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Most genetic variants associated with complex traits are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterized 14,324 RNA-sequencing samples from the Trans-Omics for Precision Medicine program and performed expression and splicing quantitative trait locus (e/sQTL) analyses in six tissues and cell types, including whole blood ( n = 6454) and lung ( n = 1291). We detected tens of thousands of secondary cis-e/sQTLs, showing that secondary cis-e/sQTL discovery remains unsaturated. We fine-mapped UK Biobank–derived genome-wide association study (GWAS) signals from 164 traits and identified e/sQTL colocalizations for 10,611 GWAS signals, including 7096 that colocalize with secondary e/sQTLs. Our results suggest that even larger e/sQTL analyses will uncover additional secondary e/sQTLs, further benefiting GWAS interpretation.

ImportanceThe Ophthalmic Knowledge Assessment Program (OKAP) has been widely used to determine readiness to take the high-stakes Written Qualifying Examination (WQE). However, it is unclear how well OKAP performance can predict WQE outcomes.ObjectiveTo examine the association between the OKAP and WQE nationally.Design, Setting, and ParticipantsThis was a retrospective cohort study conducted from 2017 to 2022. This national data analysis included residents from ophthalmology residency programs in the US. Study data were analyzed June 2023 to December 2024.ExposuresOKAP and WQE data.Main Outcomes and MeasuresThe national OKAP examination data and the WQE data were matched. Candidates who had complete data for the OKAP during postgraduate year (PGY) 2, 3, and 4 and completed the WQE were included in the study. Two-sample t tests, logistic regression analysis, receiver operating characteristic curves, and confusion matrix were used to examine the association of various test scores (PGY-2 OKAP, PGY-3 OKAP, PGY-4 OKAP, minimum OKAP, maximum OKAP, average OKAP) as predictors for WQE outcomes (pass or fail). Multiple logistic regression analyses were also used to assess the association of gender, time since graduation, program size, and WQE pass/fail outcomes.ResultsA total of 1597 residents (907 male [56.8%]) from 117 residency programs were included in this study. First-time pass rate of the WQE was 89% (1418 of 1597 residents). OKAP scores, particularly average OKAP, maximum OKAP, and PGY-4 OKAP scores (all had area under the curve = 0.88), were the most useful predictor of WQE outcomes. PGY-4 OKAP scores were used for the rest of the analysis for simplicity. A PGY-4 OKAP scaled score of 550 corresponded to 94% of candidates passing the WQE. Using PGY-4 OKAP scores to predict passing/failing, the WQE had 90.7% accuracy. Gender (odds ratio [OR], 1.50; 95% CI, 1.01-2.26; P = .048), program size (OR, 1.55; 95% CI, 0.98-2.41; P = .06), and time since residency graduation (OR, 1.00; 95% CI, 1.00-1.00; P = .14) were not included in the logistic regression model investigating the association of PGY-4 OKAP scores with the likelihood of passing the WQE.Conclusions and RelevanceResults suggest that OKAP examination scores were associated with passing the WQE after adjusting for program size, gender, and time since residency graduation. Further analyses may be warranted to predict failing the WQE so that potential interventions can be attempted.

Background The relationship between mitochondrial DNA copy number (mtDNA CN) and cardiovascular disease remains elusive. Methods and Results We performed cross‐sectional and prospective association analyses of blood‐derived mtDNA CN and cardiovascular disease outcomes in 27 316 participants in 8 cohorts of multiple racial and ethnic groups with whole‐genome sequencing. We also performed Mendelian randomization to explore causal relationships of mtDNA CN with coronary heart disease (CHD) and cardiometabolic risk factors (obesity, diabetes, hypertension, and hyperlipidemia). P <0.01 was used for significance. We validated most of the previously reported associations between mtDNA CN and cardiovascular disease outcomes. For example, 1‐SD unit lower level of mtDNA CN was associated with 1.08 (95% CI, 1.04–1.12; P <0.001) times the hazard for developing incident CHD, adjusting for covariates. Mendelian randomization analyses showed no causal effect from a lower level of mtDNA CN to a higher CHD risk (β=0.091; P =0.11) or in the reverse direction (β=−0.012; P =0.076). Additional bidirectional Mendelian randomization analyses revealed that low‐density lipoprotein cholesterol had a causal effect on mtDNA CN (β=−0.084; P <0.001), but the reverse direction was not significant ( P =0.059). No causal associations were observed between mtDNA CN and obesity, diabetes, and hypertension, in either direction. Multivariable Mendelian randomization analyses showed no causal effect of CHD on mtDNA CN, controlling for low‐density lipoprotein cholesterol level ( P =0.52), whereas there was a strong direct causal effect of higher low‐density lipoprotein cholesterol on lower mtDNA CN, adjusting for CHD status (β=−0.092; P <0.001). Conclusions Our findings indicate that high low‐density lipoprotein cholesterol may underlie the complex relationships between mtDNA CN and vascular atherosclerosis.

Background: Careful selection of patients with expiratory central airway collapse (ECAC) that may benefit from tracheobronchoplasty (TBP) can be aided by a short-term airway stent evaluation. This can be performed with either silicone Y-stents (SYSs) or uncovered self-expanding metallic airway-stents (USEMAS). No direct comparison has been made between these 2 stent types. Methods: This was a small retrospective review of consecutive patients that underwent a stent evaluation. A propensity score was used to match patients in the USEMAS and SYS groups. Outcomes included complications, changes in the health-related quality-of-life (HR-QoL), and changes in exercise capacity. Baseline measurements were compared with those obtained during stent evaluation and after TBP. Results: Forty-two patients with severe ECAC underwent USEMAS placement, while 18 patients had an SYS placed. Propensity score matching resulted in 13 matched SYS and USEMAS pairs. The SYS group had an increased rate of mucus plugging (38.5% vs. 0%, P<0.047). Although not statically significant, a clinical improvement was observed in HR-QoL and exercise capacity in the USEMAS group during stent placement. In patients who underwent TBP, both USEMAS and SYS groups had a statistically significant change in the Modified Medical Research Council Dyspnea Scale during stent evaluation and after TBP. Conclusion: In patients with severe ECAC, short-term evaluation with airway stents appears to be safe and improves respiratory symptoms, HR-QoL, and exercise capacity. The use of USEMAS led to a lower complication rate, a greater improvement in HR-QoL and exercise capacity, and appeared to better predict how the patients would respond to TBP.

Background and Purpose: Stroke is a complex disease with multiple genetic and environmental risk factors. Blacks endure a nearly 2-fold greater risk of stroke and are 2× to 3× more likely to die from stroke than European Americans. Methods: The COMPASS (Consortium of Minority Population Genome-Wide Association Studies of Stroke) has conducted a genome-wide association meta-analysis of stroke in >22 000 individuals of African ancestry (3734 cases, 18 317 controls) from 13 cohorts. Results: In meta-analyses, we identified one single nucleotide polymorphism (rs55931441) near the HNF1A gene that reached genome-wide significance ( P =4.62×10 −8 ) and an additional 29 variants with suggestive evidence of association ( P <1×10 −6 ), representing 24 unique loci. For validation, a look-up analysis for a 100 kb region flanking the COMPASS single nucleotide polymorphism was performed in SiGN (Stroke Genetics Network) Europeans, SiGN Hispanics, and METASTROKE (Europeans). Using a stringent Bonferroni correction P value of 2.08×10 −3 (0.05/24 unique loci), we were able to validate associations at the HNF1A locus in both SiGN ( P =8.18×10 −4 ) and METASTROKE ( P =1.72×10 −3 ) European populations. Overall, 16 of 24 loci showed evidence for validation across multiple populations. Previous studies have reported associations between variants in the HNF1A gene and lipids, C-reactive protein, and risk of coronary artery disease and stroke. Suggestive associations with variants in the SFXN4 and TMEM108 genes represent potential novel ischemic stroke loci. Conclusions: These findings represent the most thorough investigation of genetic determinants of stroke in individuals of African descent, to date.

AbstractBackgroundUnilateral radiotherapy (RT) of oropharyngeal carcinomas is accepted for patients with lateralized primary and low‐volume nodal disease. Utilizing prospectively defined criteria of laterality and staging positron emission tomography (PET)/CT, we studied outcomes in patients with advanced‐stage oropharyngeal cancer undergoing unilateral RT.MethodsThirty‐seven patients with oropharyngeal tumors >1 cm from midline regardless of node status underwent unilateral RT and were followed prospectively. Patient characteristics: T1 = 11; T2 = 22; T3 = 4; N0 = 3; N1 = 9; N2a = 3; N2b = 21; and Nx = 1. Dosimetry were determined and weekly National Comprehensive Cancer Network (NCCN) distress thermometer data were collected.ResultsAt median follow‐up of 32 months, 3‐year locoregional control, contralateral regional failure, distant metastasis‐free survival, and disease‐free survival were 96%, 0%, 7%, and 93%, respectively.ConclusionLow rates of contralateral neck failure are demonstrated utilizing prospectively defined criteria for unilateral RT. The tolerances of contralateral organs are respected and patients report low to moderate levels of distress throughout treatment.