Suicide attempt risk predicts inconsistent self-reported suicide attempts: A machine learning approach using longitudinal data

INTRODUCTION

Inconsistent self-reports of lifetime suicide attempts (LSAs) are a major obstacle for accurate assessment of suicidal behavior. This study is the first to posit that adolescents at higher risk report LSAs more consistently than those at lower risk, revealing a link between suicide attempt risk and consistent reporting.

METHODS

A machine learning model was trained with 70 % of the baseline assessment data of a longitudinal sample of Norwegian adolescents (n = 10,739). The model was used to estimate the LSA risk score for the remaining 30 % of the testing dataset. The relationship between these baseline risk scores and the consistency of reporting LSAs was assessed using a 2-year follow-up reassessment of the testing dataset.

RESULTS

Internalizing problems, optimism about the future, conduct problems, substance use, and disordered eating were important factors associated with suicide attempt risk. Of the participants, 63.41 % had inconsistent self-reports at the two-year follow-up. Adolescents who consistently reported LSAs had significantly higher scores of suicide attempt risk at baseline. Two logistic regression analyses confirmed an association between suicide attempt risk and inconsistent self-reported LSAs and showed that sex (being male), and lower levels of depression and conduct problems significantly predicted such inconsistencies. Those who inconsistently reported LSAs were more likely than the others to be classified by the model as false negatives at the baseline risk assessment due to their lower estimated risk scores.

LIMITATIONS

Suicide attempts were measured with a single item in this study.

CONCLUSION

These risk factors support the theory of adolescent suicidality (TAS) and could improve suicide attempt risk assessment. Inconsistent self-reported LSAs signal lower suicide attempt risk.

False negative breast cancers on imaging and associated risk factors: a single institution six-year analysis

PURPOSE

Mitigating false negative imaging studies remains an important issue given its association with worse morbidity and mortality in patients with breast cancer. We aimed to identify risk factors that predispose to false negative breast imaging exams.

METHODS

In an IRB-approved, HIPAA compliant retrospective study, we identified all patients who were diagnosed with breast cancer within 365 days of a negative imaging study assessed as BI-RADS 1-3 between January 1, 2014 and January 31, 2020. A matched cohort based on mammographic breast density was created from randomly selected studies with BI-RADS 4-5 designation that yielded breast cancer at pathology within the same time frame. Patient and cancer characteristics, prior personal history of breast cancer and gene mutation status were collected from patient charts. Pearson chi-squared and Student's t-test on two independent groups with significance at < 0.05 was used for statistical analysis.

RESULTS

We identified 155 false negative studies of 129 missed cancers and 128 breast density matched true positive cancers. False negative studies were screening mammograms in 57.42% (89/155), diagnostic mammograms in 29.68% (46/155), ultrasounds in 6.45% (10/155) and MRIs in 6.45% (10/155). Rates of personal (41.09% vs. 18.75%, p < 0.001) and family history of breast cancer (68.22% vs. 49.21%, p = 0.002) were higher in the false negative cohort and remained significant when asymptomatic MRI-detected cancers were removed.

CONCLUSION

Our findings suggest that supplemental screening may be useful in breast cancer survivors.

Effectiveness of a standardized quality control management procedure for COVID-19 RT-PCR testing: a large-scale diagnostic accuracy study in China

BACKGROUND

The study aimed to construct a standardized quality control management procedure (QCMP) and access its accuracy in the quality control of COVID-19 reverse transcriptase-polymerase chain reaction (RT-PCR).

METHODS

Considering the initial RT-PCR results without applying QCMP as the gold standard, a large-scale diagnostic accuracy study including 4,385,925 participants at three COVID-19 RT-PCR testing sites in China, Foshan (as a pilot test), Guangzhou and Shenyang (as validation sites), was conducted from May 21, 2021, to December 15, 2022.

RESULTS

In the pilot test, the RT-PCR with QCMP had a high accuracy of 99.18% with 100% specificity, 100% positive predictive value (PPV), and 99.17% negative predictive value (NPV). The rate of retesting was reduced from 1.98% to 1.16%. Its accuracy was then consistently validated in Guangzhou and Shenyang.

CONCLUSIONS

The RT-PCR with QCMP showed excellent accuracy in identifying true negative COVID-19 and relieved the labor and time spent on retesting.

The features associated with mammography-occult MRI-detected newly diagnosed breast cancer analysed by comparing machine learning models with a logistic regression model

PURPOSE

To compare machine learning (ML) models with logistic regression model in order to identify the optimal factors associated with mammography-occult (i.e. false-negative mammographic findings) magnetic resonance imaging (MRI)-detected newly diagnosed breast cancer (BC).

MATERIAL AND METHODS

The present single-centre retrospective study included consecutive women with BC who underwent mammography and MRI (no more than 45 days apart) for breast cancer between January 2018 and May 2023. Various ML algorithms and binary logistic regression analysis were utilized to extract features linked to mammography-occult BC. These features were subsequently employed to create different models. The predictive value of these models was assessed using receiver operating characteristic curve analysis.

RESULTS

This study included 1957 malignant lesions from 1914 patients, with an average age of 51.64 ± 9.92 years and a range of 20-86 years. Among these lesions, there were 485 mammography-occult BCs. The optimal features of mammography-occult BC included calcification status, tumour size, mammographic density, age, lesion enhancement type on MRI, and histological type. Among the different ML models (ANN, L1-LR, RF, and SVM) and the LR-based combined model, the ANN model with RF features was found to be the optimal model. It demonstrated the best discriminative performance in predicting mammography false- negative findings, with an AUC of 0.912, an accuracy of 86.90%, a sensitivity of 85.85%, and a specificity of 84.18%.

CONCLUSION

Mammography-occult MRI-detected breast cancers have features that should be considered when performing breast MRI to improve the detection rate for breast cancer and aid in clinician management.

Epidemiological impact of a large number of false negative SARS-CoV-2 test results in South West England during September and October 2021

During September and October 2021, a substantial number of Polymerase Chain Reaction (PCR) tests in England processed at a single laboratory were incorrectly reported as negative. We estimate the number of false negative test results issued and investigate the epidemiological impact of this incident. We estimate the number of COVID-19 cases that would have been reported had the sensitivity of the laboratory test procedure not dropped for the period 2 September to 12 October. In addition, by making comparisons between the most affected local areas and comparator populations, we estimate the number of additional infections, cases, hospitalisations and deaths that could have occurred as a result of increased transmission due to false negative test results.We estimate that around 39,000 tests may have been false negatives during this period and, as a direct result of this incident, the most affected areas in the South-West of England could have experienced between 6000 and 34,000 additional reportable cases, with a central estimate of around 24,000 additional reportable cases. Using modelled relationships between key variables, we estimate that this central estimate could have translated to approximately 55,000 additional infections.Each false negative likely led to around 1.5 additional infections. The incident is likely to have had a measurable impact on cases and infections in the affected areas in the South-West of England. IMPACT STATEMENT: These results indicate the significant negative impact of incorrect testing on COVID outcomes; and make a substantial contribution to understanding the impact of testing systems and the need to ensure high accuracy in testing and reporting of results.

Improving biosensor accuracy and speed using dynamic signal change and theory-guided deep learning

False results and time delay are longstanding challenges in biosensing. While classification models and deep learning may provide new opportunities for improving biosensor performance, such as measurement confidence and speed, it remains a challenge to ensure that predictions are explainable and consistent with domain knowledge. Here, we show that consistency of deep learning classification model predictions with domain knowledge in biosensing can be achieved by cost function supervision and enables rapid and accurate biosensing using the biosensor dynamic response. The impact and utility of the methodology were validated by rapid and accurate quantification of microRNA (let-7a) across the nanomolar (nM) to femtomolar (fM) concentration range using the dynamic response of cantilever biosensors. Data augmentation and cost function supervision based on the consistency of model predictions and experimental observations with the theory of surface-based biosensors improved the F1 score, precision, and recall of a recurrent neural network (RNN) classifier by an average of 13.8%. The theory-guided RNN (TGRNN) classifier enabled quantification of target analyte concentration and false results with an average prediction accuracy, precision, and recall of 98.5% using the initial transient or entire dynamic response, which is indicative of high prediction accuracy and low probability of false-negative and false-positive results. Classification scores were used to establish new relationships among biosensor performance characteristics (e.g., measurement confidence) and design parameters (e.g., inputs and hyperparameters of classification models and data acquisition parameters) that may be used for characterizing biosensor performance.

Are There More HER2 FISH in the Sea? An Institution's Experience in Identifying HER2 Positivity Using Fluorescent In Situ Hybridization in Patients with HER2 Negative Immunohistochemistry

BACKGROUND

Approximately 20% of breast cancers express HER2-positive receptors in the USA. HER2 receptor immunohistochemistry (IHC) staining with equivocal (2+) results commonly undergoes fluorescence in-situ hybridization (FISH) for further classification. Current guidelines do not recommend routine FISH testing in IHC-negative (0 or 1+) cases. This study investigates an institution that performs both IHC and FISH testing on all cases to identify the true HER2-positive rate.

PATIENTS AND METHODS

A retrospective chart review from 2015 to 2021 was conducted at an institution where both HER2 IHC and FISH testing were performed at the time of diagnosis for all invasive breast cancers. The rate of true HER2-positive patients was determined, and patient and tumor characteristics were further explored.

RESULTS

A total of 1835 invasive breast cancer cases were primarily treated at this institution. A total of 289 cases were HER2 positive on IHC and FISH testing (15.7%). An additional 38 cases were identified as HER2 negative on IHC, but reclassified as HER2 positive on reflex FISH testing. Total HER2 positive cases increased from 289 (15.7%) to 327 cases (17.8%) with reflex FISH testing.

CONCLUSIONS

The additional HER2-positive cases after completing FISH testing on IHC-negative tumors suggests there may be a role for routine FISH testing in addition to standard IHC staining to determine HER2 status for breast cancer. The ethical, prognostic and even  benefits of a correct diagnosis outweigh the added expense of FISH testing.

Optimizing the diagnostic performance of neural antibody testing for paraneoplastic and autoimmune encephalitis in clinical practice

The detection of neural antibodies in patients with paraneoplastic and autoimmune encephalitis has majorly advanced the diagnosis and management of neural antibody-associated diseases. Although testing for these antibodies has historically been restricted to specialized centers, assay commercialization has made this testing available to clinical chemistry laboratories worldwide. This improved test accessibility has led to reduced turnaround time and expedited diagnosis, which are beneficial to patient care. However, as the utilization of these assays has increased, so too has the need to evaluate how they perform in the clinical setting. In this chapter, we discuss assays for neural antibody detection that are in routine use, draw attention to their limitations and provide strategies to help clinicians and laboratorians overcome them, all with the aim of optimizing neural antibody testing for paraneoplastic and autoimmune encephalitis in clinical practice.

A Review of Drug Abuse, Misuse, and Related Laboratory Challenges

Various definitions can be considered for drugs and substance abuse. According to the National Institute on Abuse, the use of an over-the-counter drug in a different way than that prescribed to experience or arouse emotion is a simple form of drug abuse. The World Health Organization (WHO) also defines drug abuse as the persistent or sporadic use of drugs that are incompatible or unrelated to acceptable medical practice. With the increasing non-therapeutic use of prescription drugs, serious related consequences have also increased. Therefore, there is a need to know more precisely about the types of substances and drug abuse, which is the most important part of diagnosis and recognizing the tests that cause false positive and negative results. The purpose of this review article is to collect and summarize the most important and more common types of drugs of abuse and review the drugs that cause false results in screening tests. In addition, the most common detection methods of the drug will be reviewed and the advantages and drawbacks of each method will be discussed. In this article, we aimed to point out all the facts about the emerging problems in drug abuse, the methods of screening, and the possible false results in addition to troubleshooting strategies.

Hormesis, biological plasticity, and implications for clinical trial research

The present paper identifies a critical factor that leads to false negative results (i.e., failing to indicate efficacy when beneficial results did occur) in randomized human drug trials. The paper demonstrates that human performance can only be enhanced by a maximum of 30-60% as described by the hormetic dose response which defines the limits of biological plasticity. However, human epidemiological/clinical trials typically contain such extensive variability that often requires responses greater than 2-3 times control group responses to show statistical significance. Thus, many potentially beneficial agents may be missed because the clinical trial fails to recognize and take into consideration the limits of biological plasticity. The paper proposes that this hormesis-biological plasticity-clinical trial conundrum can be addressed successfully via the use of a weight-of-evidence methodology similar to that used by regulatory agencies such as EPA in environmental assessment of chemical toxicity.

FISH-negative BCR::ABL1-positive e19a2 chronic myeloid leukaemia: the most cryptic of insertions

BACKGROUND

Chronic myeloid leukaemia (CML) is one of the most well characterised human malignancies. Most patients have a cytogenetically visible translocation between chromosomes 9 and 22 which generates the pathognomonic BCR::ABL1 fusion gene. The derivative chromosome 22 ('Philadelphia' or Ph chromosome) usually harbours the fusion gene encoding a constitutively active ABL1 kinase domain. A small subset of patients have no visible translocation. Historically, these 'Philadelphia chromosome negative' patients caused diagnostic confusion between CML and other myeloproliferative neoplasms; it is now well established that the BCR::ABL1 fusion gene can be generated via submicroscopic intrachromosomal insertion of ABL1 sequence into BCR, or, more rarely, of BCR into ABL1. The fusion genes arising from cryptic insertions are not detectable via G-banded chromosome analysis [karyotype] but can nevertheless always be detected using fluorescence in situ hybridisation (FISH) and/or qualitative reverse transcriptase PCR.

CASE PRESENTATION

A 43-year-old female presented with suspected CML in 2007; however, contemporaneous gold standard laboratory investigations, G-banded chromosome analysis and FISH, were both negative. The reverse transcriptase quantitative PCR (RT-qPCR) assay available at the time, which was capable of detecting the common BCR::ABL1 transcripts (e13a2/e14a2), was also negative. Upon review in 2009, the newly recommended reverse transcriptase multiplex PCR (capable of detecting all BCR::ABL1 transcripts including the atypical ones) subsequently detected an e19a2 fusion. The patient then responded to tyrosine kinase inhibitor therapy. In contrast, FISH studies of both samples with three commercially available probes remained consistently negative. Retrospective whole genome sequencing, undertaken as part of the 100,000 Genomes Project, has now revealed that the patient's BCR::ABL1 fusion gene arose via a uniquely small insertion of 122 kb ABL1 sequences into BCR.

CONCLUSIONS

We present a patient with suspected chronic myeloid leukaemia whose genetic investigations were originally negative at the time of diagnosis despite the use of contemporaneous gold standard methods. This is the first report of a FISH-negative, BCR::ABL1 positive CML which demonstrates that, even after sixty years of research into one of the most well understood human malignancies, whole genome sequencing can yield novel diagnostic findings in CML.

Two cases of placental trisomy 21 mosaicism causing false-negative NIPT results

BACKGROUND

Non-invasive prenatal testing (NIPT) using cell-free DNA has been widely used for prenatal screening to detect the common fetal aneuploidies (such as trisomy 21, 18, and 13). NIPT has been shown to be highly sensitive and specific in previous studies, but false positives (FPs) and false negatives (FNs) occur. Although the prevalence of FN NIPT results for Down syndrome is rare, the impact on families and society is significant.

CASE PRESENTATION

This article described two cases of foetuses that tested "negative" for trisomy 21 by NIPT technology using the semiconductor sequencing platform. However, the fetal karyotypes of amniotic fluid were 46,XY, + 21 der(21;21)(q10;q10) and 47,XY, + 21 karyotypes, respectively. Placental biopsies confirmed that, in the first case, the chromosome 21 placenta chimerism ratio ranged from 13 to 88% with the 46,XX, + 21,der(21;21)(q10;q10)[86]/46,XX[14] karyotype of placental chorionic cells (middle of fetal-side placental tissue). However, in the second case, of all the placental biopsies, percentage of total chimerism was less than 30%; and placental biopsies taken at the middle of maternal side and middle of fetal side, also had variable trisomy 2 mosaicism levels of 10% and 8%, respectively. Ultimately, the pregnancies were interrupted at 30 gestational age (GA) and 27GA, respectively.

CONCLUSIONS

In this study, we present two cases of FN NIPT results that might have been caused by biological mechanisms, as opposed to poor quality, technical errors, or negligence. Clinical geneticists and their patients must understand that NIPT is a screening procedure.

The thoracobrachial outlet syndrome, a false negative on MRI is possible: About a case

The diagnosis of thoracobrachial outlet syndrome is one of the most discussed diagnoses. We report the case of a 33-year-old woman who presented to the consultation for pain, edema, and paresis of the left upper limb. Magnetic resonance imaging makes it possible to make the diagnosis, but it happens in certain situations that it reveals certain limits for the confirmation of this syndrome. This case highlights the false negatives of this examination in front of a very telling clinical picture.

Emergent multipath COVID-19 specimen collection problem with green corridor through variable length GA

The COVID-19 pandemic has spread worldwide exponentially. Typically, for testing, a provincial main government hospital cum testing center collects patients' specimens from remote health centers in the minimum possible time, satisfying the 'false negativity' constraint of the first collected specimen. With infrastructural developments throughout the world, multiple paths are available for transportation between two cities. Currently, the 'green corridor' is used for the transportation of human organs to be implanted, travel of VIPs, etc., in the minimum possible time. Taking these facts in consideration, for the first time, a green corridor system is suggested to provide a transportation pathway from small hospitals and urban/rural health centers to the testing center with COVID-19 specimens such as blood, nasal and throat swabs, and viral RNA, within the first collected specimen's life period. As health centers are located in different places, appropriate routing plans are needed for visiting them in the minimum possible time. A problem arises if this routing time exceeds the 'false negativity' of the first collected specimen. Thus, multipath COVID-19 specimen collection problems (MPC-19SCPs) are mathematically formulated to be collected from all health centers, and optimum routing plans are obtained using fixed and variable length genetic algorithms (VLGAs) developed for this purpose. For the first time, green corridor systems are suggested to incorporate the centers. The objectives of the models are, subject to the 'false-negative" constraint, minimization of the system time (Model A) and the green corridor time without or with mutual cooperation among the minimum number of centers for the transfer of specimens (Models B and C, respectively). The developed algorithms are based on variable length chromosomes, probabilistic selection, comparison crossover and generation-dependent mutation. Some benchmark instances from TSPLIB are solved by VLGA and GA. The competitiveness of VLGA is established through ANOVA. The models are numerically demonstrated, and some conclusions are derived.

The effect of numeric information about the likelihood of receiving a false negative or false positive result on people's attitudes towards colorectal cancer screening using faecal immunochemical testing (FIT)

OBJECTIVE

To examine the impact of numeric risk information about false negative (FN) and false positive (FP) rates in fecal immunochemical testing (FIT) on attitudes towards screening.

METHODS

102 people aged 45-55, living in the UK, read 6 hypothetical vignettes presented online about the use of FIT kits to detect colorectal cancer, in which information about FN and FP rates was systematically varied.

RESULTS

Numeric FN risk information reduced people's interest in screening, perception of screening effectiveness and lowered trust in screening compared to verbal FN information. Verbal FN information reduced perceptions of screening effectiveness and trust compared to no FN information. People with high subjective numeracy reported lower trust in screening following the provision of numeric FN information but numeracy did not moderate any other associations. FP information did not affect attitudes towards FIT testing.

CONCLUSION

Numeric FN risk information decreased people's perceptions of screening effectiveness and trust in the results of screening. While it influenced people's interest in screening, the effect was small.

PRACTICE IMPLICATIONS

Numeric FN information has a small effect on interest in screening and could promote informed decision making without affecting screening uptake.

Method for detecting rare differences between two LC-MS runs

LC-MS based multi-attribute methods (MAM) have drawn substantial attention due to their capability of simultaneously monitoring a large number of quality attributes of a biopharmaceutical product. For successful implementation of MAM, it is usually considered a requirement that the method is capable of detecting any new or missing peaks in the sample when compared to a control. Comparing a sample to a control for rare differences is also commonly practiced in many fields for investigational purpose. Because MS signal variability differs greatly between signals of different intensities, this type of comparison is often challenging, especially when the comparison is made without enough replicates. In this report we describe a statistical method for detecting rare differences between two very similar samples without replicate analyses. The method assumes that an overwhelming majority of components have equivalent abundance between the two samples, and signals with similar intensities have similar relative variability. By analyzing several monoclonal antibody peptide mapping datasets, we demonstrated that the method is suitable for new-peak detection for MAM as well as for other applications when rare differences between two samples need to be detected. The method greatly reduced false positive rate without a significant increase of false negative rate.

A ruptured thoracic aortic aneurysm and the difficulties of confirming syphilis

A 43-year-old woman died suddenly and was found at PM to have a ruptured thoracic aortic aneurysm. The endothelial surface of the aorta showed a 'tree-bark' appearance. Histology of the aneurysm wall showed a patchy, mainly perivascular, plasma cell infiltrate. Multiple spirochete-like organisms were identified on T. pallidum IHC. However, PM syphilis serology (screen including rapid plasma reagin (RPR) and T. pallidum particle agglutination (TPPA)) on femoral blood was negative. PCR testing on FFPE aortic wall tissue was negative. Further history revealed routine antenatal syphilis screening tests had been negative, no known history or risk of exposure to syphilis or other treponemes. This case raises the possibility of false negative syphilis testing. While acknowledged in RPR testing, with the modern testing regime using multiple methods, the rate of false negative results is now thought to be markedly reduced, and false positive results are a much greater problem in clinical medicine. The most common cause of false negative results is early in primary infection before an immune response has been mounted and in those patients that are immunocompromised. False negative results are also more often seen in tertiary syphilis, as in this case. Newer testing methods which include 16S rRNA sequencing have become available and early discussion with a microbiologist would be recommended. Strong macroscopic and microscopic suggestion of syphilis as the cause of the aneurysm makes it necessary to include the possibility of infection in the Post Mortem Report to Coroner as this will have implications for her sexual partners and children.

Lead in synthetic and municipal drinking water varies by field versus laboratory analysis

Water lead measurements by two field analyzers, relying on anodic stripping voltammetry (ASV) and fluorescence spectroscopy, were compared to reference laboratory measurements by inductively coupled plasma mass spectrometry (ICP-MS) in progressively complex datasets (phases A, B, C), to assess field analyzer performance. Under controlled laboratory quantitative tests of dissolved lead within the field analysis range and optimal temperature range, lead recoveries by ASV ranged within 85-106 % of reference laboratory values (corresponding linear model: y = 0.96×, r² = 0.99), compared to lower lead recoveries of 60-80 % by fluorescence (y = 0.69×, r² = 0.99) in phase A. Field analyzer performance deteriorated in three opportunistic laboratory datasets compiled for phase B that contained dissolved lead (ASV: y = 0.80×, r² = 0.98; no fluorescence data). Further lead underestimations were observed in five field datasets compiled for phase C, some of which contained known particulate lead (ASV: y = 0.54×, r² = 0.76; fluorescence: y = 0.06×, r² = 0.38). Deteriorating performance between phases was presumably due to the increasingly complex water matrices and lead particulates present in some phase C subsets (phase A < phase B < phase C). Phase C field samples had lead concentrations that were out-of-range, including a 5 % and 31 % false negative rate by ASV and by fluorescence, respectively. The range of results relevant to the diverse nature of compiled datasets, suggests that unless ideal conditions are known to be present (i.e., the lead content of water is dissolved within the field analysis range and optimal water temperature range), these field lead analyses might only be used as a water screening tool. Given the unknown conditions in many field settings, combined with the lead concentration underestimations including the false negative rates reported herein for field datasets, caution is encouraged when employing ASV and particularly fluorescence field analysis.

Toluene-mercuric modified USEPA Method 3060A to eliminate interference of sulfide-based reductants with Cr(VI) determination

The validity of USEPA Method 3060A as universal Cr(VI) analysis method for remediated soil is controversial. We investigated soil Cr(VI) remediation performance by commonly used reductants (FeSO₄, CaS_x, Na₂S) under different operating conditions (dosage, curing time and degree of mixing) using Method 3060A, and developed modified 3060A specific for sulfide-based reductants. Results showed that Cr(VI) was primarily removed during analysis stage rather than remediation stage. Thereinto, chemical dosage played a much more important role than curing time and degree of mixing. Besides, soil Cr(VI) concentration decreased to below the detection limit with residual reductant content increasing. Comparing standard and toluene-mercuric modified 3060A, Cr(VI) removal efficiency decreased from 100 % to 38.9-45.4 %, 67.1-68.8 % and 94.1-96.3 %, corresponding to mixing degree of 33 %, 67 % and 100 %, for treated soil using 1× and 2× the molar stoichiometric ratio of CaS_x. Subsequently, the optimization mechanism was revealed. Elemental sulfur, remediation product of sulfide-based reductants, was removed from soil by toluene preventing its disproportionation to sulfide at Method 3060A stage. Sulfide was fixed by mercuric oxide in species of mercuric sulfide. This method also proved suitable for different types of soils. Therefore, an effective way for scientific evaluation of soil Cr(VI) remediation was provided in this study.

Interference in ELISA

ELISA is a well-established technique used worldwide to quantify analytes present in a diverse milieu of biological samplings. It is especially important to clinicians who rely on the accuracy and precision of the test to administer patient care. Those results are to be held with great scrutiny since the assay is subject to error caused by interfering substances found in the sample matrix. In this chapter, we examine the nature of such interferences and discuss approaches to identify and offer remedies to remove the interference and validate the assay.

Interobserver Agreement among Cytopathologists in False-Negative Cases by Cytological Diagnosis with Endoscopic Ultrasound-Guided Fine Needle Aspiration in Solid Pancreatic Lesions

INTRODUCTION

Early detection and accurate pathological assessment are critical to improving prognosis of pancreatic cancer. EUS has been widely used in diagnosing pancreatic lesions and can obtain histological diagnosis by endoscopic ultrasound-guided fine needle aspiration (EUS-FNA). However, comprehensive assessment of the interobserver agreement (IOA) among cytopathologists evaluating EUS-FNA specimens is still limited. Therefore, this study evaluated IOA among cytopathologists for EUS-FNA specimens of solid pancreatic lesions, especially in false-negative cases of cytological diagnosis and analyzed the factors that influence cytological diagnosis of EUS-FNA so as to improve the diagnostic efficiency of EUS-FNA.

METHODS

We retrieved EUS-FNA samples of pancreatic solid lesions from 2017 to 2021 and collected their clinical/cytological data. Two cytopathologists independently reviewed these cases using a quoted, novel standardized cytology scoring tool. Ultimately, we calculated IOA among cytopathologists and performed a binary logistic regression analysis to evaluate factors influencing the cytological diagnosis of EUS-FNA.

RESULTS

161 patients were included, and 60 cases with a clinical diagnosis of pancreatic cancer but a cytological diagnosis of benign and atypical constituted the false-negative group. IOAs for cytological diagnosis of overall patients and the false-negative group were in perfect/moderate agreement with Kendall's W values of 0.896 and 0.462, respectively. The number of diagnostic cells in the scoring tool had the highest level of agreement (κ = 0.721) for overall patients. There was at best moderate agreement on other quantity and quality parameters for both all cases and false-negative group. Logistic regression analysis showed the number of diagnostic cells (OR = 6.110, p < 0.05) and amount of blood (OR = 0.320, p < 0.05) could influence cytological diagnosis.

CONCLUSIONS

The false-negative rate of our study as high as 37.26% (60/161) is mainly related to strict standards of cytopathologists, and their ability to standardize pancreatic cytology is still improving. Suboptimal agreement among cytopathologists for cytological diagnosis and the number of diagnostic cells may be associated with the occurrence of false-negative diagnosis. Further regression analysis confirmed that the number of diagnostic cells and obscuring blood were important factors in cytological diagnosis. Therefore, refinement of cytological diagnostic criteria, standardization of specimen quality evaluation, and training of cytopathologists may improve the agreement of cytopathologists, thus improving the repeatability of cytological diagnosis and reducing the occurrence of false-negative events.

Exploring beyond the limit: How comparative stochastic performance affects retesting outcomes in six commercial SARS CoV-2 nucleic acid amplification tests

Objectives

To examine the comparative stochasticity profile of six commercial SARS-CoV-2 nucleic acid amplification tests (NAATs) and how this may affect retesting paradigms.

Methods

Commercial quality control (QC) material was serially diluted in viral transport media to create a panel covering 10-10,000 copies/ml. The panel was tested across six commercial NAATs. A subset of high cycle threshold results was retested on a rapid PCR assay to simulate retesting protocols commonly used to discriminate false positives.

Results

Performance beyond the LOD differed among assays, with three types of stochasticity profiles observed. The ability of the rapid PCR assay to reproduce a true weak positive specimen was restricted to its own stochastic performance at the corresponding viral concentration.

Conclusion

Stochastic performance of various NAATs overlap across low viral concentrations and affect retesting outcomes. Relying on retesting alone to discriminate false positives risk missing true positives even when a more sensitive assay is deployed for confirmatory testing.

False Negative ECG Device Results May Increase the Risk of Adverse Events in Clinical Oncology Trials

Background

Sites participating in clinical trials may not have the expertise and infrastructure to accurately measure cardiac intervals on 12-lead ECGs and rely heavily on the automated ECG device generated results for clinical decision-making.

Methods

Using a dataset of over 260,000 ECGs collected in clinical oncology studies, we investigated the mean difference and the rate of false negative results between the digital ECG machine QTc and QRS measurements compared to those obtained by a centralized ECG core lab.

Results

The mean differences between the core lab and the automated algorithm QTcF and QRS measurements were + 1.8 ± 16.0 ms and − 1.0 ± 8.8 ms, respectively. Among the ECGs with a centralized QTcF value > 450 or > 470 ms, 39.5% and 47.8% respectively had a device reported QTcF value ≤ 450 ms or ≤ 470 ms. Among the ECGs with a centrally measured QTcF > 500 ms, 55.8% had a device reported value ≤ 500 ms. Automated QTcF measurements failed to detect a QTcF increase > 60 ms for 53.9% of the ECGs identified by the core lab. Automated measurements also failed to detect QRS prolongation, though to a lesser extent than failures to detect QTc prolongation. Among the ECGs with a centrally measured QRS > 110 or 120 ms, 7.9% and 7.3% respectively had a device reported QRS value ≤ 110 ms or ≤ 120 ms.

Conclusion

Relying on automated measurements from ECG devices for patient inclusion and treatment (dis)continuation decisions poses a potential risk to patients participating in oncology studies.

Effects of Menstrual Cycle on Various Morphologies of High-Grade Squamous Intraepithelial Lesions in SurePath™ Liquid-Based Cervical Cytology

INTRODUCTION

The morphology of high-grade squamous intraepithelial lesion (HSIL) on Papanicolaou (Pap) smears widely varied, including syncytial aggregates, sheets, and scattered single cells, and no particular cellular pattern is consistently observed. Therefore, this study aimed to determine whether the menstrual cycle affects the cellular pattern of HSILs, an effort to avoid false negatives due to the oversight of scattered small single HSIL cells in the cytological triage of human papillomavirus-positive women.

METHODS

A total of 147 HSIL samples of liquid-based cytology (LBC) in patients with cervical intraepithelial neoplasia grade 2 or 3 were obtained, and then, the relationship between cellular patterns, such as single-cell-like and syncytial aggregates, and menstrual cycles classified into six phases was analyzed. If a syncytial aggregate was present, the number of cells constituting the aggregate was visually counted under the microscope.

RESULTS

HSILs in scattered single cells and small sheets of <6 on LBC samples accounted for 43% (23/54) during the late proliferative phase of the menstrual cycle. A moderately strong statistically significant association was observed between cellular patterns and menstrual cycles (χ2 [3] = 9.423, p < 0.05) (Cramer's V = 0.253). The value of adjusted residuals showed a statistically significant increased proportion of single-cell-like patterns during the late proliferative phase (p < 0.01).

CONCLUSIONS

The present study demonstrated that HSIL cells in Pap smears in the late proliferation phase have a high frequency of single-cell-like patterns. In human papillomavirus-positive Pap smears with a clean background and predominantly superficial cells, careful microscopic observation by targeting single HSIL cells can potentially reduce false negatives.

SARS-CoV2 RT-PCR assays: In vitro comparison of 4 WHO approved protocols on clinical specimens and its implications for real laboratory practice through variant emergence

Introduction

RT-PCR testing on nasopharyngeal swabs is a key component in the COVID-19 fighting, provided to use sensitive and specific SARS-CoV2 genome targets. In this study, we aimed to evaluate and to compare 4 widely used WHO approved RT-PCR protocols on real clinical specimens, to decrypt the reasons of the diverging results and to propose recommendations for the choice of the genome targets.

Methods

260 nasopharyngeal samples were randomly selected among the samples tested between Week-16, 2020 and week-16 2021, in the Institut Pasteur de Tunis, Tunisia, one of the referent laboratories of COVID-19 in Tunisia. All samples were tested by Charité, Berlin protocol (singleplex envelop (E) and singleplex RNA-dependent RNA polymerase (RdRp)), Hong Kong Universiy, China protocol (singleplex nucleoprotein (N) and singleplex Open reading frame Orf1b), commercial test DAAN Gene® (using the CDC China protocol), (triplex N, Orf1ab with internal control) and Institut Pasteur Paris protocol (IPP) (triplex IP2(nsp9) and IP4 (nsp12) with internal control). For IPP, a selection from samples positive by IP2 but negative with IP4 was re-tested by exactly the same protocol but this time in singleplex. New results were described and analyzed.

Results

In vitro analysis showed discordant results in 29.2% of cases (76 out of 260). The most discordant protocol is DAAN Gene® due to the false positive late signals with N target. Discordant results between the two protocol’s targets are more frequent when viral load are low (high Ct values). Our results demonstrated that the multiplexing has worsened the sensitivity of the IP4 target.

Conclusion

We provide concise recommendations for the choice of the genome targets, the interpretation of the results and the alarm signals which makes suspect a gene mutation.

Diagnostic pitfalls in effusion fluid cytology

Effusion fluid cytology has propensity for both false positives (in up to 0.5%) and false negatives (in up to 30%) results. Methodical approach from collection step to final interpretation stage could prevent both false positives and false negatives, if the interpreter is familiar with various factors responsible for diagnostic pitfalls in effusion fluid cytology. For this discussion, these factors are categorized as mentioned below: Surface tension-related alterations in cytomorphologyImproper specimen processingMany faces of reactive mesothelial cells, overlapping with those of cancer cellsProliferation-related featuresDegenerative changes, such as nuclear hyperchromasia and cytoplasmic vacuolationUnexpected patterns and unusual entities.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Urgent care study of the LumiraDx SARS-CoV-2 Ag Test for rapid diagnosis of COVID-19

BACKGROUND

Testing individuals suspected of severe acute respiratory syndrome-like coronavirus 2 (SARS-CoV-2) infection is essential to reduce the spread of disease. The purpose of this retrospective study was to determine the false negativity rate of the LumiraDx SARS-CoV-2 Ag Test when utilized for testing individuals suspected of SARS-CoV-2 infection.

METHODS

Concurrent swab samples were collected from patients suspected of SARS-CoV-2 infection by their healthcare provider within two different urgent care centers located in Easton, MA, USA and East Bridgewater, MA, USA. One swab was tested using the LumiraDx SARS-CoV-2 Ag Test. Negative results in patients considered at moderate to high risk of SARS-CoV-2 infection were confirmed at a regional reference laboratory by polymerase chain reaction (PCR) using the additional swab sample. The data included in this study was collected retrospectively as an analysis of routine clinical practice.

RESULTS

From October 19, 2020 to January 3, 2021, a total of 2241 tests were performed using the LumiraDx SARS-CoV-2 Ag Test, with 549 (24.5%) testing positive and 1692 (75.5%) testing negative. A subset (800) of the samples rendering a negative LumiraDx SARS-CoV-2 Ag Test was also tested using a PCR-based test for SARS-CoV-2. Of this subset, 770 (96.3%) tested negative, and 30 (3.8%) tested positive. Negative results obtained with the LumiraDx SARS-CoV-2 Ag test demonstrated 96.3% agreement with PCR-based tests (CI 95%, 94.7-97.4%). A cycle threshold (C_T) was available for 17 of the 30 specimens that yielded discordant results, with an average C_T value of 31.2, an SD of 3.0, and a range of 25.2-36.3. C_T was > 30.0 in 11/17 specimens (64.7%).

CONCLUSIONS

This study demonstrates that the LumiraDx SARS-CoV-2 Ag Test had a low false-negative rate of 3.8% when used in a community-based setting.

Strain Imaging in the Evaluation of Thyroid Nodules: The Associated Factors Leading to Misdiagnosis

This study analyzed which imaging characteristics may contribute to misdiagnosis of benign and malignant thyroid nodules (TNs) through strain imaging (SI). We analyzed SI parameters and conventional ultrasound (CUS) characteristics of 264 nodules with histopathology results and we applied binary logistic regression analysis to select independent variables for incorrect SI results. The elastography imaging (EI) score and the virtual touch tissue imaging (VTI) score of malignant TNs were remarkably higher than that in benign TNs. VTI, of which the false-positive rate (FPR), the false-negative rate (FNR), and the cutoff value were 47.6% (39/82), 17.6% (32/182) and 3.5, presented higher diagnostic performance than EI. Aspect ratio (odd ratio [OR]: 14.208) and intra-nodular calcification (OR: 20.384) were significantly associated with false-positive VTI findings, while posterior acoustic feature (OR: 30.424) was significantly associated with false-negative VTI findings. Sex (OR: 0.221) and aspect ratio (OR: 0.268) were negatively associated with false-negative EI findings. In conclusion, sex and aspect ratio significantly affect the accuracy of EI results, while aspect ratio, intra-nodular calcification and posterior acoustic features notably affect the accuracy of VTI results. These CUS features of TNs should not be ignored before explaining SI examination results.

Accuracy of 18F-FDG in Detecting Stage I Lung Adenocarcinomas According to IASLC/ATS/ERS Classification

BACKGROUND

Only a small number of studies have explored the clinicopathological features of pulmonary adenocarcinoma (PA) associated with 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) false-negative (FN) results. Herein, we investigated the FDG-PET diagnostic performance by stratifying PAs according to International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society/American Thoracic Society/European Respiratory Society (IASLC/ATS/ERS) classification.

METHODS

From January 2002 to December 2016, all consecutive patients who underwent pulmonary resection for stage I PA at six thoracic surgery institutions were retrospectively reviewed. The diagnostic performance of FDG-PET was analysed according to IASLC/ATS/ERS classification and two validated subclassifications. Univariable and multivariable logistic analysis were used to identify predictors of FDG-PET FN results.

RESULTS

Five hundred and fifty (550) patients with stage I PA were included in the analyses. Most of the patients were male (n=354 [64.4%]) and smokers (n=369 [67.1%]). Ninety-seven (n=97 [17.6%]) FN cases were observed at FDG-PET imaging. On multivariable analysis, a lepidic pattern was found to be independently associated with FDG-PET FN results (odds ratio [OR], 3.20; p<0.001), while a solid pattern more commonly presented with a positive finding (OR, 0.40; p=0.066). According to Nakamura's classification, we observed an independent association between lepidic pattern and FDG-PET FN results (OR, 3.17; p<0.001), while solid/micropapillary patterns were independently related with increased FDG uptake (OR, 0.35; p=0.021). According to Yoshizawa's classification, Intermediate-grade tumours were independently correlated with FN FDG-PET results (OR, 2.78; p=0.005).

CONCLUSIONS

In our cohort, histopathological features were significantly associated with FDG uptake. In particular, some adenocarcinoma subtypes (mostly Lepidic pattern) have a tendency towards FN FDG-PET findings. The correlation between computed tomography findings, clinical characteristics, and FDG uptake is mandatory, in order to tailor the precise diagnostic and therapeutic pathway for each patient.

Improving outcomes for Colorado's IRT-IRT-DNA cystic fibrosis newborn screening algorithm by implementing floating cutoffs

The Colorado Newborn Screening Program (CO-NBS) screens for cystic fibrosis (CF) by measuring immunoreactive trypsinogen (IRT) from two screens coupled with DNA analysis (IRT/IRT/DNA). The Colorado CF Care Center identified 8 missed CF cases among 358,187 infants screened by the CO-NSP since 2016. Retrospective analysis of CO-NSP IRT data shows that a 96th percentile floating IRT cutoff with a 50 ng/mL fixed cutoff on the first screen, and second screen 50 ng/mL fixed cutoff would have identified 7 of the 8 missed cases. These efforts demonstrate the importance of continuous quality improvement in order to increase sensitivity and reduce missed cases.

False Negative Rates in Benign Thyroid Nodule Diagnosis: Machine Learning for Detecting Malignancy

BACKGROUND

Thyroid nodules are common; up to 67% of adults will show nodules on high-quality ultrasound, and 95% of these nodules are benign. FNA cytology is a crucial step in determining the risk of malignancy, and a false negative diagnosis at this stage delays cancer treatment. The purpose of this study is to develop a predictive model using machine learning which can identify false negative FNA results based on less-invasive clinical data.

MATERIALS AND METHODS

We conducted a retrospective medical record review at one academic and one community center. Inclusion criteria were thyroid nodules evaluated by ultrasound and FNA with a Bethesda II (benign) result or malignancy detected on pathology or FNA. Linear, non-linear, and ensemble models were generated with scikit-learn using 10-fold cross validation with repetition and compared with AUROC. The classification task was the prediction of malignancy using information acquired from less-invasive ultrasound and FNA.

RESULTS

A total of 604 subjects met inclusion criteria; 38 were diagnosed with malignancy. Of all algorithms tested, a Random Forest method achieved the best AUROC (0.64) in separating benign and malignant nodules, though the improvement over other tested algorithms was not statistically significant.

CONCLUSIONS

A Random Forest model performed better than random chance using readily available data obtained via standard evaluation of thyroid nodules. The diagnostic probability threshold of this model can be varied to minimize false positives at the cost of increasing the number of false negatives. Future studies will prospectively evaluate the model's performance.

A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance

More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and C_T < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.

Underrecognized Patterns of High-Grade Squamous Intraepithelial Lesion on ThinPrep Preparations

OBJECTIVES

To identify less readily identifiable patterns of high-grade squamous intraepithelial lesions (HSIL) in negative human papillomavirus (HPV)-positive Papanicolaou (Pap) tests on ThinPrep preparations.

METHODS

Of all HPV-positive Pap tests that were negative for intraepithelial lesion or malignancy (NILM) from July 2013 to June 2018, those with HSIL on subsequent histology within 6 months were identified. ThinPrep slides from the latter group (group 1) and from NILM HPV-negative Pap tests with negative follow-up (group 2) were reviewed independently by 4 participants. Group 1 cases were then reviewed together for consensus and with the ThinPrep Imaging System (TIS). Any discrepancies from the original interpretation were recorded.

RESULTS

The study cohort included 57 cases each in groups 1 and 2. On final review of group 1 cases, 17 (29.8%) were classified as NILM or unsatisfactory. Of the remaining, 4 cases revealed rare abnormal cells not flagged by the TIS in the fields of view. In the 36 cases (63.1%) with screening or interpretative errors, the key cytologic findings accounting for major discrepancies included atypical metaplastic cells, atypical repair, rare syncytial groups, and atypical immature metaplastic cells.

CONCLUSIONS

There are 3 main underrecognized patterns of HSIL in cervical cytology: atypical metaplastic cells, atypical repair, and rare syncytial groups.

A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance

More than one year into a global pandemic, SARS-CoV-2 is now defined by a variety of rapidly evolving variant lineages. Several FDA authorized molecular diagnostic tests have been impacted by viral variation, while no reports of viral variation affecting antigen test performance have occurred to date. While determining the analytical sensitivity of the Quidel Sofia SARS Antigen FIA test (Sofia 2), we uncovered a high viral load specimen that repeatedly tested negative by this antigen test. Whole genome sequencing of the specimen uncovered two mutations, T205I and D399N, present in the nucleocapsid protein of the isolate. All six SARS-CoV-2 positive clinical specimens available in our laboratory with a D399N nucleocapsid mutation and C_T < 31 were not detected by the Sofia 2 but detected by the Abbott BinaxNOW COVID-19 Ag Card, while clinical specimens with the T205I mutation were detected by both assays. Testing of recombinant SARS-CoV-2 nucleocapsid with these variants demonstrated an approximate 1000-fold loss in sensitivity for the Quidel Sofia SARS Antigen FIA test associated with the D399N mutation, while the BinaxNOW and Quidel Quickvue SARS Antigen tests were unaffected by the mutation. The D399N nucleocapsid mutation has been relatively uncommon to date, appearing in only 0.02% of genomes worldwide at time of writing. Our results demonstrate how routine pathogen genomics can be integrated into the clinical microbiology laboratory to investigate diagnostic edge cases, as well as the importance of profiling antigenic diversity outside of the spike protein for SARS-CoV-2 diagnostics.

Nationwide Rereview of Normal Cervical Cytologies before High-Grade Cervical Lesions or before Invasive Cervical Cancer

Sweden has experienced an unexpected >30% increase in cervical cancer incidence among women with normal cytological screening results. We therefore performed a nationwide assessment of false-negative cytology before invasive cervical cancer. The Swedish national cervical screening registry identified 2,150 normal cytologies taken up to 10 years before 903 cases of invasive cervical cancer. The 27 cytological laboratories in Sweden were asked to rereview the slides, and all of them completed the rereview. One thousand nine hundred fifteen slides were retrieved and reviewed. Abnormalities were found in 30% of the slides, and the proportion of slides that had a changed diagnosis on rereview increased on average by 3.9% per sampling year during 2001-2016 (p < 0.03). We also asked for rereview of normal smears taken up to 42 months before a histopathologically diagnosed high-grade squamous intraepithelial lesion (HSIL) or adenocarcinoma in situ (AIS). 19/27 laboratories responded, and out of 6,101 normal smears taken before HSIL/AIS, 5,918 were retrieved and rereviewed. The diagnosis was changed in 25% of cases. In summary, we found an increasing time trend of false-negative smears taken before invasive cervical cancer. This indicates a decreased protection of normal cytology in the screening program supporting earlier findings that this is the main reason behind the recent Swedish increase in cervical cancer. We suggest that optimal cervical cancer control may be promoted by routine nationally coordinated rereview of negative smears before high-grade cervical lesions or invasive cervical cancer.

Comparison of detection limits estimated using single- and multi-concentration spike-based and blank-based procedures

Spike- and blank-based procedures were applied to estimate the detection limits (DLs) for example analytes from inorganic and organic methods for water samples to compare with the U.S. Environmental Protection Agency's (EPA) Method Detection Limit (MDL) procedures (revisions 1.11 and 2.0). The multi-concentration spike-based procedures ASTM Within-laboratory Critical Level (DQCALC) and EPA's Lowest Concentration Minimum Reporting Level were compared in one application, with DQCALC further applied to many methods. The blank-based DLs, MDL_b99 (99th percentile) or MDL_bY (= mean blank concentration + s × t), estimated using large numbers (>100) of blank samples often provide DLs that better approach or achieve the desired ≤1% false positive risk level compared to spike-based DLs. For primarily organic methods that do not provide many uncensored blank results, spike-based DQCALC or MDL rev. 2.0 are needed to simulate the blank distribution and estimate the DL. DQCALC is especially useful for estimating DLs for multi-analyte methods having very different analyte response characteristics. Time series plots of DLs estimated using different procedures reveal that DLs are dependent on the applied procedure, should not be expected to be static over time, and seem best viewed as falling over a range versus being a single value. Use of both blank- and spike-based DL procedures help inform this DL range. Data reporting conventions that censor data at a threshold and report "less than" that threshold concentration as the reporting level have unknown and potentially high false negative risk. The U.S. Geological Survey National Water Quality Laboratory's Laboratory Reporting Level (LRL) convention (applied primarily to organic methods) attempts to simultaneously minimize both the false positive and false negative risk when <LRL is reported and data between DL and the higher LRL are allowed to be reported.

Prevalence of Plasmodium falciparum isolates lacking the histidine rich protein 2 gene among symptomatic malaria patients in Kwilu Province of the Democratic Republic of Congo

Background

Malaria rapid diagnostic tests have become a primary and critical tool for malaria diagnosis in malaria-endemic countries where Plasmodium falciparum Histidine Rich Protein 2-based rapid diagnostic tests (PfHRP2-based RDTs) are widely used. However, in the last decade, the accuracy of PfHRP2-based RDTs has been challenged by the emergence of P. falciparum strains harbouring deletions of the P. falciparum histidine rich protein 2 (pfhrp2) gene, resulting in false-negative results. In the Democratic Republic of Congo (D.R. Congo), little is known about the prevalence of the pfhrp2 gene deletion among P. falciparum isolates infecting symptomatic patients, especially in low to moderate transmission areas where pfhrp2 deletion parasites are assumed to emerge and spread. Here we determine the local prevalence and factors associated with pfhrp2 gene deletions among symptomatic malaria patients in the Kwilu Province of the D.R. Congo.

Methods

We used secondary data from a prospective health facility-based cross-sectional study conducted in 2018. Blood was collected for microscopy, PfHRP2-RDT, and spotted onto Whatman filter paper for downstream genetic analysis. Genomic DNA was extracted and used to perform PCR assays for the detection and confirmation of pfhrp2 gene deletions. Fischer’s exact and the Kruskal–Wallis tests were applied to look for associations between potential explanatory variables and the pfhrp2 gene deletion with a level of statistical significance set at P < 0.05.

Results

Of the 684 enrolled symptomatic patients, 391 (57.7%) were female. The majority (87.7%) reported the presence of mosquito breeding sites within the household’s compound, and fever was the most reported symptom (81.6%). The overall prevalence of the pfhrp2 gene deletion was 9.2% (95% CI: 6.7%–12.1%). The deletion of the pfhrp2 gene was associated with health zone of origin (P = 0.012) and age (P = 0.019). Among false-negative PfHRP2-RDT results, only 9.9% were due to pfhrp2 gene deletion.

Conclusions

P. falciparum isolates with pfhrp2 gene deletions are relatively common among symptomatic patients in Kwilu province. Further investigations are needed to provide enough evidence for policy change. Meanwhile, the use of RDTs targeting PfHRP2 and parasite lactate dehydrogenase (pLDH) antigens could limit the spread of deleted isolates.

Graphic Abstract

WEScover: selection between clinical whole exome sequencing and gene panel testing

Background

Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes.

Results

WEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage.

Conclusions

WEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04178-5.

Positive reverse transcription-polymerase chain reaction assay results in patients recovered from COVID-19: Report of two cases

BACKGROUND

Coronavirus disease 2019 (COVID-19) has spread around the globe. On February 28, 2020, the World Health Organization adjusted the risk of spread and impact of COVID-19 to “very high” at the global level. Studies have mainly focused on the etiology, epidemiology, and treatment of COVID-19 to limit further spread and the negative impact of the disease, while less attention has been devoted to the follow-up and reexamination of patients who recovered from COVID-19 or were released from quarantine.

CASE SUMMARY

This study reports two cases where patients who had negative reverse transcription-polymerase chain reaction (RT-PCR) test results and met the criteria for discharge subsequently had positive RT-PCR test results. The clinical manifestations and computed tomography (CT) findings of these patients were examined. The conversion of RT-PCR test results in these two patients may be related to false-negative and false-positive outcomes of the test. CT images helped track improvement of pulmonary lesions.

CONCLUSION

The timing of discharge of COVID-19 patients should be determined by comprehensive analysis of CT images and RT-PCR test results.

Error rates in SARS-CoV-2 testing examined with Bayes' theorem

The SARS-CoV-2 pandemic has created a demand for large scale testing, as part of the effort to understand and control transmission. It is important to quantify the error rates of test equipment under field conditions, which might differ significantly from those obtained in the laboratory. A literature review on SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) is used to construct a clinical test confusion matrix. A simple correction method for bulk test results is then demonstrated with examples. The required sensitivity and specificity of a test are explored for societal needs and use cases, before a sequential analysis of common example scenarios is explored. The analysis suggests that many of the people with mild symptoms and positive test results are unlikely to be infected with SARS-CoV-2 in some regions. It is concluded that current and foreseen alternative tests can not be used to "clear" people as being non-infected. Recommendations are given that regional authorities must establish a programme to monitor operational test characteristics before launching large scale testing; and that large scale testing for tracing infection networks in some regions is not viable, but may be possible in a focused way that does not exceed the working capacity of the laboratories staffed by competent experts. RT-PCR tests can not be solely relied upon as the gold standard for SARS-CoV-2 diagnosis at scale, instead clinical assessment supported by a range of expert diagnostic tests should be used.

Clinical utility of plasma EGFR mutation detection with quantitative PCR in advanced lung cancer: A meta-analysis

OBJECTIVES

To assess the clinical utility of quantitative PCR (qPCR) assays, a routinely used test for detection of epidermal growth factor receptor (EGFR) mutation in circulating tumour DNA (ctDNA) in treatment-naive advanced lung cancer patients.

MATERIALS AND METHODS

We performed a meta-analysis of randomized controlled trials (RCTs) with individual patient data. Eligible RCTs compared EGFR-tyrosine kinase inhibitor (EGFR-TKI) and chemotherapy in first line setting for advanced lung cancer, and included tumour EGFR+ (tEGFR+) with paired ctDNA results using real-time (quantitative) PCR. We assessed the proportion of tEGFR + detected by ctDNA, and compared the effectiveness of EGFR-TKI versus chemotherapy in ctDNA + and ctDNA- subgroups.

RESULTS

Six randomized clinical trials included 1058 tEGFR + patients with paired baseline EGFR ctDNA testing. Of these, 460 (43 %) tested ctDNA- (ctDNA+ 57 %). Progression-free survival was longer for EGFR-TKI versus chemotherapy for both ctDNA+ (HR 0.28; 95 % CI 0.22-0.36, p < 0.00001) and ctDNA- subgroups (HR 0.37; 95 % CI 0.28-0.49, p < 0.00001; p-interaction = 0.14). Objective response rate (odds ratio 6.21; 95 % CI 4.25-9.07, p < 0.00001 vs 6.44; 95 % CI 4.21-9.87, p < 0.00001) and overall survival (HR 0.82; 95 % CI 0.70-1.04 vs HR 0.77; 95CI% 0.59-1.00) similarly favoured EGFR-TKI in both ctDNA + and ctDNA- subgroups respectively.

CONCLUSION

Our findings indicate that approximately two in five tissue EGFR mutation-positive patients will not be detected using a qPCR assay, but would still potentially benefit from highly effective EGFR-TKI treatment. A negative EGFR ctDNA result via qPCR testing is therefore insufficient to exclude benefit from EGFR-TKI. Attempts should be made to repeat EGFR testing with a tissue biopsy in this patient group. As newer ctDNA assays with better sensitivity become available, the clinical impact for any false negatives will remain an important consideration.

Setting minimum clinical performance specifications for tests based on disease prevalence and minimum acceptable positive and negative predictive values: Practical considerations applied to COVID-19 testing

OBJECTIVES

Several guidelines for the evaluation of laboratory tests for severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection have recommended establishing an a priori definition of minimum clinical performance specifications before test selection and method evaluation.

METHODS

Using positive (PPV) and negative predictive values (NPV), we constructed a spreadsheet tool for determining the minimum clinical specificity (conditional on NPV or PPV, sensitivity and prevalence) and minimum clinical sensitivity (conditional on NPV or PPV, specificity and prevalence) of tests.

RESULTS

At a prevalence of 1%, there are no minimum sensitivity requirements to achieve a desired NPV of 60%-95% for a given clinical specificity above 20%. It is not possible to achieve 60-95% PPV even with 100% clinical sensitivity, except when the clinical specificity is near 100%. The opposite trend is seen in high prevalence settings (60%), where a relatively low minimum clinical sensitivity is required to achieve a desired PPV for a given clinical specificity, and a higher minimum clinical specificity is required to achieve a desired NPV for a given clinical sensitivity.

DISCUSSION

The selection of laboratory tests and the testing strategy for SARS-CoV-2 involves delicate trade-offs between NPV and PPV based on prevalence and clinical sensitivity and clinical specificity. Practitioners and health authorities should carefully consider the clinical scenarios under which the test result will be used and select the most appropriate testing strategy that fulfils the a priori defined clinical performance specification.

NSQIP Based Predictors of False Negative and Indeterminate Ultrasounds in Adults With Appendicitis

BACKGROUND

It has been well established that ultrasound (US) is the initial screening tool for children with suspected acute appendicitis. However, computed tomography (CT) has become the standard screening modality for adults presenting with abdominal pain. A recent review of National Surgical Quality Improvement Program (NSQIP) data revealed US is being utilized as a screening modality in adults. We aimed to assess the diagnostic performance of US in evaluating adults with acute appendicitis.

STUDY DESIGN

The American College of Surgeons NSQIP and NSQIP Procedure Targeted Data Files were accessed and examined for all patients in 2016 and 2017 who received an US and underwent an appendectomy. The US results were then correlated to the pathology in order to determine the diagnostic performance. Additionally, we identified predictors for indeterminate and false negative US results.

RESULTS

Our study included 3607 appendectomy patients of which 1135 (30%) had an indeterminate US, 683 (18%) had an US not consistent with appendicitis, and 1789 (49%) had an US consistent with appendicitis. Sensitivity and Specificity were 74.3% and 53.0%, respectively. Positive Predictive Value (PPV) and Negative Predictive Value (NPV) were 95.9% and 12.2%, respectively. On regression analysis, clinically relevant predictors for false negative and indeterminate studies included age, sex, and BMI.

CONCLUSIONS

Ultrasound is an effective initial imaging modality for acute appendicitis in the adult population. Females, age >30 y, and elevated BMI were more likely to have indeterminate or false negative results. These patients may benefit from CT as their initial screening test.

Preoperative false-negative transthoracic echocardiographic results in native valve infective endocarditis patients: a retrospective study from 2001 to 2018

BACKGROUND

Infective endocarditis (IE) is a lethal disease that is difficult to diagnosis early. Although echocardiography is one of the most widely used diagnostic technique, it has limited sensitivity. This study surveyed the clinical features of IE patients who underwent surgery and compared transthoracic echocardiography and histological findings to explore the factors related to false-negative echocardiographic results.

METHODS

Medical records were extracted from IE patients consecutively hospitalized between June 2001 and June 2018.

RESULTS

A total of 182 patients with native valve IE who underwent surgery were included. Compared to the non-surgery group, the surgery group was more likely to have pre-existing valvular lesions and more serious cardiac conditions and a relative lack of signs of infection and cerebrovascular events, leading to a lower proportion of "definite cases" before surgery. The false-negative rate of echocardiography was 14.5%. Echocardiography has significant disadvantages in diagnosing perivalvular abscesses, valve perforations, and left-sided endocarditis, especially for subjects with both aortic and mitral valve infections. The multivariate analysis identified congenital heart disease and small vegetations (< 10 mm) as independent predictors of false-negative echocardiography results. Conversely, fever and heart murmurs on admission served as protective factors.

CONCLUSIONS

Under some circumstances, echocardiography provides inconsistent results compared with surgical findings, and negative echocardiography results do not rule out IE. The diagnosis of IE depends on comprehensive evaluations using multiple methods.

Clinicopathological features of breast cancer without mammographic findings suggesting malignancy

Background

Mammography (MG) is widely used for screening examinations. Dense breast reduces MG screening sensitivity, possibly delaying diagnosis. However, little is known about the characteristics of breast cancers without MG findings indicative of malignancy. Hence, we investigated breast cancer patients with tumors not detected by MG.

Patients and methods

In total, 1758 Japanese patients with breast cancer, undergoing curative surgery between 2012 and 2018 without neo-adjuvant chemotherapy, were retrospectively investigated. Clinicopathological features were compared between patients without (MG-negative) and with (MG-positive) cancer-specific findings on MG. The current study included cases who came to our hospital after experiencing subjective symptoms, or whose tumors were detected by MG and/or US-screening. We reviewed results of both MG and US conducted at our institution.

Results

There were 201 MG-negative cases (11.4%). In patients with invasive disease, multivariate analysis revealed MG-negative patients to have higher breast density on MG (p < 0.001). Tumors of MG-negative patients were smaller (p < 0.001), showed less lymph node involvement (p = 0.011), and were of lower grade (p = 0.027). The majority of MG-negative tumors were found by ultrasound screening, being smaller than tumors in patients with subjective symptoms. In the MG-negative group, tumor characteristics such as tumor grade did not differ between those detected by screening versus subjective symptoms.

Conclusion

Most tumors in MG-negative group patients were identified by US screening and the diseases were found at early stages with low malignancy. The usefulness of additional ultrasound with MG-screening might merit further investigations.

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Breast cancers without cancer-specific findings on mammograms were pathologically at early stages and low-grade .

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The majority of mammogram-negative tumors were found by ultrasound screening.

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Mammogram-negative tumors were low-grade regardless of motives for visiting the hospital.

Atypical presentation of COVID-19; an observational retrospective study

BACKGROUND

COVID-19 infection may present with atypical signs and symptoms and false negative polymerase chain reaction (PCR) tests predisposing healthy people and health care workers to infection. The aim of the current study is to evaluate the features of atypical presentations in COVID-19 infection in a referral center in Tehran, Iran.

METHODS

Hospital database of inpatients admitted to Loghman Hakim hospital between February 20th and May 11th, 2020 was reviewed and all patients with final diagnosis of COVID-19 infection were evaluated for their presenting symptoms. Patients with chief complaints of "fever", "dyspnea", and/or "cough" as typical presentations of COVID-19 were excluded and those with other clinical presentations were included.

RESULTS

Nineteen patients were included with a mean age of 51 ± 19 years, of whom, 17 were males (89%). Median [IQR] Glasgow coma scale (GCS) was 14 [13, 15]. Almost 10 had referred with chief complaint of methanol poisoning and overdose on substances of abuse. Only 8 cases (42%) had positive COVID-19 test. Nine (47%) needed invasive mechanical ventilation, of whom, two had positive COVID-19 test results (p = ns). Eight patients (42%) died with three of them having positive PCRs.

CONCLUSIONS

In patients referring to emergency departments with chief complaint of poisoning (especially poisonings that can result in dyspnea including substances of abuse and toxic alcohols), gastrointestinal, and constitutional respiratory symptoms, attention should be given not to miss possible cases of COVID-19.

Evaluation of the International Society for Animal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle

A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (P_E) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10^-48 (BON) to 1.11 × 10^-54 (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.