Methods of estimating polygenic scores (PGSs) from genome-wide association studies are increasingly utilized. However, independent method evaluation is lacking, and method comparisons are often limited. Here, we evaluate polygenic scores derived via seven methods in five biobank studies (totaling about 1.2 million participants) across 16 diseases and quantitative traits, building on a reference-standardized framework. We conducted meta-analyses to quantify the effects of method choice, hyperparameter tuning, method ensembling, and the target biobank on PGS performance. We found that no single method consistently outperformed all others. PGS effect sizes were more variable between biobanks than between methods within biobanks when methods were well tuned. Differences between methods were largest for the two investigated autoimmune diseases, seropositive rheumatoid arthritis and type 1 diabetes. For most methods, cross-validation was more reliable for tuning hyperparameters than automatic tuning (without the use of target data). For a given target phenotype, elastic net models combining PGS across methods (ensemble PGS) tuned in the UK Biobank provided consistent, high, and cross-biobank transferable performance, increasing PGS effect sizes (β coefficients) by a median of 5.0% relative to LDpred2 and MegaPRS (the two best-performing single methods when tuned with cross-validation). Our interactively browsable online-results and open-source workflow prspipe provide a rich resource and reference for the analysis of polygenic scoring methods across biobanks.

BACKGROUND: Functional dyspepsia (FD) is a common gastrointestinal condition of poorly understood pathophysiology. While symptoms\' overlap with other conditions may indicate common pathogenetic mechanisms, genetic predisposition is suspected but has not been adequately investigated.
METHODS: Using healthcare, questionnaire, and genetic data from three large population-based biobanks (UK Biobank, EGCUT, and MGI), we surveyed FD comorbidities, heritability, and genetic correlations across a wide spectrum of conditions and traits in 10,078 cases and 351,282 non-FD controls of European ancestry.
RESULTS: In UK Biobank, 281 diagnoses were detected at increased prevalence in FD, based on healthcare records. Among these, gastrointestinal conditions (OR = 4.0, p < 1.0 × 10-300 ), anxiety disorders (OR = 2.3, p < 1.4 × 10-27 ), ischemic heart disease (OR = 2.2, p < 2.3 × 10-76 ), and infectious and parasitic diseases (OR = 2.1, p = 1.5 × 10-73 ) showed strongest association with FD. Similar results were obtained in an analysis of self-reported conditions and use of medications from questionnaire data. Based on a genome-wide association meta-analysis of genotypes across all cohorts, FD heritability was estimated close to 5% ( h SNP 2  = 0.047, p = 0.014). Genetic correlations indicate FD predisposition is shared with several other diseases and traits (rg  > 0.344), mostly overlapping with those also enriched in FD patients. Suggestive (p < 5.0 × 10-6 ) association with FD risk was detected for 13 loci, with 2 showing nominal replication (p < 0.05) in an independent cohort of 192 FD patients.
CONCLUSIONS: FD has a weak heritable component that shows commonalities with multiple conditions across a wide spectrum of pathophysiological domains. This new knowledge contributes to a better understanding of FD etiology and may have implications for improving its treatment.

UNASSIGNED: Obtaining patient permissions for research contact and for surplus tissue use as part of routine clinical practice can improve research participation. This study aims to investigate the difference in patient permissions for use of surplus tissues, and for direct contact for research, using 2 different methods of solicitation.
UNASSIGNED: An opt-in, population-based approach for gathering research permissions was implemented in 2 methods. The first method, applied a 2-item patient questionnaire delivered through the electronic health record patient portal. The questionnaire composed of 2 questions (1) whether de-identified surplus specimens may be used for research and (2) whether patients could be contacted about research. In the second method, the same questionnaire was physically presented in clinic within the clinical workflow. We used 1 to 1 propensity score matching and multivariate logistic regression to estimate the odds of obtaining permission and the difference between the 2 methods of solicitation.
UNASSIGNED: The propensity score model matched 8044 observations (4114 submissions in each group). Among the in-clinic submission group, 70.13% provided permission for surplus tissue compared with 66.65% in the patient portal submission group (odds ratio [OR] = 1.20; 95% confidence interval [CI] 1.09-1.32; P < 0.001). Permission for future research contact was similar among in-clinic (65.07%) and patient portal submission (66.65%) groups (OR = 0.94; 95% CI 0.85-1.03; P = 0.175). These trends were consistent among European Americans and African American patients. However, among patients of other race, higher permission for both future contact (OR = 0.58; 95% CI 0.39-0.86; P < 0.007) and surplus tissue use (OR = 0.65; 95% CI 0.43-0.97; P = 0.036) was observed among patient portal submission.
UNASSIGNED: Our findings suggest that in-clinic solicitation of patient permissions may provide the same opportunity to patients who do not use patient portals and may be associated with higher permission rate for surplus tissue. However, this was primary true for European American and African Americans patients. Patients of other race minorities might respond better to online approaches.
UNASSIGNED: Adopting a patient-centric approach that combines in-clinic and portal-based administration may be feasible and promising. Further research is required in this area.