Age and the European Society of Cardiology 0/1-hour high sensitivity troponin T algorithm for the evaluation of patients with possible acute myocardial infarction: results from the STOP-CP study

Background

The European Society of Cardiology (ESC) 0/1-hour high sensitivity troponin (hs-cTn) algorithm is widely used in the evaluation of patients presenting to the Emergency Department (ED) with symptoms suspicious for non ST-segment elevation myocardial infarction (NSTEMI). The effect of increasing patient age with its use has not been studied in any detail.

Purpose

The objective of this secondary analysis of the STOP-CP (High Sensitivity Cardiac Troponin T to Optimize Chest Pain Risk Stratification) United States (US) multicenter study was to evaluate the efficacy and safety of use of the ESC 0/1-hour hs-cTnT algorithm in younger, middle-aged, and older patients.

Methods

Patients (≥21 years old) presenting to the (ED) with symptoms suggestive of NSTEMI were enrolled (1/25/2017–9/6/2018) at 8 US medical centers. The ESC hs-cTnT 0/1-hour hs-cTnT algorithm was used to place patients into rule-out, observe, and rule-in NSTEMI zones. Algorithm performance for rapid NSTEMI rule-out and 30-day adverse outcomes was studied in 3 patient age (years) intervals: younger (21–45). middle aged (46–64) and older (≥65). Major adverse cardiovascular events (MACE) consisted of cardiac death, myocardial infarction, or coronary revascularization at 30-days. Fisher's exact tests were used to compare NSTEMI ruled out and MACE rates between patient age intervals. Negative likelihood ratios (NLR) with 95% confidence interval (CI) were calculated for 30-day MACE.

Results

Overall 1430 participants were enrolled with 15.7% (224/1430) young, 57.4% (821/1430) middle-aged, and 26.9% (385/1430) being older. The ESC 0/1 hour hs-cTnT algorithm NSTEMI rule-out rates were 79.9% (179/224), 62.1% (510/821) and 35.6% (137/385) respectively for these age groups (p<0.0001). The overall 30-day MACE rate was 14.2% (203/1430) with interval age rates of 7.1% (16/224) in younger, 13.1% (108/821) middle aged and 20.5% (79/385) older patients. Amongst NSTEMI ruled-out patients MACE occurred in 1.1% (2/179) of younger, 3.3% (17/510) middle aged and 2.9% (4/137) older individuals (p=0.320). NLR for 30-day MACE was 0.15 (95% CI 0.04, −0.54) in younger, 0.23 (95% CI 0.15–0.35) middle aged and 0.12 (95% CI 0.04–0.31) for older patients.

Conclusions

With increasing age ED patients were less often rapidly ruled out for NSTEMI during their initial cardiac evaluations. The STOP-CP US study demonstrated that older age interval alone was not an independent variable that increased the risk for 30-day MACE in patients ruled out for NSTEMI using the ESC 0/1 hour hs-cTnT algorithm. Our report suggests that cardiac risk stratification scores using age as an independent variable for predicting 30-day MACE in these patients require reevaluation.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Roche, Basel, Switzerland

Patients with known coronary artery disease who are ruled out for acute myocardial infarction using a high sensitivity troponin T 0/1-hour algorithm have increased 30-day major adverse cardiac events

Background

The European Society of Cardiology (ESC) 0/1-hour high sensitivity troponin (hs-cTn) algorithm is widely used in the evaluation of patients presenting to the Emergency Department (ED) with symptoms suspicious for non ST-segment elevation myocardial infarction (NSTEMI). There is limited data available for the use of this algorithm comparing NSTEMI rule-out rates and 30-day adverse outcomes in patients with and without known coronary artery disease (CA), defined as prior myocardial infarction [MI], coronary revascularization, or ≥70% coronary stenosis.

Purpose

The objective of this secondary analysis of the STOP-CP (High Sensitivity Cardiac Troponin T to Optimize Chest Pain Risk Stratification) United States (US) multicenter study was to compare the ESC 0/1-hour algorithm for rapid NSTEMI rule-out and 30-day adverse outcomes in patients with and without known CAD.

Methods

Patients (≥21 years old) presenting to the (ED) with symptoms suggestive of NSTEMI were enrolled (1/25/2017–9/6/2018) at 8 US medical centers. The ESC hs-cTnT 0/1-hour hs-cTnT algorithm was used to stratify patients into rule-out, observe, and rule-in zones. Algorithm performance for 30-day adverse outcomes was analyzed in patients with or without known CAD. Major adverse cardiovascular events (MACE) consisted of cardiac death, MI, or coronary revascularization. Fisher's exact tests were used to compare NSTEMI rule-out and 30-day MACE rates in patients with and without known CAD. Negative likelihood ratios (NLR) with a 95% confidence interval (CI) were calculated for 30-day MACE.

Results

Overall 1430 patients were enrolled. Of these 31.4% (449/1430) had known CAD while 14.2% (203 /1430) experienced 30-day MACE. Using the ESC 0/1-hour hs-cTnT algorithm 39.6% (178/449) of patients with known CAD were placed in the rule-out zone compared to 66.1% (648/981) without CAD (p<0.0001). Of patients with known CAD 23.2% (104/449) had 30-day MACE compared to 10.1% (99/981) of those without known CAD (p<0.0001). Additionally, amongst those patients placed in the rule-out zone, 30-day MACE occurred in 7.9% (14/178) of individuals with known CAD and 1.4% (9/648) of those without known CAD (p<0.0001). NLR for 30-day MACE was 0.28 (95% CI 0.17–0.47) in patients with known CAD and 0.13 (95% CI 0.07–0.23) in those without CAD.

Conclusions

In the multicenter US STOP-CP study patients with known CAD were less often rapidly ruled out for NSTEMI and had higher 30-day MACE rates than those without known CAD. Patients with known CAD who were rapidly ruled out for NSTEMI had a higher 30-day MACE rate compared to those without known CAD. Our analysis suggests that patients with known CAD require further cardiac reevaluations whether they are ruled out for NSTEMI by the ESC 0/1 hour hs-cTnT algorithm or not.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Roche, Basel, Switzerland

The association between melatonin and suicide: a nationwide cohort study

Introduction

Melatonin is often prescribed to patients experiencing sleep disturbances, which has been linked to elevated risks of suicide. However, it remains to be assessed whether melatonin is associated with suicide and suicide attempts.

Objectives

We aimed to investigate whether individuals in treatment with melatonin had higher rates of suicide and suicide attempt when compared to individuals not in treatment.

Methods

Using longitudinal data on all persons aged 10+ years living in Denmark between 2007-2016 were obtained. Data from the National Prescription Register was used to identify periods of being in treatment with melatonin based on number of tablets and daily defined dose. Suicide and suicide attempt were identified in hospital and cause of death registries.

Results

Among 5,798,923 included individuals, 10,577 (0.18%) were in treatment with melatonin (mean treatment length 50 days). Out of 5,952 individuals who died by suicide, 22 (0.37%) were in melatonin treatment, while 134 (0.53%) out of 25,136 had a first suicide attempt. After adjustment for sex and age-group, people in treatment with melatonin were found to have a higher rate of suicide (IRR: 4.2; 95% CI, 2.7-6.4) and suicide attempt (IRR: 6.7-fold (95% CI, 5.7-7.9) when compared to those not in treatment.

Conclusions

Treatment with melatonin was associated with higher rates of suicide and suicide attempt. The association might be explained through mediators, such as psychiatric comorbidity and sleep disorders. Our findings indicate that attention towards these issues might be warranted.

Disclosure

No significant relationships.

The association between benzodiazepine and non-benzodiazepine and suicide: a nationwide cohort study

Introduction

Benzodiazepines and non-benzodiazepines have been linked to a variety of adverse effects including addiction. Long term use of these drugs has been associated with an increased risk of suicide.

Objectives

We assessed if individuals in treatment with non-benzodiazepine (n-BZD) and benzodiazepine (BZD) had higher rates of suicide when compared to individuals not in treatment with these drugs.

Methods

We utilized a cohort design and national longitudinal data on all individuals aged 10 or above who lived in Denmark between 1995 and 2018. Treatment with either n-BZD or BZD was identified via the Danish National Prescription Registry and suicide deaths were identified in the national cause of death registries.

Results

In a total of 6,494,206 individuals, 10,862 males and 4,214 females died by suicide. Of these, 1,220 (11.2%) males and 792 (18.8%) females had been in treatment with n-BZD, resulting in adjusted IRR for suicide of 4.2 (95% CI, 4.0 – 4.5) and 3.4 (95% CI, 3.1 – 3.7) for males and females, respectively, when compared to those not in treatment. In all, 529 (4.8%) males and 395 (9.3%) females who died by suicide had been in treatment with BZD. The IRRs for suicide were 2.4 (95% CI, 2.2 – 2.6) and 2.5 (95% CI, 2.3 – 2.8) for males and females, respectively, and compared to those not in treatment.

Conclusions

In this study we find that those in treatment experienced higher suicide rates than those not in treatment, this persisted when also adjusting for a large variety of covariates.

Disclosure

No significant relationships.

Association of hospital-diagnosed sleep disorders with suicide: a nationwide cohort study

Introduction

Sleep disorders and psychiatric disease are closely related, and psychiatric diseases are associated with elevated suicide risks. Yet, the association between sleep disorders and suicide remains to be assessed using a consistent measure of sleep disorders.

Objectives

The aim of this study was to examine whether people with a hospital-diagnosis of sleep disorders had higher suicide rates than people with no diagnosis.

Methods

In a cohort study, nationwide data on all persons aged 15+ years living in Denmark during 1980-2016 were analysed. Sleep disorders were identified through diagnoses recorded during contacts to somatic hospitals. Incidence Rate Ratios (IRR) were estimated using Poisson regression models and adjusted for relevant covariates.

Results

In all, 3,674,563 males and 3,688,164 females were included, of whom 82,223 (2.2%, mean age: 50.2, SD: 17.5) males and 40,003 (1.1%, mean age: 50.6, SD: 19.9) females had sleep disorder diagnoses. Compared to those with no sleep disorders, the adjusted IRRs for suicide were 1.6 (95% CI, 1.4-1.7) and 2.2 (95% CI, 1.8-2.6) for males and females with sleep disorders, respectively. Excess rates for narcolepsy were found for males (IRR:1.2, 95% CI, 1.0-1.5) and females (IRR:3.3, 95% CI, 3.0-4.1), and for sleep apnea in males (IRR:1.8, 95% CI, 1.5-2.2). Males and females had IRRs of 4.1 (95% CI, 3.1-5.5) and 7.0 (95% CI, 4.8-10.1), respectively, 6 months after being diagnosed with a sleep disorder.

Conclusions

Sleep disorders were associated with higher suicide rates even after adjusting for pre-existing mental disorders. Our findings suggest attention towards suicidal ideation in patients suffering from sleep disorders is warranted.

Disclosure

Disclosures and Acknowledgements: Adam Spira has received honoraria for serving as a consultant to Merck and from Springer Nature Switzerland AG for guest editing special issues of Current Sleep Medicine Reports. The other authors report no conflict of in

Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii)

Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.

Evaluation of European Society of Cardiology (ESC) 0/1-hour algorithm in the diagnosis of 90-day major adverse cardiovascular events: a multicenter United States cohort study

Background

The ESC 0/1-hour algorithm using high sensitivity troponin (ESC 0/1-h) is a rapid triage protocol for diagnosing acute coronary syndrome, however the classification performance of the algorithm in the US population is uncertain. Further, evidence for the use of ESC 0/1-h in the long-term diagnosis of major adverse cardiovascular events (MACE) remains limited.

Purpose

To evaluate the performance of the ESC 0/1-h algorithm in diagnosing 90-day MACE in a diverse US cohort.

Methods

In this prospective, multicenter, observational cohort study, adult emergency department patients who were evaluated for suspected ACS were enrolled at eight sites in the US. Serial 1-hour blood samples were collected and high sensitivity troponin T (hs-cTnT) concentrations were measured in a central laboratory using the hs-cTnT assay. Primary outcome included major adverse cardiovascular events (MACE) within 90 (+30) days of enrollment. MACE defined as myocardial infarction (MI), cardiovascular or uncertain death, and coronary revascularization. Presence of MI and cardiovascular death were adjudicated by independent reviewers blinded to hs-cTnT results. Each participant was stratified to one of three risk groups as determined by ESC 0/1-h algorithm. Diagnostic classification performance metrics with exact confidence intervals (i.e. negative predictive value [NPV], positive predicted value [PPV], sensitivity, and specificity) were evaluated for each risk group where appropriate.

Results

Among 1430 eligible participants, 45.8% (655/1430) were women and 36.6% (524/1430) were African American with a mean age of 57.6±12.8 years. MACE at 90-days occurred in 15.5% (221/1430). ESC 0/1-h stratified 59.5% (851/1430) subjects in Rule-Out range and 13.0% (186/1430) subjects in Rule-In range. The Rule-Out criteria had an NPV and sensitivity for 90-day MACE of 96.8% (95% CI: 95.4–97.9%) and 87.8% (95% CI: 82.7–91.8%), respectively. For 90-day cardiovascular death or MI, Rule-Out criteria had an NPV of 98.2% (95% CI: 97.1–99.0%) and sensitivity was 92.4% (95% CI: 87.8–95.7%). The Rule-In criteria had a PPV of 60.8% (95% CI: 53.3–67.8%) for both outcomes. Rule-In criteria had a specificity for 90-day MACE and 90-day cardiovascular death or MI of 94.0% (95% CI: 92.5–95.2%) and 94.1% (95% CI: 92.6–95.3%), respectively. Among the 27.5% (393/1430) participants classified in neither risk groups, the prevalence of 90-day MACE was 20.6% (81/393) and the prevalence of 90-day cardiovascular death or MI was 17.8% (70/393)

Conclusion

In a prospective, multicenter, US cohort, the ESC 0/1-h algorithm was unable to achieve a sufficiently high NPV to safely exclude the diagnosis of MACE within 90 days after emergency department presentation. New hs-cTn algorithms specific to the US population may be warranted.

ESC 0/1-h 90 Day Outcomes

Funding Acknowledgement

Type of funding source: Private company. Main funding source(s): Roche Diagnostics

High suicide rates during psychiatric inpatient stay and shortly after discharge

OBJECTIVE

Over recent decades, intense efforts to address suicides in psychiatric admitted people have been initiated. The aim was to calculate suicide rates, rate ratios, population attributable risks (PAR) and trends among people admitted to or recently discharged from psychiatric wards.

METHODS

Using a cohort design, we obtained nationwide register data on 6 292 932 individuals aged 15+ living in Denmark during 1995-2016. Of these, 178 703 (5.73%) males and 201 033 females (6.33%) had been admitted to psychiatric hospital. Incidence rate ratios (IRR) were obtained using Poisson regression analyses while adjusting for age and calendar period. Trends were assessed using joinpoint analyses.

RESULTS

In total, 15 075 persons died by suicide, of which 6174 had been psychiatrically admitted. Among males, the suicide rate during the first week of admission and after discharge was 3409 and 3148 per 100 000 person-years, respectively. The corresponding values for females were 1267 and 1631. Generally, estimated suicide rates were highest in those with affective or anxiety stress disorders. During first week of hospitalization, the IRR was 237 for males and of 322 for females when compared with those never hospitalized. In first week after discharge, the IRR was 225 and 425 for males and females, respectively. PAR estimates indicated 6% of male suicides and 13% of female suicides attributes to first week of admission and discharge. The inpatient suicide rate decreased annually 2.5% until 2009 followed by a 7.5% annual percentage increase. The suicide rate after discharge decreased steadily annually over the study period.

CONCLUSION

Despite finding declining post-discharge suicide rates, the period surrounding a psychiatric admission was still associated with extremely high suicide rates.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.

EBADIMEX: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples

DNA methylation and gene expression are interdependent and both implicated in cancer development and progression, with many individual biomarkers discovered. A joint analysis of the two data types can potentially lead to biological insights that are not discoverable with separate analyses. To optimally leverage the joint data for identifying perturbed genes and classifying clinical cancer samples, it is important to accurately model the interactions between the two data types. Here, we present EBADIMEX for jointly identifying differential expression and methylation and classifying samples. The moderated t-test widely used with empirical Bayes priors in current differential expression methods is generalised to a multivariate setting by developing: (1) a moderated Welch t-test for equality of means with unequal variances; (2) a moderated F-test for equality of variances; and (3) a multivariate test for equality of means with equal variances. This leads to parametric models with prior distributions for the parameters, which allow fast evaluation and robust analysis of small data sets. EBADIMEX is demonstrated on simulated data as well as a large breast cancer (BRCA) cohort from TCGA. We show that the use of empirical Bayes priors and moderated tests works particularly well on small data sets.

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation

Motivation

Understanding the mutational processes that act during cancer development is a key topic of cancer biology. Nevertheless, much remains to be learned, as a complex interplay of processes with dependencies on a range of genomic features creates highly heterogeneous cancer genomes. Accurate driver detection relies on unbiased models of the mutation rate that also capture rate variation from uncharacterized sources.

Results

Here, we analyse patterns of observed-to-expected mutation counts across 505 whole cancer genomes, and find that genomic features missing from our mutation-rate model likely operate on a megabase length scale. We extend our site-specific model of the mutation rate to include the additional variance from these sources, which leads to robust significance evaluation of candidate cancer drivers. We thus present ncdDetect v.2, with greatly improved cancer driver detection specificity. Finally, we show that ranking candidates by their posterior mean value of their effect sizes offers an equivalent and more computationally efficient alternative to ranking by their P-values.

Availability and implementation

ncdDetect v.2 is implemented as an R-package and is freely available at http://github.com/TobiasMadsen/ncdDetect2

Supplementary information

Supplementary data are available at Bioinformatics online.

P2247Pregnancies and childbirth in women with arrhythmogenic right ventricular cardiomyopathy are associated with low risk of ventricular arrhythmias

Background

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is associated with a risk of ventricular arrhythmias (VA) and sudden cardiac death (SCD). Even though female patients with ARVC are considered to be at lower risk of VA, the impact of pregnancy and child birth on the arrhythmic risk and development of arrhythmic substrate in the context of ARVC remains insufficiently studied.

Objective

To assess the risk of VA in relation to childbirth in women with ARVC and the impact of multiple pregnancies on progression of arrhythmic manifestations of the disease.

Methods

The study included 186 females with definite ARVC (n=107, 70 probands) or unaffected mutation-carriers (n=79) with median age at the end of follow up of 48 (IQR 34–60) years. Seventeen women had 1, 59 had 2 and 29 had ≥3 child births by the age of 40 years. VA was defined as ventricular tachycardia, appropriate ICD therapy, aborted cardiac arrest or SCD. Proportions of patients who experienced VA by the age of 40 years were compared between nulliparous women (n=81) and those with reported child births (n=105). VA-free survival after accomplished pregnancies was assessed for women ≥40 years of age (n=119). Cumulative probability of VA for each pregnancy (n=230) was assessed from conception through 2 years after child birth and compared between those that occurred before ARVC diagnosis (Pre-Ds, n=164), after it (Post-Ds, n=11) and in unaffected mutation carriers (No-Ds, n=55).

Results

The nulliparous women had lower age at ARVC diagnosis (37 vs 44, p=0.023) and more often had VA before the age of 40 (31% vs 13%, p=0.003) while the number of child births was not related to the prevalence of VA (18% among women with 1 childbirth, 12% in those with 2 and 14% in those with 3 or more, ns). Three women suffered SCD before the age of 40. VA-free survival after 40 years did not differ between nulliparous and those who gave birth (Figure A). Only four pregnancy-related events were documented (Figure B): 1 in the Post-Ds group and three in the Pre-Ds group. No pregnancy-related events were reported in the unaffected mutation carriers.

Conclusion

In this Scandinavian cohort of women with ARVC we observed no indication of an increased VA risk either associated with pregnancies or during long-term follow up after the last child birth.

P992Incidence, predictors, and success of ventricular tachycardia catheter ablation in arrhythmogenic right ventricular cardiomyopathy (ARVC): A long-term cohort study from the Nordic ARVC registry

Background

Catheter ablation may reduce ventricular tachycardia (VT) burden in arrhythmogenic right ventricular cardiomyopathy (ARVC) patients. However, little is known about factors predicting need for ablation and various outcomes have been reported.

Purpose

We sought to investigate predictors and use of VT ablation and to evaluate the post-procedural outcome in ARVC patients.

Methods

We studied 435 patients from the Nordic ARVC registry including 220 probands with definite ARVC according to the 2010 task force criteria and 215 mutation-carrying relatives identified through cascade screening. Patients were followed until first-time VT ablation, death, heart transplantation, or January 1st 2018. Additionally, patients undergoing VT ablation were further followed from the time of ablation for recurrent ventricular arrhythmias.

Results

Cumulative use of VT ablation was 4% (95% CI 3%-6%) and 11% (95% CI 8%-15%) after 1 and 10 years. All procedures were performed in probands in whom the cumulative use was 8% (95% CI 5%-12%) and 20% (95% CI 15%-26%). In adjusted analyses restricted to probands, only young age predicted need for ablation. In patients undergoing ablation, risk of recurrent arrhythmias was 59% (95% CI 44%-71%) and 74% (95% CI 59%-84%) 1 and 5 years after the procedure. Despite high recurrence rates, the burden of ventricular arrhythmias was reduced after ablation (p=0.0042). Young age, use of several antiarrhythmic drugs and inducibility to VT immediately after ablation were associated with an unfavorable outcome.

Conclusions

Twenty percent of ARVC probands developed a clinical indication for VT ablation within 10 years after diagnosis whereas mutation-carrying relatives were without such need. Although the burden of ventricular arrhythmias decreased after ablation, risk of recurrence was substantial.

Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments

Background

Motif analysis methods have long been central for studying biological function of nucleotide sequences. Functional genomics experiments extend their potential. They typically generate sequence lists ranked by an experimentally acquired functional property such as gene expression or protein binding affinity. Current motif discovery tools suffer from limitations in searching large motif spaces, and thus more complex motifs may not be included. There is thus a need for motif analysis methods that are tailored for analyzing specific complex motifs motivated by biological questions and hypotheses rather than acting as a screen based motif finding tool.

Methods

We present Regmex (REGular expression Motif EXplorer), which offers several methods to identify overrepresented motifs in ranked lists of sequences. Regmex uses regular expressions to define motifs or families of motifs and embedded Markov models to calculate exact p-values for motif observations in sequences. Biases in motif distributions across ranked sequence lists are evaluated using random walks, Brownian bridges, or modified rank based statistics. A modular setup and fast analytic p value evaluations make Regmex applicable to diverse and potentially large-scale motif analysis problems.

Results

We demonstrate use cases of combined motifs on simulated data and on expression data from micro RNA transfection experiments. We confirm previously obtained results and demonstrate the usability of Regmex to test a specific hypothesis about the relative location of microRNA seed sites and U-rich motifs. We further compare the tool with an existing motif discovery tool and show increased sensitivity.

Conclusions

Regmex is a useful and flexible tool to analyze motif hypotheses that relates to large data sets in functional genomics. The method is available as an R package (https://github.com/muhligs/regmex).

Electronic supplementary material

The online version of this article (10.1186/s13015-018-0135-2) contains supplementary material, which is available to authorized users.

Comparing post-deployment mental health services utilization in soldiers deployed to Balkan, Iraq and Afghanistan

OBJECTIVE

Insight on how different missions have impacted rates of mental health service (MHS) utilization is unexplored. We compared postdeployment MHS utilization in a national cohort of first-time deployed to missions in Balkan, Iraq, and Afghanistan respectively.

METHODS

A prospective national cohort study of 13 246 first-time deployed in the period 1996 through 2012 to missions in Balkan area, Iraq, or Afghanistan respectively. Soldiers 'MHS utilization was also compared with a 5:1 sex-, age-, and calendar year-matched never-deployed background population. Postdeployment utilization of MHS was retrieved from national coverage registers. Using Cox survival analyses, participants were followed and compared with regard to receiving three different types of psychiatric services: (i) admission to psychiatric hospital, (ii) psychiatric outpatient contact, and (iii) prescriptions of psychotropics.

RESULTS

Utilizing of psychiatric outpatient services and psychotropics was significantly higher in first-time deployed to Iraq and Afghanistan compared with deployed to Balkan. However, the rate of postdeployment admission to psychiatric hospital did not differ between missions. Postdeployment rates of psychiatric admission and psychiatric outpatient treatment were significantly higher in Afghanistan-deployed personnel compared with the background population.

CONCLUSIONS

Utilization of MHS differed significantly between mission areas and was highest after the latest mission to Afghanistan.

Significance evaluation in factor graphs

BACKGROUND

Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of both genomics data as well as data from other scientific fields. Owing to the ever larger data sets encountered in genomics and the multiple-testing issues accompanying them, accurate significance evaluation is of great importance. We here address the problem of evaluating statistical significance of observations from factor graph models.

RESULTS

Two novel numerical approximations for evaluation of statistical significance are presented. First a method using importance sampling. Second a saddlepoint approximation based method. We develop algorithms to efficiently compute the approximations and compare them to naive sampling and the normal approximation. The individual merits of the methods are analysed both from a theoretical viewpoint and with simulations. A guideline for choosing between the normal approximation, saddle-point approximation and importance sampling is also provided. Finally, the applicability of the methods is demonstrated with examples from cancer genomics, motif-analysis and phylogenetics.

CONCLUSIONS

The applicability of saddlepoint approximation and importance sampling is demonstrated on known models in the factor graph framework. Using the two methods we can substantially improve computational cost without compromising accuracy. This contribution allows analyses of large datasets in the general factor graph framework.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

Non-coding mutations may drive cancer development. Statistical detection of non-coding driver regions is challenged by a varying mutation rate and uncertainty of functional impact. Here, we develop a statistically founded non-coding driver-detection method, ncdDetect, which includes sample-specific mutational signatures, long-range mutation rate variation, and position-specific impact measures. Using ncdDetect, we screened non-coding regulatory regions of protein-coding genes across a pan-cancer set of whole-genomes (n = 505), which top-ranked known drivers and identified new candidates. For individual candidates, presence of non-coding mutations associates with altered expression or decreased patient survival across an independent pan-cancer sample set (n = 5454). This includes an antigen-presenting gene (CD1A), where 5'UTR mutations correlate significantly with decreased survival in melanoma. Additionally, mutations in a base-excision-repair gene (SMUG1) correlate with a C-to-T mutational-signature. Overall, we find that a rich model of mutational heterogeneity facilitates non-coding driver identification and integrative analysis points to candidates of potential clinical relevance.

Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX

The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.

PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification

MOTIVATION

Cancer development and progression is driven by a complex pattern of genomic and epigenomic perturbations. Both types of perturbations can affect gene expression levels and disease outcome. Integrative analysis of cancer genomics data may therefore improve detection of perturbed genes and prediction of disease state. As different data types are usually dependent, analysis based on independence assumptions will make inefficient use of the data and potentially lead to false conclusions.

MODEL

Here, we present PINCAGE (Probabilistic INtegration of CAncer GEnomics data), a method that uses probabilistic integration of cancer genomics data for combined evaluation of RNA-seq gene expression and 450k array DNA methylation measurements of promoters as well as gene bodies. It models the dependence between expression and methylation using modular graphical models, which also allows future inclusion of additional data types.

RESULTS

We apply our approach to a Breast Invasive Carcinoma dataset from The Cancer Genome Atlas consortium, which includes 82 adjacent normal and 730 cancer samples. We identify new biomarker candidates of breast cancer development (PTF1A, RABIF, RAG1AP1, TIMM17A, LOC148145) and progression (SERPINE3, ZNF706). PINCAGE discriminates better between normal and tumour tissue and between progressing and non-progressing tumours in comparison with established methods that assume independence between tested data types, especially when using evidence from multiple genes. Our method can be applied to any type of cancer or, more generally, to any genomic disease for which sufficient amount of molecular data is available.

AVAILABILITY AND IMPLEMENTATION

R scripts available at http://moma.ki.au.dk/prj/pincage/

CONTACT

: michal.switnicki@clin.au.dk or jakob.skou@clin.au.dk

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Aquatic Risk Assessment of Enzymes used in Household Detergents

Exposure and effect assessment including risk characterisation of enzymes used in household detergents were conducted. Predicted environmental concentrations were calculated by use of traditional methods and detailed transport and fate modelling. Predicted no effect concentrations were derived from the results of ecotoxicological studies conducted with subtilisin and other available information on the acute and chronic aquatic toxicity. Risk characterisation ratios were defined as the ratio between the predicted environmental concentration and the predicted no effect concentration. Risk characterisation ratios were calculated for fresh and marine water and were found to be between 0.0002 and 0.06, i.e. all well below 1. This shows that under the given conditions, the use of enzymes in household detergents does not present a risk to the aquatic environment.

Aquatic Risk Assessment of Alcohol Ethoxylates, Alcohol Ethoxysulphates and Linear Alkylbenzene Sulphonate used in Household Detergents

Exposure and effect assessments including risk characterisation of the surfactants alcohol ethoxylates, alcohol ethoxysulphates and linear alkylbenzene sulphonates used in household detergents were conducted. Predicted environmental concentrations were calculated by use of traditional methods and detailed transport and fate modelling. Predicted no effect concentrations were derived from the available information on the acute and chronic aquatic toxicity. Risk characterisation ratios were defined as the ratio of the predicted environmental concentration to the predicted no effect concentration. Risk characterisation ratios were calculated for fresh water and marine water and were below 1. This indicates that based on the methods employed in this study the use of alcohol ethoxylates, alcohol ethoxysulphates and linear alkylbenzene sulphonate in household detergents does not appear to present a risk to the aquatic environment.

The effect of low-dose marine n-3 fatty acids on the biosynthesis of pro-inflammatory 5-lipoxygenase pathway metabolites in overweight subjects: a randomized controlled trial

INTRODUCTION

Marine n-3 polyunsaturated fatty acids (PUFA) have a variety of anti-inflammatory properties. This study evaluated the effect of n-3 PUFA in a low, but recommended cardioprotective dosage on the formation of 5-lipoxygenase pathway metabolites in overweight subjects.

MATERIALS AND METHODS

Fifty subjects were randomized to 1.1g of n-3 PUFA or olive oil for 6 weeks.

RESULTS

Leukotriene B(4) formation decreased by 14% in the n-3 PUFA group which proved to be significant within the group (p=0.005) but not between groups (p=0.25). The formation of 5-hydroxyeicosatetraenoic acid (5-HETE) did not differ significantly between the groups. In the n-3 PUFA group, both 5-hydroxyeicosapentaenoic (5-HEPE) acid and leukotriene B(5) increased significantly compared to the control group (p<0.001).

CONCLUSION

In conclusion, we did not observe any significant net anti-inflammatory effect on the 5-lipoxygenase pathway from a daily supplement of 1.1g marine n-3 PUFA for 6 weeks.

Effects of sulfuroxy anions on degradation of pentachlorophenol by a methanogenic enrichment culture

We studied the degradation of pentachlorophenol (PCP) under methanogenic and sulfate-reducing conditions with an anaerobic mixed culture derived from sewage sludge. The consortium degraded PCP via 2,3,4,5-tetrachlorophenol, 3,4,5-trichlorophenol, and 3,5-dichlorophenol and eventually accumulated 3-chlorophenol. Dechlorination of PCP and metabolites was inhibited in the presence of sulfate, thiosulfate, and sulfite. A decrease in the rate of PCP transformation was noted when the endogenous dissolved H(2) was depleted below 0.11 muM in sulfate-reducing cultures. The effect on dechlorination observed with sulfate could be relieved by addition of molybdate, a competitive inhibitor of sulfate reduction. Addition of H(2) reduced the inhibition observed with sulfuroxy anions. The inhibitory effect of sulfuroxy anions may be due to a competition for H(2) between sulfate reduction and dechlorination. When cultured under methanogenic conditions, the consortium degraded several chlorinated and brominated phenols.