Diagnostic Accuracy of the Cepheid 3-gene Host Response Fingerstick Blood Test in a Prospective, Multi-site Study: Interim Results

BACKGROUND

The development of a fast and accurate, non-sputum-based point-of-care triage test for tuberculosis (TB) would have a major impact on combating the TB burden worldwide. A new fingerstick blood test has been developed by Cepheid (the Xpert MTB Host Response [MTB-HR] prototype), which generates a "TB score" based on messenger RNA (mRNA) expression of 3 genes. Here we describe the first prospective findings of the MTB-HR prototype.

METHODS

Fingerstick blood from adults presenting with symptoms compatible with TB in South Africa, The Gambia, Uganda, and Vietnam was analyzed using the Cepheid GeneXpert MTB-HR prototype. Accuracy of the Xpert MTB-HR cartridge was determined in relation to GeneXpert Ultra results and a composite microbiological score (GeneXpert Ultra and liquid culture) with patients classified as having TB or other respiratory diseases (ORD).

RESULTS

When data from all sites (n = 75 TB, 120 ORD) were analyzed, the TB score discriminated between TB and ORD with an area under the curve (AUC) of 0.94 (95% confidence interval [CI], .91-.97), sensitivity of 87% (95% CI, 77-93%) and specificity of 94% (88-97%). When sensitivity was set at 90% for a triage test, specificity was 86% (95% CI, 75-97%). These results were not influenced by human immunodeficiency virus (HIV) status or geographical location. When evaluated against a composite microbiological score (n = 80 TB, 111 ORD), the TB score was able to discriminate between TB and ORD with an AUC of 0.88 (95% CI, .83-.94), 80% sensitivity (95% CI, 76-85%) and 94% specificity (95% CI, 91-96%).

CONCLUSIONS

Our interim data indicate the Cepheid MTB-HR cartridge reaches the minimal target product profile for a point of care triage test for TB using fingerstick blood, regardless of geographic area or HIV infection status.

Automatic cough classification for tuberculosis screening in a real-world environment

Objective.The automatic discrimination between the coughing sounds produced by patients with tuberculosis (TB) and those produced by patients with other lung ailments.Approach.We present experiments based on a dataset of 1358 forced cough recordings obtained in a developing-world clinic from 16 patients with confirmed active pulmonary TB and 35 patients suffering from respiratory conditions suggestive of TB but confirmed to be TB negative. Using nested cross-validation, we have trained and evaluated five machine learning classifiers: logistic regression (LR), support vector machines, k-nearest neighbour, multilayer perceptrons and convolutional neural networks.Main Results.Although classification is possible in all cases, the best performance is achieved using LR. In combination with feature selection by sequential forward selection, our best LR system achieves an area under the ROC curve (AUC) of 0.94 using 23 features selected from a set of 78 high-resolution mel-frequency cepstral coefficients. This system achieves a sensitivity of 93% at a specificity of 95% and thus exceeds the 90% sensitivity at 70% specificity specification considered by the World Health Organisation (WHO) as a minimal requirement for a community-based TB triage test.Significance.The automatic classification of cough audio sounds, when applied to symptomatic patients requiring investigation for TB, can meet the WHO triage specifications for the identification of patients who should undergo expensive molecular downstream testing. This makes it a promising and viable means of low cost, easily deployable frontline screening for TB, which can benefit especially developing countries with a heavy TB burden.

Evaluation of Triage Tests When Existing Test Capacity Is Constrained: Application to Rapid Diagnostic Testing in COVID-19

Objectives

A triage test is used to determine which patients will undergo an existing or “reference” test. This article explores the potential value of using triage tests before reference tests when the capacity of the reference test is constrained.

Methods

We developed a simple model with inputs: prevalence, sensitivity, specificity, and reference test capacity. We included a case study of rapid diagnostic tests for SARS-CoV-2 antigens used as triage tests before a reference polymerase chain reaction test. Performance data were obtained from an evaluation performed by an academic center on 425 samples from testing centers in the United Kingdom and Germany.

Results

When reference test capacity is constrained, the use of a triage test leads to a relative expansion of the population tested and cases identified; both are higher with a high-specificity triage test. When reference test capacity is not constrained, the potential advantages of introducing a triage test can be assessed using a standard cost-utility framework, balancing the utility of the reduction in the number of reference tests required against the disutility of missed cases associated with the use of a lower-sensitivity triage test. In the constrained case, the advantage of a triage testing strategy in terms of population covered and cases identified is reduced as the prevalence increases. In the unconstrained case, the reduction in reference tests required is reduced and the number of cases missed increase as the prevalence rises.

Conclusion

When the availability of the reference test is constrained, tests added in a triage position do not need high levels of accuracy to increase the number of cases diagnosed. This has implications in many disease areas, including COVID-19.

p16/Ki-67 dual-stained cytology used for triage in cervical cancer opportunistic screening

Objective

To evaluate the efficiency of p16/Ki-67 dual stain used as a triage in cervical cancer screening.

Methods

In this study, we did 468 p16/Ki-67 dual stain in human papillomavirus (HPV) 16/18-positive or 12 other high-risk HPV (OHR-HPV) positive Thinprep cytologic test (TCT) atypical squamous cells of undetermined significance (ASCUS)/ lower-grade squamous intraepithelial lesion (LSIL) women. We evaluated the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the triage test.

Results

The sensitivity, specificity, PPV and NPV of p16/Ki-67 dual stain in HPV 16/18-positive women were 91.5%/68.4%, 77.0%/75.0%, 73.9%/59.1% and 92.8%/81.8%. In 12 OHR-HPV positive TCT ASCUS/LSIL women, the results were 79.1%/95.0%, 88.5%/66.7%, 88.5%/70.4% and 89.2%/94.1%. The risk of precancerous lesions in p16/Ki-67 dual stain positive cases was much higher than before, and the negative cases had lower risk. Besides, there was no cervical intraepithelial neoplasia (CIN) III case missed after triaged by p16/Ki-67 dual-stained cytology. In p16/Ki-67 dual-stained cytology positive women with benign pathology or CIN I, the 1-year progression rate is 20.5% and in p16/Ki-67 dual-stained cytology negative women, the 1-year progression rate is 5.6%.

Conclusions

hr-HPV genotyping test plays an important role in cervical cancer screening. p16/Ki-67 dual stain may be a promising triage test. As for chronic cervicitis or CIN I patients, a positive p16/Ki-67 dual-stained cytology suggests a high risk in progression and need to be followed up closely.

DNA methylation markers as a triage test for identification of cervical lesions in a high risk human papillomavirus positive screening cohort

Objective triage strategies are required to prevent unnecessary referrals for colposcopy in population‐based screening programs using primary high‐risk human papillomavirus (hrHPV) testing. We have identified several DNA methylation markers with high sensitivity and specificity for detection of high‐grade cervical intraepithelial neoplasia or worse (CIN2+) in women referred for colposcopy. Our study assessed diagnostic potential of these methylation markers in a hrHPV‐positive screening cohort. All six markers (JAM3, EPB41L3, C13orf18, ANKRD18CP, ZSCAN1 and SOX1) showed similar association across histology in the hrHPV‐positive cohort when compared to the Dutch cohort (each p > 0.15). Sensitivity for CIN2+ was higher using methylation panel C13orf18/EPB41L3/JAM3 compared to the other 2 panels (80% vs. 60% (ANKRD18CP/C13orf18/JAM3) and 63% (SOX1/ZSCAN1), p = 0.01). For CIN3+ all three methylation panels showed comparable sensitivity ranging from 68% (13/19) to 95% (18/19). Specificity of SOX1/ZSCAN1 panel (84%, 167/200) was considerably higher compared to ANKRD18CP/C13orf18/JAM3 (68%, 136/200, p = 2 × 10⁻⁵) and C13orf18/EPB41L3/JAM3 (66%, 132/200, p = 2 × 10⁻⁷). High negative predictive value (NPV) (91–95% and 96–99%) was observed for CIN2+ and CIN3+, for all three methylation panels, while positive predictive value (PPV) varied from 25 to 40% for CIN2+ and 15–27% for CIN3+. Interestingly, 118/235 samples were negative for all six markers (including 106 controls (89.8%), 6 CIN1 (5.1%), 5 CIN2 (4.2%) and 1 CIN3 (0.8%)). Methylation results from both independent cohorts were comparable as well as high sensitivity for detection of cervical cancer and its high‐grade precursors in hrHPV‐positive population. Our study therefore validates these methylation marker panels as triage test either in hrHPV‐based or abnormal cytology‐based screening programs.

What's new?

In cervical cancer screening, HPV testing provides greater sensitivity than cytology, but its lower specificity leads to some unnecessary treatment referrals. DNA methylation assays could potentially provide better specificity for identifying CIN2+ in women carrying high risk HPV. These authors investigated six previously identified CIN2+ methylation markers. They tested three different combinations of markers, and found high levels of sensitivity and specificity, making these markers potentially useful as part of a population‐based screening program.

Prehospital stroke scale (FAST PLUS Test) predicts patients with intracranial large vessel occlusion

BACKGROUND AND PURPOSE

Mechanical thrombectomy (MT) is indicated for the treatment of large vessel occlusion (LVO) stroke. MT should be provided as quickly as possible; therefore, a test identifying suspected LVO in the prehospitalization stage is needed to ensure direct transport to a comprehensive stroke center (CSC). We assume that patients with clinically severe hemiparesis have a high probability of LVO stroke. We modified the FAST test into the FAST PLUS test: The first part is the FAST test and the second part evaluates the presence of severe arm or leg motor deficit. This prospective multicenter study evaluates the specificity and sensitivity of the FAST PLUS test in detecting LVO stroke.

METHODS

Paramedics were trained through e-learning to conduct the FAST PLUS test. All prehospital suspected stroke patients who were administered the FAST PLUS test were included. Demographics, National Institutes of Health Stroke Scale (NIHSS) score, brain computed tomography (CT), and CT angiography (CTA) were recorded. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and receiver operating curve (ROC) area for LVO were calculated.

RESULTS

The study included 435 patients. LVO were found in 124 patients (28%). Sensitivity was 93%, specificity was 47%, PPV was 41%, NPV was 94%, and ROC area for ICA/MCA occlusion was 0.65. Intracerebral hemorrhage (ICH) was identified in 48 patients (11%).

CONCLUSION

We found that the FAST PLUS test had a high sensitivity for LVO stroke. Of the 435 patients, 41% were all directly transported to a CSC based on positive FAST PLUS test scores and were potential candidates for MT.

Analytic and Diagnostic Performances of Human Papillomavirus E6/E7 mRNA Test on up-to 11-Year-Old Liquid-Based Cervical Samples. A Biobank-Based Longitudinal Study

Human Papillomavirus (HPV) E6/E7 mRNA test demonstrated high specificity in detecting HPV infections, but studies assessing its efficacy in terms of cancer risk stratification are lacking. Follow-up studies are arduous and expensive. Biobank would be the answer to the problem, although data investigating the effects of long-term storage on RNA preservation are still needed. We addressed these issues by retrieving 202 residual liquid-based cervical specimens, collected from 149 women attending cervical cancer screening during the years 2001–2012. Samples were stored in Adriatic Biobank at room temperature and without any handing. After calculation of RNA yield and purity, E6/E7 mRNA test was retrospectively performed on each samples, to assess analytic and diagnostic performances. Using automated extraction procedures, RNA of good quantity and quality was obtained. The mean value of RNA concentration was 27.5 ng/μL. The mean A260/A280 ratio was 2.1. An invalid mRNA test result was found in 11.9% of the specimens. Neither RNA integrity, nor analytic performances of mRNA test were influenced by the year of sample collection. In total, 62.4% of the specimens tested as mRNA positive; among these, 89.2% were CIN2+. E6/E7 mRNA was detected in all Squamous Cervical Cancer (SCC) cases. Percentage of positive samples increased with the severity of histological diagnosis. mRNA testing, showing specificity and predictive values of 75.6% and 84.4%, respectively, significantly improved the corresponding values for DNA testing. Thus, the reflex mRNA test was demonstrated to be suitable to triage women with persistent cervical lesions. A “one sample for all” approach is possible, with practical benefits for Biobank-based long-term longitudinal studies, diseases prevention, prediction, diagnosis and treatment.

Performance of multiparametric MRI in men at risk of prostate cancer before the first biopsy: a paired validating cohort study using template prostate mapping biopsies as the reference standard

BACKGROUND

Multiparametric magnetic resonance imaging (mpMRI) has the potential to serve as a non-invasive triage test for men at risk of prostate cancer. Our objective was to determine the performance characteristics of mpMRI in men at risk before the first biopsy using 5 mm template prostate mapping (TPM) as the reference standard.

METHODS

One hundred and twenty-nine consecutive men with clinical suspicion of prostate cancer, who had no prior biopsy, underwent mpMRI (T1/T2-weighted, diffusion-weighting, dynamic contrast enhancement) followed by TPM. The primary analysis used were as follows: (a) radiological scores of suspicion of ≥3 attributed from a five-point ordinal scale, (b) a target condition on TPM of any Gleason pattern ≥4 and/or a maximum cancer core length of ≥4 mm and (c) two sectors of analysis per prostate (right and left prostate halves). Secondary analyses evaluated the impact of changing the mpMRI score threshold to ≥4 and varying the target definition for clinical significance.

RESULTS

One hundred and forty-one out of 258 (55%) sectors of analysis showed 'any cancer' and 77/258 (30%) had the target histological condition for the purpose of deriving the primary outcome. Median (with range) for age, PSA, gland volume and number of biopsies taken were 62 years (41-82), 5.8 ng ml(-1) (1.2-20), 40 ml (16-137) and 41 cores (20-93), respectively. For the primary outcome sensitivity, specificity, positive and negative predictive values and area under the receiver-operating curve (with 95% confidence intervals) were 94% (88-99%), 23% (17-29%), 34% (28-40%), 89% (79-98%) and 0.72 (0.65-0.79), respectively.

CONCLUSIONS

MpMRI demonstrated encouraging diagnostic performance characteristics in detecting and ruling out clinically significant prostate cancer in men at risk, who were biopsy naive.