scholarly journals Efficiency of a Randomized Confirmatory Basket Trial Design Constrained to Control the False Positive Rate by Indication

2020 ◽  
Author(s):  
Linchen He ◽  
Yuru Ren ◽  
Han Chen ◽  
Daphne Guinn ◽  
Deepak Parashar ◽  
...  
Keyword(s):  
False Positive ◽  
Power Efficiency ◽  
Statistical Significance ◽  
False Positive Rate ◽  
Pooled Analysis ◽  
Positive Control ◽  
Design Parameters ◽  
Molecular Oncology ◽  
Basket Trial ◽  
Basket Trials

PURPOSEMolecular oncology determines biomarker-defined niche indications. Basket trials pool histologic indications sharing molecular pathophysiology, potentially improving development efficiency. Currently basket trials have been confirmatory only for exceptional therapies. Our previous randomized basket design may be generally suitable in the resource-intensive confirmatory phase, maintains high power, and provides nearly k-fold increased efficiency for k indications, but controls false positives for the pooled result only. Since false positive control by indications (FWER) may sometimes be required, we now simulate a variant of this basket design controlling FWER at 0.025k, the total FWER of k separate randomized trials.METHODSThe previous design eliminated indications at an interim analysis, conducting a final pooled analysis of remaining indications. To control FWER, we rechecked individual indications at a prospectively defined level of statistical significance after any positive pooled result. We simulated this modified design under numerous scenarios varying design parameters. Only designs controlling FWER and minimizing estimation bias were allowable.RESULTSSequential analyses (interim, pooled, and post-individual tests)) result in cumulative power losses. Optimal performance results when k = 3,4. We report efficiency (expected # true positives/expected sample size) relative to k parallel studies, at 90% power (“uncorrected”) or at the power achieved in the basket trial (“corrected”, because conventional designs could also increase efficiency by sacrificing power). Efficiency and power (percentage active indications identified) improve with higher percentage of initial indications active. Up to 92% uncorrected and 38% corrected efficiency improvement is possible, with power ≈ 60%.CONCLUSIONSEven under FWER control, randomized confirmatory basket trials substantially improve development efficiency. Initial indication selection is critical. The design is particularly attractive when enrollment challenges preclude full powering of individual indications.

Marginal Effects in Interaction Models: Determining and Controlling the False Positive Rate

2017 ◽  
Vol 51 (9) ◽  
pp. 1144-1176 ◽  
Author(s):  
Justin Esarey ◽  
Jane Lawrence Sumner
Keyword(s):  
Political Parties ◽  
False Positive ◽  
Software Package ◽  
Statistical Significance ◽  
False Positive Rate ◽  
Marginal Effect ◽  
Marginal Effects ◽  
Political Studies ◽  
Positive Rate ◽  
The Relationship

When a researcher suspects that the marginal effect of [Formula: see text] on [Formula: see text] varies with [Formula: see text], a common approach is to plot [Formula: see text] at different values of [Formula: see text] along with a pointwise confidence interval generated using the procedure described in Brambor, Clark, and Golder to assess the magnitude and statistical significance of the relationship. Our article makes three contributions. First, we demonstrate that the Brambor, Clark, and Golder approach produces statistically significant findings when [Formula: see text] at a rate that can be many times larger or smaller than the nominal false positive rate of the test. Second, we introduce the interactionTest software package for R to implement procedures that allow easy control of the false positive rate. Finally, we illustrate our findings by replicating an empirical analysis of the relationship between ethnic heterogeneity and the number of political parties from Comparative Political Studies.

scholarly journals The impact of P-hacking on "Redefine statistical significance"

2017 ◽  
Author(s):  
Harry Crane
Keyword(s):  
False Positive ◽  
Statistical Significance ◽  
False Positive Rate ◽  
Perceived Benefits ◽  
Replication Rate ◽  
Recent Proposal ◽  
Positive Rate ◽  
Replication Crisis ◽  
The Impact ◽  
Lower Cutoff

A recent proposal to "redefine statistical significance" (Benjamin, et al. Nature Human Behaviour, 2017) claims that false positive rates "would immediately improve" by factors greater than two and replication rates would double simply by changing the conventional cutoff for 'statistical significance' from P<0.05 to P<0.005. I analyze the veracity of these claims, focusing especially on how Benjamin, et al neglect the effects of P-hacking in assessing the impact of their proposal. My analysis shows that once P-hacking is accounted for the perceived benefits of the lower threshold all but disappear, prompting two main conclusions: (i) The claimed improvements to false positive rate and replication rate in Benjamin, et al (2017) are exaggerated and misleading. (ii) There are plausible scenarios under which the lower cutoff will make the replication crisis worse.

scholarly journals Inferring the genetic architecture of expression variation from replicated high throughput allele-specific expression experiments

2019 ◽  
Author(s):  
Xinwen Zhang ◽  
J.J. Emerson
Keyword(s):  
False Positive ◽  
Statistical Significance ◽  
False Positive Rate ◽  
Regulatory Sequences ◽  
Binomial Model ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Expression Variation ◽  
Positive Rate ◽  
Allele Specific

AbstractGene expression variation between alleles in a diploid cell is mediated by variation in cis regulatory sequences, which usually refers to the differences in DNA sequence between two alleles near the gene of interest. Expression differences caused by cis variation has been estimated by the ratio of the expression level of the two alleles under a binomial model. However, the binomial model underestimates the variance among replicated experiments resulting in the exaggerated statistical significance of estimated cis effects and thus many false discoveries of cis-affected genes. Here we describe a beta-binomial model that estimates the cis-effect for each gene while permitting overdispersion of variance among replicates. We demonstrated with simulated null data (data without true cis-effect) that the new model fits the true distribution better, resulting in approximately 5% false positive rate under 5% significance level in all null datasets, considerably better than the 6%-40% false positive rate of the binomial model. Additional replicates increase the performance of the beta-binomial model but not of the binomial model. We also collected new allele-specific expression data from an experiment comprised of 20 replicates of a yeast hybrid (YPS128/RM11-1a). We eliminated the mapping bias problem with de novo assemblies of the two parental genomes. By applying the beta-binomial model to this dataset, we found that cis effects are ubiquitous, affecting around 70% of genes. However, most of these changes are small in magnitude. The high number of replicates enabled us a better approximation of cis landscape within species and also provides a resource for future exploration for better models.

Improving diagnosis of acute appendicitis with atypical findings by Tc-99m HMPAO leukocyte scan

2002 ◽  
Vol 41 (01) ◽  
pp. 37-41 ◽  
Author(s):  
S. Shung-Shung ◽  
S. Yu-Chien ◽  
Y. Mei-Due ◽  
W. Hwei-Chung ◽  
A. Kao
Keyword(s):  
Acute Appendicitis ◽  
False Positive ◽  
False Positive Rate ◽  
Accurate Method ◽  
Clinical Findings ◽  
Pathological Findings ◽  
Lower Quadrant ◽  
Predictive Values ◽  
Positive Rate

Summary Aim: Even with careful observation, the overall false-positive rate of laparotomy remains 10-15% when acute appendicitis was suspected. Therefore, the clinical efficacy of Tc-99m HMPAO labeled leukocyte (TC-WBC) scan for the diagnosis of acute appendicitis in patients presenting with atypical clinical findings is assessed. Patients and Methods: Eighty patients presenting with acute abdominal pain and possible acute appendicitis but atypical findings were included in this study. After intravenous injection of TC-WBC, serial anterior abdominal/pelvic images at 30, 60, 120 and 240 min with 800k counts were obtained with a gamma camera. Any abnormal localization of radioactivity in the right lower quadrant of the abdomen, equal to or greater than bone marrow activity, was considered as a positive scan. Results: 36 out of 49 patients showing positive TC-WBC scans received appendectomy. They all proved to have positive pathological findings. Five positive TC-WBC were not related to acute appendicitis, because of other pathological lesions. Eight patients were not operated and clinical follow-up after one month revealed no acute abdominal condition. Three of 31 patients with negative TC-WBC scans received appendectomy. They also presented positive pathological findings. The remaining 28 patients did not receive operations and revealed no evidence of appendicitis after at least one month of follow-up. The overall sensitivity, specificity, accuracy, positive and negative predictive values for TC-WBC scan to diagnose acute appendicitis were 92, 78, 86, 82, and 90%, respectively. Conclusion: TC-WBC scan provides a rapid and highly accurate method for the diagnosis of acute appendicitis in patients with equivocal clinical examination. It proved useful in reducing the false-positive rate of laparotomy and shortens the time necessary for clinical observation.

Predicting Fetal Chromosome Anomalies in the First Trimester Using Pregnancy Associated Plasma Protein-A: A Comparison of Statistical Methods

1993 ◽  
Vol 32 (02) ◽  
pp. 175-179 ◽  
Author(s):  
B. Brambati ◽  
T. Chard ◽  
J. G. Grudzinskas ◽  
M. C. M. Macintosh
Keyword(s):  
Logistic Regression ◽  
General Population ◽  
Likelihood Ratio ◽  
False Positive ◽  
False Positive Rate ◽  
Ratio Method ◽  
Detection Rates ◽  
Gaussian Distributions ◽  
Positive Rate ◽  
Likelihood Ratio Method

Abstract:The analysis of the clinical efficiency of a biochemical parameter in the prediction of chromosome anomalies is described, using a database of 475 cases including 30 abnormalities. A comparison was made of two different approaches to the statistical analysis: the use of Gaussian frequency distributions and likelihood ratios, and logistic regression. Both methods computed that for a 5% false-positive rate approximately 60% of anomalies are detected on the basis of maternal age and serum PAPP-A. The logistic regression analysis is appropriate where the outcome variable (chromosome anomaly) is binary and the detection rates refer to the original data only. The likelihood ratio method is used to predict the outcome in the general population. The latter method depends on the data or some transformation of the data fitting a known frequency distribution (Gaussian in this case). The precision of the predicted detection rates is limited by the small sample of abnormals (30 cases). Varying the means and standard deviations (to the limits of their 95% confidence intervals) of the fitted log Gaussian distributions resulted in a detection rate varying between 42% and 79% for a 5% false-positive rate. Thus, although the likelihood ratio method is potentially the better method in determining the usefulness of a test in the general population, larger numbers of abnormal cases are required to stabilise the means and standard deviations of the fitted log Gaussian distributions.

Identification of and Correction for Publication Bias: Comment

2019 ◽  
Author(s):  
Amanda Kvarven ◽  
Eirik Strømland ◽  
Magnus Johannesson
Keyword(s):  
Publication Bias ◽  
False Positive ◽  
Large Scale ◽  
Meta Analysis ◽  
False Positive Rate ◽  
Effect Sizes ◽  
Replication Studies ◽  
Moderate Reduction ◽  
Positive Rate ◽  
Meta Analyses

Andrews & Kasy (2019) propose an approach for adjusting effect sizes in meta-analysis for publication bias. We use the Andrews-Kasy estimator to adjust the result of 15 meta-analyses and compare the adjusted results to 15 large-scale multiple labs replication studies estimating the same effects. The pre-registered replications provide precisely estimated effect sizes, which do not suffer from publication bias. The Andrews-Kasy approach leads to a moderate reduction of the inflated effect sizes in the meta-analyses. However, the approach still overestimates effect sizes by a factor of about two or more and has an estimated false positive rate of between 57% and 100%.

Characteristics of false-positive alerts on transcranial motor evoked potential monitoring during pediatric scoliosis and adult spinal deformity surgery: an “anesthetic fade” phenomenon

2020 ◽  
Vol 32 (3) ◽  
pp. 423-431 ◽  
Author(s):  
Hiroki Ushirozako ◽  
Go Yoshida ◽  
Tomohiko Hasegawa ◽  
Yu Yamato ◽  
Tatsuya Yasuda ◽  
...  
Keyword(s):  
Spinal Deformity ◽  
False Positive ◽  
Adult Spinal Deformity ◽  
False Positive Rate ◽  
Multivariate Logistic Regression Analysis ◽  
Motor Evoked Potential ◽  
Scoliosis Surgery ◽  
True Negative ◽  
Duration Of Surgery ◽  
Spinal Deformity Surgery

OBJECTIVETranscranial motor evoked potential (TcMEP) monitoring may be valuable for predicting postoperative neurological complications with a high sensitivity and specificity, but one of the most frequent problems is the high false-positive rate. The purpose of this study was to clarify the differences in the risk factors for false-positive TcMEP alerts seen when performing surgery in patients with pediatric scoliosis and adult spinal deformity and to identify a method to reduce the false-positive rate.METHODSThe authors retrospectively analyzed 393 patients (282 adult and 111 pediatric patients) who underwent TcMEP monitoring while under total intravenous anesthesia during spinal deformity surgery. They defined their cutoff (alert) point as a final TcMEP amplitude of ≤ 30% of the baseline amplitude. Patients with false-positive alerts were classified into one of two groups: a group with pediatric scoliosis and a group with adult spinal deformity.RESULTSThere were 14 cases of false-positive alerts (13%) during pediatric scoliosis surgery and 62 cases of false-positive alerts (22%) during adult spinal deformity surgery. Compared to the true-negative cases during adult spinal deformity surgery, the false-positive cases had a significantly longer duration of surgery and greater estimated blood loss (both p < 0.001). Compared to the true-negative cases during pediatric scoliosis surgery, the false-positive cases had received a significantly higher total fentanyl dose and a higher mean propofol dose (0.75 ± 0.32 mg vs 0.51 ± 0.18 mg [p = 0.014] and 5.6 ± 0.8 mg/kg/hr vs 5.0 ± 0.7 mg/kg/hr [p = 0.009], respectively). A multivariate logistic regression analysis revealed that the duration of surgery (1-hour difference: OR 1.701; 95% CI 1.364–2.120; p < 0.001) was independently associated with false-positive alerts during adult spinal deformity surgery. A multivariate logistic regression analysis revealed that the mean propofol dose (1-mg/kg/hr difference: OR 3.117; 95% CI 1.196–8.123; p = 0.020), the total fentanyl dose (0.05-mg difference; OR 1.270; 95% CI 1.078–1.497; p = 0.004), and the duration of surgery (1-hour difference: OR 2.685; 95% CI 1.131–6.377; p = 0.025) were independently associated with false-positive alerts during pediatric scoliosis surgery.CONCLUSIONSLonger duration of surgery and greater blood loss are more likely to result in false-positive alerts during adult spinal deformity surgery. In particular, anesthetic doses were associated with false-positive TcMEP alerts during pediatric scoliosis surgery. The authors believe that false-positive alerts during pediatric scoliosis surgery, in particular, are caused by “anesthetic fade.”

scholarly journals PRATD: A Phased Remote Access Trojan Detection Method with Double-Sided Features

Electronics ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1894
Author(s):  
Chun Guo ◽  
Zihua Song ◽  
Yuan Ping ◽  
Guowei Shen ◽  
Yuhei Cui ◽  
...  
Keyword(s):  
False Positive ◽  
Detection Method ◽  
False Positive Rate ◽  
True Positive Rate ◽  
Remote Access ◽  
Detection Methods ◽  
Security Threats ◽  
True Positive ◽  
Trojan Detection ◽  
Positive Rate

Remote Access Trojan (RAT) is one of the most terrible security threats that organizations face today. At present, two major RAT detection methods are host-based and network-based detection methods. To complement one another’s strengths, this article proposes a phased RATs detection method by combining double-side features (PRATD). In PRATD, both host-side and network-side features are combined to build detection models, which is conducive to distinguishing the RATs from benign programs because that the RATs not only generate traffic on the network but also leave traces on the host at run time. Besides, PRATD trains two different detection models for the two runtime states of RATs for improving the True Positive Rate (TPR). The experiments on the network and host records collected from five kinds of benign programs and 20 famous RATs show that PRATD can effectively detect RATs, it can achieve a TPR as high as 93.609% with a False Positive Rate (FPR) as low as 0.407% for the known RATs, a TPR 81.928% and FPR 0.185% for the unknown RATs, which suggests it is a competitive candidate for RAT detection.

Evidence for Age-Adjusted D-Dimer to Rule out Pulmonary Embolism: An Institutional Study

2020 ◽  
Vol 154 (Supplement_1) ◽  
pp. S5-S5
Author(s):  
Ridin Balakrishnan ◽  
Daniel Casa ◽  
Morayma Reyes Gil
Keyword(s):  
Pulmonary Embolism ◽  
False Positive ◽  
False Positive Rate ◽  
Moderate Risk ◽  
Older Population ◽  
Statistical Measures ◽  
Positive Rate ◽  
Risk Patients ◽  
D Dimer ◽  
Rule Out

Abstract The diagnostic approach for ruling out suspected acute pulmonary embolism (PE) in the ED setting includes several tests: ultrasound, plasma d-dimer assays, ventilation-perfusion scans and computed tomography pulmonary angiography (CTPA). Importantly, a pretest probability scoring algorithm is highly recommended to triage high risk cases while also preventing unnecessary testing and harm to low/moderate risk patients. The d-dimer assay (both ELISA and immunoturbidometric) has been shown to be extremely sensitive to rule out PE in conjunction with clinical probability. In particularly, d-dimer testing is recommended for low/moderate risk patients, in whom a negative d-dimer essentially rules out PE sparing these patients from CTPA radiation exposure, longer hospital stay and anticoagulation. However, an unspecific increase in fibrin-degradation related products has been seen with increase in age, resulting in higher false positive rate in the older population. This study analyzed patient visits to the ED of a large academic institution for five years and looked at the relationship between d-dimer values, age and CTPA results to better understand the value of age-adjusted d-dimer cut-offs in ruling out PE in the older population. A total of 7660 ED visits had a CTPA done to rule out PE; out of which 1875 cases had a d-dimer done in conjunction with the CT and 5875 had only CTPA done. Out of the 1875 cases, 1591 had positive d-dimer results (&gt;0.50 µg/ml (FEU)), of which 910 (57%) were from patients older than or equal to fifty years of age. In these older patients, 779 (86%) had a negative CT result. The following were the statistical measures of the d-dimer test before adjusting for age: sensitivity (98%), specificity (12%); negative predictive value (98%) and false positive rate (88%). After adjusting for age in people older than 50 years (d-dimer cut off = age/100), 138 patients eventually turned out to be d-dimer negative and every case but four had a CT result that was also negative for a PE. The four cases included two non-diagnostic results and two with subacute/chronic/subsegmental PE on imaging. None of these four patients were prescribed anticoagulation. The statistical measures of the d-dimer test after adjusting for age showed: sensitivity (96%), specificity (20%); negative predictive value (98%) and a decrease in the false positive rate (80%). Therefore, imaging could have been potentially avoided in 138/779 (18%) of the patients who were part of this older population and had eventual negative or not clinically significant findings on CTPA if age-adjusted d-dimers were used. This data very strongly advocates for the clinical usefulness of an age-adjusted cut-off of d-dimer to rule out PE.

Sign in / Sign up

Export Citation Format

Share Document