SmCCNet 2.0: A Comprehensive Tool for Multi-omics Network Inference with Shiny Visualization

Summary

Sparse multiple canonical correlation network analysis (SmCCNet) is a machine learning technique for integrating omics data along with a variable of interest (e.g., phenotype of complex disease), and reconstructing multi-omics networks that are specific to this variable. We present the second-generation SmCCNet (SmCCNet 2.0) that adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. In addition, this new package offers a streamlined setup process that can be configured manually or automatically, ensuring a flexible and user-friendly experience.

Availability

This package is available in both CRAN: https://cran.r-project.org/web/packages/SmCCNet/index.html and Github: https://github.com/KechrisLab/SmCCNet under the MIT license. The network visualization tool is available at https://smccnet.shinyapps.io/smccnetnetwork/.

Type 2 Diabetes Modifies the Association of CAD Genomic Risk Variants With Subclinical Atherosclerosis

BACKGROUND

Individuals with type 2 diabetes (T2D) have an increased risk of coronary artery disease (CAD), but questions remain about the underlying pathology. Identifying which CAD loci are modified by T2D in the development of subclinical atherosclerosis (coronary artery calcification [CAC], carotid intima-media thickness, or carotid plaque) may improve our understanding of the mechanisms leading to the increased CAD in T2D.

METHODS

We compared the common and rare variant associations of known CAD loci from the literature on CAC, carotid intima-media thickness, and carotid plaque in up to 29 670 participants, including up to 24 157 normoglycemic controls and 5513 T2D cases leveraging whole-genome sequencing data from the Trans-Omics for Precision Medicine program. We included first-order T2D interaction terms in each model to determine whether CAD loci were modified by T2D. The genetic main and interaction effects were assessed using a joint test to determine whether a CAD variant, or gene-based rare variant set, was associated with the respective subclinical atherosclerosis measures and then further determined whether these loci had a significant interaction test.

RESULTS

Using a Bonferroni-corrected significance threshold of P<1.6×10-4, we identified 3 genes (ATP1B1, ARVCF, and LIPG) associated with CAC and 2 genes (ABCG8 and EIF2B2) associated with carotid intima-media thickness and carotid plaque, respectively, through gene-based rare variant set analysis. Both ATP1B1 and ARVCF also had significantly different associations for CAC in T2D cases versus controls. No significant interaction tests were identified through the candidate single-variant analysis.

CONCLUSIONS

These results highlight T2D as an important modifier of rare variant associations in CAD loci with CAC.

Clustering-based COPD subtypes have distinct longitudinal outcomes and multi-omics biomarkers

Introduction

Chronic obstructive pulmonary disease (COPD) can progress across several domains, complicating the identification of the determinants of disease progression. In our previous work, we applied k-means clustering to spirometric and chest radiological measures to identify four COPD-related subtypes: ‘relatively resistant smokers (RRS)’, ‘mild upper lobe-predominant emphysema (ULE)’, ‘airway-predominant disease (AD)’ and ‘severe emphysema (SE)’. In the current study, we examined the associations of these subtypes to longitudinal COPD-related health measures as well as blood transcriptomic and plasma proteomic biomarkers.

Methods

We included 8266 non-Hispanic white and African-American smokers from the COPDGene study. We used linear regression to investigate cluster associations to 5-year prospective changes in spirometric and radiological measures and to gene expression and protein levels. We used Cox-proportional hazard test to test for cluster associations to prospective exacerbations, comorbidities and mortality.

Results

The RRS, ULE, AD and SE clusters represented 39%, 15%, 26% and 20% of the studied cohort at baseline, respectively. The SE cluster had the greatest 5-year FEV₁ (forced expiratory volume in 1 s) and emphysema progression, and the highest risks of exacerbations, cardiovascular disease and mortality. The AD cluster had the highest diabetes risk. After adjustments, only the SE cluster had an elevated respiratory mortality risk, while the ULE, AD and SE clusters had elevated all-cause mortality risks. These clusters also demonstrated differential protein and gene expression biomarker associations, mostly related to inflammatory and immune processes.

Conclusion

COPD k-means subtypes demonstrate varying rates of disease progression, prospective comorbidities, mortality and associations to transcriptomic and proteomic biomarkers. These findings emphasise the clinical and biological relevance of these subtypes, which call for more study for translation into clinical practice.

Trail registration number

NCT00608764.

Co-Morbidity Patterns Identified Using Latent Class Analysis of Medications Predict All-Cause Mortality Independent of Other Known Risk Factors: The COPDGene® Study

PURPOSE

Medication patterns include all medications in an individual's clinical profile. We aimed to identify chronic co-morbidity treatment patterns through medication use among COPDGene participants and determine whether these patterns were associated with mortality, acute exacerbations of chronic obstructive pulmonary disease (AECOPD) and quality of life.

MATERIALS AND METHODS

Participants analyzed here completed Phase 1 (P1) and/or Phase 2 (P2) of COPDGene. Latent class analysis (LCA) was used to identify medication patterns and assign individuals into unobserved LCA classes. Mortality, AECOPD, and the St. George's Respiratory Questionnaire (SGRQ) health status were compared in different LCA classes through survival analysis, logistic regression, and Kruskal-Wallis test, respectively.

RESULTS

LCA identified 8 medication patterns from 32 classes of chronic comorbid medications. A total of 8110 out of 10,127 participants with complete covariate information were included. Survival analysis adjusted for covariates showed, compared to a low medication use class, mortality was highest in participants with hypertension+diabetes+statin+antiplatelet medication group. Participants in hypertension+SSRI+statin medication group had the highest odds of AECOPD and the highest SGRQ score at both P1 and P2.

CONCLUSION

Medication pattern can serve as a good indicator of an individual's comorbidities profile and improves models predicting clinical outcomes.

Visual Emphysema at Chest CT in GOLD Stage 0 Cigarette Smokers Predicts Disease Progression: Results from the COPDGene Study

Background The clinical significance of visually evident emphysema on CT images in individuals without spirometric evidence of chronic obstructive pulmonary disease (COPD) by current diagnostic criteria is, to the knowledge of the authors, unknown. Purpose To evaluate whether participants with visually evident emphysema at CT were more likely to have progressive disease and increased mortality at 5 years compared with those without visual emphysema. Materials and Methods This secondary analysis of the prospective Genetic Epidemiology of COPD study evaluated current or former smokers enrolled between 2008 and 2011 who did not meet current criteria for COPD (defined as Global Initiative for Obstructive Lung Disease stage 0). Statistical analysis was performed by using linear mixed models to estimate mean physiologic, imaging, and clinical outcomes for those with and without visual emphysema. Hazard ratios for mortality were calculated by using Cox regression models with emphysema as the main predictor. Results Of the 4095 participants, 48.3% (1979 participants; 1096 men and 883 women; mean age, 57 years ± 8 [standard deviation]) had trace or greater visual emphysema at CT and 51.7% (2116 participants; 1068 men and 1048 women; mean age, 56 years ± 8) had no emphysema at CT. At 5 years, participants with visual emphysema at CT demonstrated progressive airflow obstruction with lower values of ratio of forced expiratory volume in 1 second (FEV₁)-to-functional vital capacity (FVC) ratio (-1.7 vs -0.7) and greater progression in quantitative emphysema measured by 15th percentile lung density (-3.3 vs -0.3 HU), adjusted lung density (-3.1 vs -0.2 g/L), and percentage of lung voxels with CT attenuation less than -950 HU (0.17 vs -0.20) than participants without emphysema (P < .001 for each). The rate of quantitative emphysema progression increased with greater grades of emphysema severity within the emphysema group. Conclusion The presence of visual emphysema at CT in current and former Global Initiative for Obstructive Lung Disease stage 0 smokers predicted structural and physiologic disease progression. © RSNA, 2020 Online supplemental material is available for this article. See also the editorial by Grenier in this issue.

Long-term Outcomes of Lifestyle Intervention to Prevent Diabetes in American Indian and Alaska Native Communities: The Special Diabetes Program for Indians Diabetes Prevention Program

OBJECTIVE

Evidence for long-term translational effectiveness of lifestyle interventions in minority populations is scarce. This article reports long-term outcomes, for up to 10 years, of such an intervention to prevent diabetes in American Indian and Alaska Native (AI/AN) communities.

RESEARCH DESIGN AND METHODS

From January 2006 to July 2016, the Special Diabetes Program for Indians Diabetes Prevention Program implemented the Diabetes Prevention Program lifestyle intervention among 46 AI/AN health care programs. Enrolled participants underwent a thorough clinical assessment at baseline, after completing the Lifestyle Balance Curriculum (postcurriculum assessment), and annually thereafter. Proportional hazards regression was used to estimate the association between diabetes incidence and postcurriculum weight loss status.

RESULTS

Of 8,652 enrolled participants, 65% finished the postcurriculum assessment. The assessment completion rate diminished over time to 13% in year 10. Among those with postcurriculum weight measurements, 2,028 (36%) lost >5% of their initial weight, 978 (17%) lost 3-5%, whereas 2,604 (47%) had <3% weight loss (average weight loss 3.8%). Compared with those with <3% weight loss, participants with >5% weight loss had a 64% (95% CI 54-72) lower risk of developing diabetes during the first 6 years of follow-up, whereas those with 3-5% weight loss had 40% (95% CI 24-53) lower risk.

CONCLUSIONS

Moderate to small weight loss was associated with substantially reduced long-term risk of diabetes in diverse AI/AN communities. High participant attrition rates and nonoptimal postcurriculum weight loss are important challenges found in this translational effort implemented in an underserved population.

Case management to reduce cardiovascular disease risk in American Indians and Alaska Natives with diabetes: results from the Special Diabetes Program for Indians Healthy Heart Demonstration Project

OBJECTIVES

We evaluated cardiovascular disease (CVD) risk factors in American Indians/Alaska Natives (AI/ANs) with diabetes in the Special Diabetes Program for Indians Healthy Heart (SDPI-HH) Demonstration Project.

METHODS

Multidisciplinary teams implemented an intensive case management intervention among 30 health care programs serving 138 tribes. The project recruited 3373 participants, with and without current CVD, between 2006 and 2009. We examined data collected at baseline and 1 year later to determine whether improvements occurred in CVD risk factors and in Framingham coronary heart disease (CHD) risk scores, aspirin use, and smoking status.

RESULTS

A1c levels decreased an average of 0.2% (P < .001). Systolic and diastolic blood pressure, low-density lipoprotein (LDL) cholesterol, and triglyceride levels decreased, with the largest significant reduction in LDL cholesterol (∆ = -5.29 mg/dL; P < .001). Average Framingham CHD risk scores also decreased significantly. Aspirin therapy increased significantly, and smoking decreased. Participants with more case management visits had significantly greater reductions in LDL cholesterol and A1c values.

CONCLUSIONS

SDPI-HH successfully translated an intensive case management intervention. Creative retention strategies and an improved understanding of organizational challenges are needed for future Indian health translational efforts.

Factor analyses of condom attitudes, norms, and self-efficacy measures in diverse samples

Measurement of condom attitudes, norms, and self-efficacy is variable, reducing research generalizability. The purpose of this study was to assess reliability and construct validity of measures of condom attitudes, norms, and self-efficacy across 3,989 youth. Data were collected at computer kiosks and on the Internet. Analyses included internal consistency reliability assessments and exploratory and confirmatory factor analyses of three constructs in a 32-item a priori instrument. Reliability estimates ranged between 0.68 and 0.89, and goodness of fit indices all exceeded 0.90. Factor analysis results supported the compatibility of the items from the three subscales with their conceptual domains. Final scales include measures of positive and negative outcome expectancies related to condom use, peer and partner condom norms, self-efficacy for condom negotiation, and self-efficacy for condom use. These measures of condom attitudes, norms, and self-efficacy can be employed for assessments to improve standardization of measures and generalizability of research, particularly related to HIV prevention.

Care of undocumented individuals with ESRD: a national survey of US nephrologists

BACKGROUND

Although Medicare covers most dialysis therapy for US citizens with end-stage renal disease (ESRD), no national standards for dialysis provision exist for undocumented (ie, immigrant) patients with ESRD.

STUDY DESIGN

Cross-sectional survey.

SETTING & PARTICIPANTS

Mail and internet survey from October 2006 to February 2007 of American Society of Nephrology member nephrologists.

PREDICTORS

Region of the country, practicing in a state with a high undocumented population, inpatient and outpatient practice setting, and practice location.

OUTCOMES

Characteristics of nephrologists who report caring for undocumented patients with ESRD and those who perceive that such patients have access to maintenance dialysis therapy.

RESULTS

Response rate was 57% (990 of 1,723). Of nephrologists surveyed, 65%, representing 44 states, reported providing care to undocumented patients with ESRD and 61% reported increasing prevalence. Being from a state with a high undocumented population (OR, 1.67; 95% CI, 1.21 to 2.30) was associated with undocumented ESRD patient care; being from the Northeastern United States (OR, 0.55; 95% CI, 0.34 to 0.88) or a small town/rural area (OR, 0.27; 95% CI, 0.18 to 0.40) were negatively associated. Of the respondents, 91% reported that undocumented patients had access to emergent dialysis, but only 51% reported access to maintenance dialysis therapy. The characteristic associated with reporting access to maintenance dialysis was practicing in a state with a high undocumented population (OR, 1.91; 95% CI, 1.37 to 2.66), whereas practicing in the Southern United States was negatively associated (OR, 0.37; 95% CI, 0.24 to 0.57). Emergent-only dialysis for undocumented patients was reported by 28%. Of respondents knowledgeable about reimbursement, most reported inadequate compensation and 35% reported that outpatient dialysis units provide uncompensated dialysis care to undocumented patients with ESRD.

LIMITATIONS

Selection and information biases inherent to survey methods.

CONCLUSIONS

Dialysis for undocumented patients with ESRD is an increasing problem involving the majority of US nephrologists. Inadequately compensated or uncompensated care may limit the availability of long-term maintenance dialysis therapy for undocumented patients with ESRD. Regional variations argue for more rational and uniform national policy regarding this issue.

Relationship of Processes and Structures of Care in General Surgery to Postoperative Outcomes: A Descriptive Analysis

BACKGROUND

The systematic collection of quantitative data on structures and processes from surgical services participating in the National Surgical Quality Improvement Program (NSQIP) has not been a focus to date. Efficient collection of useful measures of structures and processes may improve understanding of surgical outcomes and strategies for improving the quality of surgical care, as NSQIP continues to expand. The purpose of this article was to describe results of a quantitative survey designed to measure surgical care structures and processes within NSQIP sites.

STUDY DESIGN

A cross-sectional survey was mailed to 123 Department of Veteran Affairs (VA) and 14 private sector sites participating in the Agency for Healthcare Research and Quality (AHRQ)-funded Patient Safety in Surgery (PSS) Study. The survey included questions about organizational structures and processes of preoperative, intraoperative, and postoperative general surgical care services. For this study, we included only data from 90 VA sites that returned a survey (73% response rate). We used descriptive statistics and examined the bivariate association of structures and processes items or scales with risk-adjusted observed-to-expected (O/E) ratios of surgical morbidity and mortality.

RESULTS

Examination of frequency or means and standard deviations of items and scales revealed substantial variation in the structures and processes of surgical care services in participating VA sites, with correlation analyses demonstrating that, of 35 process and structure variables, there was a statistically significant relationship with the hospital's observed-to-expected ratio for 14 variables for morbidity, but only 4 variables for mortality.

CONCLUSIONS

This descriptive analysis provides support for the potential importance of measuring organizational structures and processes of care in addition to risk-adjusted morbidity and mortality.

Adoption and use of an online patient portal for diabetes (Diabetes-STAR)

Online patient portals, which provide patients with personal information and facilitate electronic doctor-patient communication, can help patients manage chronic diseases. These systems will be most beneficial if they have broad and durable appeal. In a randomized trial, we compared a portal providing generic diabetes self-management information to one providing personalized information (Diabetes-STAR). We assessed (1) the characteristics of patient-users and (2) whether including personalized content promotes sustained use.