Evidence for a role of Anopheles stephensi in the spread of drug- and diagnosis-resistant malaria in Africa

Anopheles stephensi, an Asian malaria vector, continues to expand across Africa. The vector is now firmly established in urban settings in the Horn of Africa. Its presence in areas where malaria resurged suggested a possible role in causing malaria outbreaks. Here, using a prospective case-control design, we investigated the role of An. stephensi in transmission following a malaria outbreak in Dire Dawa, Ethiopia in April-July 2022. Screening contacts of patients with malaria and febrile controls revealed spatial clustering of Plasmodium falciparum infections around patients with malaria in strong association with the presence of An. stephensi in the household vicinity. Plasmodium sporozoites were detected in these mosquitoes. This outbreak involved clonal propagation of parasites with molecular signatures of artemisinin and diagnostic resistance. To our knowledge, this study provides the strongest evidence so far for a role of An. stephensi in driving an urban malaria outbreak in Africa, highlighting the major public health threat posed by this fast-spreading mosquito.

Process mining to discover patterns in patient outcomes in a Psychological Therapies Service

In the mental health sector, Psychological Therapies face numerous challenges including ambiguities over the client and service factors that are linked to unfavourable outcomes. Better understanding of these factors can contribute to effective and efficient use of resources within the Service. In this study, process mining was applied to data from the Northern Health and Social Care Trust Psychological Therapies Service (NHSCT PTS). The aim was to explore how psychological distress severity pre-therapy and attendance factors relate to outcomes and how clinicians can use that information to improve the service. Data included therapy episodes (N = 2,933) from the NHSCT PTS for adults with a range of mental health difficulties. Data were analysed using Define-Measure-Analyse model with process mining. Results found that around 11% of clients had pre-therapy psychological distress scores below the clinical cut-off and thus these individuals were unlikely to significantly improve. Clients with fewer cancelled or missed appointments were more likely to significantly improve post-therapy. Pre-therapy psychological distress scores could be a useful factor to consider at assessment for estimating therapy duration, as those with higher scores typically require more sessions. This study concludes that process mining is useful in health services such as NHSCT PTS to provide information to inform caseload planning, service management and resource allocation, with the potential to improve client's health outcomes.

Distinct and shared genetic architectures of Gestational diabetes mellitus and Type 2 Diabetes Mellitus

Gestational diabetes mellitus (GDM) affects more than 16 million pregnancies annually worldwide and is related to an increased lifetime risk of Type 2 diabetes (T2D). The diseases are hypothesized to share a genetic predisposition, but there are few GWAS studies of GDM and none of them is sufficiently powered to assess whether any variants or biological pathways are specific to GDM. We conducted the largest genome-wide association study of GDM to date in 12,332 cases and 131,109 parous female controls in the FinnGen Study and identified 13 GDM-associated loci including 8 novel loci. Genetic features distinct from T2D were identified both at the locus and genomic scale. Our results suggest that the genetics of GDM risk falls into two distinct categories - one part conventional T2D polygenic risk and one part predominantly influencing mechanisms disrupted in pregnancy. Loci with GDM-predominant effects map to genes related to islet cells, central glucose homeostasis, steroidogenesis, and placental expression. These results pave the way for an improved biological understanding of GDM pathophysiology and its role in the development and course of T2D.

Inherited cancer predisposing mutations in patients with therapy-related myeloid neoplasms

Some patients with therapy-related myeloid neoplasms (t-MN) may have unsuspected inherited cancer predisposition syndrome (CPS). We propose a set of clinical criteria to identify t-MN patients with high risk of CPS (HR-CPS). Among 225 t-MN patients with an antecedent non-myeloid malignancy, our clinical criteria identified 52 (23%) HR-CPS patients. Germline whole-exome sequencing identified pathogenic or likely pathogenic variants in 10 of 27 HR-CPS patients compared to 0 of 9 low-risk CPS patients (37% vs. 0%, p = 0.04). These simple clinical criteria identify t-MN patients most likely to benefit from genetic testing for inherited CPS.

Measurement properties of the WHO Disability Assessment Schedule 2.0 for evaluating functional status after inpatient surgery

BACKGROUND

Expert recommendations propose the WHO Disability Assessment Schedule (WHODAS) 2.0 as a core outcome measure in surgical studies, yet data on its long-term measurement properties remain limited. These were evaluated in a secondary analysis of the Measurement of Exercise Tolerance before Surgery (METS) prospective cohort.

METHODS

Participants were adults (40 years of age or older) who underwent inpatient non-cardiac surgery. The 12-item WHODAS and EQ-5DTM-3L questionnaires were administered preoperatively (in person) and 1 year postoperatively (by telephone). Responsiveness was characterized using standardized response means (SRMs) and correlation coefficients between change scores. Construct validity was evaluated using correlation coefficients between 1-year scores and comparisons of WHODAS scores across clinically relevant subgroups.

RESULTS

The analysis included 546 patients. There was moderate correlation between changes in WHODAS and various EQ-5DTM subscales. The strongest correlation was between changes in WHODAS and changes in the functional domains of the EQ-5D-3L-for example, mobility (Spearman's rho 0.40, 95 per cent confidence interval [c.i.] 0.32 to 0.48) and usual activities (rho 0.45, 95 per cent c.i. 0.30 to 0.52). When compared across quartiles of EQ-5D index change, median WHODAS scores followed expected patterns of change. In subgroups with expected functional status changes, the WHODAS SRMs ranged from 'small' to 'large' in the expected directions of change. At 1 year, the WHODAS demonstrated convergence with the EQ-5D-3L functional domains, and good discrimination between patients with expected differences in functional status.

CONCLUSION

The WHODAS questionnaire has construct validity and responsiveness as a measure of functional status at 1 year after major surgery.

Mutational and splicing landscape in a cohort of 43,000 patients tested for hereditary cancer

DNA germline genetic testing can identify individuals with cancer susceptibility. However, DNA sequencing alone is limited in its detection and classification of mRNA splicing variants, particularly those located far from coding sequences. Here we address the limitations of splicing variant identification and interpretation by pairing DNA and RNA sequencing and describe the mutational and splicing landscape in a clinical cohort of 43,524 individuals undergoing genetic testing for hereditary cancer predisposition.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

First Leptophobic Dark Matter Search from the Coherent-CAPTAIN-Mills Liquid Argon Detector

We report the first results of a search for leptophobic dark matter (DM) from the Coherent-CAPTAIN-Mills (CCM) liquid argon (LAr) detector. An engineering run with 120 photomultiplier tubes (PMTs) and 17.9×10^{20} protons on target (POT) was performed in fall 2019 to study the characteristics of the CCM detector. The operation of this 10-ton detector was strictly light based with a threshold of 50 keV and used coherent elastic scattering off argon nuclei to detect DM. Despite only 1.5 months of accumulated luminosity, contaminated LAr, and nonoptimized shielding, CCM's first engineering run has already achieved sensitivity to previously unexplored parameter space of light dark matter models with a baryonic vector portal. With an expected background of 115 005 events, we observe 115 005+16.5 events which is compatible with background expectations. For a benchmark mediator-to-DM mass ratio of m_{V_{B}}/m_{χ}=2.1, DM masses within the range 9  MeV≲m_{χ}≲50  MeV are excluded at 90% C. L. in the leptophobic model after applying the Feldman-Cousins test statistic. CCM's upgraded run with 200 PMTs, filtered LAr, improved shielding, and 10 times more POT will be able to exclude the remaining thermal relic density parameter space of this model, as well as probe new parameter space of other leptophobic DM models.

The prevalence and clinical significance of a reduced ventricular ejection fraction in asymptomatic young elite endurance athletes

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Health and Medical Research Council of Australia

Background

Ventricular ejection fraction (EF) is the most widely used parameter to evaluate ventricular systolic function. Endurance athletes presenting with a reduced ventricular EF often raise the question of an underlying dilated or arrhythmogenic cardiomyopathy. The clinical significance of a reduced EF in athletes remains to be elucidated.

Purpose

To investigate the prevalence and clinical significance of a reduced EF in asymptomatic endurance athletes.

Methods

Two hundred eighteen asymptomatic young elite endurance athletes were evaluated at baseline. Cardiac magnetic resonance imaging (CMR) was performed to assess cardiac volumes, left ventricular and right ventricular EF (LVEF and RVEF), mass and fibrosis. Athletes with reduced EF (ATrEF) were defined as those having LVEF<50% and/or RVEF<45%. Ventricular systolic and diastolic function were assessed by trans-thoracic echocardiography. A 12-lead ECG and 24-hour holtermonitoring assessed electrical alterations and arrhythmias. In 145 athletes, LV and RV contractile reserve was evaluated by exercise CMR. Cardiopulmonary testing was performed in all athletes to measure maximal oxygen uptake (VO2max).

Results

Thirty-one ATrEF (14.2%) were compared to 187 athletes with a preserved EF (ATpEF). ATrEF were more frequently males (93 vs 77% male, p=0.033) but did not differ from ATpEF with regard to age (18.8±2.1 vs 18.3±2.1 years, p=0.25). Ten athletes had an isolated reduced LVEF, 10 had an isolated reduced RVEF and 11 had both a reduced LVEF and RVEF. ATrEF had similar end-diastolic volumes and cardiac mass but differed by higher end-systolic volumes.

Peak exercise LVEF and RVEF determined by exercise CMR remained lower in ATrEF (68±3 vs 73±4% and 62±6 vs 69±5%, p<0.001) but contractile reserve was greater (ΔLVEF 18±5 vs 14±4% and ΔRVEF 19±5 vs 15±5%, p<0.01).

A reduced EF was not associated with lower exercise capacity, in fact VO2max was higher in ATrEF than in ATpEF (65±6 vs 62±9mL/kg/min, p=0.020) and the percentage of predicted VO2max by the Wasserman equation were similar (151±14 vs 149±21%, p=0.533).

Fibrosis was present in 3 ATrEF and 18 ATpEF (9.7 vs 9.6%, p=0.993) and was isolated to the RV hinge-points in all but 3 ATpEF who had midmyocardial LV lateral wall fibrosis. LV systolic strain (-17.5±2.0 vs -19±2.1%, p<0.001) was lower in ATrEF whereas RV free wall systolic strain (-24.9±3.7 vs -25.1±3.5%, p=0.776) was similar. Diastolic function was normal in all ATrEF and ATpEF. Pathologic T-wave inversions were present in 2 ATrEF and 13 ATpEF (6.5 vs 7%, p=0.999). Ventricular premature beats (VPB) were infrequent but more prevalent in ATrEF than in ATpEF (2[0-18] vs 1[0-2]/24h, p=0.025; 16.1 vs 2.7% >100/24h, p=0.006).

Conclusion

A reduced ventricular EF is common in asymptomatic young elite endurance athletes, is more frequent in males but is not associated with structural, functional or electrical abnormalities apart from a minor excess in VPB.

Greater cardiorespiratory fitness reduces incidence of atrial fibrillation: a meta-analysis

Funding Acknowledgements

Type of funding sources: None.

Introduction

 Atrial Fibrillation (AF) is the most common sustained cardiac arrhythmia affecting 1-2% of the global population, with the prevalence of AF increasing dramatically over the past two decades. Although low levels of cardiorespiratory fitness (CRF) and physical activity are predictive of cardiovascular disease onset and mortality, only recently has this emerged as a potential risk factor for AF.

Purpose

The aim of this meta-analysis was therefore to quantify the relationship between CRF, measured by a symptom limited exercise stress test, and incident AF. We hypothesised that there would be an inverse relationship between CRF and the incidence of AF.

Methods

The systematic literature review was conducted using PUBMED, MEDLINE and EMBASE databases, with seven studies meeting the inclusion criteria. A random-effects meta-analysis was then used to compare the multivariate risk estimates of the lowest CRF group from each cohort with the group of the highest CRF.

Results

Data from 206,925 individuals (55.8% males) was used for analysis with a mean age of 55 ± 2.5 years and a mean follow-up period of 10.3 ± 5 years. The total number of AF events across the studies was 19,913. The overall pooled risk of AF in the high-CRF group versus the low-CRF group showed a significant lower risk of incident AF in those with high-CRF (OR: 0.52, 95% CI, 0.44-0.605, p < 0.001). There was evidence of statistical heterogeneity between the studies (I2 = 81%, p < 0.001). AF incidence rates demonstrated an overall decline in rates across the CRF quartiles from low to high. The mean incidence rate for low-CRF was 21 ± 13.4 compared to 6.9 ± 0.7 per 1000 person-years for the high CRF group (p = 0.03).

Conclusion

There is an inverse association between a lower CRF and an increased risk of AF, with a higher level of CRF protective against AF. This study highlights that low-CRF may be an additional risk factor for AF along with already other established lifestyle-based risk factors such as obesity and hypertension. Exercise interventions should be promoted as a primary prevention strategy in those at risk of developing AF with known risk factors. Future studies are warranted to identify the mechanism(s) through which improved CRF confers a reduction in AF incidence.

Abstract Figure. AF risk between high and low-CRF

Hinge point fibrosis in athletes is not associated with structural, functional or electrical consequences: a comparison between young and middle-aged elite endurance athletes

Background

The health benefits of extensive endurance training have been debated due to the report of myocardial fibrosis (MF), arrhythmias and temporary post-race cardiac impairment in middle-aged and veteran athletes. The extent of these changes is unknown in elite young athletes.

Purpose

To assess the prevalence of MF and its structural, functional and electrical impact in highly trained young endurance athletes (YA, 15–23 years) as compared to middle-aged athletes (MA, 30–50 years). We hypothesised that MF would be more frequent in MA and associated with more structural, functional and electrical abnormalities.

Methods

We prospectively assessed 197 YA and 34 MA. All had ECG, maximal oxygen consumption (VO2max) testing, cardiac magnetic resonance imaging (CMR), echocardiography and 24h-holter. Indexed left ventricular and right ventricular end diastolic volume (LVEDVi, RVEDVi), ejection fraction (LVEF, RVEF), left ventricular mass (LVMi), and MF defined as delayed gadolinium enhancement were assessed by CMR. LV and RV free wall strain (LVSL, RVfwSL) were assessed by 2D speckle tracking echocardiography. Ventricular premature beats (VPB) and non-sustained ventricular tachycardia (nsVT) were assessed by 24h-holter.

Results

YA and MA (18±2 vs 38±5 years [p<0.01]; 78% vs 80% male [p=0.99]) with an elite level of fitness (VO2max 61±8 vs 54±10 mL/min/kg [p<0.01]; % predicted VO2max 150±20 vs 158±30 [p=0.02]) had a large variance in LV and RV remodelling (Figure 1). MF was seen in 28 athletes (12.5%) and more prevalent in MA than in YA (23.5 vs 10.5%, p=0.048). MF was limited to the hinge points in all 8 MA with MF and 17 YA. 3 YA had LV lateral wall subepicardial MF. 27 of 187 (14.4%) male athletes had MF compared to 1 of 50 (2%) female athletes (p=0.01).

MF+ MA(A) and YA(B) as well as MF− MA(C) and YA(D) had similar structural remodelling (LVEDVi 110±14 vs 118±14 vs 113±19 vs 110±16 mL/m2; RVEDVi 120±14 vs 128±17 vs 117±19 vs 125±23mL/m2; LVMi 77±11 vs 83±14 vs 81±14 vs 77±15g/m2, p>0.05). LVEF, LVSL and RVSL were similar (59±3 vs 58±5 vs 61±6 vs 58±6%; −18.8±2 vs −18.8±2 vs −19.8±2 vs −19.3±2%; −26.3±2.4 vs −24.4±2.4; −26.3±3 vs −25.8±3.5% respectively, p>0.05). LVEF <50% was seen in 19 (8.2%) athletes (0 [0%] vs [5%] 1 vs 1 [3.8%] vs 17 [9.6%]; p=0.51). RVEF was higher in D compared to C without further differences between groups (54±4 vs 54±6 vs 53±6 vs 57±5, p=0.005). RVEF<45% was seen 21 (9.1%) athletes (0 [0%] vs 1 [5%] vs 0 [0%] vs 20 [11.3%]; p=0.14). Abnormal T-wave inversion was similar (12.5 vs 5 vs 7.4 vs 6.2%, p=0.93) as was the prevalence of >100VPB/24h (12.5 vs 5 vs 11.1 vs 5.1%, p=0.42). 2 athletes had nsVT, both in D. All had similar exercise capacity (% predicted VO2max 157±26 vs 152±15 vs 147±24 vs 158±32%; p=0.11).

Conclusion

Hinge-point fibrosis was more prevalent in MA, possibly due to repeated hemodynamic stress during exercise, but is not associated with structural, functional or electrical consequences.

Figure 1. Cardiac remodelling in elite athletes

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Fonds voor Wetenschappelijk Onderzoek (FWO)

70Autonomic dysfunction in atrial fibrillation (AF) patients: absent vasomotor reflex to decreased cardiac venous return during af in comparison to sinus rhythm; implications for earlier rhythm control

Funding Acknowledgements

Dr Malik is supported by an Australian Postgraduate Award Scholarship from the University of Adelaide.

OnBehalf

Centre for Heart Rhythm Disorders, University of Adelaide & Royal Adelaide Hospital

Background

A bi-directional relationship exists between AF and the autonomic nervous system (ANS). Patients with AF studied in sinus rhythm (SR) have impaired vasomotor responses to decreased cardiac volume. Whether autonomic dysfunction worsens during AF itself, is unknown. 

Purpose

We examined haemodynamic responses to lower body negative pressure (LBNP) in patients with persistent AF compared to AF studied in SR. LBNP decreases cardiac volume, deactivates atrial stretch receptors and induces a reflex to maintain blood pressure by increasing systemic vascular resistance (SVR). 

Methods

21 consecutive patients with paroxysmal or persistent AF were studied; during AF (n = 8) or SR (n = 13). Anti-arrhythmic and anti-hypertensives were withheld for 5 half-lives. Patients underwent LBNP using a custom-made chamber sealing both lower limbs. Negative pressure at sham (-0 mmHg), low (-20 mmHg) and high level (-40 mmHg) was applied for 5 minutes each. Finger photo plethysmography was used for beat-beat-blood pressure. Computation of SVR during AF is not feasible with this method. Therefore, the right forearm was used to perform venous occlusion plethysmography (VOP); non-invasive, well validated with LBNP and impervious to AF: to estimate forearm blood flow (FBF) and SVR (inversely proportional). 

Results

Baseline characteristics and responses to LBNP are presented in Table 1. MAP was maintained, and HR rose slightly, in the SR group. MAP and HR decreased in the AF group. VOP demonstrates a reduction in FBF in the SR group (vasoconstriction); whereas the vasomotor response to LBNP was absent during AF. Figure 1 (Panels A-C). 

Conclusion

The presence of AF is associated with autonomic dysfunction from impaired cardiac volume regulation. This novel finding may contribute to the known risk of falls and syncope due to AF. Further studies are needed to evaluate whether abnormal cardiac reflexes are involved in atrial remodelling and AF progression.

Table 1 Baseline Characteristics During AF During SR P Value Age 65 ± 5 59 ± 3 0.4 AAD & Anti-HTN medications withheld (%) 75 85 0.6 Resting mean arterial pressure (MAP) 109 ± 9 93 ± 6 0.1 Resting heart rate (HR) 94 ± 6 60 ± 4 0.0001* Haemodynamic response to LBNP % Δ MAP due to LBNP -9 ± 5 +0.5 ± 3 0.2 % Δ HR due to LBNP -6 ± 3 +5 ± 3 0.03* % Δ FBF due to LBNP +75 ± 59 -27 ± 8 0.02* AAD Anti-arrhthmic. HTN: Hypertension. Mean +/- SEM.

Abstract Figure. Vasomotor response to LBNP: in AF vs SR

Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013-2019

The aim of this study was to review microbiology results from testing >2500 raw drinking milk and dairy products made with unpasteurised milk examined in England between 2013 and 2019. Samples were collected as part of incidents of contamination, investigation of infections or as part of routine monitoring and were tested using standard methods for a range of both pathogens and hygiene indicators. Results from testing samples of raw cow's milk or cheese made from unpasteurised milk for routine monitoring purposes were overall of better microbiological quality than those collected during incident or investigations of infections. Results from routine monitoring were satisfactory for 62% of milks, 82% of cream, 100% of ice-cream, 51% of butter, 63% of kefir and 79% of cheeses, with 5% of all samples being considered potentially hazardous. Analysis of data from cheese demonstrated a significant association between increasing levels of indicator Escherichia coli with elevated levels of coagulase positive staphylococci and decreased probability of isolation of Shiga toxin-producing E. coli. These data highlight the public health risk associated with these products and provide further justification for controls applied to raw drinking milk and dairy products made with unpasteurised milk.

Cancer Risks Associated With Germline PALB2 Pathogenic Variants: An International Study of 524 Families

PURPOSE

To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized.

METHODS

We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes.

RESULTS

We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 × 10-76), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 × 10-3), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 × 10-3), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 × 10-2). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 × 10-3). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer.

CONCLUSION

These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers.

Splicing profile by capture RNA-seq identifies pathogenic germline variants in tumor suppressor genes

Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.

P3794MOODS: a novel risk score to identify patients with atrial fibrillation and sleep apnoea

Background

Sleep-disordered breathing (SDB) is an important risk factor for developing atrial fibrillation (AF), and treatment of concomitant SDB can improve AF rhythm outcomes. Diagnosis of SDB requires sleep studies which can pose a significant time and resource burden. We sought to develop a prediction score based on clinical characteristics that can help identify AF patients who require further assessment for SDB.

Methods

Prospectively-collected data for 442 consecutive patients treated for AF from 2009 to 2017 were analysed. All patients were considered candidates for rhythm-control and therefore referred for sleep studies. The diagnosis of SDB was confirmed using in-lab polysomnography and classified using the apnoea-hypopnoea-index (AHI), with cut-offs of ≥15/hr and ≥30/hr indicating moderate-to-severe and severe SDB respectively. Patients treated up to 2015 formed the derivation cohort (n=311) and the remainder (n=113) formed the validation cohort. Multivariate logistic regression analysis was used to identify clinical variables predictive of moderate-to-severe SDB. A risk score model was developed based on regression coefficients and tested using receiver-operating-characteristics analyses on the validation cohort.

Results

Overall, mean age was 60±11 years, mean body mass index (BMI) was 30±5 kg/m2 and 69% were men. The prevalence of moderate-to-severe SDB was 33.7%. There were no significant differences in baseline characteristics between the derivation and validation cohorts. Male gender (score=1), overweight (BMI: 25–29 kg/m2, score=2), obesity (BMI≥30 kg/m2, score=3), diabetes (score=1), and stroke (score=2) were significantly independently predictive of moderate-to-severe SDB and formulated the score. The score performed well to predict moderate-to-severe SDB with a C-statistic of 0.73 (95% CI: 0.67–0.79, P<0.001) in the derivation cohort, and 0.67 (95% CI: 0.57–0.77, P<0.001) in the validation cohort. As a rule-out test, a score of ≤3 had a negative predictive value of 77% for moderate-to-severe SDB (91% for severe SDB). A score of ≥4 had an intermediate positive likelihood ratio (PLR) of 2 for moderate-to-severe SDB (2.2 for severe SDB), while a score of ≥5 had a high PLR of 6.5 and 6.8 for moderate-to-severe SDB and severe SDB respectively.

Sensitivity and specificity table

Conclusion

A novel risk score comprising clinical characteristics can identify patients with AF likely to benefit from further assessment for SDB. Application of this model may aid optimise resource utilisation and facilitate timely patient care.

Assessment of Diagnostic Outcomes of RNA Genetic Testing for Hereditary Cancer

IMPORTANCE

Performing DNA genetic testing (DGT) for hereditary cancer genes is now a well-accepted clinical practice; however, the interpretation of DNA variation remains a challenge for laboratories and clinicians. Adding RNA genetic testing (RGT) enhances DGT by clarifying the clinical actionability of hereditary cancer gene variants, thus improving clinicians' ability to accurately apply strategies for cancer risk reduction and treatment.

OBJECTIVE

To evaluate whether RGT is associated with improvement in the diagnostic outcome of DGT and in the delivery of personalized cancer risk management for patients with hereditary cancer predisposition.

DESIGN, SETTING, AND PARTICIPANTS

Diagnostic study in which patients and/or families with inconclusive variants detected by DGT in genes associated with hereditary breast and ovarian cancer, Lynch syndrome, and hereditary diffuse gastric cancer sent blood samples for RGT from March 2016 to April 2018. Clinicians who ordered genetic testing and received a reclassification report for these variants were surveyed to assess whether RGT-related variant reclassifications changed clinical management of these patients. To quantify the potential number of tested individuals who could benefit from RGT, a cohort of 307 812 patients who underwent DGT for hereditary cancer were separately queried to identify variants predicted to affect splicing. Data analysis was conducted from March 2016 and September 2018.

MAIN OUTCOMES AND MEASURES

Variant reclassification outcomes following RGT, clinical management changes associated with RGT-related variant reclassifications, and the proportion of patients who would likely be affected by a concurrent DGT and RGT multigene panel testing approach.

RESULTS

In total, 93 if 909 eligible families (10.2%) submitted samples for RGT. Evidence from RGT clarified the interpretation of 49 of 56 inconclusive cases (88%) studied; 26 (47%) were reclassified as clinically actionable and 23 (41%) were clarified as benign. Variant reclassifications based on RGT results changed clinical management recommendations for 8 of 18 patients (44%) and 14 of 18 families (78%), based on responses from 18 of 45 clinicians (40%) surveyed. A total of 7265 of 307 812 patients who underwent DGT had likely pathogenic variants or variants of uncertain significance potentially affecting splicing, indicating that approximately 1 in 43 individuals could benefit from RGT.

CONCLUSIONS AND RELEVANCE

In this diagnostic study, conducting RNA testing resolved a substantial proportion of variants of uncertain significance in a cohort of individuals previously tested for cancer predisposition by DGT. Performing RGT might change the diagnostic outcome of at least 1 in 43 patients if performed in all individuals undergoing genetic evaluation for hereditary cancer.

P5657Fibrosis detected by late-gadolinium enhancement cardiac MRI is associated with atrial fibrillation and poorer ablation outcome: A meta-analysis

Background

Fibrosis is a hallmark of atrial fibrillation (AF) substrate. Recent data suggests that fibrosis detected by late-gadolinium enhancement (LGE) cardiac MRI (CMR) can predict AF. However, this relationship is not well described.

Objective

To delineate the association of cardiac fibrosis detected by LGE CMR with AF prevalence, AF recurrence after catheter ablation.

Methods

PubMed, Embase, Web of Science and Ovid MEDLINE were searched through November 2018, using the keywords: LGE AND Fibrosis AND CMR AND AF. Inclusion criteria: 1. LGE CMR of left atrial (LA LGE), ventricular wall (LV LGE) or right ventricular wall (RV LGE); 2. Studies reporting AF or recurrent arrhythmia after ablation; 3. Patient ≥18 years; and 4. ≥50 participants. Included studies were pooled in a random effects meta-analysis and reported as: mean difference (MD); unadjusted risk ratios (RR); adjusted hazard ratios (HR); and 95% confidence intervals (95% CI).

Results

After exclusions, we identified 9 studies (2,307 patients [65.9% males, 34.1% females]) conducted between 2003 and 2015 for LGE and AF. Fibrosis was present in 666 (35.1%) and detected by LV LGE in 7 (78%) and RV LGE in 2 (22%). The presence of AF was higher in patients positive for ventricular LGE than those negative, trending towards significance (RR: 1.51, 95% CI: 0.94–2.45, p=0.09). Pooled LV fibrosis associated with AF progression (RR [NPAF vs. PAF]: 2.2, 95% CI: 1.22–3.94, p=0.009). We identified 8 studies (2,041 patients [65.8% males, 34.2% females]) conducted between 2006 and 2016 reporting LGE and AF recurrence after catheter ablation, with fibrosis detected in 644 (31.6%) by LA LGE in 8 (88.9%, biased towards one centre). After 17.8±14.2 follow-up years, atrial fibrosis was significantly greater in recurrent AF than controls (MD: 4.97%, 95% CI: 1.23–8.7, p<0.01), and predicted 16% increased risk of AF recurrence (RR: 1.16, 95% CI: 1.07–1.26, p<0.05).

Conclusion

Myocardial fibrosis detected by LGE associates with prevalence and progress of AF and is predictive of AF recurrence post ablation. This further supports the proarrhythmic role of fibrosis and selection of patients for ablation therapy based on LGE.

P661Nocturnal hypoxemic burden in ambulatory patients with atrial fibrillation: a disease-orientated assessment of sleep-disordered breathing severity

Background

Studies investigating the relationship between sleep-disordered breathing (SDB) and atrial fibrillation (AF) have largely assessed SDB-severity by the apnea–hypopnea index (AHI). However, the AHI does not incorporate nocturnal hypoxemic burden, which may increase the risk of non-paroxysmal AF (nPAF) as the clinical manifestation of more progressed AF substrates. This investigation sought to systematically characterize and compare the composition of AHI and hypoxemic burden with the aim to defining a disease-orientated metric for SDB-severity best associated with prevalent nPAF.

Methods

Polysomnography including overnight oximetry data were obtained in 435 consecutive ambulatory AF patients to determine the composition of AHI (apneas vs. hypopneas), the number of acute episodic desaturations per hour (oxygen desaturation index, ODI) and the composition of total time spent below 90% oxygen saturation (T90Total) attributed to acute desaturations (T90Desaturation). Logistic regression analysis was used to characterize the association with prevalent nPAF.

Results

One hundred sixty-nine AF patients (38%) had nPAF and one third (n=149, 34%) had moderate-to-severe SDB (AHI>15). 82% of the median total AHI (9.4 [3.6–20.1]) could be attributed to hypopneas. Only 29% of events were associated with episodic desaturations, which contributed to 96% (T90Desaturation) of the variation in T90Total. The high variability in durations and nadirs of distinct desaturation events can expose patients to long T90Total, even if the AHI is low. Not AHI, but T90Total and ODI were associated with nPAF independent of gender and age. However, diabetes, hypertension and body mass index contributed more significantly to the overall risk of nPAF.

Conclusions

In AF patients, hypopneas constitute a majority of respiratory events during sleep. Patients with low AHI can still be exposed to high nocturnal hypoxemic burden, which is mainly a cumulative consequence of episodic desaturations. T90Total and ODI, but not AHI, were associated with nPAF independent of gender and age, but concomitant modifiable risk factors made a more significant contribution to the overall risk of nPAF versus PAF.

Cold Preflush of Porcine Kidney Grafts Prior to Normothermic Machine Perfusion Aggravates Ischemia Reperfusion Injury

Normothermic machine perfusion (NMP) of kidney grafts is a promising new preservation method to improve graft quality and clinical outcome. Routinely, kidneys are washed out of blood remnants and cooled using organ preservation solutions prior to NMP. Here we assessed the effect of cold preflush compared to direct NMP. After 30 min of warm ischemia, porcine kidneys were either preflushed with cold histidine-tryptophan-ketoglutarate solution (PFNMP group) prior to NMP or directly subjected to NMP (DNMP group) using a blood/buffer solution. NMP was performed at a perfusion pressure of 75 mmHg for 6 h. Functional parameters were assessed as well as histopathological and biochemical analyses. Renal function as expressed by creatinine clearance, fractional excretion of sodium and total output of urine was inferior in PFNMP. Urine protein and neutrophil gelatinase-associated lipocalin (NGAL) concentrations as markers for kidney damage were significantly higher in the PFNMP group. Additionally, increased osmotic nephropathy was found after PFNMP. This study demonstrated that cold preflush prior to NMP aggravates ischemia reperfusion injury in comparison to direct NMP of warm ischemia-damaged kidney grafts. With increasing use of NMP systems for kidneys and other organs, further research into graft flushing during retrieval is warranted.

Association of Breast and Ovarian Cancers With Predisposition Genes Identified by Large-Scale Sequencing

Importance

Since the discovery of BRCA1 and BRCA2, multiple high- and moderate-penetrance genes have been reported as risk factors for hereditary breast cancer, ovarian cancer, or both; however, it is unclear whether these findings represent the complete genetic landscape of these cancers. Systematic investigation of the genetic contributions to breast and ovarian cancers is needed to confirm these findings and explore potentially new associations.

Objective

To confirm reported and identify additional predisposition genes for breast or ovarian cancer.

Design, Setting, and Participants

In this sample of 11 416 patients with clinical features of breast cancer, ovarian cancer, or both who were referred for genetic testing from 1200 hospitals and clinics across the United States and of 3988 controls who were referred for genetic testing for noncancer conditions between 2014 and 2015, whole-exome sequencing was conducted and gene-phenotype associations were examined. Case-control analyses using the Genome Aggregation Database as a set of reference controls were also conducted.

Main Outcomes and Measures

Breast cancer risk associated with pathogenic variants among 625 cancer predisposition genes; association of identified predisposition breast or ovarian cancer genes with the breast cancer subtypes invasive ductal, invasive lobular, hormone receptor-positive, hormone receptor-negative, and male, and with early-onset disease.

Results

Of 9639 patients with breast cancer, 3960 (41.1%) were early-onset cases (≤45 years at diagnosis) and 123 (1.3%) were male, with men having an older age at diagnosis than women (mean [SD] age, 61.8 [12.8] vs 48.6 [11.4] years). Of 2051 women with ovarian cancer, 445 (21.7%) received a diagnosis at 45 years or younger. Enrichment of pathogenic variants were identified in 4 non-BRCA genes associated with breast cancer risk: ATM (odds ratio [OR], 2.97; 95% CI, 1.67-5.68), CHEK2 (OR, 2.19; 95% CI, 1.40-3.56), PALB2 (OR, 5.53; 95% CI, 2.24-17.65), and MSH6 (OR, 2.59; 95% CI, 1.35-5.44). Increased risk for ovarian cancer was associated with 4 genes: MSH6 (OR, 4.16; 95% CI, 1.95-9.47), RAD51C (OR, not estimable; false-discovery rate-corrected P = .004), TP53 (OR, 18.50; 95% CI, 2.56-808.10), and ATM (OR, 2.85; 95% CI, 1.30-6.32). Neither the MRN complex genes nor CDKN2A was associated with increased breast or ovarian cancer risk. The findings also do not support previously reported breast cancer associations with the ovarian cancer susceptibility genes BRIP1, RAD51C, and RAD51D, or mismatch repair genes MSH2 and PMS2.

Conclusions and Relevance

The results of this large-scale exome sequencing of patients and controls shed light on both well-established and controversial non-BRCA predisposition gene associations with breast or ovarian cancer reported to date and may implicate additional breast or ovarian cancer susceptibility gene candidates involved in DNA repair and genomic maintenance.

Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing

PURPOSE

Structural variation (SV) is associated with inherited diseases. Next-generation sequencing (NGS) is an efficient method for SV detection because of its high-throughput, low cost, and base-pair resolution. However, due to lack of standard NGS protocols and a limited number of clinical samples with pathogenic SVs, comprehensive standards for SV detection, interpretation, and reporting are to be established.

METHODS

We performed SV assessment on 60,000 clinical samples tested with hereditary cancer NGS panels spanning 48 genes. To evaluate NGS results, NGS and orthogonal methods were used separately in a blinded fashion for SV detection in all samples.

RESULTS

A total of 1,037 SVs in coding sequence (CDS) or untranslated regions (UTRs) and 30,847 SVs in introns were detected and validated. Across all variant types, NGS shows 100% sensitivity and 99.9% specificity. Overall, 64% of CDS/UTR SVs were classified as pathogenic/likely pathogenic, and five deletions/duplications were reclassified as pathogenic using breakpoint information from NGS.

CONCLUSION

The SVs presented here can be used as a valuable resource for clinical research and diagnostics. The data illustrate NGS as a powerful tool for SV detection. Application of NGS and confirmation technologies in genetic testing ensures delivering accurate and reliable results for diagnosis and patient care.

DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes

PURPOSE

Gross duplications are ambiguous in terms of clinical interpretation due to the limitations of the detection methods that cannot infer their context, namely, whether they occur in tandem or are duplicated and inserted elsewhere in the genome. We investigated the proportion of gross duplications occurring in tandem in breast cancer predisposition genes with the intent of informing their classifications.

METHODS

The DNA breakpoint assay (DBA) is a custom, paired-end, next-generation sequencing (NGS) method designed to capture and detect deep-intronic DNA breakpoints in gross duplications in BRCA1, BRCA2, ATM, CDH1, PALB2, and CHEK2.

RESULTS

DBA allowed us to ascertain breakpoints for 44 unique gross duplications from 147 probands. We determined that the duplications occurred in tandem in 114 (78%) carriers from this cohort, while the remainder have unknown tandem status. Among the tandem gross duplications that were eligible for reclassification, 95% of them were upgraded to pathogenic.

CONCLUSION

DBA is a novel, high-throughput, NGS-based method that informs the tandem status, and thereby the classification of, gross duplications. This method revealed that most gross duplications in the investigated genes occurred in tandem and resulted in a pathogenic classification, which helps to secure the necessary treatment options for their carriers.

Quantitative Analysis of BRCA1 and BRCA2 Germline Splicing Variants Using a Novel RNA-Massively Parallel Sequencing Assay

Clinical genetic testing for hereditary breast and ovarian cancer (HBOC) is becoming widespread. However, the interpretation of variants of unknown significance (VUS) in HBOC genes, such as the clinically actionable genes BRCA1 and BRCA2, remain a challenge. Among the variants that are frequently classified as VUS are those with unclear effects on splicing. In order to address this issue we developed a high-throughput RNA-massively parallel sequencing assay—CloneSeq—capable to perform quantitative and qualitative analysis of transcripts in cell lines and HBOC patients. This assay is based on cloning of RT-PCR products followed by massive parallel sequencing of the cloned transcripts. To validate this assay we compared it to the RNA splicing assays recommended by members of the ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium. This comparison was performed using well-characterized lymphoblastoid cell lines (LCLs) generated from carriers of the BRCA1 or BRCA2 germline variants that have been previously described to be associated with splicing defects. CloneSeq was able to replicate the ENIGMA results, in addition to providing quantitative characterization of BRCA1 and BRCA2 germline splicing alterations in a high-throughput fashion. Furthermore, CloneSeq was used to analyze blood samples obtained from carriers of BRCA1 or BRCA2 germline sequence variants, including the novel uncharacterized alteration BRCA1 c.5152+5G>T, which was identified in a HBOC family. CloneSeq provided a high-resolution picture of all the transcripts induced by BRCA1 c.5152+5G>T, indicating it results in significant levels of exon skipping. This analysis proved to be important for the classification of BRCA1 c.5152+5G>T as a clinically actionable likely pathogenic variant. Reclassifications such as these are fundamental in order to offer preventive measures, targeted treatment, and pre-symptomatic screening to the correct individuals.