Ancestry, ethnicity, and race: explaining inequalities in cardiometabolic disease

Population differences in cardiometabolic disease remain unexplained. Misleading assumptions over genetic explanations are partly due to terminology used to distinguish populations, specifically ancestry, race, and ethnicity. These terms differentially implicate environmental and biological causal pathways, which should inform their use. Genetic variation alone accounts for a limited fraction of population differences in cardiometabolic disease. Research effort should focus on societally driven, lifelong environmental determinants of population differences in disease. Rather than pursuing population stratifiers to personalize medicine, we advocate removing socioeconomic barriers to receipt of and adherence to healthcare interventions, which will have markedly greater impact on improving cardiometabolic outcomes. This requires multidisciplinary collaboration and public and policymaker engagement to address inequalities driven by society rather than biology per se.

Identifying and ranking novel independent features for cardiovascular disease prediction in people with type 2 diabetes

Background

CVD prediction models do not perform well in people with diabetes. We therefore aimed to identify novel predictors for six facets of CVD, (including coronary heart disease (CHD), Ischemic stroke, heart failure (HF), and atrial fibrillation (AF)) in people with T2DM.

Methods

Analyses were conducted using the UK biobank and were stratified on history of CVD and of T2DM: 459,142 participants without diabetes or a history of CVD, 14,610 with diabetes but without CVD, and 4,432 with diabetes and a history of CVD. Replication was performed using a 20% hold-out set, ranking features on their permuted c-statistic.

Results

Out of the 600+ candidate features, we identified a subset of replicated features, ranging between 32 for CHD in people with diabetes to 184 for CVD+HF+AF in people without diabetes. Classical CVD risk factors (e.g. parental or maternal history of heart disease, or blood pressure) were relatively highly ranked for people without diabetes. The top predictors in the people with diabetes without a CVD history included: cystatin C, self-reported health satisfaction, biochemical measures of ill health (e.g. plasma albumin). For people with diabetes and a history of CVD top features were: self-reported ill health, and blood cell counts measurements (e.g. red cell distribution width). We additionally identified risk factors unique to people with diabetes, consisting of information on dietary patterns, mental health and biochemistry measures. Consideration of these novel features improved risk classification, for example per 1000 people with diabetes 133 CVD and 165 HF cases appropriately received a higher risk.

Conclusion

Through data-driven feature selection we identified a substantial number of features relevant for prediction of cardiovascular risk in people with diabetes, the majority of which related to non-classical risk factors such as mental health, general illness markers, and kidney disease.

Heterozygous APOE ε4 carriage associates with improved myocardial efficiency in older age

Background

Carriage of the ancestral APOE ε4 allele confers a risk of developing Alzheimer's and coronary artery disease, but its persistence in human populations also suggests some potential survival advantages. To date it remains unclear whether APOE ε4 carriage independently associates with a better or worse long-term cardiac phenotype.

Purpose

Using data from the 1946 National Survey of Health and Development (NSHD) birth cohort, we investigated whether APOE ε4 carriage associates with adverse or beneficial left ventricular (LV) size and function parameters by echocardiography in older age.

Methods

Based on the presence or absence of APOE ε4, genotypes were divided into: non-APOE ε4 (ε2ε2, ε2ε3, ε3ε3), heterozygous-APOE ε4 (ε2ε4 and ε3ε4) and homozygous-APOE ε4 (ε4ε4). Echocardiographic data at 60–64 years included: left ventricular ejection fraction (LV EF), E/e', systolic and diastolic LV posterior wall and interventricular septal thickness (LVPWTs/d, IVSs/d), and body-surface area indexed LV mass (LVmassi) and myocardial contraction fraction (MCFi). Generalized linear models explored associations between APOE ε4 genotypes as exposures and echocardiographic biomarkers as outcomes. As a combination of gene variants, APOE ε genotype is expected to be an instrumental variable and therefore unconfounded. Thus, Model 1 was unadjusted. To obtain more precise regression estimates, Model 2 was adjusted for factors associated with the outcome, namely sex and socio-economic position (SEP). To explore the mechanistic pathway downstream of APOE ε genotype but upstream of the echocardiographic outcomes, subsequent models were adjusted for mediators as follows: Model 3 for body mass index, Model 4 for the presence of cardiovascular disease (CVD), Model 5 for diabetes, Model 6 for high cholesterol and Model 7 for hypertension.

Results

1464 participants were included. Compared to non-APOE ε4 and homozygous groups, heterozygous-APOE ε4 individuals had similar cardiac phenotypes in terms of EF, E/e', LVPWTs/d, IVSs/d and LVmassi but had a 7% higher MCFi 95% confidence interval [CI]: 1%-13%, p=0.017) which persisted even after adjustment for sex and SEP (95% CI 1%-12%, p=0.026) that was attenuated to 6% after adjustment for CVD (95% CI 0–13% p=0.050) and hypertension (95% CI 1–13% p=0.022).

Conclusion

The heterozygous-APOE ε4 state associates with improved myocardial shortening in older age resulting in greater LV stroke volume generation per 1 mL of myocardium. As we found no association between APOE ε4 carriage and LVPWTs/d, IVSs/d or LVmassi, MCFi enhancement may be mediated by improved myocardial energetics and contractility, with calcium and androgens potentially implicated, rather than through pathological ventricular thickening. Although a dose relationship is normally expected with ε4 carriage, any benefit from increased energetics and contractility is likely to be counterbalances by the higher risk of CVD and cardiovascular risk factors.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): UK Medical Research Council British Heart Foundation

Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.

Myocardial strain by 3D-speckle tracking echocardiography predicts long-term risk of cardiovascular morbidity and mortality in the general population: the Southall And Brent Revisited (SABRE) study

Background

Both left ventricular (LV) ejection fraction (EF) and Global Longitudinal Strain (GLS) by 2D-echocardiography predict mortality and cardiac events, and GLS may be superior to EF. 3D-speckle tracking echocardiography (3D-STE), a recently validated method, allows simultaneous assessment of EF, GLS and principal tangential strain (PTS), but its prognostic utility in the general population is unknown.

Purpose

We hypothesized that 3D-STE derived LV myocardial strains predict a composite of cardiac endpoints, and that GLS would be a better prognostic marker than EF. We also investigated the utility of PTS compared with GLS and EF.

Methods

A total of 529 individuals (69±6y; 76.6% male) from SABRE study, a UK-based tri-ethnic community cohort, underwent health examinations. The association between 3D-STE EF or multidirectional myocardial strains and a composite cardiac endpoints comprising coronary heart disease (fatal/non-fatal), heart failure hospitalization, new-onset arrhythmia was determined using Cox proportional hazards models with and without adjustment for potential confounders and Harrell's C statistics were calculated. Associations with cardiovascular (CV) mortality was examined as a secondary objective. The incremental value of 3D-STE EF, GLS and PTS in improving CV risk stratification by the established Framingham risk score (FRS) was investigated using a likelihood ratio test on a series of nested Cox proportional hazards models.

Results

During follow-up (median, 8y), there were 56 composite cardiac endpoints and 24 CV deaths. EF and radial strain were negatively associated, while GLS, global circumferential strain and PTS were positively associated with the composite cardiac endpoints in unadjusted models (Table 1). Associations were only marginally affected by adjustment for potential confounders although confidence intervals of the estimate increased slightly (Table 1). There was little difference in the C-statistics for EF, GLS or PTS for the composite cardiac endpoints (Table 1). Associations with CV mortality were generally weaker and only GLS showed some evidence of a positive association with CV mortality in unadjusted and adjusted models (Table 1). Compared to EF and GLS, PTS most improved the predictive value (model fit) of FRS for composite cardiac endpoints (Table 2). None of the measures convincingly improved calibration for CV mortality.

Conclusions

3D-STE-derived LV myocardial strains predicted adverse cardiac events and CV mortality in a multi-ethnic sample of the UK general population. PTS/3D-strain was an independent predictor of cardiac events with some evidence of it being a slightly better predictor than conventional indices of LV function (GLS and EF). Future prospective studies are needed to confirm and extend these findings.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): The main SABRE study is supported by the Wellcome Trust and BHF.

Arterial stiffness increase from adolescence to young adulthood is accelerated by smoking and alcohol use

Background

Smoking tobacco and drinking alcohol are associated with increased arterial stiffness, a critical intermediate endpoint for cardiovascular disease, in adults and in teenagers. The relationship between these risky behaviours and changes in arterial stiffness from late adolescence to early adulthood is not known.

Purpose

To investigate associations between smoking and drinking habits and the change in arterial stiffness between ages 17 and 24 using a large population-based cohort.

Methods

Participants underwent repeated measurements of arterial stiffness (carotid-femoral pulse wave velocity (cfPWV)), anthropometrics, resting blood pressure and blood biomarkers, at ages 17 and 24 years. Participants were grouped and scored by alcohol (never, medium intensity (MI): ≤4 drinks on a typical day of drinking, high intensity (HI): >5) and smoking (never, past, MI, <10 cigarettes a day HI, ≥10) exposure at both clinics. Average scores between clinics were taken (scores 0–5) and composite alcohol (never, MI, HI) and smoking (never, past, MI, HI) groups were created. Multivariable regression analysis was performed to investigate associations between smoking/drinking habits and change in cfPWV from 17 to 24 years (ΔPWV). Associations were adjusted for age, gender, and socioeconomic status (model 1). Model 2 was additionally adjusted for body mass index, systolic blood pressure, LDL cholesterol, glucose, and C-reactive protein at age 24. Data are presented as means (95% confidence intervals).

Results

1,655 participants (1,013 females and 642 males) had cfPWV recorded at both ages. cfPWV increased from 17 to 24 years in both women (ΔPWV 0.56m/s (0.50, 0.62), p<0.001) and men (0.65m/s (0.56, 0.74), p<0.001). There was a 0.05m/s (0.00, 0.10) increase in ΔPWV per 1 unit increase in average alcohol score (p=0.039). Compared to never drinkers, ΔPWV increased by 0.18m/s (−0.03, 0.38) in MI (p=0.09), and 0.21m/s (−0.01, 0.41) in HI drinkers (p=0.055). There was no association between ΔPWV and average smoking score (β=0.03m/s (−0.03, 0.08), p=0.4). Compared to never smokers, HI smokers had a slightly greater ΔPWV (0.17m/s (−0.08, 0.42), p=0.18). After stratifying by sex, this difference was evident in women (0.32m/s (0.04, 0.60), p=0.028) while no association was seen in men (−0.12m/s (−0.59, 0.35), p=0.6). No differences were found between never-smokers and ex-smokers (difference = 0.04m/s (−0.08, 0.16), p=0.5). Adjustment for potential confounders (model 2) did not attenuate these associations. Figure shows estimated marginal means for ΔPWV between (a) alcohol and (b) smoking groups from model 1. Error bars represent 95% confidence intervals.

Conclusion

Smoking and alcohol use in young adulthood is associated with an accelerated increase in arterial stiffness, with evidence of a graded adverse association for alcohol. Our findings also suggest that adverse effects of smoking in youth may be reversible with smoking cessation.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation

Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method

Background

Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. However, mapping sequenced data to a reference genome remains a computationally-intensive task due to the dependence on edit distance for dealing with INDELs and mismatches introduced by sequencing. All modern aligners use seed–filter–extend methodology and rely on filtration heuristics to reduce the overhead of edit distance computation. However, filtering has inherent performance–accuracy trade-offs that limits its effectiveness.

Results

Motivated by algorithmic advances in randomized low-distortion embedding, we introduce SEE, a new methodology for developing sequence mappers and aligners. While SFE focuses on eliminating sub-optimal candidates, SEE focuses instead on identifying optimal candidates. To do so, SEE transforms the read and reference strings from edit distance regime to the Hamming regime by embedding them using a randomized algorithm, and uses Hamming distance over the embedded set to identify optimal candidates. To show that SEE performs well in practice, we present Accel-Align an SEE-based short-read sequence mapper and aligner that is 3–12\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document}× faster than state-of-the-art aligners on commodity CPUs, without any special-purpose hardware, while providing comparable accuracy.

Conclusions

As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be achieved by using edit distance. Thus, the techniques presented in this paper have a much broader scope as they can be used for other applications like graph alignment, multiple sequence alignment, and sequence assembly.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-021-04162-z.

Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study

Background

The role of primary immunodeficiencies (PID) in susceptibility to sepsis remains unknown. It is unclear whether children with sepsis benefit from genetic investigations. We hypothesized that sepsis may represent the first manifestation of underlying PID. We applied whole-exome sequencing (WES) to a national cohort of children with sepsis to identify rare, predicted pathogenic variants in PID genes.

Methods

We conducted a multicenter, population-based, prospective study including previously healthy children aged ≥28 days and <17 years admitted with blood culture-proven sepsis. Using a stringent variant filtering procedure, analysis of WES data was restricted to rare, predicted pathogenic variants in 240 PID genes for which increased susceptibility to bacterial infection has been reported.

Results

There were 176 children presenting with 185 sepsis episodes who underwent WES (median age, 52 months; interquartile range, 15.4–126.4). There were 41 unique predicted pathogenic PID variants (1 homozygous, 5 hemizygous, and 35 heterozygous) found in 35/176 (20%) patients, including 3/176 (2%) patients carrying variants that were previously reported to lead to PID. The variants occurred in PID genes across all 8 PID categories, as defined by the International Union of Immunological Societies. We did not observe a significant correlation between clinical or laboratory characteristics of patients and the presence or absence of PID variants.

Conclusions

Applying WES to a population-based cohort of previously healthy children with bacterial sepsis detected variants of uncertain significance in PID genes in 1 out of 5 children. Future studies need to investigate the functional relevance of these variants to determine whether variants in PID genes contribute to pediatric sepsis susceptibility.

Cardiovascular disease recurrence and long-term mortality in a tri-ethnic British cohort: a retrospective study

Background

People of South Asian and of African Caribbean descent have elevated risks of some cardiovascular diseases compared to Europeans. How ethnicity relates to recurrent risk, and explanations for between ethnic group differences in recurrence are unclear. We characterized long-term risk of major adverse cardiovascular event (MACE) and mortality following a non-fatal cardiovascular event in a tri-ethnic British cohort.

Methods

We linked hospital and mortality records of a population-based cohort of South Asian, African Caribbean and European men and women aged 40–69 years with no prior history of cardiovascular disease. We identified index and recurrent cardiovascular events (stroke, transient ischaemic attack, myocardial infarction, or ischaemic heart disease), and mortality from 1988 to 2017. Using multivariable proportional hazards models, we separately calculated the adjusted hazard ratios (HR) of MACE and death following index event. We adjusted for demographics, vascular and lifestyle risk factors. We used interaction terms to evaluate if diabetes or decade of index event modified the association between ethnicity and outcomes.

Results

We included 801 participants with first non-fatal cardiovascular events, 647 coronary and 127 cerebrovascular, of whom 335 (41.8%) were European, 396 (49.5%) South Asian, and 70 (8.7%) African Caribbean. During a mean follow-up of 5.3 years, 537 patients developed MACE and 338 died. Crude incidence rate of MACE was higher in South Asians (135.9 per 1000-person-years) compared to Europeans (117.1) and African Caribbeans (123.6). Higher risk of MACE in South Asian compared to Europeans was eliminated in the adjusted models (HR 0.97, 95% confidence interval 0.77–1.21), whereas their mortality advantage was eliminated when the younger age at index event was accounted for (HR 0.95, 0.72–1.26). African Caribbeans had similar outcomes to Europeans (HR MACE 1.04, 0.74–1.47; and HR death 1.07, 0.70–1.64). There was no modification by diabetes for outcomes, whereas survival following index event improved more in South Asian, than African Caribbean, compared to European over three decades (Pinteraction = 0.04).

Conclusions

Baseline vascular risk factors explained the observed ethnic variation in cardiovascular disease recurrence and long-term mortality, with a relative improvement in survival of minority ethnic groups over time.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): UK Medical Research Council, Wellcome Trust

Ethnic differences in the severity and clinical management of type 2 diabetes at time of diagnosis: A cohort study in the UK Clinical Practice Research Datalink

AIMS

To characterize ethnic differences in the severity and clinical management of type 2 diabetes at initial diagnosis.

METHODS

An observational cohort study of 179,886 people with incident type 2 diabetes between 2004 and 2017 in the Clinical Practice Research Datalink was undertaken; 63.4% of the cohort were of white ethnicity, 3.9% south Asian, and 1.6% black. Ethnic differences in clinical profile at diagnosis, consultation rates, and risk factor recording were derived from linear and logistic regression. Cox-proportional hazards regression was used to determine ethnic differences in time to initiation of therapeutic and non-therapeutic management following diagnosis. All analyses adjusted for age, sex, deprivation, and clustering by practice.

RESULTS

In the 12 months prior to diagnosis, non-white groups had fewer consultations compared to white groups, but risk factor recording was better than or equivalent to white groups for 9/10 risk factors for south Asian groups and 8/10 risk factors for black groups (p < 0.002). Blood pressure, BMI, cholesterol, eGFR, and CVD risk levels were more favourable in non-white groups, and prevalence of macrovascular disease was significantly lower (p < 0.003). Time to initiation of antidiabetic treatment and first risk assessment was faster in non-white groups relative to white groups, while time to risk factor measurement and diabetes review was slower.

CONCLUSIONS

We find limited evidence of systematic ethnic inequalities around the time of type 2 diabetes diagnosis. Ethnic disparities in downstream consequences may relate to genetic risk factors, or manifest later in the care pathway, potentially in relation to long-term risk factor control.

Gnomonious projections for bend-free textures: thoughts on the splay-twist phase

The Hopf fibration has inspired any number of geometric structures in physical systems, in particular, in chiral liquid crystalline materials. Because the Hopf fibration lives on the three sphere,S 3 , some method of projection or distortion must be employed to realize textures in flat space. Here, we explore the geodesic-preserving gnomonic projection of the Hopf fibration, and show that this could be the basis for a new liquid crystalline texture with only splay and twist. We outline the structure and show that it is defined by the tangent vectors along the straight line rulings on a series of hyperboloids. The phase is defined by a lack of bend deformations in the texture, and is reminiscent of the splay-bend and twist-bend nematic phases. We show that domains of this phase may be stabilized through anchoring and saddle-splay.

4950Adiposity gain from 17 to 25 years has a substantial effect on cardiac structure, independent of haemodynamics

Introduction

Body mass index (BMI) is independently associated with increased left ventricle mass (LVM) and remodeling in children. However associations from adolescence to emerging adulthood are unknown.

Purpose

To investigate associations between the change (Δ) in BMI to Δ in cardiac structure from 17 to 25 yrs using a large population-based sample of echocardiography in youth, and to explore the role of possible haemodynamic mediators.

Methods

901 participants (61% female) underwent echocardiography, anthropometry and sitting blood pressure (BP) measurements aged 17 yrs and had repeated measures aged 25 yrs. BMI, LVM, concentricity0.67 (LVM/end-diastolic volume0.67), total arterial compliance (TACI), peripheral resistance (TPR) and effective arterial elastance (Ea) were calculated. Regression analysis was used to investigate associations between ΔBMI and ΔLVM indexed to height2.7 (ΔLVMI) and Δconcentricity0.67.

Results

From 17 to 25 yrs BMI increased by 2.05±2.1 g/m2 in males and 1.80±3.1 kg/m2 in females, LVMI increased by 3.10±6.2g/m2.7 and 2.01±6.0g/m2.7 and concentricity0.67 increased by 0.91±1.2g/ml0.67 and 0.03±1.1g/ml0.67. ΔBMI was associated with ΔLVMI and Δconcentricity0.67 independently of age, socioeconomic status (SES) and smoking status. Haemodynamic measures did not substantially mediate these associations.

Table 1 ΔLVMI (g/m2.7) ΔConcentricity0.67 (g/m0.67) Males Females Males Females Model 1: Age, SES and smoking @25 0.78±0.15** 0.53±0.08** 0.12±0.03** 0.083±0.02** + ΔSystolic BP (mmHg) 0.68±0.16** 0.46±0.09** 0.10±0.03* 0.069±0.016** + ΔDiastolic BP (mmHg) 0.83±0.16** 0.47±0.08** 0.12±0.03** 0.074±0.015** + ΔMean Arterial Pressure (mmHg) 0.77±0.17** 0.46±0.08** 0.11±0.03** 0.069±0.015** + ΔPulse Pressure (mmHg) 0.72±0.15** 0.54±0.08** 0.11±0.03** 0.083±0.015** + ΔTACI (ml/m2/mmHg) 0.68±0.16** 0.53±0.08 0.12±0.03** 0.091±0.015** + ΔTPR (mmHg/min/L) 0.76±0.17** 0.65±0.08** 0.10±0.03* 0.072±0.016** + ΔEa (mmHg/ml) 0.73±0.17** 0.54±0.08** 0.11±0.03** 0.083±0.015** Data are β±SE. *p<0.01, **p<0.0001.

Discussion

BMI gain from adolescence to emerging adulthood has a substantial effect on cardiac structure, independent of haemodynamics. These findings highlight the importance of weight control in early adulthood for good cardiovascular health.

Acknowledgement/Funding

BHF

P2444Comparison of 3D and 2D echocardiography-derived indices of left ventricular function and structure to predict long-term mortality in the general population: Southall And Brent Revisited (SABRE) study

Background

Three-dimensional echocardiography (3DE) may have advantages over two-dimensional echocardiography (2DE) for the assessment of left ventricular (LV) function and structure. However, studies comparing 3DE and 2DE-derived indices in relation to mortality are limited, particularly in the general population.

Purpose

We examined associations between 2DE and 3DE-derived LV ejection fractions (LVEF) and volumes for all-cause mortality in a population-based sample.

Methods

A total of 899 individuals (age, 69.6±6.1 years; 77.5%male) from the SABRE study, a UK-based tri-ethnic community cohort, underwent a comprehensive transthoracic echocardiography examination. 2D LVEF and volumes were calculated, and full-volume 3D LV datasets acquired over 4 sub-volumes were obtained using a matrix-array transducer and were analysed offline using Qlab advanced, v7.0. The associations between both 2D- and 3D-derived LVEF (≥55% vs. <55%), body surface area indexed end-diastolic volume (iEDV) and end-systolic volume (iESV), and all-cause mortality were determined using Cox proportional hazards models. Survival curves were constructed using the Kaplan-Meier method.

Results

Of the 899 individuals, 118 (13.1%) died over a median follow-up period of 8 years to 2018. Kaplan Meier survival estimates (Figure 1 illustrates LVEF) and Cox regression revealed that 2D and 3D LVEF, iEDV and iESV were associated with increased risk of all-cause mortality (LVEF (≥55% vs. <55%), 3DE: HR=0.53 (0.35, 0.80); 2DE: HR=0.51 (0.34, 0.75), iEDV (per 1SD increment), 3DE: HR=1.20 (1.0, 1.41); 2DE: HR=1.19 (1.0–1.41), iESV (per 1SD increment), 3DE: HR=1.27 (1.1, 1.52), 2DE: HR=1.32 (1.15, 0.1.51)). However, 3DE associations tended to be stronger in models adjusted for classical risk factors including age, sex, ethnicity, systolic blood pressure, cholesterol:HDL ratio, body mass index, antihypertensive medications, diabetes, and smoking (LVEF (≥55% vs. <55%), 3DE: HR=0.59 (0.39, 0.90); 2DE: HR=0.69 (0.46, 1.0), iEDV (per 1SD increment), 3DE: HR=1.20 (1.0, 1.41); 2DE: HR=1.10 (0.93, 1.31), iESV (per 1SD increment), 3DE: HR=1.27 (1.1, 1.52), 2DE: HR=1.20 (1.04, 0.1.39)).

Figure 1. Kaplan-Meier curves.

Conclusions

In this population-based study, both 2DE and 3DE-derived indices of LV structure and function were associated with all-cause mortality independently of classical risk factors, with some indication that strengths of association were greater for 3DE-derived indices.

Acknowledgement/Funding

SABRE is funded by BHF, Diabetes UK, the MRC and the Wellcome Trust. LA holds a scholarship grant from Imam Abdulrahman Bin Faisal University, SA

6070Association of blood pressure measures with brain structure and function: the Southall and Brent REvisited (SABRE) study

Background

In our rapidly ageing society, dementia and neurocognitive decline are significant global public health problems. Blood pressure (BP), an established cardiovascular risk factor, has been extensively studied with respect to brain structure and function; however, findings across the literature differ depending on the BP component in consideration, and the use of brachial rather than central BP.

Purpose

We set out to assess associations between detailed measures of brain structure and function with comprehensive measures of central and peripheral BP. Furthermore, we performed comprehensive mediation analyses on the associations to investigate potential micro and macro vascular mediatory pathways.

Methods

A community-based sample of 1438 individuals (69.7±6.2 years) from a tri-ethnic cohort. underwent vascular, cognitive and MRI based structural brain measures. BP measures included central (cSBP (Pulsecor)) and peripheral systolic BP (pSBP), diastolic BP (DBP), brachial (bPP) and central pulse pressure (cPP), and mean arterial pressure (MAP). Cognitive assessments comprised tests which explored global/overall function (CSID), executive function and memory. For brain structure, hippocampal brain volume was our key measure. Potential macro- and microvascular mediators included: arterial stiffness (cfPWV), carotid intima-media thickness, retinopathy, white matter hyperintensities and infarcts. Multivariable regression analyses were used to assess associations of BP components with cognitive function scores and brain volumes, adjusted for age, sex and ethnicity as well as macro- and microvascular risk factors. Multiple imputation was performed to account for missing data.

Results

After adjusting for age, sex and ethnicity, both cSBP and pSBP were negatively associated with memory (data are β±SE (z-score) −0.014±0.006, p=0.04), while DBP was positively associated with hippocampal volume (0.006±0.003, p=0.03). cPP was negatively associated with memory (−0.020±0.009, p=0.03), executive function (−0.018±0.006, p=0.002) and hippocampal volume (−0.007±0.003, p=0.005), while bPP was negatively associated with CSID (−0.008±0.004, p=0.04), memory (−0.020±0.008, p=0.02), executive function (−0.016±0.005, p=0.002) and hippocampal volume (−0.006±0.002, p=0.007). There was a stronger association between both PP measures and brain structure and function than with the other BP components, especially MAP. There was little difference in association between cPP and bPP measures with brain structure and function. Furthermore, these associations do not appear to be mediated by either macro- or microvascular disease.

Conclusion

These results suggest that there is a direct association between increased PP and a decline in brain structure and function. This implies that older patients with suboptimal PP control may be at increased risk of developing cognitive impairment and that measuring PP offers mechanistic information above and beyond conventional BP measures.

Acknowledgement/Funding

Wellcome Trust, British Heart Foundation

Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and response to interferon-based treatment. Here, we evaluate associations between IFN-λ polymorphism and HCV variation in 8729 patients (Europeans 77%, Asians 13%, Africans 8%) infected with various viral genotypes, predominantly 1a (41%), 1b (22%) and 3a (21%). We searched for associations between rs12979860 genotype and variants in the NS3, NS4A, NS5A and NS5B HCV proteins. We report multiple associations in all tested proteins, including in the interferon-sensitivity determining region of NS5A. We also assessed the combined impact of human and HCV variation on pretreatment viral load and report amino acids associated with both IFN-λ polymorphism and HCV load across multiple viral genotypes. By demonstrating that IFN-λ variation leaves a large footprint on the viral proteome, we provide evidence of pervasive viral adaptation to innate immune pressure during chronic HCV infection.

Birth weight and cardiac function assessed by echocardiography in adolescence: Avon Longitudinal Study of Parents and Children

OBJECTIVE

Maternal hemodynamics in pregnancy is associated with fetal growth and birth weight, which in turn are associated with offspring cardiovascular disease later in life. The aim of this study was to quantify the extent to which birth weight is associated with cardiac structure and function in adolescence.

METHODS

A subset of offspring (n = 1964; 55% female) of the Avon Longitudinal Study of Parents and Children were examined with echocardiography at a mean age of 17.7 (SD, 0.3) years. The associations of birth-weight Z-score for sex and gestational age with cardiac structure (assessed by relative wall thickness, left ventricular mass index (LVMI) and left atrial diameter index), systolic function (assessed by ejection fraction and left ventricular wall velocity) and diastolic function (assessed by early/late mitral inflow velocity (E/A) and early mitral inflow velocity/mitral annular early diastolic velocity (E/e')) were evaluated. Linear regression models were adjusted for several potential confounders, including maternal prepregnancy body mass index, age, level of education and smoking during pregnancy.

RESULTS

Higher birth-weight Z-score was associated with lower E/A (mean difference, -0.024; 95% CI, -0.043 to -0.005) and E/e' (mean difference, -0.05; 95% CI, -0.10 to -0.001) and higher LVMI (mean difference, 0.38 g/m2.7 ; 95% CI, 0.09 to 0.67). There was no or inconsistent evidence of associations of birth-weight Z-score with relative wall thickness, left atrial diameter and measurements of systolic function. Further analyses suggested that the association between birth-weight Z-score and LVMI was driven mainly by an association observed in participants born small-for-gestational age and it did not persist when risk factors in adolescence were accounted for.

CONCLUSIONS

Higher birth weight adjusted for sex and gestational age was associated with differences in measures of diastolic function in adolescence, but the observed associations were small. It remains to be determined the extent to which these associations translate into increased susceptibility to cardiovascular disease later in life. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Mechanisms to splay-bend nematic phases

While twist-bend nematic phases have been extensively studied, the experimental observation of two dimensional, oscillating splay-bend phases is recent. We consider two theoretical models that have been used to explain the formation of twist-bend phases-flexoelectricity and bond orientational order-as mechanisms to induce splay-bend phases. Flexoelectricity is a viable mechanism, and splay and bend flexoelectric couplings can lead to splay-bend phases with different modulations. We show that while bond orientational order circumvents the need for higher order terms in the free energy, the important role of nematic symmetry and phase chirality rules it out as a basic mechanism.

Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipients

Acute liver failure (ALF) or fulminant hepatitis is a rare, yet severe outcome of infection with hepatitis B virus (HBV) that carries a high mortality rate. The occurrence of a life-threatening condition upon infection with a prevalent virus in individuals without known risk factors is suggestive of pathogen-specific immune dysregulation. In the absence of established differences in HBV virulence, we hypothesized that ALF upon primary infection with HBV could be due to rare deleterious variants in the human genome. To search for such variants, we performed exome sequencing in 21 previously healthy adults who required liver transplantation upon fulminant HBV infection and 172 controls that were positive for anti-HBc and anti-HBs but had no clinical history of jaundice or liver disease. After a series of hypothesis-driven filtering steps, we searched for putatively pathogenic variants that were significantly associated with case-control status. We did not find any causal variant or gene, a result that does not support the hypothesis of a shared monogenic basis for human susceptibility to HBV-related ALF in adults. This study represents a first attempt at deciphering the human genetic contribution to the most severe clinical presentation of acute HBV infection in previously healthy individuals.

A test for detecting differential indirect trans effects between two groups of samples

Integrative analysis of copy number and gene expression data can help in understanding the cis and trans effect of copy number aberrations on transcription levels of genes involved in a pathway. To analyse how these copy number mediated gene-gene interactions differ between groups of samples we propose a new method, named dNET. Our method uses ridge regression to model the network topology involving one gene's expression level, its gene dosage and the expression levels of other genes in the network. The interaction parameters are estimated by fitting the model per gene for all samples together. However, instead of testing for differential network topology per gene, dNET tests for an overall difference in estimated parameters between two groups of samples and produces a single p-value. With the help of several simulation studies, we show that dNET can detect differential network nodes with high accuracy and low rate of false positives even in the presence of differential cis effects. We also apply dNET to publicly available TCGA cancer datasets and identify pathways where copy number mediated gene-gene interactions differ between samples with cancer stage lower than stage 3 and samples with cancer stage 3 or above.

Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes

Studies of host genetic determinants of pathogen sequence variations can identify sites of genomic conflicts, by highlighting variants that are implicated in immune response on the host side and adaptive escape on the pathogen side. However, systematic genetic differences in host and pathogen populations can lead to inflated type I (false positive) and type II (false negative) error rates in genome-wide association analyses. Here, we demonstrate through a simulation that correcting for both host and pathogen stratification reduces spurious signals and increases power to detect real associations in a variety of tested scenarios. We confirm the validity of the simulations by showing comparable results in an analysis of paired human and HIV genomes.

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

BACKGROUND

Humoral immune responses to infectious agents or vaccination vary substantially among individuals, and many of the factors responsible for this variability remain to be defined. Current evidence suggests that human genetic variation influences (i) serum immunoglobulin levels, (ii) seroconversion rates, and (iii) intensity of antigen-specific immune responses. Here, we evaluated the impact of intrinsic (age and sex), environmental, and genetic factors on the variability of humoral response to common pathogens and vaccines.

METHODS

We characterized the serological response to 15 antigens from common human pathogens or vaccines, in an age- and sex-stratified cohort of 1000 healthy individuals (Milieu Intérieur cohort). Using clinical-grade serological assays, we measured total IgA, IgE, IgG, and IgM levels, as well as qualitative (serostatus) and quantitative IgG responses to cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1 and 2, varicella zoster virus, Helicobacter pylori, Toxoplasma gondii, influenza A virus, measles, mumps, rubella, and hepatitis B virus. Following genome-wide genotyping of single nucleotide polymorphisms and imputation, we examined associations between ~ 5 million genetic variants and antibody responses using single marker and gene burden tests.

RESULTS

We identified age and sex as important determinants of humoral immunity, with older individuals and women having higher rates of seropositivity for most antigens. Genome-wide association studies revealed significant associations between variants in the human leukocyte antigen (HLA) class II region on chromosome 6 and anti-EBV and anti-rubella IgG levels. We used HLA imputation to fine map these associations to amino acid variants in the peptide-binding groove of HLA-DRβ1 and HLA-DPβ1, respectively. We also observed significant associations for total IgA levels with two loci on chromosome 2 and with specific KIR-HLA combinations.

CONCLUSIONS

Using extensive serological testing and genome-wide association analyses in a well-characterized cohort of healthy individuals, we demonstrated that age, sex, and specific human genetic variants contribute to inter-individual variability in humoral immunity. By highlighting genes and pathways implicated in the normal antibody response to frequently encountered antigens, these findings provide a basis to better understand disease pathogenesis.

TRIALS REGISTRATION

ClinicalTrials.gov , NCT01699893.

Performance Analysis of GaN Capping Layer Thickness on GaN/AlGaN/GaN High Electron Mobility Transistors

In this paper, we present an investigation of the impact of GaN capping layer and AlGaN layer thickness on the two-dimensional (2D)-electron mobility and the carrier concentration which was formed close to the AlGaN/GaN buffer layer for Al0.25Ga0.75N/GaN and GaN/Al0.25Ga0.75N/GaN heterostructures deposited on sapphire substrates. The results of our analysis clearly indicate that expanding the GaN capping layer thickness from 1 nm to 100 nm prompts an increment in the electron concentration at hetero interface. As consequence of which drain current was additionally increments with GaN cap layer thicknesses, and eventually saturates at approximately 1.85 A/mm for capping layer thickness greater than 40 nm. Interestingly, for the same structure, the 2D-electron mobility, decrease monotonically with GaN capping layer thickness, and saturate at approximately 830 cm2/Vs for capping layer thickness greater than 50 nm. A device with a GaN cap layer didn't exhibit gate leakage current. Furthermore, it was observed that the carrier concentration was first decrease 1.03 × 1019/cm3 to 6.65 × 1018/cm3 with AlGaN Layer thickness from 5 to 10 nm and after that it increases with the AlGaN layer thickness from 10 to 30 nm. The same trend was followed for electric field distributions. Electron mobility decreases monotonically with AlGaN layer thickness. Highest electron mobility 1354 cm2/Vs were recorded for the AlGaN layer thickness of 5 nm. Results obtained are in good agreement with published experimental data.

Bullseye's representation of cerebral white matter hyperintensities

BACKGROUND AND PURPOSE

Visual rating scales have limited capacities to depict the regional distribution of cerebral white matter hyperintensities (WMH). We present a regional-zonal volumetric analysis alongside a visualization tool to compare and deconstruct visual rating scales.

MATERIALS AND METHODS

3D T1-weighted, T2-weighted spin-echo and FLAIR images were acquired on a 3T system, from 82 elderly participants in a population-based study. Images were automatically segmented for WMH. Lobar boundaries and distance to ventricular surface were used to define white matter regions. Regional-zonal WMH loads were displayed using bullseye plots. Four raters assessed all images applying three scales. Correlations between visual scales and regional WMH as well as inter and intra-rater variability were assessed. A multinomial ordinal regression model was used to predict scores based on regional volumes and global WMH burdens.

RESULTS

On average, the bullseye plot depicted a right-left symmetry in the distribution and concentration of damage in the periventricular zone, especially in frontal regions. WMH loads correlated well with the average visual rating scores (e.g. Kendall's tau [Volume, Scheltens]=0.59 CI=[0.53 0.62]). Local correlations allowed comparison of loading patterns between scales and between raters. Regional measurements had more predictive power than global WMH burden (e.g. frontal caps prediction with local features: ICC=0.67 CI=[0.53 0.77], global volume=0.50 CI=[0.32 0.65], intra-rater=0.44 CI=[0.23 0.60]).

CONCLUSION

Regional-zonal representation of WMH burden highlights similarities and differences between visual rating scales and raters. The bullseye infographic tool provides a simple visual representation of regional lesion load that can be used for rater calibration and training.

The risk of cardiac failure following metal-on-metal hip arthroplasty

AIMS

The aim of this study was to determine whether patients with metal-on-metal (MoM) arthroplasties of the hip have an increased risk of cardiac failure compared with those with alternative types of arthroplasties (non-MoM).

PATIENTS AND METHODS

A linkage study between the National Joint Registry, Hospital Episodes Statistics and records of the Office for National Statistics on deaths was undertaken. Patients who underwent elective total hip arthroplasty between January 2003 and December 2014 with no past history of cardiac failure were included and stratified as having either a MoM (n = 53 529) or a non-MoM (n = 482 247) arthroplasty. The primary outcome measure was the time to an admission to hospital for cardiac failure or death. Analysis was carried out using data from all patients and from those matched by propensity score.

RESULTS

The risk of cardiac failure was lower in the MoM cohort compared with the non-MoM cohort (adjusted hazard ratio (aHR) 0.901; 95% confidence interval (CI) 0.853 to 0.953). The risk of cardiac failure was similar following matching (aHR 0.909; 95% CI 0.838 to 0.987) and the findings were consistent in subgroup analysis.

CONCLUSION

The risk of cardiac failure following total hip arthroplasty was not increased in those in whom MoM implants were used, compared with those in whom other types of prostheses were used, in the first seven years after surgery. Cite this article: Bone Joint J 2018;100-B:20-7.

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus

Outcomes of hepatitis C virus (HCV) infection and treatment depend on viral and host genetic factors. We use human genome-wide genotyping arrays and new whole-genome HCV viral sequencing technologies to perform a systematic genome-to-genome study of 542 individuals chronically infected with HCV, predominately genotype 3. We show that both HLA alleles and interferon lambda innate immune system genes drive viral genome polymorphism, and that IFNL4 genotypes determine HCV viral load through a mechanism that is dependent on a specific polymorphism in the HCV polyprotein. We highlight the interplay between innate immune responses and the viral genome in HCV control.

A global × global test for testing associations between two large sets of variables

In high-dimensional omics studies where multiple molecular profiles are obtained for each set of patients, there is often interest in identifying complex multivariate associations, for example, copy number regulated expression levels in a certain pathway or in a genomic region. To detect such associations, we present a novel approach to test for association between two sets of variables. Our approach generalizes the global test, which tests for association between a group of covariates and a single univariate response, to allow high-dimensional multivariate response. We apply the method to several simulated datasets as well as two publicly available datasets, where we compare the performance of multivariate global test (G2) with univariate global test. The method is implemented in R and will be available as a part of the globaltest package in R.

Ethnic differences in cross-sectional associations between impaired glucose regulation, identified by oral glucose tolerance test or HbA1c values, and cardiovascular disease in a cohort of European and South Asian origin

AIMS

We contrasted impaired glucose regulation (prediabetes) prevalence, defined according to oral glucose tolerance test or HbA1c values, and studied cross-sectional associations between prediabetes and subclinical/clinical cardiovascular disease (CVD) in a cohort of European and South Asian origin.

METHODS

For 682 European and 520 South Asian men and women, aged 58-85 years, glycaemic status was determined by oral glucose tolerance test or HbA1c thresholds. Questionnaires, record review, coronary artery calcification scores and cerebral magnetic resonance imaging established clinical plus subclinical coronary heart and cerebrovascular disease.

RESULTS

Prediabetes was more prevalent in South Asian participants when defined by HbA1c rather than by oral glucose tolerance test criteria. Accounting for age, sex, smoking, systolic blood pressure, triglycerides and waist-hip ratio, prediabetes was associated with coronary heart disease and cerebrovascular disease in European participants, most obviously when defined by HbA1c rather than by oral glucose tolerance test [odds ratios for HbA1c -defined prediabetes 1.60 (95% CI 1.07, 2.39) for coronary heart disease and 1.57 (95% CI 1.00, 2.51) for cerebrovascular disease]. By contrast, non-significant associations were present between oral glucose tolerance test-defined prediabetes only and coronary heart disease [odds ratio 1.41 (95% CI 0.84, 2.36)] and HbA1c -defined prediabetes only and cerebrovascular disease [odds ratio 1.39 (95% CI 0.69, 2.78)] in South Asian participants. Prediabetes defined by HbA1c or oral glucose tolerance test criteria was associated with cardiovascular disease (defined as coronary heart and/or cerebrovascular disease) in Europeans [odds ratio 1.95 (95% CI 1.31, 2.91) for HbA1c prediabetes criteria] but not in South Asian participants [odds ratio 1.00 (95% CI 0.62, 2.66); ethnicity interaction P = 0.04].

CONCLUSIONS

Prediabetes appeared to be less associated with cardiovascular disease in the South Asian than in the European group. These findings have implications for screening, and early cardiovascular prevention strategies in South Asian populations.

Is a reduction in albuminuria associated with renal and cardiovascular protection? A post hoc analysis of the ALTITUDE trial

AIMS

To investigate whether the degree of albuminuria reduction observed in the ALTITUDE trial is associated with renal and cardiovascular protection, and secondly, whether the reduction in albuminuria was too small to afford clinical benefit.

METHODS

In a post hoc analysis of the ALTITUDE trial in 8561 patients with type 2 diabetes and chronic kidney disease or cardiovascular disease we examined the effect of albuminuria changes at 6 months on renal and cardiovascular outcomes using Cox proportional hazard regression.

RESULTS

The median change in albuminuria in the first 6 months in the aliskiren arm of the trial was -12% (25th to 75th percentile: -48.7_to_ +41.9%) and 0.0% (25th to 75th percentile: -40.2_to_55%) in the placebo arm. Changes in albuminuria in the first 6 months were linearly associated with renal and cardiovascular endpoints: a >30% reduction in albuminuria in the first 6 months was associated with a 62% reduction in renal risk and a 25% reduction in cardiovascular risk compared with an increase in albuminuria. The association between changes at 6 months in albuminuria and renal or cardiovascular endpoints was similar in the two treatment groups (p for interaction >0.1 for both endpoints).

CONCLUSIONS

The addition of aliskiren to angiotensin-converting enzyme inhibitor/angiotensin receptor blocker therapy resulted in albuminuria changes that were associated with renal and cardiovascular risk changes. This did not translate into renal or cardiovascular protection because the overall reduction in albuminuria in the aliskiren arm was too small and nearly similar to that in the placebo arm.

Grey Matter Atrophy in Multiple Sclerosis: Clinical Interpretation Depends on Choice of Analysis Method

Background

Studies disagree on the location of grey matter (GM) atrophy in the multiple sclerosis (MS) brain.

Aim

To examine the consistency between FSL, FreeSurfer, SPM for GM atrophy measurement (for volumes, patient/control discrimination, and correlations with cognition).

Materials and Methods

127 MS patients and 50 controls were included and cortical and deep grey matter (DGM) volumetrics were performed. Consistency of volumes was assessed with Intraclass Correlation Coefficient/ICC. Consistency of patients/controls discrimination was assessed with Cohen’s d, t-tests, MANOVA and a penalized double-loop logistic classifier. Consistency of association with cognition was assessed with Pearson correlation coefficient and ANOVA. Voxel-based morphometry (SPM-VBM and FSL-VBM) and vertex-wise FreeSurfer were used for group-level comparisons.

Results

The highest volumetry ICC were between SPM and FreeSurfer for cortical regions, and the lowest between SPM and FreeSurfer for DGM. The caudate nucleus and temporal lobes had high consistency between all software, while amygdala had lowest volumetric consistency. Consistency of patients/controls discrimination was largest in the DGM for all software, especially for thalamus and pallidum. The penalized double-loop logistic classifier most often selected the thalamus, pallidum and amygdala for all software. FSL yielded the largest number of significant correlations. DGM yielded stronger correlations with cognition than cortical volumes. Bilateral putamen and left insula volumes correlated with cognition using all methods.

Conclusion

GM volumes from FreeSurfer, FSL and SPM are different, especially for cortical regions. While group-level separation between MS and controls is comparable, correlations between regional GM volumes and clinical/cognitive variables in MS should be cautiously interpreted.

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene’s tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10⁻⁴). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases.

Genome sequencing provides evidence for large numbers of putative protein truncating variants in humans. Most truncating variants are only observed in few individuals but are collectively prevalent and widely distributed across the coding genome. Most of the truncating variants are so rare that they are only observed in heterozygosis. The current study identifies 10% of genes where heterozygous truncations are not observed and describes their biological characteristics. In addition, for genes where rare truncations are observed, we argue that these are an unexplored source of diversity of phenotypic traits and diseases.

Depressive symptoms are doubled in older British South Asian and Black Caribbean people compared with Europeans: associations with excess co-morbidity and socioeconomic disadvantage

BACKGROUND

Despite elevated risk profiles for depression among South Asian and Black Caribbean people in the UK, prevalences of late-life depressive symptoms across the UK's three major ethnic groups have not been well characterized.

METHOD

Data were collected at baseline and 20-year follow-up from 632 European, 476 South Asian and 181 Black Caribbean men and women (aged 58-88 years), of a community-based cohort study from north-west London. The 10-item Geriatric Depression Scale was interviewer-administered during a clinic visit (depressive symptoms defined as a score of ⩾4 out of 10), with clinical data (adiposity, diabetes, cardiovascular disease, cognitive function) also collected. Sociodemographic, psychosocial, behavioural, disability, and medical history information was obtained by questionnaire.

RESULTS

Prevalence of depressive symptoms varied by ethnic group, affecting 9.7% of White European, 15.5% of South Asian, and 17.7% of Black Caribbean participants. Compared with White Europeans, South Asian and Black Caribbean participants were significantly more likely to have depressive symptoms (odds ratio 1.79, 95% confidence interval 1.24-2.58 and 1.80, 1.11-2.92, respectively). Adjustment for co-morbidities had most effect on the excess South Asian odds, and adjustment for socioeconomic position had most effect on the elevated Black Caribbean odds.

CONCLUSIONS

Higher prevalence of depressive symptoms observed among South Asian people were attenuated after adjustment for physical health, whereas the Black Caribbean increased prevalence was most explained by socioeconomic disadvantage. It is important to understand the reasons for these ethnic differences to identify opportunities for interventions to address inequalities.

Ethnicity-specific obesity cut-points in the development of Type 2 diabetes - a prospective study including three ethnic groups in the United Kingdom

AIMS

Conventional definitions of obesity, e.g. body mass index (BMI) ≥ 30 kg/m² or waist circumference cut-points of 102 cm (men) and 88 cm (women), may underestimate metabolic risk in non-Europeans. We prospectively identified equivalent ethnicity-specific obesity cut-points for the estimation of diabetes risk in British South Asians, African-Caribbeans and Europeans.

METHODS

We studied a population-based cohort from London, UK (1356 Europeans, 842 South Asians, 335 African-Caribbeans) who were aged 40-69 years at baseline (1988-1991), when they underwent anthropometry, fasting and post-load (75 g oral glucose tolerance test) blood tests. Incident Type 2 diabetes was identified from primary care records, participant recall and/or follow-up biochemistry. Ethnicity-specific obesity cut-points in association with diabetes incidence were estimated using negative binomial regression.

RESULTS

Diabetes incidence rates (per 1000 person years) at a median follow-up of 19 years were 20.8 (95% CI: 18.4, 23.6) and 12.0 (8.3, 17.2) in South Asian men and women, 16.5 (12.7, 21.4) and 17.5 (13.0, 23.7) in African-Caribbean men and women, and 7.4 (6.3, 8.7), and 7.2 (5.3, 9.8) in European men and women. For incidence rates equivalent to those at a BMI of 30 kg/m² in European men and women, age- and sex-adjusted cut-points were: South Asians, 25.2 (23.4, 26.6) kg/m²; and African-Caribbeans, 27.2 (25.2, 28.6) kg/m². For South Asian and African-Caribbean men, respectively, waist circumference cut-points of 90.4 (85.0, 94.5) and 90.6 (85.0, 94.5) cm were equivalent to a value of 102 cm in European men. Waist circumference cut-points of 84.0 (74.0, 90.0) cm in South Asian women and 81.2 (71.4, 87.4) cm in African-Caribbean women were equivalent to a value of 88 cm in European women.

CONCLUSIONS

In prospective analyses, British South Asians and African-Caribbeans had equivalent diabetes incidence rates at substantially lower obesity levels than the conventional European cut-points.

A test for comparing two groups of samples when analyzing multiple omics profiles

BACKGROUND

A number of statistical models has been proposed for studying the association between gene expression and copy number data in integrated analysis. The next step is to compare association patterns between different groups of samples.

RESULTS

We propose a method, named dSIM, to find differences in association between copy number and gene expression, when comparing two groups of samples. Firstly, we use ridge regression to correct for the baseline associations between copy number and gene expression. Secondly, the global test is applied to the corrected data in order to find differences in association patterns between two groups of samples. We show that dSIM detects differences even in small genomic regions in a simulation study. We also apply dSIM to two publicly available breast cancer datasets and identify chromosome arms where copy number led gene expression regulation differs between positive and negative estrogen receptor samples. In spite of differing genomic coverage, some selected arms are identified in both datasets.

CONCLUSION

We developed a flexible and robust method for studying association differences between two groups of samples while integrating genomic data from different platforms. dSIM can be used with most types of microarray/sequencing data, including methylation and microRNA expression. The method is implemented in R and will be made part of the BioConductor package SIM.

Fused lasso algorithm for Cox' proportional hazards and binomial logit models with application to copy number profiles

This paper presents an efficient algorithm based on the combination of Newton Raphson and Gradient Ascent, for using the fused lasso regression method to construct a genome-based classifier. The characteristic structure of copy number data suggests that feature selection should take genomic location into account for producing more interpretable results for genome-based classifiers. The fused lasso penalty, an extension of the lasso penalty, encourages sparsity of the coefficients and their differences by penalizing the L1-norm for both of them at the same time, thus using genomic location. The major advantage of the algorithm over other existing fused lasso optimization techniques is its ability to predict binomial as well as survival response efficiently. We apply our algorithm to two publicly available datasets in order to predict survival and binary outcomes.