A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables.

The identification and understanding of gene-environment interactions can provide insights into the pathways and mechanisms underlying complex diseases. However, testing for gene-environment interaction remains a challenge since a.) statistical power is often limited and b.) modeling of environmental effects is nontrivial and such model misspecifications can lead to false positive interaction findings. To address the lack of statistical power, recent methods aim to identify interactions on an aggregated level using, for example, polygenic risk scores. While this strategy can increase the power to detect interactions, identifying contributing genes and pathways is difficult based on these relatively global results. Here, we propose RITSS (Robust Interaction Testing using Sample Splitting), a gene-environment interaction testing framework for quantitative traits that is based on sample splitting and robust test statistics. RITSS can incorporate sets of genetic variants and/or multiple environmental factors. Based on the user's choice of statistical/machine learning approaches, a screening step selects and combines potential interactions into scores with improved interpretability. In the testing step, the application of robust statistics minimizes the susceptibility to main effect misspecifications. Using extensive simulation studies, we demonstrate that RITSS controls the type 1 error rate in a wide range of scenarios, and we show how the screening strategy influences statistical power. In an application to lung function phenotypes and human height in the UK Biobank, RITSS identified highly significant interactions based on subcomponents of genetic risk scores. While the contributing single variant interaction signals are weak, our results indicate interaction patterns that result in strong aggregated effects, providing potential insights into underlying gene-environment interaction mechanisms.

The Mediating Role of Anxiety Sensitivity in Uncontrolled Drinking: A Look at Gender-Specific Parental Influences.

BACKGROUND: Anxiety sensitivity (AS) reflects an individual's belief that experiencing anxiety will cause illness or embarrassment, and may be a reason individuals self-medicate with alcohol. Harsh or indulgent parenting could contribute to the development of AS. We examined the direct and indirect associations between parenting styles and alcohol-related variables through AS and impaired control over drinking (IC; i.e., perceived failure to adhere to limits on alcohol consumption in the future). METHODS: A multiple-group structural equation model with 614 university students (344 men; 270 women) was examined. Structural invariance tests were conducted to evaluate moderation by gender. We used a bias corrected bootstrap technique to obtain the mediated effects. RESULTS: Father authoritarianism and mother permissiveness were directly linked to AS among women, whereas father permissiveness was directly linked to AS among men. This suggests unique parental influences based on gender regarding AS. While AS was directly linked to alcohol-related problems for both men and women, several gender-specific associations were found. AS was directly linked to IC for men but not for women. For men, father permissiveness was directly related to AS, and AS mediated the indirect link between father permissiveness and IC along both the heavy episodic drinking and alcohol-related problems pathways. Similar to other internalizing constructs (e.g., neuroticism and depression), higher AS was directly associated with less heavy episodic drinking but more alcohol-related problems. CONCLUSIONS: Our findings highlight the dangers of AS for men as an important correlate of under-controlled drinking behaviors. Additionally, permissive parenting of the same-gender parent was associated with AS, which is consistent with the gender-matching hypothesis. Together, these results underscore the importance of measuring the independent influence of both parents.

Asthma exacerbations and eosinophilia in the UK Biobank: a genome-wide association study.

Background: Asthma exacerbations reflect disease severity, affect morbidity and mortality, and may lead to declining lung function. Inflammatory endotypes (e.g. T2-high (eosinophilic)) may play a key role in asthma exacerbations. We aimed to assess whether genetic susceptibility underlies asthma exacerbation risk and additionally tested for an interaction between genetic variants and eosinophilia on exacerbation risk. Methods: UK Biobank data were used to perform a genome-wide association study of individuals with asthma and at least one exacerbation compared to individuals with asthma and no history of exacerbations. Individuals with asthma were identified using self-reported data, hospitalisation data and general practitioner records. Exacerbations were identified as either asthma-related hospitalisation, general practitioner record of asthma exacerbation or an oral corticosteroid burst prescription. A logistic regression model adjusted for age, sex, smoking status and genetic ancestry via principal components was used to assess the association between genetic variants and asthma exacerbations. We sought replication for suggestive associations (p<5×10-6) in the GERA cohort. Results: In the UK Biobank, we identified 11 604 cases and 37 890 controls. While no variants reached genome-wide significance (p<5×10-8) in the primary analysis, 116 signals were suggestively significant (p<5×10-6). In GERA, two single nucleotide polymorphisms (rs34643691 and rs149721630) replicated (p<0.05), representing signals near the NTRK3 and ABCA13 genes. Conclusions: Our study has identified reproducible associations with asthma exacerbations in the UK Biobank and GERA cohorts. Confirmation of these findings in different asthma subphenotypes in diverse ancestries and functional investigation will be required to understand their mechanisms of action and potentially inform therapeutic development.

Examining the Effect of Genes on Depression as Mediated by Smoking and Modified by Sex.

Depression is heritable, differs by sex, and has environmental risk factors such as cigarette smoking. However, the effect of single nucleotide polymorphisms (SNPs) on depression through cigarette smoking and the role of sex is unclear. In order to examine the association of SNPs with depression and smoking in the UK Biobank with replication in the COPDGene study, we used counterfactual-based mediation analysis to test the indirect or mediated effect of SNPs on broad depression through the log of pack-years of cigarette smoking, adjusting for age, sex, current smoking status, and genetic ancestry (via principal components). In secondary analyses, we adjusted for age, sex, current smoking status, genetic ancestry (via principal components), income, education, and living status (urban vs. rural). In addition, we examined sex-stratified mediation models and sex-moderated mediation models. For both analyses, we adjusted for age, current smoking status, and genetic ancestry (via principal components). In the UK Biobank, rs6424532 [LOC105378800] had a statistically significant indirect effect on broad depression through the log of pack-years of cigarette smoking (p = 4.0 × 10-4) among all participants and a marginally significant indirect effect among females (p = 0.02) and males (p = 4.0 × 10-3). Moreover, rs10501696 [GRM5] had a marginally significant indirect effect on broad depression through the log of pack-years of cigarette smoking (p = 0.01) among all participants and a significant indirect effect among females (p = 2.2 × 10-3). In the secondary analyses, the sex-moderated indirect effect was marginally significant for rs10501696 [GRM5] on broad depression through the log of pack-years of cigarette smoking (p = 0.01). In the COPDGene study, the effect of an SNP (rs10501696) in GRM5 on depressive symptoms and medication was mediated by log of pack-years (p = 0.02); however, no SNPs had a sex-moderated mediated effect on depressive symptoms. In the UK Biobank, we found SNPs in two genes [LOC105378800, GRM5] with an indirect effect on broad depression through the log of pack-years of cigarette smoking. In addition, the indirect effect for GRM5 on broad depression through smoking may be moderated by sex. These results suggest that genetic regions associated with broad depression may be mediated by cigarette smoking and this relationship may be moderated by sex.

GSDMB/ORMDL3 Rare/Common Variants Are Associated with Inhaled Corticosteroid Response among Children with Asthma.

Inhaled corticosteroids (ICS) are efficacious in the treatment of asthma, which affects more than 300 million people in the world. While genome-wide association studies have identified genes involved in differential treatment responses to ICS in asthma, few studies have evaluated the effects of combined rare and common variants on ICS response among children with asthma. Among children with asthma treated with ICS with whole exome sequencing (WES) data in the PrecisionLink Biobank (91 White and 20 Black children), we examined the effect and contribution of rare and common variants with hospitalizations or emergency department visits. For 12 regions previously associated with asthma and ICS response (DPP10, FBXL7, NDFIP1, TBXT, GLCCI1, HDAC9, TBXAS1, STAT6, GSDMB/ORMDL3, CRHR1, GNGT2, FCER2), we used the combined sum test for the sequence kernel association test (SKAT) adjusting for age, sex, and BMI and stratified by race. Validation was conducted in the Biorepository and Integrative Genomics (BIG) Initiative (83 White and 134 Black children). Using a Bonferroni threshold for the 12 regions tested (i.e., 0.05/12 = 0.004), GSDMB/ORMDL3 was significantly associated with ICS response for the combined effect of rare and common variants (p-value = 0.003) among White children in the PrecisionLink Biobank and replicated in the BIG Initiative (p-value = 0.02). Using WES data, the combined effect of rare and common variants for GSDMB/ORMDL3 was associated with ICS response among asthmatic children in the PrecisionLink Biobank and replicated in the BIG Initiative. This proof-of-concept study demonstrates the power of biobanks of pediatric real-life populations in asthma genomic investigations.

The Role of Sex in Genetic Association Studies of Depression.

Depression is the most common mental illness in the U.S. affecting nearly 40 million adults age 18 years and older. Depression has both genetic and environmental influences. In addition, women are more likely to be affected by depression than men. However, the relationship between genes and depression is complex and may be influenced by sex. Understanding the genetic basis of sex-specific differences for depression has the potential to lead to new biological understanding of the etiology of depression in females compared to males and to promote the development of novel and more effective pharmacotherapies. This review examines the role of sex in genetic associations with depression for both genome-wide association and candidate gene studies. While the genetic association signals of depression differ by sex, the role of sex in the heritability of depression is complex and warrants further investigation.

Supportive interventions for childhood cancer: An umbrella review of randomized evidence.

Therapeutic advancements have improved pediatric cancer prognosis, shifting the interest towards the management of psychosocial burden and treatment-related morbidity. To critically appraise the available evidence, we conducted an umbrella review of meta-analyses of randomized controlled trials on supportive interventions for childhood cancer. Thirty-four publications (92 meta-analyses, 1 network, 14,521 participants) were included. The most concrete data showed a reduction in procedure-related pain and distress through hypnosis. Moreover, exercise improved the functional mobility of the patients. Regarding pharmacological interventions, most of the meta-analyses pertained to the treatment of nausea/vomiting (ondansetron was effective) and infections/febrile neutropenia [granulocyte-(macrophage) colony-stimulating factors showed benefits]. Substantial heterogeneity was detected in 31 associations. Conclusively, supportive interventions for pediatric cancer are being thoroughly evaluated. However, most of the studies are small and of moderate quality, highlighting the need for more randomized evidence in order to increase precision in improving the quality of life of patients, survivors and their families.

Covariate adjustment of spirometric and smoking phenotypes: The potential of neural network models.

To increase power and minimize bias in statistical analyses, quantitative outcomes are often adjusted for precision and confounding variables using standard regression approaches. The outcome is modeled as a linear function of the precision variables and confounders; however, for many complex phenotypes, the assumptions of the linear regression models are not always met. As an alternative, we used neural networks for the modeling of complex phenotypes and covariate adjustments. We compared the prediction accuracy of the neural network models to that of classical approaches based on linear regression. Using data from the UK Biobank, COPDGene study, and Childhood Asthma Management Program (CAMP), we examined the features of neural networks in this context and compared them with traditional regression approaches for prediction of three outcomes: forced expiratory volume in one second (FEV1), age at smoking cessation, and log transformation of age at smoking cessation (due to age at smoking cessation being right-skewed). We used mean squared error to compare neural network and regression models, and found the models performed similarly unless the observed distribution of the phenotype was skewed, in which case the neural network had smaller mean squared error. Our results suggest neural network models have an advantage over standard regression approaches when the phenotypic distribution is skewed. However, when the distribution is not skewed, the approaches performed similarly. Our findings are relevant to studies that analyze phenotypes that are skewed by nature or where the phenotype of interest is skewed as a result of the ascertainment condition.

Therapeutic interventions for childhood cancer: An umbrella review of randomized evidence.

Treatment advancements in pediatric cancer have improved prognosis, but the strength of supporting evidence has not been thoroughly evaluated. To critically appraise it, we performed an umbrella review of meta-analyses of randomized controlled trials examining the efficacy and safety of therapeutic interventions for pediatric malignancies. Fourteen publications (68 meta-analyses, 31,496 participants) were eligible. Acute lymphoblastic leukemia (ALL) was investigated at most. Substantial heterogeneity was detected in 10 associations, with limited indications for small-study effects and excess-significance bias. The most concrete evidence pertained to the use of methotrexate and vincristine-prednisone pulses for ALL, improving event-free survival. Evidence regarding other cancers was relatively weak. Conclusively, we found few small meta-analyses focusing mainly on ALL. Randomized evidence stemming from adult populations still seems to serve as valuable indirect evidence backup. More randomized evidence and individual patient data meta-analyses are needed to increase certainty and precision in the care of pediatric cancer patients.

The Role of SNP Interactions when Determining Independence of Novel Signals in Genetic Association Studies-An Application to ARG1 and Bronchodilator Response.

Genome-wide association studies (GWAS) play a critical role in identifying many loci for common diseases and traits. There has been a rapid increase in the number of GWAS over the past decade. As additional GWAS are being conducted, it is unclear whether a novel signal associated with the trait of interest is independent of single nucleotide polymorphisms (SNPs) in the same region that has been previously associated with the trait of interest. The general approach to determining whether the novel association is independent of previous signals is to examine the association of the novel SNP with the trait of interest conditional on the previously identified SNP and/or calculate linkage disequilibrium (LD) between the two SNPs. However, the role of epistasis and SNP by SNP interactions are rarely considered. Through simulation studies, we examined the role of SNP by SNP interactions when determining the independence of two genetic association signals. We have created an R package on Github called gxgRC to generate these simulation studies based on user input. In genetic association studies of asthma, we considered the role of SNP by SNP interactions when determining independence of signals for SNPs in the ARG1 gene and bronchodilator response.

Age by Single Nucleotide Polymorphism Interactions on Bronchodilator Response in Asthmatics.

An unaddressed and important issue is the role age plays in modulating response to short acting ß2-agonists in individuals with asthma. The objective of this study was to identify whether age modifies genetic associations of single nucleotide polymorphisms (SNPs) with bronchodilator response (BDR) to ß2-agonists. Using three cohorts with a total of 892 subjects, we ran a genome wide interaction study (GWIS) for each cohort to examine SNP by age interactions with BDR. A fixed effect meta-analysis was used to combine the results. In order to determine if previously identified BDR SNPs had an age interaction, we also examined 16 polymorphisms in candidate genes from two published genome wide association studies (GWAS) of BDR. There were no significant SNP by age interactions on BDR using the genome wide significance level of 5 × 10-8. Using a suggestive significance level of 5 × 10-6, three interactions, including one for a SNP within PRAG1 (rs4840337), were significant and replicated at the significance level of 0.05. Considering candidate genes from two previous GWAS of BDR, three SNPs (rs10476900 (near ADRB2) [p-value = 0.009], rs10827492 (CREM) [p-value = 0.02], and rs72646209 (NCOA3) [p-value = 0.02]) had a marginally significant interaction with age on BDR (p < 0.05). Our results suggest age may be an important modifier of genetic associations for BDR in asthma.

Association of Inclusion of Medicare Advantage Patients in Hospitals' Risk-Standardized Readmission Rates, Performance, and Penalty Status.

Importance: The Hospital Readmissions Reduction Program publicly reports and financially penalizes hospitals according to 30-day risk-standardized readmission rates (RSRRs) exclusively among traditional Medicare (TM) beneficiaries but not persons with Medicare Advantage (MA) coverage. Exclusively reporting readmission rates for the TM population may not accurately reflect hospitals' readmission rates for older adults. Objective: To examine how inclusion of MA patients in hospitals' performance is associated with readmission measures and eligibility for financial penalties. Design, Setting, and Participants: This is a retrospective cohort study linking the Medicare Provider Analysis and Review file with the Healthcare Effectiveness Data and Information Set at 4070 US acute care hospitals admitting both TM and MA patients. Participants included patients admitted and discharged alive with a diagnosis of acute myocardial infarction (AMI), congestive heart failure (CHF), or pneumonia between 2011 and 2015. Data analyses were conducted between April 1, 2018, and November 20, 2020. Exposures: Admission to an acute care hospital. Main Outcomes and Measures: The outcome was readmission for any reason occurring within 30 days after discharge. Each hospital's 30-day RSRR was computed on the basis of TM, MA, and all patients and estimated changes in hospitals' performance and eligibility for financial penalties after including MA beneficiaries for calculating 30-day RSRRs. Results: There were 748 033 TM patients (mean [SD] age, 76.8 [83] years; 360 692 [48.2%] women) and 295 928 MA patients (mean [SD] age, 77.5 [7.9] years; 137 422 [46.4%] women) hospitalized and discharged alive for AMI; 1 327 551 TM patients (mean [SD] age, 81 [8.3] years; 735 855 [55.4%] women) and 457 341 MA patients (mean [SD] age, 79.8 [8.1] years; 243 503 [53.2%] women) for CHF; and 2 017 020 TM patients (mean [SD] age, 80.7 [8.5] years; 1 097 151 [54.4%] women) and 610 790 MA patients (mean [SD] age, 79.6 [8.2] years; 321 350 [52.6%] women) for pneumonia. The 30-day RSRRs for TM and MA patients were correlated (correlation coefficients, 0.31 for AMI, 0.40 for CHF, and 0.41 for pneumonia) and the TM-based RSRR systematically underestimated the RSRR for all Medicare patients for each condition. Of the 2820 hospitals with 25 or more admissions for at least 1 of the outcomes of AMI, CHF, and pneumonia, 635 (23%) had a change in their penalty status for at least 1 of these conditions after including MA data. Changes in hospital performance and penalty status with the inclusion of MA patients were greater for hospitals in the highest quartile of MA admissions. Conclusions and Relevance: In this cohort study, the inclusion of data from MA patients changed the penalty status of a substantial fraction of US hospitals for at least 1 of 3 reported conditions. This suggests that policy makers should consider including all hospital patients, regardless of insurance status, when assessing hospital quality measures.