Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data.

BACKGROUND: Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods. METHODS: Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. We separated the resulting sequencing data into regions with dense CpG data, and differentially methylated regions (DMRs) were inferred with the SOMNiBUS region-level test, adjusted for age. Pathway enrichment analysis was performed with ingenuity pathway analysis (IPA). We compared the results obtained by SOMNiBUS and bumphunter. RESULTS: Of 8268 CpG regions of ≥ 60 CpGs eligible for analysis with SOMNiBUS, we identified 131 DMRs and 125 differentially methylated genes (DMGs; p-values less than Bonferroni-corrected threshold of 6.05-06 controlling family-wise error rate at 0.05; 1.6% of the regions). In comparison, bumphunter identified 821,929 CpG regions, 599 DMRs (of which none had ≥ 60 CpGs) and 340 DMGs (q-value of 0.05; 0.04% of all regions). The top ranked gene identified by SOMNiBUS was FLT4, a lymphangiogenic orchestrator, and the top ranked gene on chromosome X was CHST7, known to catalyze the sulfation of glycosaminoglycans in the extracellular matrix. The top networks identified by IPA included connective tissue disorders. CONCLUSIONS: SOMNiBUS is a complementary method of analyzing WGBS data that enhances biological insights into SSc and provides novel avenues of investigation into its pathogenesis.

Novel mobility index tracks COVID-19 transmission following stay-at-home orders.

Considering the emergence of SARS-CoV-2 variants and low vaccine access and uptake, minimizing human interactions remains an effective strategy to mitigate the spread of SARS-CoV-2. Using a functional principal component analysis, we created a multidimensional mobility index (MI) using six metrics compiled by SafeGraph from all counties in Illinois, Ohio, Michigan and Indiana between January 1 to December 8, 2020. Changes in mobility were defined as a time-updated 7-day rolling average. Associations between our MI and COVID-19 cases were estimated using a quasi-Poisson hierarchical generalized additive model adjusted for population density and the COVID-19 Community Vulnerability Index. Individual mobility metrics varied significantly by counties and by calendar time. More than 50% of the variability in the data was explained by the first principal component by each state, indicating good dimension reduction. While an individual metric of mobility was not associated with surges of COVID-19, our MI was independently associated with COVID-19 cases in all four states given varying time-lags. Following the expiration of stay-at-home orders, a single metric of mobility was not sensitive enough to capture the complexity of human interactions. Monitoring mobility can be an important public health tool, however, it should be modelled as a multidimensional construct.

Interactive online informational and peer support application for patients with low anterior resection syndrome: patient survey and protocol for a multicentre randomized controlled trial.

AIM: Low anterior resection syndrome (LARS) refers to a constellation of bowel symptoms that affect the majority of patients following restorative proctectomy. LARS is associated with poorer quality of life (QoL), and can lead to distress, anxiety and isolation. Peer support could be an important resource for people living with LARS, helping them normalize and validate their experience. The aim of this work is to describe the development of an interactive online informational and peer support app for LARS and the protocol for a randomized controlled trial. METHOD: A multicentre, randomized, assessor-blind, parallel-groups pragmatic trial will involve patients from five large colorectal surgery practices across Canada. The trial will evaluate the impact of an interactive online informational and peer support app for LARS, consisting of LARS informational modules and a closed forum for peers and trained peer support mentors, on patient-reported outcomes of people living with LARS. The primary outcome will be global QoL at 6 months following app exposure. The treatment effect on global QoL will be modelled using generalized estimating equations. Secondary outcomes will include patient activation and bowel function as measured by LARS scores. RESULTS: In order to better understand patients' interest and preferences for an online peer support intervention for LARS, we conducted a single institution cross-sectional survey study of rectal cancer survivors. In total, 35/69 (51%) participants reported interest in online peer support for LARS. Age <65 years (OR 9.1; 95% CI 2.3-50) and minor/major LARS (OR 20; 95% CI 4.2-100) were significant predictors of interest in LARS online peer support. CONCLUSION: There is significant interest in the use of online peer support for LARS among younger patients and those with significant bowel dysfunction. Based on results of the needs assessment study, the app content and features were modified reflect patients' needs and preferences. We are now in an optimal position to rigorously test the potential effects of this initiative on patient-centered outcomes using a randomized controlled trial.

Polygenic Risk Score for Low-Density Lipoprotein Cholesterol Is Associated With Risk of Ischemic Heart Disease and Enriches for Individuals With Familial Hypercholesterolemia.

BACKGROUND: The clinical implications of a polygenic risk score (PRS) for LDL-C (low-density lipoprotein cholesterol) are not well understood, both within the general population and individuals with familial hypercholesterolemia (FH). METHODS: We developed the LDL-C PRS using Least Absolute Shrinkage and Selection Operator regression in 377 286 White British participants from UK Biobank and tested its association with LDL-C according to FH variant carrier status in another 41 748 whole-exome sequenced individuals. Next, we tested for an enrichment of FH variant carriers among individuals with severe hypercholesterolemia and low LDL-C PRS. Last, we contrasted the effect of the LDL-C PRS, measured LDL-C and FH variant carrier status on risk of ischemic heart disease among 3010 cases and 38 738 controls. RESULTS: Among the 41 748 whole-exome sequenced White British individuals, 1-SD increase in the LDL-C PRS was associated with elevated LDL-C among both FH variant carriers (0.34 [95% CI, 0.22-0.47] mmol/L) and noncarriers (0.42 [95% CI, 0.42-0.43] mmol/L). Among individuals with severe hypercholesterolemia, FH variant carriers were enriched in those with a low LDL-C PRS (odds ratio, 2.20 [95% CI, 1.66-2.71] per SD). Each SD increase in the LDL-C PRS was associated with risk of ischemic heart disease to the comparable magnitude as measured LDL-C (odds ratio, 1.24 [95% CI, 1.20-1.29] and odds ratio, 1.15 [95% CI, 1.09-1.23], respectively). The LDL-C PRS was not strongly associated with other traditional ischemic heart disease risk factors. CONCLUSIONS: An LDL-C PRS could be used to identify individuals with a higher probability of harboring FH variants. The association between ischemic heart disease and the LDL-C PRS was comparable to measured LDL-C, likely because the PRS reflects lifetime exposure to LDL-C levels.

Development and evaluation of a patient-centred program for low anterior resection syndrome: protocol for a randomized controlled trial.

INTRODUCTION: Low anterior resection syndrome (LARS) is described as disordered bowel function after rectal resection that leads to a detriment in quality of life, and affects the majority of individuals following restorative proctectomy for rectal cancer. The management of LARS includes personalised troubleshooting and effective self-management behaviours. Thus, affected individuals need to be well informed and appropriately engaged in their own LARS management. This manuscript describes the development of a LARS patient-centred programme (LPCP) and the study protocol for its evaluation in a randomised controlled trial. METHODS AND ANALYSIS: This will be a multicentre, randomised, assessor-blind, parallel-groups, pragmatic trial evaluating the impact of an LPCP, consisting of an informational booklet, patient diaries and nurse support, on patient-reported outcomes after restorative proctectomy for rectal cancer. The informational booklet was developed by a multidisciplinary LARS team, and was vetted in a focus group and semistructured interviews involving patients, caregivers, and healthcare professionals. The primary outcome will be global quality of life (QoL), as measured by the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (QLQ-C30), at 6 months after surgery. The treatment effect on global QoL will be modelled using generalised estimating equations. Secondary outcomes include symptom change, patient activation, bowel function measures, emotional distress, knowledge about LARS and satisfaction with the LPCP. ETHICS AND DISSEMINATION: The Research Ethics Committee (REC) at the Integrated Health and Social Services Network for West-Central Montreal (health network responsible for the Jewish General Hospital) is the overseeing REC for all Quebec sites. They have granted ethical approval (MP-05-2019-1628) for all Quebec hospitals (Jewish General Hospital, McGill University Health Center, CHU de Quebec) and have granted full authorisation to begin research at the Jewish General Hospital. Patient recruitment will not begin at the other Quebec sites until inter-institutional contracts are finalised and feasibility/authorisation for research is granted by their respective REC. The results of this study will be presented at national and international conferences, and a manuscript with results will be submitted for publication in a high-impact peer-reviewed journal. TRIAL REGISTRATION NUMBER: NCT03828318; Pre-results.

Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models.

Complex traits are known to be influenced by a combination of environmental factors and rare and common genetic variants. However, detection of such multivariate associations can be compromised by low statistical power and confounding by population structure. Linear mixed effects models (LMM) can account for correlations due to relatedness but have not been applicable in high-dimensional (HD) settings where the number of fixed effect predictors greatly exceeds the number of samples. False positives or false negatives can result from two-stage approaches, where the residuals estimated from a null model adjusted for the subjects' relationship structure are subsequently used as the response in a standard penalized regression model. To overcome these challenges, we develop a general penalized LMM with a single random effect called ggmix for simultaneous SNP selection and adjustment for population structure in high dimensional prediction models. We develop a blockwise coordinate descent algorithm with automatic tuning parameter selection which is highly scalable, computationally efficient and has theoretical guarantees of convergence. Through simulations and three real data examples, we show that ggmix leads to more parsimonious models compared to the two-stage approach or principal component adjustment with better prediction accuracy. Our method performs well even in the presence of highly correlated markers, and when the causal SNPs are included in the kinship matrix. ggmix can be used to construct polygenic risk scores and select instrumental variables in Mendelian randomization studies. Our algorithms are available in an R package available on CRAN (https://cran.r-project.org/package=ggmix).

Trends in cause-specific mortality in HIV-hepatitis C coinfection following hepatitis C treatment scale-up.

OBJECTIVE: Hepatitis C virus (HCV) treatment may reduce liver-related mortality but with competing risks, other causes of mortality may undermine benefits. We examined changes in cause-specific mortality among HIV-HCV coinfected patients before and after scale-up of HCV treatment. DESIGN: Prospective multicentre HIV-HCV cohort study in Canada. METHODS: Cause-specific deaths, classified using a modified 'Coding of Cause of Death in HIV' protocol, were determined for two time periods, 2003-2012 and 2013-2017, stratified by age (20-49; 50-80 years). Comparison of trends between periods was performed using Poisson regression. To account for competing risks, multinomial regression was used to estimate the cause-specific hazard ratios of time and age on cause of death, from which end-stage liver disease (ESLD)-specific 5-year cumulative incidence functions were estimated. RESULTS: Overall, 1634 participants contributed 8248 person-years of follow-up; 273 (17%) died. Drug overdose was the most common cause of death overall, followed by ESLD and smoking-related deaths. In 2013-2017, ESLD was surpassed by drug overdose and smoking-related deaths among those aged 20-49 and 50-80, respectively. After accounting for competing risks, comparing 2003-2012 to 2013-2017, ESLD deaths declined (adjusted hazards ratio: 0.18, 95% confidence interval 0.05-0.62). However, both early and late period cumulative incidence functions demonstrated increased risk of death from ESLD for patients with poor HIV control and advanced fibrosis. CONCLUSION: The gains made in overall mortality with HCV therapy may be thwarted if modifiable harms are not addressed. Although ESLD-related deaths have decreased over time, treatment should be further expanded, prioritizing those with advanced fibrosis.

Impact of adipose tissue on prostate cancer aggressiveness - analysis of a high-risk population.

Background We investigated whether visceral adiposity is associated with more aggressive disease at prostatectomy. Materials and methods Four hundred and seventy-four patients referred for postoperative adjuvant or salvage radiotherapy were included in this study. Primary endpoints were positive surgical margins (pSM) or extracapsular extension (ECE). Visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) were manually contoured. Univariate and multivariate logistic regression was performed. Results In univariate analysis, VAT volume (p = 0.006), adipose tissue ratio (VAT/SAT, p = 0.003), density of the SAT (p = 0.04), as well as age (p < 0.001) were associated with pSM. In the univariate analysis, SAT density was associated with a trend towards a higher rate of ECE (p = 0.051) but visceral fat volume (p = 0.01), as well as the adipose tissue ratio (p = 0.03) were both protective factors. None of the adipose tissue measurements or BMI had an influence on biochemical recurrence or overall survival (all p ≥ 0.5). Conclusions SAT-volume and increased SAT-density were generally associated with more aggressive prostate cancers whereas VAT as a protective factor. These findings emphasize a possible mechanism for the association between obesity and prostate cancer aggressiveness.

Assessing transmission ratio distortion in extended families: a comparison of analysis methods.

A statistical departure from Mendel's law of segregation is known as transmission ratio distortion. Although well documented in many other organisms, the extent of transmission ratio distortion and its influence in the human genome remains incomplete. Using Genetic Analysis Workshop 19 whole genome sequence data from 20 large Mexican American pedigrees, our goal was to identify potentially distorted regions in the genome using family-based association methods such as the transmission disequilibrium test, the pedigree disequilibrium test, and the family-based association test. Preliminary results showed an unusually high number of transmission ratio distortion signals identified by the transmission disequilibrium test, but this phenomenon could not be replicated by the pedigree disequilibrium test or family-based association test. Applying these tests to different subsets of the data, we found the transmission disequilibrium test to be very sensitive to imputed genotypes. Regression analysis of transmission ratio distortion test p values controlling for minor allele frequency and quality control checks showed that Hardy Weinberg p values are associated with this inflation. Although the transmission disequilibrium test appears confounded by imputation of single nucleotide polymorphisms, the pedigree disequilibrium test and family-based association test seem to offer more robust alternatives when searching for transmission ratio distortion loci in whole genome sequence data from extended families.

Joint analysis of multiple blood pressure phenotypes in GAW19 data by using a multivariate rare-variant association test.

INTRODUCTION: Large-scale sequencing studies often measure many related phenotypes in addition to the genetic variants. Joint analysis of multiple phenotypes in genetic association studies may increase power to detect disease-associated loci. METHODS: We apply a recently developed multivariate rare-variant association test to the Genetic Analysis Workshop 19 data in order to test associations between genetic variants and multiple blood pressure phenotypes simultaneously. We also compare this multivariate test with a widely used univariate test that analyzes phenotypes separately. RESULTS: The multivariate test identified 2 genetic variants that have been previously reported as associated with hypertension or coronary artery disease. In addition, our region-based analyses also show that the multivariate test tends to give smaller p values than the univariate test. CONCLUSIONS: Hence, the multivariate test has potential to improve test power, especially when multiple phenotypes are correlated.