Evaluation of Kernfeld et al.: Toward best practices for tackling false positives in regulatory network inference.

One snapshot of the peer review process for "Transcriptome data are insufficient to control false discoveries in regulatory network inference" (Kernfeld et al., 2024).1.

Analytical interference in CA 19-9 immunoassay generates false-positive results in a young woman with a low-grade appendiceal tumor: An educational case report and brief literature review.

CA 19-9 (carbohydrate antigen 19-9) is a tumor marker widely used for the follow-up of patients with pancreatic cancer and other digestive neoplasia. This case report describes a discrepancy between the results of serum CA 19-9 analyses using the Alinity analytical platform (Abbott™) and two other techniques, Kryptor Gold (ThermoFisher Scientific™) and Cobas E411 (Roche™), in the context of a young woman with appendiceal mucocele. In this context, when the serum concentration of CA 19-9 is high, it may raise concerns about potential malignancy or rupture of the mucocele that may lead to tumoral dissemination in the abdominal cavity. In the present case, we observed with Alinity a false elevation in CA 19-9 concentration at 190 kU/L (normal range < 37 kU/L) before appendix resection that continued to increase until reaching 619 kU/L six months after surgery. This situation led to unnecessary additional tests, increased hospitalization time and stress for the patient who also had to interrupt her medically assisted reproduction project. We solved this case using new measurements in CA 19-9 concentration with two other techniques, Kryptor Gold and Cobas E411, and we identified an analytical interference caused by the presence of heterophile antibodies. In all cases, abnormal result initially obtained with Alinity was found below normal range not only with the two other techniques but also with Alinity after a neutralisation step by using Heterophile Blocking Tubes (Scantibodies Laboratory™). Analytical interferences in medical tests can lead to inappropriate medical care. It is an important issue requiring a continuing training of biologists who must be aware of these problems, which are recurring concerns and are not always easy to identify in laboratories of medical biology, in particular when immunoassays are used. This case report also provides an opportunity to do a brief review of the literature and to remind some recommendations and actions to take into consideration in the presence of discrepancies between the clinic and the biology, in particular, one of them is to measure the biological analyte with a different technique. Moreover, the use of Heterophile Blocking Tubes neutralizing specifically the heterophile antibodies may be useful. In all cases, dialogue between clinicians and biologists remains essential.

False Discovery Rate Control for Lesion-Symptom Mapping With Heterogeneous Data via Weighted p-Values.

Lesion-symptom mapping studies provide insight into what areas of the brain are involved in different aspects of cognition. This is commonly done via behavioral testing in patients with a naturally occurring brain injury or lesions (e.g., strokes or brain tumors). This results in high-dimensional observational data where lesion status (present/absent) is nonuniformly distributed, with some voxels having lesions in very few (or no) subjects. In this situation, mass univariate hypothesis tests have severe power heterogeneity where many tests are known a priori to have little to no power. Recent advancements in multiple testing methodologies allow researchers to weigh hypotheses according to side information (e.g., information on power heterogeneity). In this paper, we propose the use of p-value weighting for voxel-based lesion-symptom mapping studies. The weights are created using the distribution of lesion status and spatial information to estimate different non-null prior probabilities for each hypothesis test through some common approaches. We provide a monotone minimum weight criterion, which requires minimum a priori power information. Our methods are demonstrated on dependent simulated data and an aphasia study investigating which regions of the brain are associated with the severity of language impairment among stroke survivors. The results demonstrate that the proposed methods have robust error control and can increase power. Further, we showcase how weights can be used to identify regions that are inconclusive due to lack of power.

False-Positive Circulating Tumor DNA Results Do Not Explain Lack of Efficacy for PARP Inhibitors in Patients With Castration-Resistant Prostate Cancer Harboring ATM and CHEK2 Mutations.

False-positive ctDNA results do not explain lack of efficacy for PARPi in patients with ATMm and CHEK2m CRPC.

Clinical Evaluation of a New Chemiluminescence Assay for the Detection of Treponema Pallidum Antibodies.

BACKGROUND: A new chemiluminescence assay, the Anti-TP-Ⅱ assay, is going to be commercially available in clinical laboratories in China and other countries. This study examined the performance of the new assay for the detection of TP infection and compared it with that of the Anti-TP assay by using large amounts of clinical samples. METHODS: The precision, accuracy, anti-interference ability, and the clinical sensitivity and specificity of the Anti-TP-Ⅱ assay were evaluated. In addition, compared with those of the Anti-TP assay, the false positive and false negative rates of the Anti-TP-Ⅱ assay were evaluated for 2,436 clinical routine samples and 711 preselected Anti-TP assay reactive samples. Discrepancy of the samples was investigated with the recomLinec Treponema IgM/IgG kit or the Elecsys syphilis assay. RESULTS: The precision, accuracy, and anti-interference ability of the Anti-TP-Ⅱ assay met the national standard of China, and there was an overall agreement of 96.75% (Kappa = 0.91) between the two assays. The sensitivity and specificity of the Anti-TP-Ⅱ assay were 100% (95% CI: 94.13% to 100%) and 99.92% (95% CI: 99.70% to 99.99%), respectively. Compared with the Anti-TP assay, the Anti-TP-Ⅱ assay significantly reduced the number of borderline samples and the false positive rate. CONCLUSIONS: Considering its excellent performance, the Anti-TP-Ⅱ assay is a good screening test for high-throughput laboratories and can replace the previous generation of reagents, the Anti-TP assay, with a superior specificity.

Pseudo-Elevation of Anti Double Stranded DNA IgG Antibody Caused by Rheumatoid Factor.

BACKGROUND: The examination of anti-double stranded DNA (ds-DNA) IgG antibody is of great significance for the diagnosis, differential diagnosis, assessment of disease activity, and prognosis of disease recurrence in SLE. METHODS: We used a chemiluminescence method to detect ds-DNA IgG and found that the levels of ds-DNA IgG antibody in the patient's serum were significantly increased and the indirect immunofluorescence (IIF) test result was negative. Laboratory tests show that the patient's RF level far exceeds the upper limit of their reference range. RESULTS: RF 110.6 IU/mL, ds-DNA IgG 753 IU/mL; After PEG6000 treatment, the RF was 108.7 IU/mL, and then the ds-DNA IgG was measured at 23.5 IU/mL. CONCLUSIONS: The RF IgM subtype is the main cause of RF interference in IgG antibody detection, mainly due to the binding of the Fc region of RF to the Fab segment of IgG. Combining with capture antibodies and labeled antibodies leads to the formation of non-specific detection signals, or directly reacting with the detected substance, resulting in false positive test results.

A Case of False Insulin Test Results Due to the Megaloblastic Anemia.

BACKGROUND: Megaloblastic anemia is a subtype of anemia with increased red blood cell volume. These megaloblastic cells can be easily destroyed in the bone marrow and spleen, leading to ineffective hematopoiesis. Insulin-degrading enzymes (IDE) in erythrocytes can break down the insulin into amino acid fragments; thus, when hemolysis occurs, IDE can be released into the blood, resulting in low insulin measurement values. METHODS: This article reports a case of false insulin test results due to the hemolysis resulting from megaloblastic anemia. RESULTS: The patient's first fasting glucose results indicated that the glucose and C-peptide levels were within the normal range while her insulin level was abnormally low. After hemolysis was corrected, the relevant indicators were re-evaluated and all the results were normal. CONCLUSIONS: This article reports a patient diagnosed with megaloblastic anemia, whose dysmorphic erythrocytes cause severe extravascular hemolysis. It was the occurrence of hemolysis that the IDE released into the blood, leading to the abnormal insulin test result.

Two Cases of False Elevation of MCHC.

BACKGROUND: Mean corpuscular hemoglobin concentration (MCHC) is one of the parameters detected by blood cell analyzers, often used together with mean corpuscular volume (MCV) and mean corpuscular hemoglobin content (MCH) as diagnostic indicators for anemia classification. It has important clinical value in early detection of the cause of anemia and the underlying etiology of anemia. Therefore, the accuracy of MCHC results is of great significance for the diagnosis and treatment of diseases. METHODS: We reported two cases of false elevation of MCHC. Considering the possibility of cold agglutination and lipid blood interference detection, we used 37℃ water bath and plasma exchange to correct for interference on the sample. RESULTS: After correcting the interference, MCHC returned to normal, consistent with the patient's disease status. Therefore, the two cases of abnormal elevation of MCHC are considered to be pseudo elevation caused by interference. CONCLUSIONS: For specimens with abnormally elevated MCHC levels, experimenters should first analyze possible interfering factors and choose effective methods to correct different interferences, providing accurate testing reports for doctors and patients.

A Case of False Decrease of Plasma D-Dimer.

BACKGROUND: D-dimer, a specific product of cross-linked fibrin degradation, is of great clinical value in the early diagnosis of thrombotic diseases and in monitoring the efficacy of thrombolysis; therefore, the accuracy of D-dimer test results is crucial. METHODS: This article reports a case of a patient with disseminated intravascular coagulation (DIC) who experienced a false decrease in D-dimer due to the hook effect. RESULTS: The three D-dimer test results for DIC patients were 1.09 mg/L, 0.93 mg/L, and 1.43 mg/L. After sample dilution, the results were: first time (1:128) 842.24 mg/L, second time (1:128) 1,505.28 mg/L, third time (1:32) 415.68 mg/L. There was a significant difference in the three test results before and after dilution, because the D-dimer concentration was too high, exceeding the detection range and causing the hook effect, which falsely lowered the D-dimer value. CONCLUSIONS: When the D-dimer value of DIC patients does not match the clinical situation, the possibility of the hook effect should be considered, and the false decrease can be ruled out by the sample dilution method. In this way, accurate clinical results can be obtained to avoid delaying the diagnosis and treatment of DIC patients.

Deep Learning Reconstruction of Accelerated MRI: False-Positive Cartilage Delamination Inserted in MRI Arthrography Under Traction.

OBJECTIVES: The radiological imaging industry is developing and starting to offer a range of novel artificial intelligence software solutions for clinical radiology. Deep learning reconstruction of magnetic resonance imaging data seems to allow for the acceleration and undersampling of imaging data. Resulting reduced acquisition times would lead to greater machine utility and to greater cost-efficiency of machine operations. MATERIALS AND METHODS: Our case shows images from magnetic resonance arthrography under traction of the right hip joint from a 30-year-old, otherwise healthy, male patient. RESULTS: The undersampled image data when reconstructed by a deep learning tool can contain false-positive cartilage delamination and false-positive diffuse cartilage defects. CONCLUSIONS: In the future, precision of this novel technology will have to be put to thorough testing. Bias of systems, in particular created by the choice of training data, will have to be part of those assessments.

[Development of a PCR Method to Detect a Mysid Species Causing False Positives in Tests for Crustacean Allergens].

Mysids are small crustaceans that are closely related to shrimp/prawns and crabs but not subject to food allergen labeling requirements for raw materials. In the past, a processed food that contained Japanese smelt (wakasagi) was suspected of producing a false-positive result in shrimp/prawn and crab allergen test because of the presence of consumed mysids. However, there was no reported methods to confirm mysid presence. Therefore, we developed a PCR method to detect mysids. The developed PCR method had high specificity for a mysid species, with no amplification observed from samples of shrimp, crab, krill, mantis shrimp, or the meat of Japanese smelt. In addition, DNA extracted from the internal organs of Japanese smelt was amplified by this PCR method, and sequencing revealed mysid DNA. This confirmed that mysids remained in the internal organs of Japanese smelt following consumption. This PCR method for mysid detection even amplified Japanese smelt-containing processed food samples that were suspected to have produced a false-positive result in shrimp/prawn and crab ELISA. Thus, this PCR method would enable to detect such false positives are caused by mysid contamination.

Controlling false discovery rate for mediator selection in high-dimensional data.

The need to select mediators from a high dimensional data source, such as neuroimaging data and genetic data, arises in much scientific research. In this work, we formulate a multiple-hypothesis testing framework for mediator selection from a high-dimensional candidate set, and propose a method, which extends the recent development in false discovery rate (FDR)-controlled variable selection with knockoff to select mediators with FDR control. We show that the proposed method and algorithm achieved finite sample FDR control. We present extensive simulation results to demonstrate the power and finite sample performance compared with the existing method. Lastly, we demonstrate the method for analyzing the Adolescent Brain Cognitive Development (ABCD) study, in which the proposed method selects several resting-state functional magnetic resonance imaging connectivity markers as mediators for the relationship between adverse childhood events and the crystallized composite score in the NIH toolbox.

Kaiser score diagnosis of breast MRI lesions: Factors associated with false-negative and false-positive results.

PURPOSE: We sought factors associated with false-negative and false-positive results in the diagnosis of breast lesions using the Kaiser score (KS) on breast magnetic resonance imaging (MRI). METHODS: We retrospectively analyzed 1058 patients with 1058 breast lesions who underwent preoperative breast MRI with successful histopathologic results. Two radiologists assessed each lesion according to KS criteria, and clinicopathologic features and MRI findings were analyzed. Multivariate regression analysis was conducted to identify factors associated with false-negative and false-positive KS results. RESULTS: Of the 1058 lesions, 859 were malignant and 199 were benign. Particularly high misdiagnosis rates were observed for intraductal papilloma, inflammatory lesion, and mucinous carcinoma. For breast cancer, KS yielded 821 (95.6 %) true-positive and 38 (4.4 %) false-negative results. Multivariate analysis showed that smaller lesion size (≤1 cm) (OR, 3.698; 95 %CI, 1.430-9.567; p = 0.007), absence of ipsilateral breast hypervascularity (OR, 3.029; 95 %CI, 1.370-6.693; p = 0.006), and presence of hyperintensity on T2WI (OR, 2.405; 95 %CI, 1.121-5.162; p = 0.024) were significantly associated with false-negative breast cancer results. For benign lesions, KS yielded 141 (70.9 %) true-negative and 58 (29.1 %) false-positive results. Multivariate regression analysis revealed that non-mass enhancement lesions (OR, 4.660; 95 %CI, 2.018-10.762; p＜0.001), moderate/high background parenchymal enhancement (OR, 2.402; 95 %CI, 1.180-4.892; p = 0.016), and the presence of hyperintensity on T2WI (OR, 2.986; 95 %CI, 1.386-6.433; p = 0.005) were significantly associated with false-positive KS results. CONCLUSION: Several clinicopathologic and MRI features influence the accuracy of KS diagnosis. Understanding these factors may facilitate appropriate use of KS and guide alternative diagnostic approaches, ultimately improving diagnostic accuracy in the evaluation of breast lesions.

Improved efficiency using sequential automated immunoassays for syphilis screening in blood donors.

Using sequential immunoassays for the screening of blood donors is well described for viral serology testing but not for the screening of syphilis. In this study, we report the evaluation results and 2-year sequential testing data using two highly sensitive automated serology assays, the Alinity s Syphilis chemiluminescent immunoassay for screening, with all repeatedly reactive samples then tested on the Elecsys Syphilis electrochemiluminescence immunoassay. We screened 1,767,782 blood donor samples between 7 July 2021 and 6 July 2023 and found the Alinity false-positive rate to be low at 0.08% (1,456/1,767,782). The common false-positive rate between the two assays was also low (3.83%, 58/1,514). Concordantly reactive samples were further tested using a Treponema pallidum particle agglutination test, a rapid plasma reagin test, and a fluorescent treponemal antibody absorption test. There were 262/1,376 concordantly reactive Alinity and Elecsys blood donor samples with reactivity on one or more of the confirmatory tests. A total of 26/1,376 donors had a current syphilis infection, 152/1,376 reported a past history of syphilis and had been treated, and 84/1,376 did not report a past history of syphilis. We suggest that future studies could explore the use of sequential immunoassays to aid in the serodiagnosis for syphilis. IMPORTANCE: The serodiagnosis for syphilis usually follows two methodologies-a "traditional" algorithm using a non-treponemal test followed by confirmation using a treponemal test, or a "reverse" algorithm using a treponemal test followed by a non-treponemal test. There are limited reports in the literature of using a modified reverse algorithm (treponemal test followed by a second treponemal test), and to the best of knowledge, there are currently no published articles using two highly sensitive automated immunoassays to aid the serodiagnosis of syphilis. In addition, the Treponema pallidum particle agglutination (TPPA) assay is commonly used as a confirmatory test for the diagnosis of syphilis. With the withdrawal of the TPPA assay from Australia and presumably from the global market also, alternative testing algorithms are now required. This study provides proof of concept for using sequential immunoassays in the diagnosis of syphilis.

Factors Associated with False Positive Breast Cancer Results in the Real-Time Sonoelastography Evaluation of Solid Breast Lesions.

Background and Objectives: Breast cancer is one of the most widespread cancers among the female population around the world and is curable if diagnosed in an early stage. Consequently, breast cancer screening imaging techniques have greatly evolved and adjusted over the last decades. Alongside mammography, sonoelastography became an important tool for breast cancer detection. However, sonoelastography still has its limitations, namely, there is still a high occurrence of false positive results in the BIRADS 4 category. The aim of our study is to identify potential false positive predictors and to ascertain the factors influencing the quality of strain ultrasound elastography for the evaluation of suspicious solid breast lesions categorized as BIRADS 4B, 4C, and 5. Materials and Methods: We conducted a retrospective study in a single private medical center in Timisoara between January 2017 and January 2022 analyzing 1625 solid breast lesions by the sonoelastography strain using a standardized BIRADS-US lexicon. Results: Our study showed that most sonoelastography factors linked to incorrect and overdiagnosis were due to a nodule dimension (OR = 1.02 per unit increase), posterior acoustic shadowing (OR = 12.26), reactive adenopathy (OR = 6.35), and an increased TES score (TES3 OR = 6.60; TES4 OR = 23.02; TES5 OR = 108.24). Regarding patient characteristics, age (OR = 1.09 per unit increase), BMI, (OR = 1.09 per unit increase), and breastfeeding history (OR = 3.00) were observed to increase the likelihood of false positive results. On the other hand, the nodules less likely to be part of the false positive group exhibited the following characteristics: a regular shape (OR = 0.27), homogenous consistency (OR = 0.42), and avascularity (OR = 0.22). Conclusions: Older age, high BMI, patients with a breastfeeding history, and those who exhibit the following specific nodule characteristics were most often linked to false positive results: large tumors with posterior acoustic shadowing and high elasticity scores, accompanied by reactive adenopathy. On the other hand, homogenous, avascular nodules with regular shapes were less likely to be misdiagnosed.

Effects of Various Concentrations of Pronase on Flow Cytometric Crossmatching Patients Treated With Rituximab and Donor HLA-Specific Antibodies.

Background: Pronase pretreatment can reduce rituximab (RTX) interference by degrading CD20 in B-cell flow cytometry crossmatch (FCXM) testing. However, it may also reduce the assay sensitivity by degrading HLA molecules. We investigated the effects of various pronase concentrations on RTX interference and the analytical sensitivity of B-cell FCXM testing. Methods: Using 59 patient serum samples and 38 donor lymphocyte samples, we designed 97 recipient-donor pairs and divided them into three groups according to RTX use and the presence of weak-to-moderate donor HLA-specific antibody (DSA) reactions: RTX+/DSA-, RTX+/DSA+, and RTX-/DSA+. FCXM was performed after pretreating lymphocytes with six different pronase concentrations (0, 0.5, 1, 2, 3, and 4 mg/mL). Results: With B-FCXM testing, false-positive results due to RTX in the RTX+/DSA- group markedly decreased with increasing pronase concentrations. The median channel shift values in the RTX+/DSA+ and RTX-/DSA+ groups did not significantly decrease when the pronase concentration was increased from 1 mg/mL to 2 or 3 mg/mL. All eight RTX+/DSA+ cases that were positive at 1 mg/mL pronase but negative at 2 or 3 mg/mL had mean fluorescence intensity (MFI) DSA values of less than 3,000 except for DQ5 (MFI: 5,226). With T-cell FCXM, false-positive results were observed in 2.9% of 315 FCXM tests with pronase pretreatment. Conclusions: Higher concentrations (2 or 3 mg/mL) of pronase effectively eliminated RTX interference but still carried a risk for false negativity for weak DSA reactions in B-cell FCXM. Higher pronase concentrations can be used as an auxiliary method to detect moderate-to-strong DSA reactions in RTX-treated patients.