Population genomic evidence of a putative 'far-west' African cryptic taxon in the Anopheles gambiae complex.

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identified a putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather may have originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Health economic analysis of polygenic risk score use in primary prevention of coronary artery disease - A system dynamics model.

Background: Primary prevention programs utilising traditional risk scores fail to identify all individuals who suffer acute cardiovascular events. We aimed to model the impact and cost effectiveness of incorporating a Polygenic risk scores (PRS) into the cardiovascular disease CVD primary prevention program in Australia, using a whole-of-system model. Methods: System dynamics models, encompassing acute and chronic CVD care in the Australian healthcare setting, assessing the cost-effectiveness of incorporating a CAD-PRS in the primary prevention setting. The time horizon was 10-years. Results: Pragmatically incorporating a CAD-PRS in the Australian primary prevention setting in middle-aged individuals already attending a Heart Health Check (HHC) who are determined to be at low or moderate risk based on the 5-year Framingham risk score (FRS), with conservative assumptions regarding uptake of PRS, could have prevented 2, 052 deaths over 10-years, and resulted in 24, 085 QALYs gained at a cost of $19, 945 per QALY with a net benefit of $724 million. If all Australians overs the age of 35 years old had their FRS and PRS performed, and acted upon, 12, 374 deaths and 60, 284 acute coronary events would be prevented, with 183, 682 QALYs gained at a cost of $18, 531 per QALY, with a net benefit of $5, 780 million. Conclusions: Incorporating a CAD-PRS in a contemporary primary prevention setting in Australia would result in substantial health and societal benefits and is cost-effective. The broader the uptake of CAD-PRS in the primary prevention setting in middle-aged Australians, the greater the impact and the more cost-effective the strategy.

Ancestry-specific polygenic risk scores are risk enhancers for clinical cardiovascular disease assessments.

Clinical implementation of new prediction models requires evaluation of their utility in a broad range of intended use populations. Here we develop and validate ancestry-specific Polygenic Risk Scores (PRSs) for Coronary Artery Disease (CAD) using 29,389 individuals from diverse cohorts and genetic ancestry groups. The CAD PRSs outperform published scores with an average Odds Ratio per Standard Deviation of 1.57 (SD = 0.14) and identify between 12% and 24% of individuals with high genetic risk. Using this risk factor to reclassify borderline or intermediate 10 year Atherosclerotic Cardiovascular Disease (ASCVD) risk improves assessments for both CAD (Net Reclassification Improvement (NRI) = 13.14% (95% CI 9.23-17.06%)) and ASCVD (NRI = 10.70 (95% CI 7.35-14.05)) in an independent cohort of 9,691 individuals. Our analyses demonstrate that using PRSs as Risk Enhancers improves ASCVD risk assessments outlining an approach for guiding ASCVD prevention with genetic information.

Cost-effectiveness analysis of implementing polygenic risk score in a workplace cardiovascular disease prevention program.

Background: Polygenic risk score for coronary artery disease (CAD-PRS) improves precision in assessing the risk of cardiovascular diseases and is cost-effective in preventing cardiovascular diseases in a health system and may be cost-effective in other settings and prevention programs such as workplace cardiovascular prevention programs. Workplaces provide a conducitve environment for cardiovascular prevention interventions, but the cost-effectiveness of CAD-PRS in a workplace setting remains unknown. This study examined the cost-effectiveness of integrating CAD-PRS in a workplace cardiovascular disease prevention program compared to the standard cardiovascular workplace program without CAD-PRS and no-workplace prevention program. Methods: We developed a cohort simulation model to project health benefits (quality-adjusted life years gained) and costs over a period of 5 years in a cohort of employees with a mean age of 50 years. The model health states reflected the risk of disease (coronary artery disease and ischemic stroke) and statin prevention therapy side effects (diabetes, hemorrhagic stroke, and myopathy). We considered medical and lost productivity costs. Data were obtained from the literature, and the analysis was performed from a self-insured employer perspective with future costs and quality-adjusted life years discounted at 3% annually. Uncertainty in model parameter inputs was assessed using deterministic and probabilistic sensitivity analyses. Three programs were compared: (1) a workplace cardiovascular program that integrated CAD-PRS with the pooled cohort equation-a standard of care for assessing the risk of cardiovascular diseases (CardioriskSCORE); (2) a workplace cardiovascular prevention program without CAD-PRS (Standard-WHP); and (3) no-workplace health program (No-WHP). The main outcomes were total costs (US $2019), incremental costs, incremental quality-adjusted life years, and incremental cost-effectiveness ratio. Results: CardioriskSCORE lowered employer costs ($53 and $575) and improved employee quality-adjusted life years (0.001 and 0.005) per employee screened compared to Standard-WHP and No-WHP, respectively. The effectiveness of statin prevention therapy, employees' baseline cardiovascular risk, the proportion of employees that enrolled in the program, and statin adherence had the largest effect size on the incremental net monetary benefit. However, despite the variation in parameter input values, base case results remained robust. Conclusion: Polygenic testing in a workplace cardiovascular prevention program improves employees' quality of life and simultaneously lowers health costs and productivity monetary loss for employers.

Incorporating a polygenic risk score-triaged coronary calcium score into cardiovascular disease examinations to identify subclinical coronary artery disease (ESCALATE): Protocol for a prospective, nonrandomized implementation trial.

BACKGROUND: Identifying and targeting established modifiable risk factors has been a successful strategy for reducing the burden of coronary artery disease (CAD) at the population-level. However, up to 1-in-4 patients who present with ST elevation myocardial infarction do so in the absence of such risk factors. Polygenic risk scores (PRS) have demonstrated an ability to improve risk prediction models independent of traditional risk factors and self-reported family history, but a pathway for implementation has yet to be clearly identified. The aim of this study is to examine the utility of a CAD PRS to identify individuals with subclinical CAD via a novel clinical pathway, triaging low or intermediate absolute risk individuals for noninvasive coronary imaging, and examining the impact on shared treatment decisions and participant experience. TRIAL DESIGN: The ESCALATE study is a 12-month, prospective, multicenter implementation study incorporating PRS into otherwise standard primary care CVD risk assessments, to identify patients at increased lifetime CAD risk for noninvasive coronary imaging. One-thousand eligible participants aged 45 to 65 years old will enter the study, which applies PRS to those considered low or moderate 5-year absolute CVD risk and triages those with CAD PRS ≥80% for a coronary calcium scan. The primary outcome will be the identification of subclinical CAD, defined as a coronary artery calcium score (CACS) >0 Agatston units (AU). Multiple secondary outcomes will be assessed, including baseline CACS ≥100 AU or ≥75th age-/sex-matched percentile, the use and intensity of lipid- and blood pressure-lowering therapeutics, cholesterol and blood pressure levels, and health-related quality of life (HRQOL). CONCLUSION: This novel trial will generate evidence on the ability of a PRS-triaged CACS to identify subclinical CAD, as well as subsequent differences in traditional risk factor medical management, pharmacotherapy utilization, and participant experience. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry, ACTRN12622000436774. Trial was prospectively registered on March 18, 2022. https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=383134.

Integrating a Polygenic Risk Score for Coronary Artery Disease as a Risk-Enhancing Factor in the Pooled Cohort Equation: A Cost-Effectiveness Analysis Study.

Background Cardiovascular diseases are the leading cause of death in the United States, yet a significant proportion of adults at high risk remain undetected by standard screening practices. Polygenic risk score for coronary artery disease (CAD-PRS) improves precision in determining the 10-year risk of atherosclerotic cardiovascular disease but health benefits and health care costs associated with CAD-PRS are unknown. We examined the cost-effectiveness of including CAD-PRS as a risk-enhancing factor in the pooled cohort equation (PCE)-the standard of care for determining the risk of atherosclerotic cardiovascular disease-versus PCE alone. Methods and Results We applied a Markov model on a cohort of 40-year-old individuals with borderline or intermediate 10-year risk (5% to <20%) for atherosclerotic cardiovascular disease to identify those in the top quintile of the CAD-PRS distribution who are at high risk and eligible for statin prevention therapy. Health outcomes examined included coronary artery disease (CAD; ie, myocardial infarction) and ischemic stroke. The model projected medical costs (2019 US$) of screening for CAD, statin prevention therapy, treatment, and monitoring patients living with CAD or ischemic stroke and quality-adjusted life-years for PCE+CAD-PRS versus PCE alone. Deterministic and probabilistic sensitivity analyses and scenario analyses were performed to examine uncertainty in parameter inputs. PCE+CAD-PRS was dominant compared with PCE alone in the 5- and 10-year time horizons. We found that, respectively, PCE+CAD-PRS had 0.003 and 0.011 higher mean quality-adjusted life-years and $40 and $181 lower mean costs per person screened, with 29 and 50 fewer events of CAD and ischemic stroke in a cohort of 10 000 individuals compared with PCE alone. The risk of developing CAD, the effectiveness of statin prevention therapy, and the cost of treating CAD had the largest impact on the cost per quality-adjusted life-year gained. However, this cost remained below the $50 000 willingness-to-pay threshold except when the annual risk of developing CAD was <0.006 in the 5-year time horizon. Results from Monte Carlo simulation indicated that PCE+CAD-PRS would be cost-effective. with the probability of 94% and 99% at $50 000 willingness-to-pay threshold in the 5- and 10-year time horizon, respectively. Conclusions Implementing CAD-PRS as a risk-enhancing factor in the PCE to determine the risk of atherosclerotic cardiovascular disease reduced the mean cost per individual, improved quality-adjusted life-years, and averted future events of CAD and ischemic stroke when compared with PCE alone.

[Progress in cardiovascular prevention: from risk charts to polygenic risk score and precision prevention]. / Progressi in prevenzione cardiovascolare: dalle carte del rischio allo score poligenico e alla prevenzione di precisione.

In the last few decades, great epidemiological studies identified the main risk factors and their causative role in cardiovascular diseases (CVD). In this field, the pivotal study was the Framingham Heart Study for the evaluation of classical risk factors and for the production of initial instruments of risk calculation. The Seven Countries Study of Cardiovascular Diseases was the first to compare the influence of different cultural environments on the risks of developing atherosclerosis. In 1980, the Italian Journal of Cardiology published an extensive evaluation of risk factors in nine Italian communities. Since the early '90s, the first risk charts for global and individual risk evaluation were available (Framingham, SCORE, PROCAM, CUORE). Mortality reduction in the period of 1980-2000 can be attributed to risk factor reduction in primary prevention (55%) and to pharmacological treatment in the acute phase of the disease or in secondary prevention (40%). Two important longitudinal studies have been conducted in Italy in the periods of 1998-2002 and 2008-2012 thanks to the cooperation of the National Association of Hospital Cardiologists (ANMCO) and the National Health Institute (ISS), which became the reference point for the influence of lifestyle and risk factors on CVD. During the last 15 years, genetic studies allowed the construction of polygenic risk scores (PRS), that are strongly predictive of developing CVD in the future, thanks to big genomic datasets of individuals followed for more than 10 years (e.g. UK Biobank). PRS can be used as an adjunctive tool to the common risk charts for a better classification of individual risk profile. In addition to PRS, inflammation biomarkers and imaging tools like ultrasound and coronary calcium score and their integration with machine learning can help in the best definition of cardiovascular risk. Precision prevention by the study of "metabotypes" and community prevention provide possible future development of cardiovascular prevention.

Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae.

The two most efficient and most recently radiated Afrotropical vectors of human malaria - Anopheles coluzzii and An. gambiae - are identified by single-locus diagnostic PCR assays based on species-specific markers in a 4 Mb region on chromosome-X centromere. Inherently, these diagnostic assays cannot detect interspecific autosomal admixture shown to be extensive at the westernmost and easternmost extremes of the species range. The main aim of this study was to develop novel, easy-to-implement tools for genotyping An. coluzzii and An. gambiae-specific ancestral informative markers (AIMs) identified from the Anopheles gambiae 1000 genomes (Ag1000G) project. First, we took advantage of this large set of data in order to develop a multilocus approach to genotype 26 AIMs on all chromosome arms valid across the species range. Second, we tested the multilocus assay on samples from Guinea Bissau, The Gambia and Senegal, three countries spanning the westernmost hybridization zone, where conventional species diagnostic is problematic due to the putative presence of a novel "hybrid form". The multilocus assay was able to capture patterns of admixture reflecting those revealed by the whole set of AIMs and provided new original data on interspecific admixture in the region. Third, we developed an easy-to-use, cost-effective PCR approach for genotyping two AIMs on chromosome-3 among those included in the multilocus approach, opening the possibility for advanced identification of species and of admixed specimens during routine large scale entomological surveys, particularly, but not exclusively, at the extremes of the range, where WGS data highlighted unexpected autosomal admixture.

New prevention scenarios: polygenic risk.

Although coronary heart disease is a highly preventable disease, it is still the leading cause of morbidity and mortality in developed countries. This is also due to the fact that the risk models used in clinical practice have proved ineffective in identifying people at risk: up to 30% of cases of myocardial infarction do not have traditional risk factors used in risk estimation models. Although the genetic component of myocardial infarction has been known for many years, with an inheritance rate of between 40% and 60%, it is not yet used as a risk factor in primary prevention models such as the Heart Card or the European SCORE. Recent advances in genomics and the use of clinical big data have allowed the development of genetic risk scores called Polygenic Risk Score (PRS), capable of identifying populations with average LDL-C levels, but with the same risk of heart attack of carriers of hypercholesterolaemia. The clinical usefulness of the PRS lies precisely in identifying high-risk individuals who are invisible to traditional models. The clinical applications of PRS for coronary artery disease are discussed in this report.

Massive introgression drives species radiation at the range limit of Anopheles gambiae.

Impacts of introgressive hybridisation may range from genomic erosion and species collapse to rapid adaptation and speciation but opportunities to study these dynamics are rare. We investigated the extent, causes and consequences of a hybrid zone between Anopheles coluzzii and Anopheles gambiae in Guinea-Bissau, where high hybridisation rates appear to be stable at least since the 1990s. Anopheles gambiae was genetically partitioned into inland and coastal subpopulations, separated by a central region dominated by A. coluzzii. Surprisingly, whole genome sequencing revealed that the coastal region harbours a hybrid form characterised by an A. gambiae-like sex chromosome and massive introgression of A. coluzzii autosomal alleles. Local selection on chromosomal inversions may play a role in this process, suggesting potential for spatiotemporal stability of the coastal hybrid form and providing resilience against introgression of medically-important loci and traits, found to be more prevalent in inland A. gambiae.

Glutathione S-transferase M1 null genotype, household pesticides exposure and cutaneous melanoma.

Glutathione S-transferase (GST) activity is believed to play a critical role in cellular protection against toxic chemicals. We evaluated the role of GSTM1 polymorphisms in modifying the association between indoor pesticide exposure and cutaneous melanoma. Peripheral blood samples were collected from 325 individuals (177 patients with cutaneous melanoma and 148 controls). Genotyping was performed using the PCR method. Participants were interviewed to collect data on pesticides used indoors, sociodemographic characteristics, medical history, sun exposure and pigmented characteristics. Odds ratio and 95% confidence intervals (CIs) were calculated by unconditional logistic regression. After adjustment for sex, age, education, hair colour, skin photo-type, solar lentigines, number of nevi and sunburns episodes in childhood, a 2.76-fold (95% CI: 1.08-7.08) increase in the risk of cutaneous melanoma was observed for GSTM1 null individuals highly exposed to indoor pesticides (≥2 times/year) in comparison with GSTM1 active individuals who received low exposure (<2 times/year). Participants exposed to these products for 10 years or more and with GSTM1 null genotype also had an increased risk of cutaneous melanoma (odds ratio: 2.78; 95% CI: 1.01-7.66) in comparison with participants with a low duration of exposure (<10 years) and active GSTM1. These findings suggest that the GSTM1 null genotype is a risk modifier for cutaneous melanoma.

Assessment of the Effectiveness of a Seasonal-Long Insecticide-Based Control Strategy against Aedes albopictus Nuisance in an Urban Area.

Seasonal-long larvicide treatments and/or outdoor space-spray applications of insecticides are frequently applied to reduce Aedes albopictus nuisance in urban areas of temperate regions, where the species has become a permanent pest affecting people's quality of life and health. However, assessments of the effectiveness of sequential interventions is a difficult task, as it requires to take into account the cumulative and combined effect of multiple treatments, as well as the mosquito seasonal dynamics (rather than mosquito abundance before and after single treatments). We here present the results of the effectiveness assessment of a seasonal-long calendar-based control intervention integrating larvicide treatments of street catch basins and night-time adulticide ground spraying in the main University hospital in Rome (Italy). Cage-experiments and an intensive monitoring of wild mosquito abundance in treated and untreated sites were carried out along an entire season. Sticky traps were used to monitor adult abundance and site-specific eco-climatic variations (by recording water left over in each trap), in order to disentangle the effect of insecticide treatments from eco-climatic drivers on mosquito seasonal dynamics. Despite the apparent limited impact of single adulticide sprayings assessed based on mortality in caged and wild mosquitoes, the results of the temporal analysis showed that mosquito seasonal patterns were initially comparable in the two sites, diverged in the absence of diverging eco-climatic conditions and remained stable afterwards. This allowed to attribute the lack of the expected Ae. albopictus population expansion in the treated site to the combined effect of multiple adulticide sprayings and larvicide treatments carried out during the whole season. The approach proposed was proved to be successful to assess effects of seasonal-long control treatments on adult mosquito population dynamics and could represent a valuable instrument to assess the effectiveness of other control interventions, to evaluate their actual cost-benefits and to possibly minimize space-spraying applications to reduce mosquito nuisance.

The protective effect of coffee consumption on cutaneous melanoma risk and the role of GSTM1 and GSTT1 polymorphisms.

PURPOSES: The authors examined the association between coffee consumption and cutaneous melanoma and the implication of GSTM1 and GSTT1 polymorphisms. METHODS: A hospital-based case-control study was conducted in the inpatient wards of IDI-San Carlo Rome, Italy, including 304 incident cases of cutaneous melanoma and 305 controls. Information on socio-demographic characteristics, medical history, smoking, sun exposure, pigmentary characteristics and diet was collected for all subjects. Within the study, individual patterns at two polymorphic genes (GSTM1 and GSTT1) belonging to glutathione S-transferases family were investigated in 188 cases of cutaneous melanoma and 152 controls. Logistic regression was the method used to estimate odds ratio and 95 % confidence intervals. RESULTS: High frequency of coffee drinking (>once daily), compared with low-frequency consumption of coffee (≤7 times weekly) was associated with a protective effect for cutaneous melanoma (OR 0.46; 95 % CI 0.31-0.68) after adjusting for sex, age, education, hair colour, common nevi, skin phototype, and sunburn episodes in childhood. When stratified by GSTM1 and GSTT1 genotype, the protective effect of coffee was extremely high for subjects with both GSTM1 and GSTT1 null polymorphisms (OR 0.01; 95 % CI 0.0003-0.54). CONCLUSIONS: Our results show a protective effect of coffee consumption for cutaneous melanoma, in particular for those with homozygous deletion for GSTM1 and GSTT1.