Post COVID-19 condition (PCC) is known to affect a large proportion of COVID-19 survivors. Robust study design and methods are needed to understand post-COVID-19 diagnosis patterns in all survivors, not just those clinically diagnosed with PCC.
We applied a case-crossover Phenome-Wide Association Study (PheWAS) in a retrospective cohort of COVID-19 survivors, comparing the occurrences of 1,671 diagnosis-based phenotype codes (PheCodes) pre- and post-COVID-19 infection periods in the same individual using a conditional logistic regression. We studied how this pattern varied by COVID-19 severity and vaccination status, and we compared to test negative and test negative but flu positive controls.
In 44,198 SARS-CoV-2-positive patients, we foundenrichment in respiratory,circulatory, and mental health disorders post-COVID-19-infection. Top hits included anxiety disorder (p = 2.8e-109, OR = 1.7 [95 % CI: 1.6-1.8]), cardiac dysrhythmias (p = 4.9e-87, OR = 1.7 [95 % CI: 1.6-1.8]), and respiratory failure, insufficiency, arrest (p = 5.2e-75, OR = 2.9 [95 % CI: 2.6-3.3]). In severe patients, we found stronger associations with respiratory and circulatory disorders compared to mild/moderate patients. Fully vaccinated patients had mental health and chronic circulatory diseases rise to the top of the association list, similar to the mild/moderate cohort. Both control groups (test negative, test negative and flu positive) showed a different pattern of hits to SARS-CoV-2 positives.
Patients experience myriad symptoms more than 28 days after SARS-CoV-2 infection, but especially respiratory, circulatory, and mental health disorders. Our case-crossover PheWAS approach controls for within-person confounders that are time-invariant. Comparison to test negatives and test negative but flu positive patients with a similar design helped identify enrichment specific to COVID-19. This design may be applied other emerging diseases with long-lasting effects other than a SARS-CoV-2 infection. Given the potential for bias from observational data, these results should be considered exploratory. As we look into the future, we must be aware of COVID-19 survivors\' healthcare needs.

Subgroup analyses are an essential part of fully understanding the complete results from confirmatory clinical trials. However, they come with substantial methodological challenges. In case no statistically significant overall treatment effect is found in a clinical trial, this does not necessarily indicate that no patients will benefit from treatment. Subgroup analyses could be conducted to investigate whether a treatment might still be beneficial for particular subgroups of patients. Assessment of the level of evidence associated with such subgroup findings is primordial as it may form the basis for performing a new clinical trial or even drawing the conclusion that a specific patient group could benefit from a new therapy. Previous research addressed the overall type I error and the power associated with a single subgroup finding for continuous outcomes and suitable replication strategies. The current study aims at investigating two scenarios as part of a nonconfirmatory strategy in a trial with dichotomous outcomes: (a) when a covariate of interest is represented by ordered subgroups, eg, in case of biomarkers, and thus, a trend can be studied that may reflect an underlying mechanism, and (b) when multiple covariates, and thus multiple subgroups, are investigated at the same time. Based on simulation studies, this paper assesses the credibility of subgroup findings in overall nonsignificant trials and provides practical recommendations for evaluating the strength of evidence of subgroup findings in these settings.

A number of sophisticated estimators of longitudinal effects have been proposed for estimating the intervention-specific mean outcome. However, there is a relative paucity of research comparing these methods directly to one another. In this study, we compare various approaches to estimating a causal effect in a longitudinal treatment setting using both simulated data and data measured from a human immunodeficiency virus cohort. Six distinct estimators are considered: (i) an iterated conditional expectation representation, (ii) an inverse propensity weighted method, (iii) an augmented inverse propensity weighted method, (iv) a double robust iterated conditional expectation estimator, (v) a modified version of the double robust iterated conditional expectation estimator, and (vi) a targeted minimum loss-based estimator. The details of each estimator and its implementation are presented along with nuisance parameter estimation details, which include potentially pooling the observed data across all subjects regardless of treatment history and using data adaptive machine learning algorithms. Simulations are constructed over six time points, with each time point steadily increasing in positivity violations. Estimation is carried out for both the simulations and applied example using each of the six estimators under both stratified and pooled approaches of nuisance parameter estimation. Simulation results show that double robust estimators remained without meaningful bias as long as at least one of the two nuisance parameters were estimated with a correctly specified model. Under full misspecification, the bias of the double robust estimators remained better than that of the inverse propensity estimator under misspecification, but worse than the iterated conditional expectation estimator. Weighted estimators tended to show better performance than the covariate estimators. As positivity violations increased, the mean squared error and bias of all estimators considered became worse, with covariate-based double robust estimators especially susceptible. Applied analyses showed similar estimates at most time points, with the important exception of the inverse propensity estimator which deviated markedly as positivity violations increased. Given its efficiency, ability to respect the parameter space, and observed performance, we recommend the pooled and weighted targeted minimum loss-based estimator.

Assessing the statistical significance of risk factors when screening large numbers of 2 × 2 tables that cross-classify disease status with each type of exposure poses a challenging multiple testing problem. The problem is especially acute in large-scale genomic case-control studies. We develop a potentially more powerful and computationally efficient approach (compared with existing methods, including Bonferroni and permutation testing) by taking into account the presence of complex dependencies between the 2 × 2 tables. Our approach gains its power by exploiting Monte Carlo simulation from the estimated null distribution of a maximally selected log-odds ratio. We apply the method to case-control data from a study of a large collection of genetic variants related to the risk of early onset stroke.

Functional Magnetic Resonance Imaging is a widespread technique in cognitive psychology that allows visualizing brain activation. The data analysis encompasses an enormous number of simultaneous statistical tests. Procedures that either control the familywise error rate or the false discovery rate have been applied to these data. These methods are mostly validated in terms of average sensitivity and specificity. However, procedures are not comparable if requirements on their error rates differ. Moreover, less attention has been given to the instability or variability of results. In a simulation study in the context of imaging, we first compare the Bonferroni and Benjamini-Hochberg procedures. Considering Bonferroni as a way to control the expected number of type I errors enables more lenient thresholding compared to familywise error rate control and a direct comparison between both procedures. We point out that while the same balance is obtained between average sensitivity and specificity, the Benjamini-Hochberg procedure appears less stable. Secondly, we have implemented the procedure of Gordon et al. () (originally proposed for gene selection) that includes stability, measured through bootstrapping, in the decision criterion. Simulations indicate that the method attains the same balance between sensitivity and specificity. It improves the stability of Benjamini-Hochberg but does not outperform Bonferroni, making this computationally heavy bootstrap procedure less appealing. Third, we show how stability of thresholding procedures can be assessed using real data. In a dataset on face recognition, we again find that Bonferroni renders more stable results.