Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects.

Genome-wide association studies (GWASs) have been performed to identify host genetic factors for a range of phenotypes, including for infectious diseases. The use of population-based common control subjects from biobanks and extensive consortia is a valuable resource to increase sample sizes in the identification of associated loci with minimal additional expense. Non-differential misclassification of the outcome has been reported when the control subjects are not well characterized, which often attenuates the true effect size. However, for infectious diseases the comparison of affected subjects to population-based common control subjects regardless of pathogen exposure can also result in selection bias. Through simulated comparisons of pathogen-exposed cases and population-based common control subjects, we demonstrate that not accounting for pathogen exposure can result in biased effect estimates and spurious genome-wide significant signals. Further, the observed association can be distorted depending upon strength of the association between a locus and pathogen exposure and the prevalence of pathogen exposure. We also used a real data example from the hepatitis C virus (HCV) genetic consortium comparing HCV spontaneous clearance to persistent infection with both well-characterized control subjects and population-based common control subjects from the UK Biobank. We find biased effect estimates for known HCV clearance-associated loci and potentially spurious HCV clearance associations. These findings suggest that the choice of control subjects is especially important for infectious diseases or outcomes that are conditional upon environmental exposures.

Development of the multivariate administrative data cystectomy model and its impact on misclassification bias.

BACKGROUND: Misclassification bias (MB) is the deviation of measured from true values due to incorrect case assignment. This study compared MB when cystectomy status was determined using administrative database codes vs. predicted cystectomy probability. METHODS: We identified every primary cystectomy-diversion type at a single hospital 2009-2019. We linked to claims data to measure true association of cystectomy with 30 patient and hospitalization factors. Associations were also measured when cystectomy status was assigned using billing codes and by cystectomy probability from multivariate logistic regression model with covariates from administrative data. MB was the difference between measured and true associations. RESULTS: 500 people underwent cystectomy (0.12% of 428 677 hospitalizations). Sensitivity and positive predictive values for cystectomy codes were 97.1% and 58.6% for incontinent diversions and 100.0% and 48.4% for continent diversions, respectively. The model accurately predicted cystectomy-incontinent diversion (c-statistic [C] 0.999, Integrated Calibration Index [ICI] 0.000) and cystectomy-continent diversion (C:1.000, ICI 0.000) probabilities. MB was significantly lower when model-based predictions was used to impute cystectomy-diversion type status using for both incontinent cystectomy (F = 12.75; p < .0001) and continent cystectomy (F = 11.25; p < .0001). CONCLUSIONS: A model using administrative data accurately returned the probability that cystectomy by diversion type occurred during a hospitalization. Using this model to impute cystectomy status minimized MB. Accuracy of administrative database research can be increased by using probabilistic imputation to determine case status instead of individual codes.

Does misclassification of former tobacco smokers explain the 'smoker's paradox' in the risk of COVID-19? Insights from the Stockholm Public Health Cohort.

BACKGROUND: The association between tobacco smoking and the risk of COVID-19 and its adverse outcomes is controversial, as studies reported contrasting findings. Bias due to misclassification of the exposure in the analyses of current versus non-current smoking could be a possible explanation because former smokers may have higher background risks of the disease due to co-morbidity. The aim of the study was to investigate the extent of this potential bias by separating non-, former, and current smokers when assessing the risk or prognosis of diseases. METHODS: We analysed data from 43,400 participants in the Stockholm Public Health Cohort, Sweden, with information on smoking obtained prior to the pandemic. We estimated the risk of COVID-19, hospital admissions and death for (a) former and current smokers relative to non-smokers, (b) current smokers relative to non-current smokers, that is, including former smokers; adjusting for potential confounders (aRR). RESULTS: The aRR of a COVID-19 diagnosis was elevated for former smokers compared with non-smokers (1.07; 95% confidence interval (CI) =1.00-1.15); including hospital admission with any COVID-19 diagnosis (aRR= 1.23; 95% CI = 1.03-1.48); or with COVID-19 as the main diagnosis (aRR=1.23, 95% CI= 1.01-1.49); and death within 30 days with COVID-19 as the main or a contributory cause (aRR=1.40; 95% CI=1.00-1.95). Current smoking was negatively associated with risk of COVID-19 (aRR=0.79; 95% CI=0.68-0.91). CONCLUSIONS: Separating non-smokers from former smokers when assessing the disease risk or prognosis is essential to avoid bias. However, the negative association between current smoking and the risk of COVID-19 could not be entirely explained by misclassification.

Alcohol and early mortality (before 65 years) in the 'Seguimiento Universidad de Navarra' (SUN) cohort: does any level reduce mortality?

The aim of this study was to assess the association between alcohol intake and premature mortality (younger than 65 years) and to explore the effect of potential alcohol underreporting by heavy drinkers. We followed-up 20 272 university graduates. Four categories of alcohol intake were considered (abstainer, light, moderate and heavy consumption). Repeated measurements of alcohol intake and updated information on confounders were used in time-dependent Cox models. Potential underreporting of alcohol intake by some heavy drinkers (likely misclassified as light or moderate drinkers) was explicitly addressed in an attempt to correct potential underreporting by using indirect information. During 12·3 years of median follow-up (interquartile range: 6·8-15·0), 226 participants died before their 65th birthday. A higher risk of early mortality was found for the highest category of alcohol intake (≥50 g/d) in comparison with abstention (multivariable-adjusted hazard ratio (HR) = 2·82, 95 % CI 1·38, 5·79). In analyses of alcohol as a continuous variable, the multivariable-adjusted HR was 1·17 (95 % CI 1·08, 1·26), for each 10 g/d of alcohol. This harmful linear association was present both in uncorrected models and in models corrected for potential underreporting. No significant inverse association between light or moderate alcohol intake and premature mortality was observed, even after correcting for potential misclassification. Alcohol intake exhibited a harmful linear dose-response association with premature mortality (<65 years) in this young and highly educated Mediterranean cohort. Our attempts to correct for potential misclassification did not substantially change these results.

Bias correction methods for test-negative designs in the presence of misclassification.

The test-negative design (TND) has become a standard approach for vaccine effectiveness (VE) studies. However, previous studies suggested that it may be more vulnerable than other designs to misclassification of disease outcome caused by imperfect diagnostic tests. This could be a particular limitation in VE studies where simple tests (e.g. rapid influenza diagnostic tests) are used for logistical convenience. To address this issue, we derived a mathematical representation of the TND with imperfect tests, then developed a bias correction framework for possible misclassification. TND studies usually include multiple covariates other than vaccine history to adjust for potential confounders; our methods can also address multivariate analyses and be easily coupled with existing estimation tools. We validated the performance of these methods using simulations of common scenarios for vaccine efficacy and were able to obtain unbiased estimates in a variety of parameter settings.

Conditional validation sampling for consistent risk estimation with binary outcome data subject to misclassification.

PURPOSE: Misclassification of a binary outcome can introduce bias in estimation of the odds-ratio associated with an exposure of interest in pharmacoepidemiology research. It has been previously demonstrated that utilizing information from an internal randomly selected validation sample can help mitigate this bias. METHODS: Using a Monte Carlo simulation-based approach, we study the properties of misclassification bias-adjusted odds-ratio estimators in a contingency table setting. We consider two methods of internal validation sampling; namely, simple random sampling and sampling conditional on the original (possibly incorrect) outcome status. Additional simulation studies are conducted to investigate these sampling approaches in a multi-table setting. RESULTS: We demonstrate that conditional validation sampling, across a range of subsampling fractions, can produce better estimates than those based on an unconditional simple random sample. This approach allows for greater flexibility in the chosen categorical composition of the validation data, as well as the potential for obtaining a more efficient estimator of the odds-ratio. We further demonstrate that this relationship holds for the Mantel-Haenszel misclassification bias-adjusted odds-ratio in stratified samples. Recommendations for the choice of validation subsampling fraction are also provided. CONCLUSIONS: Careful consideration when choosing the sampling scheme used to draw internal validation samples can improve the properties of the outcome misclassification bias-adjusted odds-ratio estimator in a (multiple) contingency table.

Combining population-based administrative health records and electronic medical records for disease surveillance.

BACKGROUND: Administrative health records (AHRs) and electronic medical records (EMRs) are two key sources of population-based data for disease surveillance, but misclassification errors in the data can bias disease estimates. Methods that combine information from error-prone data sources can build on the strengths of AHRs and EMRs. We compared bias and error for four data-combining methods and applied them to estimate hypertension prevalence. METHODS: Our study included rule-based OR and AND methods that identify disease cases from either or both data sources, respectively, rule-based sensitivity-specificity adjusted (RSSA) method that corrects for inaccuracies using a deterministic rule, and probabilistic-based sensitivity-specificity adjusted (PSSA) method that corrects for error using a statistical model. Computer simulation was used to estimate relative bias (RB) and mean square error (MSE) under varying conditions of population disease prevalence, correlation amongst data sources, and amount of misclassification error. AHRs and EMRs for Manitoba, Canada were used to estimate hypertension prevalence using validated case definitions and multiple disease markers. RESULTS: The OR method had the lowest RB and MSE when population disease prevalence was 10%, and the RSSA method had the lowest RB and MSE when population prevalence increased to 20%. As the correlation between data sources increased, the OR method resulted in the lowest RB and MSE. Estimates of hypertension prevalence for AHRs and EMRs alone were 30.9% (95% CI: 30.6-31.2) and 24.9% (95% CI: 24.6-25.2), respectively. The estimates were 21.4% (95% CI: 21.1-21.7), for the AND method, 34.4% (95% CI: 34.1-34.8) for the OR method, 32.2% (95% CI: 31.8-32.6) for the RSSA method, and ranged from 34.3% (95% CI: 34.1-34.5) to 35.9% (95% CI, 35.7-36.1) for the PSSA method, depending on the statistical model. CONCLUSIONS: The OR and AND methods are influenced by correlation amongst the data sources, while the RSSA method is dependent on the accuracy of prior sensitivity and specificity estimates. The PSSA method performed well when population prevalence was high and average correlations amongst disease markers was low. This study will guide researchers to select a data-combining method that best suits their data characteristics.

Weighted estimation for confounded binary outcomes subject to misclassification.

In the presence of confounding, the consistency assumption required for identification of causal effects may be violated due to misclassification of the outcome variable. We introduce an inverse probability weighted approach to rebalance covariates across treatment groups while mitigating the influence of differential misclassification bias. First, using a simplified example taken from an administrative health care dataset, we introduce the approach for estimation of the marginal causal odds ratio in a simple setting with the use of internal validation information. We then extend this to the presence of additional covariates and use simulated data to investigate the finite sample properties of the proposed weighted estimators. Estimation of the weights is done using logistic regression with misclassified outcomes, and a bootstrap approach is used for variance estimation.

Short communication: Model for metritis severity predicts that disease misclassification underestimates projected milk production losses.

The objective of this research was to determine the effect of disease misclassification on the estimated effect of metritis on milk production. Misclassification introduces bias that usually results in an underestimation of the association between exposure (disease) and the outcome of interest (milk production). This distorted measure of association results from the comparison of an affected population (some of which may not truly be affected) to a nonaffected population (which often includes affected subjects that are unidentified). A convenience sample of DairyComp305 (Valley Agricultural Software, Tulare, CA) data representing 1 yr of calvings (n = 3,277) from 1 Midwestern Holstein herd was used. This herd was chosen because of its ongoing efforts to consistently and completely record all clinical diseases, including the incidence of both mild and severe metritis cases. Metritis was defined as the presence of a flaccid uterus containing fetid fluids or a foul watery discharge within 14 d of calving. Cows that appeared clinically normal other than the discharge were considered mild and those with systemic signs of disease were classified as severe. The original data set included metritis recorded as mild, severe, or not recorded (NR), where no metritis was observed, and was considered to contain the metritis true severity (TrS). First, to evaluate the effect of misclassification bias, we retrospectively randomized 45% of mild metritis to be classified as NR to simulate inconsistent disease recording (IR); then, in a separate model, all mild metritis cases were changed to NR to simulate a situation of very poor disease recording (PR), where only the most severe cases are recorded. The TrS, IR, and PR data sets were analyzed separately in JMP (SAS Institute Inc., Cary, NC). An ANOVA was conducted for second test 305-d mature-equivalent milk projection (2nd305ME), and nonsignificant variables were removed, but the variable metritis was forced into all models. Based upon the TrS model, adjusting for effects of lactation group, month of calving, dystocia, twins, retained placenta, early-lactation mastitis, displaced abomasum, and significant interactions, a case of mild metritis was associated with 384 kg less 2nd305ME and a case of severe metritis was associated with 847 kg less 2nd305ME compared with no metritis. For the IR model, a case of mild metritis was associated with 315 kg less 2nd305ME and a case of severe metritis was associated with 758 kg less 2nd305ME compared with no metritis. For the PR model, severe metritis was associated with 680 kg less 2nd305ME compared with NR. The IR and PR models underestimated 2nd305ME loss for severe metritis cases by 89 and 166 kg/cow, and resulted in 180,441 and 330,256 kg of total milk loss unaccounted for at the herd level, respectively, compared with TrS. Overall, misclassification of metritis cases results in greater bias and largely underestimates the true association between metritis and the consequence costs of the disease.