Identifying genetic risk variants for coronary heart disease in familial hypercholesterolemia: an extreme genetics approach

Comparison of mixed model based approaches for correcting for population substructure with application to extreme phenotype sampling

Background

Mixed models are used to correct for confounding due to population stratification and hidden relatedness in genome-wide association studies. This class of models includes linear mixed models and generalized linear mixed models. Existing mixed model approaches to correct for population substructure have been previously investigated with both continuous and case-control response variables. However, they have not been investigated in the context of extreme phenotype sampling (EPS), where genetic covariates are only collected on samples having extreme response variable values. In this work, we compare the performance of existing binary trait mixed model approaches (GMMAT, LEAP and CARAT) on EPS data. Since linear mixed models are commonly used even with binary traits, we also evaluate the performance of a popular linear mixed model implementation (GEMMA).

Results

We used simulation studies to estimate the type I error rate and power of all approaches assuming a population with substructure. Our simulation results show that for a common candidate variant, both LEAP and GMMAT control the type I error rate while CARAT’s rate remains inflated. We applied all methods to a real dataset from a Québec, Canada, case-control study that is known to have population substructure. We observe similar type I error control with the analysis on the Québec dataset. For rare variants, the false positive rate remains inflated even after correction with mixed model approaches. For methods that control the type I error rate, the estimated power is comparable.

Conclusions

The methods compared in this study differ in their type I error control. Therefore, when data are from an EPS study, care should be taken to ensure that the models underlying the methodology are suitable to the sampling strategy and to the minor allele frequency of the candidate SNPs.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-022-08297-y).

Risk Assessment and Clinical Management of Children and Adolescents with Heterozygous Familial Hypercholesterolaemia. A Position Paper of the Associations of Preventive Pediatrics of Serbia, Mighty Medic and International Lipid Expert Panel

Heterozygous familial hypercholesterolaemia (FH) is among the most common genetic metabolic lipid disorders characterised by elevated low-density lipoprotein cholesterol (LDL-C) levels from birth and a significantly higher risk of developing premature atherosclerotic cardiovascular disease. The majority of the current pediatric guidelines for clinical management of children and adolescents with FH does not consider the impact of genetic variations as well as characteristics of vascular phenotype as assessed by recently developed non-invasive imaging techniques. We propose a combined integrated approach of cardiovascular (CV) risk assessment and clinical management of children with FH incorporating current risk assessment profile (LDL-C levels, traditional CV risk factors and familial history) with genetic and non-invasive vascular phenotyping. Based on the existing data on vascular phenotype status, this panel recommends that all children with FH and cIMT ≥0.5 mm should receive lipid lowering therapy irrespective of the presence of CV risk factors, family history and/or LDL-C levels Those children with FH and cIMT ≥0.4 mm should be carefully monitored to initiate lipid lowering management in the most suitable time. Likewise, all genetically confirmed children with FH and LDL-C levels ≥4.1 mmol/L (160 mg/dL), should be treated with lifestyle changes and LLT irrespective of the cIMT, presence of additional RF or family history of CHD.

A Cautionary Note on the Effects of Population Stratification Under an Extreme Phenotype Sampling Design

Extreme phenotype sampling (EPS) is a popular study design used to reduce genotyping or sequencing costs. Assuming continuous phenotype data are available on a large cohort, EPS involves genotyping or sequencing only those individuals with extreme phenotypic values. Although this design has been shown to have high power to detect genetic effects even at smaller sample sizes, little attention has been paid to the effects of confounding variables, and in particular population stratification. Using extensive simulations, we demonstrate that the false positive rate under the EPS design is greatly inflated relative to a random sample of equal size or a “case-control”-like design where the cases are from one phenotypic extreme and the controls randomly sampled. The inflated false positive rate is observed even with allele frequency and phenotype mean differences taken from European population data. We show that the effects of confounding are not reduced by increasing the sample size. We also show that including the top principal components in a logistic regression model is sufficient for controlling the type 1 error rate using data simulated with a population genetics model and using 1,000 Genomes genotype data. Our results suggest that when an EPS study is conducted, it is crucial to adjust for all confounding variables. For genetic association studies this requires genotyping a sufficient number of markers to allow for ancestry estimation. Unfortunately, this could increase the costs of a study if sequencing or genotyping was only planned for candidate genes or pathways; the available genetic data would not be suitable for ancestry correction as many of the variants could have a true association with the trait.

Predicting cardiovascular disease in familial hypercholesterolemia

PURPOSE OF REVIEW

Familial hypercholesterolemia is a frequent genetic disease associated with a high lifetime risk of cardiovascular disease (CVD). Statins are the cornerstone of treatment of familial hypercholesterolemia; however, with the advent of novel LDL-cholesterol lowering therapies, it has become necessary to identify familial hypercholesterolemia subjects presenting a significant residual CVD risk. The aim of this review is to provide an update on the recent literature concerning cardiovascular risk stratification in familial hypercholesterolemia.

RECENT FINDINGS

Recently, several clinical and genetic factors have been shown to be independent predictors of CVD in familial hypercholesterolemia. These include clinical scores such as the Montreal-FH-SCORE, novel protein biomarkers, carotid plaque score and genetic predictors such as genetic risk scores as well as single-nucleotide polymorphisms.

SUMMARY

Although there has been recent progress in cardiovascular risk stratification in familial hypercholesterolemia, there is still a need to further refine our knowledge concerning phenotype modifiers in this disease. Indeed, current known predictors do not explain the entirety of cardiovascular risk. More precise individual risk stratification in familial hypercholesterolemia could help to better tailor the proper therapy for each patient.

Progress in the care of common inherited atherogenic disorders of apolipoprotein B metabolism

Familial hypercholesterolaemia, familial combined hyperlipidaemia (FCH) and elevated lipoprotein(a) are common, inherited disorders of apolipoprotein B metabolism that markedly accelerate the onset of atherosclerotic cardiovascular disease (ASCVD). These disorders are frequently encountered in clinical lipidology and need to be accurately identified and treated in both index patients and their family members, to prevent the development of premature ASCVD. The optimal screening strategies depend on the patterns of heritability for each condition. Established therapies are widely used along with lifestyle interventions to regulate levels of circulating lipoproteins. New therapeutic strategies are becoming available, and could supplement traditional approaches in the most severe cases, but their long-term cost-effectiveness and safety have yet to be confirmed. We review contemporary developments in the understanding, detection and care of these highly atherogenic disorders of apolipoprotein B metabolism.

Cardiovascular risk stratification in familial hypercholesterolaemia

Familial hypercholesterolaemia (FH) is a common autosomal-dominant disorder in most European countries. Patients with FH are characterised by a raised level of low-density lipoprotein cholesterol and a high risk of premature coronary heart disease (CHD). Currently there is no consensus regarding the clinical utility to predict future coronary events or testing for the presence of subclinical atherosclerotic disease in asymptomatic patients with FH. Family screening of patients with FH as recommended by the UK National Institute of Health and Care Excellence guideline would result in finding many young individuals with a diagnosis of FH who are clinically asymptomatic. The traditional CHD risk scores, that is, the Framingham score, are insufficient in risk prediction in this group of young individuals. In addition, a better understanding of the genetic aetiology of the FH phenotype and CHD risk in monogenic FH and polygenic hypercholesterolaemia is needed. Non-invasive imaging methods such as carotid intima-media thickness measurement might produce more reliable information in finding high-risk patients with FH. The potential market authorisation of novel therapeutic agents such as PCSK9 monoclonal inhibitors makes it essential to have a better screening programme to prioritise the candidates for treatment with the most severe form of FH and at higher risk of coronary events. The utility of new imaging techniques and new cardiovascular biomarkers remains to be determined in prospective trials.

Cascade Screening in Familial Hypercholesterolemia: Advancing Forward

Familial hypercholesterolemia is a genetic disorder associated with elevated LDL-cholesterol and high lifetime cardiovascular risk. Both clinical and molecular cascade screening programs have been implemented to increase early definition and treatment. In this systematic review, we discuss the main issues found in 65 different articles related to cascade screening and familial hypercholesterolemia, covering a range of topics including different types/strategies, considerations both positive and negative regarding cascade screening in general and associated with the different strategies, cost and coverage consideration, direct and indirect contact with patients, public policy around life insurance and doctor-patient confidentiality, the "right to know," and public health concerns regarding familial hypercholesterolemia.

Recent advances in the understanding and care of familial hypercholesterolaemia: significance of the biology and therapeutic regulation of proprotein convertase subtilisin/kexin type 9

Familial hypercholesterolaemia (FH) is an autosomal co-dominant disorder that markedly raises plasma low-density lipoprotein-cholesterol (LDL-C) concentration, causing premature atherosclerotic coronary artery disease (CAD). FH has recently come under intense focus and, although there is general consensus in recent international guidelines regarding diagnosis and treatment, there is debate about the value of genetic studies. Genetic testing can be cost-effective as part of cascade screening in dedicated centres, but the full mutation spectrum responsible for FH has not been established in many populations, and its use in primary care is not at present logistically feasible. Whether using genetic testing or not, cholesterol screening of family members of index patients with an abnormally raised LDL-C must be used to determine the need for early treatment to prevent the development of CAD. The metabolic defects in FH extend beyond LDL, and may affect triacylglycerol-rich and high-density lipoproteins, lipoprotein(a) and oxidative stress. Achievement of the recommended targets for LDL-C with current treatments is difficult, but this may be resolved by new drug therapies. Lipoprotein apheresis remains an effective treatment for severe FH and, although expensive, it costs less than the two recently introduced orphan drugs (lomitapide and mipomersen) for homozygous FH. Recent advances in understanding of the biology of proprotein convertase subtilisin/kexin type 9 (PCSK9) have further elucidated the regulation of lipoprotein metabolism and led to new drugs for effectively treating hypercholesterolaemia in FH and related conditions, as well as for treating many patients with statin intolerance. The mechanisms of action of PCSK9 inhibitors on lipoprotein metabolism and atherosclerosis, as well as their impact on cardiovascular outcomes and cost-effectiveness, remain to be established.