool to protect their well-being. We developed a participatory mapping activity to elicit spatially explicit perceptions of forest change and its drivers across 43 mangrove-dependent communities in Pemba, Tanzania. We administered this activity along with a questionnaire regarding conservation preferences and behaviors to 423 individuals across those 43 communities. We analyzed these data with a set of Bayesian hierarchical statistical models. Perceived cover loss in 50% of a community's mangrove area drove individuals to decrease proposed limits on fuelwood bundles from 2.74 (forest perceived as intact) to 2.37 if participants believed resultant gains in mangrove cover would not be stolen by outsiders. Conversely, individuals who believed their community mangrove forests were at high risk of theft loosened their proposed harvest limits from 1.26 to 2.75 bundles of fuelwood in response to the same perceived forest decline. High rates of intergroup competition and mangrove loss were thus driving a self-reinforcing increase in unsustainable harvesting preferences in community forests in this system. This finding demonstrates a mechanism by which increasing environmental decline may cause communities to forgo conservation practices, rather than adopt them, as is often assumed in much community-based conservation planning. However, we also found that when effective boundaries were present, individuals were willing to limit their own harvests to stem such perceived decline.

Efectos de las percepciones del cambio forestal y la competencia intergrupal en los comportamientos de conservación comunitarios Resumen Aproximadamente una cuarta parte de la población mundial aprovecha directamente los recursos naturales para satisfacer sus necesidades diarias. Estos individuos se ven desproporcionadamente obligados a alterar sus comportamientos en respuesta a la creciente variabilidad climática y la pérdida de biodiversidad global. Gran parte de la ambiciosa agenda de conservación global se basa en la adopción voluntaria de comportamientos de conservación en dichas poblaciones. Por lo tanto, es fundamental comprender cómo esas personas perciben el cambio ambiental y utilizan las prácticas de conservación como herramienta para proteger su bienestar. Desarrollamos una actividad de mapeo participativo para generar percepciones espacialmente explícitas del cambio forestal y sus causantes en 43 comunidades dependientes de manglares en Pemba, Tanzania. Administramos esta actividad junto con un cuestionario sobre preferencias y comportamientos de conservación a 423 personas en esas 43 comunidades. Analizamos estos datos mediante un conjunto de modelos estadísticos jerárquicos bayesianos. La pérdida de cobertura percibida en el 50% del área de manglares de una comunidad llevó a los individuos a reducir los límites propuestos para los paquetes de leña de 2.74 (bosque percibido como intacto) a 2.37 si los participantes creían que las ganancias resultantes en la cobertura de manglares no serían robadas por personas ajenas a la comunidad. Por el contrario, las personas que creían que los bosques de manglares de su comunidad corrían un alto riesgo de robo flexibilizaron los límites de cosecha propuestos de 1.26 a 2.75 haces de leña en respuesta a la misma disminución percibida del bosque. Por lo tanto, las altas tasas de competencia entre grupos y pérdida de manglares estaban impulsando un aumento, que se auto reforzaba, en las preferencias de aprovechamiento insostenibles en los bosques comunitarios de este sistema. Este hallazgo muestra un mecanismo por el cual el creciente deterioro ambiental puede hacer que las comunidades renuncien a las prácticas de conservación, en lugar de adoptarlas, como a menudo se supone en gran parte de la planificación de la conservación basada en la comunidad. Sin embargo, también encontramos que cuando existían límites efectivos, los individuos estaban dispuestos a restringir sus propias cosechas para frenar esa disminución percibida.

Risk stratification of HPV-positive results using extended genotyping and cytology: Data from the baseline phase of the Onclarity trial.

BACKGROUND: Optimizing the balance between colposcopy referrals and the detection of high-grade cervical intraepithelial neoplasia (CIN) during cervical cancer screening requires robust triage strategies. We evaluated the performance of extended HPV genotyping (xGT), in combination with cytology triage, and compared it to previously published performance data for high-grade CIN detection by HPV16/18 primary screening in combination with p16/Ki-67 dual staining (DS). METHODS AND MATERIALS: The baseline phase of the Onclarity trial enrolled 33,858 individuals, yielding 2978 HPV-positive participants. Risk values for ≥CIN3 were determined for Onclarity result groupings corresponding to HPV16, not HPV16 but HPV18 or 31, not HPV16/18/31 but HPV33/58 or 52, not HPV16/18/31/33/58/52 but HPV35/39/68 or 45 or 51 or 56/59/66 across all cytology categories. Published data from the IMPACT trial for HPV16/18 plus DS was utilized as a comparator during ROC analyses. RESULTS: There were 163 ≥ CIN3 cases detected. The ≥CIN3 risk stratum hierarchy (% risk of ≥CIN3) that resulted from this analysis included: >LSIL (39.4%); HPV16, ≤LSIL (13.3%); HPV18/31, ≤LSIL (5.9%); HPV33/58/52/45, ASC-US/LSIL (2.4%); HPV33/58/52, NILM (2.1%); HPV35/39/68/51/56/59/66, ASC-US/LSIL (0.9%); and HPV45/35/39/68/51/56/59/66, NILM (0.6%). For ≥CIN3 ROC analysis, the optimal cutoff for sensitivity versus specificity was approximated between not HPV16 but HPV18 or 31, any cytology (≥CIN3 sensitivity = 85.9% and colposcopy-to- ≥ CIN3 = 7.4) and not HPV16/18/31 but HPV33/58/52, NILM (≥CIN3 sensitivity = 94.5% and colposcopy-to- ≥CIN3 = 10.8). HPV16/18 with DS triage showed a sensitivity of 94.3%, with a colposcopy-to- ≥ CIN3 ratio of 11.4. CONCLUSIONS: xGT performed similarly compared to HPV primary screening plus DS for detection of high-grade CIN. xGT provides results that stratify risk in a flexible and reliable manner for colposcopy risk thresholds set by different guidelines or organizations.

Detection of high-grade cervical neoplasia using extended genotyping: Performance data from the longitudinal phase of the Onclarity trial.

OBJECTIVES: The Onclarity cervical cancer screening trial was designed to establish the clinical validity of the Onclarity HPV assay for extended genotyping (xGT) during detection of high-grade cervical neoplasia grades 2 or 3 (≥CIN2 or ≥CIN3). Here, three-year follow up data is presented to evaluate the overall efficacy of these screening strategies, compared to the baseline data. METHODS: At baseline 29,513 women, ≥25 years, had evaluable cytology and valid high-risk HPV results. Women with atypical squamous cells-undetermined significance or worse cytology or a positive HPV test were referred for colposcopy/biopsy. Participants that did not reach the study end point (treatment for ≥CIN2) continued into the longitudinal phase that included the same protocol as baseline. RESULTS: The three-year cumulative incident risk (CIR) for ≥CIN3 in HPV-negative women was 0.15% [95%CI: 0.06, 0.26] and for HPV- and cytology-negative women was 0.12% [95% CI: 0.03,0.23]. HPV16 carried the highest baseline and three-year ≥CIN3 CIR, followed by HPV31 and HPV18. At least one year of genotype-specific persistence increased ≥CIN3 risk for xGT results compared to genotype non-persistence, HPV clearance, or new infection over the same time period. Risk-based screening with immediate colposcopy for HPV16/18/31 and further xGT triage resulted in better ≥CIN3 sensitivity (79.2% versus 72.3%; relative difference of 6.9 [95%CI: 3.3, 10.4]) and a lower colposcopy/≥CIN3 ratio (9.2 versus 11.2; relative difference of -1.9 [95%CI: -2.6, -1.3]) when compared to primary HPV16/18-based screening. CONCLUSIONS: An HPV-negative result offers the same assurance of no disease over three years of follow up as that offered by a negative co-testing result. xGT facilitates risk-based screening and persistence tracking and can help optimize disease detection during screening without excessive colposcopic procedures.

Practical guide to coproduction in conservation science.

We considered a series of conservation-related research projects on the island of Pemba, Tanzania, to reflect on the broad significance of Beier et al.'s recommendations for linking conservation science with practical conservation outcomes. The implementation of just some of their suggestions can advance a successful coproduction of actionable science by small research teams. Key elements include, first, scientists and managers working together in the field to ensure feedback in real time; second, questions jointly identified by managers and researchers to facilitate engaged collaboration; third, conducting research at multiple sites, thereby broadening managers' abilities to reach multiple stakeholders; and fourth, establishing a multidisciplinary team because most of the concerns of local managers require input from multiple disciplines.

Consideramos una serie de proyectos de investigación relacionados con la conservación en la isla de Pemba, Tanzania, para reflexionar sobre la importancia de las recomendaciones de Beier et al. para vincular las ciencias de la conservación con sus resultados prácticos. La implementación de sólo algunas de sus sugerencias puede impulsar una coproducción exitosa de ciencia práctica hecha por pequeños equipos de investigación. Los elementos clave incluyen, primero, a los científicos y administrados trabajando juntos en el campo para asegurar respuestas en tiempo real; segundo, preguntas identificadas en conjunto por los administradores y los investigadores para facilitar la colaboración participativa; tercero, realizar investigaciones en sitios diferentes y ampliar con esto las habilidades de los administradores para llegar a múltiples actores; y cuarto, establecer un equipo multidisciplinario ya que la mayoría de los intereses de los administradores locales requieren información de múltiples disciplinas.

Radiation treatment response and hypoxia biomarkers revealed by machine learning assisted Raman spectroscopy in tumour cells and xenograft tissues.

Recent advancements in anatomical imaging of tumours as treatment targets have led to improvements in RT. However, it is unlikely that improved anatomical imaging alone will be the sole driver for new advances in personalised RT. Biochemically based radiobiological information is likely to be required for next-generation improvements in the personalisation of radiotherapy dose prescriptions to individual patients. In this paper, we use Raman spectroscopy (RS), an optical technique, to monitor individual biochemical response to radiation within a tumour microenvironment. We spatially correlate individual biochemical responses to augmentatively derived hypoxic maps within the tumour microenvironment. Furthermore, we pair RS with a data analytical framework combining (i) group and basis restricted non-negative matrix factorization (GBR-NMF), (ii) a random forest (RF) classifier, (iii) and a feature metric importance calculation method, Shapley Additive exPlanations (SHAP), in order to ascertain the relative importance of individual biochemicals in describing the overall biological response as observed with RS. The current study found that the GBR-NMF-RF-SHAP model helped identify a wide range of radiation response biomarkers and hypoxia indicators (e.g., glycogen, lipids, DNA, amino acids) in H460 human lung cancer cells and H460 xenografts. Correlations between the hypoxic regions and Raman chemical biomarkers (e.g., glycogen, alanine, and arginine) were also identified in H460 xenografts. To summarize, GBR-NMF-RF-SHAP combined with RS can be applied to monitor the RT-induced biochemical response within cellular and tissue environments. Individual biochemicals were identified that (i) contributed to overall biological response to radiation, and (ii) spatially correlated with hypoxic regions of the tumour. RS combined with our analytical pipeline shows promise for further understanding of individual biochemical dynamics in radiation response for use in cancer therapy.

Research integrity in clinical trials: innocent errors and spin versus scientific misconduct.

PURPOSE OF REVIEW: High-quality research underpins the best healthcare practice. This article focuses on analyzing the current literature to promote research integrity across clinical trials. RECENT FINDINGS: Recent admissions of questionable practices by researchers have undermined practitioner and public confidence. There is limited evidence specifically for ethical and professional standards in clinical trials to guide researchers and institutions to embed integrity into research practice. SUMMARY: Unintentional errors and spin in research are not uncommon as training in design and conduct of clinical trials is not part of health education for medical and allied health professions. There is unfamiliarity with procedures, such as prospective registration, a priori documentation of statistical analysis plans, openness in data sharing, and so forth. This, combined with the academic culture of secrecy, has led to an environment where scientific suspicion, instead of trust, is the norm. Existing science integrity documents are devoid of specific recommendations about how to translate any guidance into clinical trial practice. There is a need for constructive, supportive and multidisciplinary approaches based on open dialogue and continuous training, targeting the research environment. Research integrity now needs to take centre stage to re-instill confidence in randomized trial evidence to inform clinical practice.

Antigen-Based Testing but Not Real-Time Polymerase Chain Reaction Correlates With Severe Acute Respiratory Syndrome Coronavirus 2 Viral Culture.

BACKGROUND: Individuals can test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by molecular assays following the resolution of their clinical disease. Recent studies indicate that SARS-CoV-2 antigen-based tests are likely to be positive early in the disease course, when there is an increased likelihood of high levels of infectious virus. METHODS: Upper respiratory specimens from 251 participants with coronavirus disease 2019 symptoms (≤7 days from symptom onset) were prospectively collected and tested with a lateral flow antigen test and a real-time polymerase chain reaction (rt-PCR) assay for detection of SARS-CoV-2. Specimens from a subset of the study specimens were utilized to determine the presence of infectious virus in the VeroE6TMPRSS2 cell culture model. RESULTS: The antigen test demonstrated a higher positive predictive value (90%) than rt-PCR (70%) when compared to culture-positive results. The positive percentage agreement for detection of infectious virus for the antigen test was similar to rt-PCR when compared to culture results. CONCLUSIONS: The correlation between SARS-CoV-2 antigen and SARS-CoV-2 culture positivity represents a significant advancement in determining the risk for potential transmissibility beyond that which can be achieved by detection of SARS-CoV-2 genomic RNA. SARS-CoV-2 antigen testing can facilitate low-cost, scalable, and rapid time-to-result, while providing good risk determination of those who are likely harboring infectious virus, compared to rt-PCR.

The Potential Clinical and Economic Value of a Human Papillomavirus Primary Screening Test That Additionally Identifies Genotypes 31, 45, 51, and 52 Individually.

BACKGROUND: Although current human papillomavirus (HPV) genotype screening tests identify genotypes 16 and 18 and do not specifically identify other high-risk types, a new extended genotyping test identifies additional individual (31, 45, 51, and 52) and groups (33/58, 35/39/68, and 56/59/66) of high-risk genotypes. METHODS: We developed a Markov model of the HPV disease course and evaluated the clinical and economic value of HPV primary screening with Onclarity (BD Diagnostics, Franklin Lakes, NJ) capable of extended genotyping in a cohort of women 30 years or older. Women with certain genotypes were later rescreened instead of undergoing immediate colposcopy and varied which genotypes were rescreened, disease progression rate, and test cost. RESULTS: Assuming 100% compliance with screening, HPV primary screening using current tests resulted in 25,194 invasive procedures and 48 invasive cervical cancer (ICC) cases per 100,000 women. Screening with extended genotyping (100% compliance) and later rescreening women with certain genotypes averted 903 to 3163 invasive procedures and resulted in 0 to 3 more ICC cases compared with current HPV primary screening tests. Extended genotyping was cost-effective ($2298-$7236/quality-adjusted life year) when costing $75 and cost saving (median, $0.3-$1.0 million) when costing $43. When the probabilities of disease progression increased (2-4 times), extended genotyping was not cost-effective because it resulted in more ICC cases and accrued fewer quality-adjusted life years. CONCLUSIONS: Our study identified the conditions under which extended genotyping was cost-effective and even cost saving compared with current tests. A key driver of cost-effectiveness is the risk of disease progression, which emphasizes the need to better understand such risks in different populations.

Human Papillomavirus Same Genotype Persistence and Risk: A Systematic Review.

OBJECTIVE: The aim of the study was to examine whether high-grade cervical intraepithelial neoplasia (CIN) was more closely associated with human papillomavirus (HPV) same-genotype persistence (SGTP) versus clearance of prior infection with a subsequent infection by a new genotype (genotype switch [GS]), clearance of HPV infection, or acquisition of a new HPV infection after a negative infection status, during a follow-up testing subsequent to abnormal screening results. MATERIALS AND METHODS: MEDLINE, Cochrane Library, Health Technology Assessment, and clinicaltrials.gov were searched from January 2000 to July 2019 for prospective controlled trials and observational studies of women and retrospective studies using HPV assays with extended- or full-genotype reporting. The primary outcome was high-grade CIN after at least 2 rounds of testing. Overall quality of evidence for the risk estimate outcomes was assessed. Of the 830 identified abstracts, 66 full-text articles were reviewed, and 7 studies were included in the synthesis. The study protocol was registered with the PROSPERO International Prospective Register of Systematic Reviews (CRD42018091093). RESULTS: Continued HPV-positive women falls in 2 equally large groups: SGTP and GS. Sensitivity, positive predictive value, and positive likelihood ratio of SGTP were significantly higher than for GS. Human papillomavirus genotypes may be ranked into 3 tiers (immediate colposcopy, follow-up testing, return to routine screening), according to associated risk of persistence for high-grade CIN and to prevailing clinical action thresholds. CONCLUSIONS: There is moderately high-quality evidence to support the clinical utility of SGTP to improve risk discrimination for high-grade CIN compared with qualitative HPV testing without genotype-specific information.

Clinical Evaluation of BD Veritor SARS-CoV-2 Point-of-Care Test Performance Compared to PCR-Based Testing and versus the Sofia 2 SARS Antigen Point-of-Care Test.

The clinical performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 nucleocapsid antigen (Veritor), a chromatographic immunoassay used for SARS-CoV-2 point-of-care testing, was evaluated using nasal specimens from individuals with COVID-19 symptoms. Two studies were completed to determine clinical performance. In the first study, nasal specimens and either nasopharyngeal or oropharyngeal specimens from 251 participants with COVID-19 symptoms (≤7 days from symptom onset [DSO], ≥18 years of age) were utilized to compare Veritor with the Lyra SARS-CoV-2 PCR assay (Lyra). In the second study, nasal specimens from 361 participants with COVID-19 symptoms (≤5 DSO, ≥18 years of age) were utilized to compare performance of Veritor to that of the Sofia 2 SARS Antigen FIA test (Sofia 2). The positive, negative, and overall percent agreement (PPA, NPA, and OPA, respectively) were the primary outcomes. In study 1, the PPA for Veritor, compared to Lyra, ranged from 81.8 to 87.5% across the 0 to 1 and 0 to 6 DSO ranges. In study 2, Veritor had PPA, NPA, and OPA values of 97.4, 98.1, and 98.1%, respectively, with Sofia 2. Discordant analysis showed one Lyra positive missed by Veritor and five Lyra positives missed by Sofia 2; one Veritor positive result was negative by Lyra. Veritor met FDA emergency use authorization (EUA) acceptance criteria for SARS-CoV-2 antigen testing for the 0 to 5 and 0 to 6 DSO ranges (PPA values of 83.9% and 82.4%, respectively). Veritor and Sofia 2 showed a high degree of agreement for SARS-CoV-2 detection. The Veritor test allows for more rapid COVID-19 testing utilizing easy-to-collect nasal swabs but demonstrated <100% PPA compared to PCR.

Clinical Utility of Human Papillomavirus Genotyping in Cervical Cancer Screening: A Systematic Review.

OBJECTIVE: Thirteen human papillomavirus (HPV) genotypes are associated with the highest risk of cervical disease/cancer; however, the risk of disease progression and cancer is genotype dependent. The objective of this systematic review was to examine evidence for high-grade cervical intraepithelial neoplasia (≥CIN 3) risk discrimination using HPV genotyping. MATERIALS AND METHODS: A systematic review of English and non-English articles through MEDLINE, Cochrane, clinicaltrials.gov, and abstracts presented at relevant professional society conferences were searched from 2000 to 2019. Search terms included: cervical cancer screening, HPV genotyping, CIN, HPV persistence, humans, and colposcopy; prospective, controlled trials, observational studies, and retrospective studies of residual specimens; evidence included HPV genotyping (beyond genotypes 16/18/45) results. Data were obtained independently by authors using predefined fields. Risk of bias was evaluated with a modified Newcastle-Ottawa Scale. The Grading of Recommendations, Assessment, Development and Evaluation methodology facilitated overall quality of evidence evaluation for risk estimation. The study protocol was registered with the PROSPERO International Prospective Register of Systematic Reviews (CRD42018091093). The primary outcome was CIN 3 or worse risk both at baseline and at different follow-up periods. RESULTS: Of 236 identified sources, 60 full texts were retrieved and 16 articles/sources were included. Risk of bias was deemed low; the overall quality of evidence for CIN 3 or worse risk with negative for intraepithelial lesions or malignancies or low-grade squamous intraepithelial cytology was assessed as moderate; that with atypical squamous cells-undetermined significance and "all cytology" was assessed as high. Clinical and methodological heterogeneity precluded meta-analysis. Human papillomavirus genotyping discriminated risk of CIN 3 or worse to a clinically significant degree, regardless of cytology result. CONCLUSIONS: The evidence supports a clinical utility for HPV genotyping in risk discrimination during cervical cancer screening.

Longitudinal linear combination test for gene set analysis.

BACKGROUND: Although microarray studies have greatly contributed to recent genetic advances, lack of replication has been a continuing concern in this area. Complex study designs have the potential to address this concern, though they remain undervalued by investigators due to the lack of proper analysis methods. The primary challenge in the analysis of complex microarray study data is handling the correlation structure within data while also dealing with the combination of large number of genetic measurements and small number of subjects that are ubiquitous even in standard microarray studies. Motivated by the lack of available methods for analysis of repeatedly measured phenotypic or transcriptomic data, herein we develop a longitudinal linear combination test (LLCT). RESULTS: LLCT is a two-step method to analyze multiple longitudinal phenotypes when there is high dimensionality in response and/or explanatory variables. Alternating between calculating within-subjects and between-subjects variations in two steps, LLCT examines if the maximum possible correlation between a linear combination of the time trends and a linear combination of the predictors given by the gene expressions is statistically significant. A generalization of this method can handle family-based study designs when the subjects are not independent. This method is also applicable to time-course microarray, with the ability to identify gene sets that exhibit significantly different expression patterns over time. Based on the results from a simulation study, LLCT outperformed its alternative: pathway analysis via regression. LLCT was shown to be very powerful in the analysis of large gene sets even when the sample size is small. CONCLUSIONS: This self-contained pathway analysis method is applicable to a wide range of longitudinal genomics, proteomics, metabolomics (OMICS) data, allows adjusting for potentially time-dependent covariates and works well with unbalanced and incomplete data. An important potential application of this method could be time-course linkage of OMICS, an attractive possibility for future genetic researchers. AVAILABILITY: R package of LLCT is available at: https://github.com/its-likeli-jeff/LLCT.

Stratified risk of high-grade cervical disease using onclarity HPV extended genotyping in women, ≥25 years of age, with NILM cytology.

OBJECTIVES: Increasing evidence suggests that extended human papillomavirus (HPV) genotyping (beyond 16/18) is effective for risk stratification in women with normal cytology. This report provides extended genotyping results, using the BD Onclarity HPV Assay, for individual genotypes HPV16, 18, 31, 45, 51, and 52 ̶ and three pooled genotype results for HPV33/58, 35/39/68, and 56/59/66. METHODS: 27,037 women with normal cytology, ≥25 years, were enrolled into the Onclarity HPV trial during routine screening. Women positive for any HPV genotype were referred to colposcopy/biopsy. Hierarchical-ranked prevalence and risk values, associated with cervical intraepithelial neoplasia, grade 2 or worse (≥CIN2) or ≥CIN3, were calculated based on extended genotyping results. RESULTS: HPV 16 and 31 carried the highest risk for ≥CIN2 (11.6% and 12.1%, respectively) and ≥CIN3 (8.1% and 7.5%, respectively); these genotypes were the most prevalent in both ≥CIN2 (29.6% and 19.3%, respectively) and ≥CIN3 (43.7% and 22.5%, respectively). Of the other 12 genotypes, HPV 18, 33/58, and 52 comprised an intermediate risk band (≥CIN2 risk range: 4.9-6.8%; ≥CIN3 risk range: 3.9-5.0%). Genotypes 45, 51, 35/39/68, and 56/59/66 constituted the lowest risk band for both disease grades (≥CIN2 value risk range: 1.7-3.0%; ≥CIN3 value risk range: 1.2-3.6%). CONCLUSIONS: Extended genotyping stratifies risk for ≥CIN2/3 in the ≥25 year-old, normal cytology population. While baseline HPV 16/31 values exceeded the risk threshold for colposcopy referral, the management of women with normal cytology who were positive for the intermediate- or lower-risk genotypes may evolve based on refined risk estimates as well as clinical factors.

Risk detection for high-grade cervical disease using Onclarity HPV extended genotyping in women, ≥21 years of age, with ASC-US or LSIL cytology.

OBJECTIVES: There is growing interest in using human papillomavirus (HPV) genotyping as a risk-based triage approach for women with atypical squamous cells-undetermined significance (ASC-US) and low-grade squamous intraepithelial lesions (LSIL) cytology. METHODS: This analysis includes 2807 subjects with ASC-US or LSIL cytology, ≥21 years, from the baseline phase of the Onclarity HPV trial. All women were referred to colposcopy/biopsy. Hierarchical-ranked prevalence and risk values, associated with high-grade cervical disease, were calculated based on extended genotyping. RESULTS: HPV 16 carried the highest risk for cervical intraepithelial neoplasia grade 2 or worse (≥CIN2) in both the ASC-US and LSIL populations. Risk of ≥CIN3 and ≥CIN2 associated with the other 13 genotypes varied somewhat for women with ASC-US and LSIL, however, HPV 31, 18, 33/58, 51 and 52 appear to comprise an intermediate risk band. Risk associated with HPV 35/39/68, 45, and 56/59/66, in either cytology population, was relatively low and beneath the benchmark threshold risk for immediate colposcopy. Restricting the analysis to women 21-24 years, ≥25 years, or ≥30 years produced similar results. CONCLUSIONS: HPV genotyping identified multiple risk bands for ≥CIN3 and ≥CIN2 in the ≥21 year-old ASC-US and LSIL populations. These results support a 1-year follow-up period to preclude immediate colposcopy for ASC-US or LSIL women positive for the lowest-risk HPV genotypes.

Identifying factors of activities of daily living important for cost and caregiver outcomes in Alzheimer's disease.

BACKGROUND: We aimed to obtain a better understanding of how different aspects of patient functioning affect key cost and caregiver outcomes in Alzheimer's disease (AD). METHODS: Baseline data from a prospective observational study of community-living AD patients (GERAS) were used. Functioning was assessed using the Alzheimer's Disease Cooperative Study-Activities of Daily Living Scale. Generalized linear models were conducted to analyze the relationship between scores for total activities of daily living (ADL), basic ADL (BADL), instrumental ADL (IADL), ADL subdomains (confirmed through factor analysis) and individual ADL questions, and total societal costs, patient healthcare and social care costs, total and supervision caregiver time, and caregiver burden. RESULTS: Four distinct ADL subdomains were confirmed: basic activities, domestic/household activities, communication, and outside activities. Higher total societal costs were associated with impairments in all aspects of ADL, including all subdomains; patient costs were associated with total ADL and BADL, and basic activities subdomain scores. Both total and supervision caregiver hours were associated with total ADL and IADL scores, and domestic/household and outside activities subdomain scores (greater hours associated with greater functional impairments). There was no association between caregiver burden and BADL or basic activities subdomain scores. The relationship between total ADL, IADL, and the outside activities subdomain and outcomes differed between patients with mild and moderate-to-severe AD. CONCLUSIONS: Identification of ADL subdomains may lead to a better understanding of the association between patient function and costs and caregiver outcomes at different stages of AD, in particular the outside activities subdomain within mild AD.

Baseline characteristics and hospitalizations in patients with schizophrenia receiving olanzapine long-acting injection: an interim analysis from a non-interventional, prospective observational safety study.

BACKGROUND: Depot antipsychotics are a treatment option for medication nonadherence in patients with schizophrenia. Nonadherence can lead to increased relapse and hospitalization rates. This article reports hospitalization data before and after initiation of olanzapine long-acting injection (LAI), a depot antipsychotic. METHODS: Data were assessed from an ongoing, multinational, prospective, observational post-authorisation safety study being conducted to evaluate post-injection delirium/sedation syndrome (PDSS), an adverse reaction that can occur following injection of olanzapine LAI. Eligible patients were aged ≥18 years, diagnosed with schizophrenia, were prescribed olanzapine LAI, and lived outside the United States. Psychiatric hospitalization and medication data were collected retrospectively for the 6-month period before study entry and prospectively throughout the study. Paired t-tests and McNemar's tests were used to assess changes in hospitalization incidence and duration. Stepwise Cox proportional hazards models assessed factors associated with hospitalizations. Analyses were based on data from the first 3 years of the continuously enrolling study (N = 668). RESULTS: The average duration of olanzapine LAI exposure for all patients was 0.768 years. Of the 529 patients who received at least 1 injection of olanzapine LAI and were not hospitalized at study entry, 8.1% had at least 1 subsequent psychiatric hospitalization with a mean duration of 2.0 days. Of the 288 patients who had a >6-month follow-up, 8.3% had at least 1 post-baseline psychiatric hospitalization with a mean duration of 2.3 days. The incidence of hospitalizations in the 6-month period after treatment was significantly lower than that in the 6-month period prior to treatment (8.3 vs 32.6%, respectively; P < 0.001). Furthermore, mean hospitalization duration decreased from 11.5 days in the 6-month period before treatment to 2.3 days in the 6-month period after treatment (P < 0.001). Psychiatric hospitalization in the prior 12 months (P < 0.0001) and recreational drug use within 24 h of baseline visit (P = 0.015) were identified as potential predictors of time to first psychiatric hospitalization after beginning to take olanzapine LAI. At the time of interim analysis, 5 PDSS events had occurred, which was too few for a full analysis of those events. CONCLUSIONS: Results indicate a significant reduction in the incidence and days of hospitalization from the 6-month period before to the 6-month period after olanzapine LAI initiation, which suggests reduced relapse and hospitalization during treatment. Results should be interpreted with caution due to the observational nature of the study and use of retrospective baseline data.

Lower Anogenital Tract Disease Therapy Outcomes, COMET, and CROWN: Call for Research Submissions.

OBJECTIVES: There is a problem of inconsistent and inappropriate outcome selection for research studies. We can improve the relevance of research results for women and for their physicians and clinicians by encouraging researchers to critically evaluate outcome measures, and use valid, appropriate, standardized measures. To this purpose, and to facilitate synthesis of the evidence, outcomes reported by clinical studies should be standardized for different disease conditions through the development of core outcome sets (COS). METHODS: There is an international effort for reaching consensus on outcome measures and establishing COS that represent agreed-upon standardized collections of outcome measures that will be reported in all studies within a clinical area. Across clinical specialties, the Core Outcome Measures in Effectiveness Trials (COMET) initiative launched in 2010. In 2014, the editors of women's health journals answered the challenge of COMET and formed the Core Outcomes in Women's Health initiative. The Journal of Lower Genital Tract Diseases is a participating member of the Core Outcomes in Women's Health consortium. RESULTS: There is broad inconsistency in outcome measures and reporting in the field of lower anogenital tract diseases. No core outcome sets currently exist. Suggested target conditions in anogenital disease are vulvar dermatoses, cervical intraepithelial neoplasia, and vulvodynia. CONCLUSIONS: Investigators are encouraged to conduct secondary systematic research to determine previously reported primary outcome measures and suggest domains for COS. Core Outcomes in Women's health initiative and COMET encourage the formation of consensus panels of stakeholders (researchers, health care providers, patients, and others) to recommend outcome domains and COS and then publish their report.