Gene-based sequencing identifies lipid-influencing variants with ethnicity-specific effects in African Americans

Triglyceride to high-density lipoprotein ratio as a predictor for 10-year cardiovascular disease in individuals with diabetes in Thailand

BACKGROUND

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality worldwide. The triglyceride to high-density lipoprotein cholesterol (TG/HDL) ratio has emerged as a potential marker for CVD risk. However, its predictive value for high 10-year predicted Cardiovascular (CV) risk remains unclear; This study evaluates the predictive value of the TG/HDL-C ratio for 10-year cardiovascular risk using the Framingham Heart Study (FHS) risk prediction model in individuals with Type 2 Diabetes Mellitus (T2DM).

METHODS

A cross-sectional study was conducted on 61,004 adults from 2014,2015, and 2018 aged 30-74 years with T2DM, without a history of CVD. The FHS model was used to estimate 10-year predicted CV risk, and high CVD risk was defined as ≥ 20%. ROC curve analysis was used to determine the optimal TG/HDL cutoff for high 10-year predicted CV risk in the overall population and age-specific subgroups. Logistic regression was performed to find the association between TG/HDL and high 10-year predicted CV risk, adjusting for potential confounders.

RESULTS

The optimal TG/HDL-C cutoff was 2.52 (AUC = 0.618, 95% CI: 0.612-0.624), with 67% sensitivity and 50% specificity. Higher TG/HDL were associated with increased odds of high predicted CVD risk in a dose-dependent manner, with an adjusted odds ratio (AOR) of 5.16 (95% CI: 4.86-5.49) in the highest TG/HDL quartile (> 4.91). Age-stratified analysis identified lower cutoffs for older adults (≥ 60 years: 2.42, AUC = 0.694) than younger individuals (< 60 years: 2.98, AUC = 0.636), indicating stronger predictive performance in older adults.

CONCLUSIONS

The TG/HDL ratio is significantly associated with 10-year predicted CVD risk in T2DM with age-specific differences in predictive value. The lower cutoff for older adults (2.42) suggests even modest elevations indicate increased risk. These findings support TG/HDL integration into routine CVD risk assessments and highlight the importance of age-specific cutoffs for improved risk stratification.

Associations Between Lipid Traits and Breast Cancer Risk: A Mendelian Randomization Study in African Women

BACKGROUND

Blood lipids are implicated in the development of breast cancer (BC), though the genetic connection remains unclear, particularly in African populations. Observational studies on this topic are limited by confounding factors and reverse causation, potentially affecting the reliability of findings.

METHODS

We applied univariate and multivariable two-sample Mendelian randomization to assess the causal association between blood lipids (total cholesterol [TC], high-density lipoprotein [HDL], low-density lipoprotein [LDL], and triglycerides [TG]) and BC. Summary-level data for lipid traits were sourced from the Africa Wits-INDEPTH partnership for Genomic Research (AWI-Gen) (N = 10,603 women). BC data were obtained from the largest genome-wide association study of BC in African women, comprising 18,034 BC cases and 22,104 controls.

RESULTS

Our analysis revealed that genetically predicted TG was associated with a decreased BC risk (OR = 0.73, 95% CI = 0.56-0.95, p = 0.018. In contrast, no significant associations were found between TC, HDL, or LDL levels and BC risk: TC (OR = 1.04, 95% CI = 0.93-1.18, p = 0.467), HDL (OR = 1.29, 95% CI = 0.93-1.79, p = 0.121), and LDL (OR = 1.04, 95% CI = 0.90-1.20, p = 0.577). After adjusting for the effects of other lipid traits, the association between TG and BC was attenuated, and no associations were observed for TC, HDL, or LDL. No causal relationship was found between lipid traits and BC subtypes.

CONCLUSIONS

This study provides evidence that elevated triglycerides may be associated with a reduced risk of BC, whereas no significant associations were observed for TC, HDL, or LDL. Further research is needed to better understand the underlying mechanisms and potential clinical implications of these findings.

Lipoprotein Lipase: Structure, Function, and Genetic Variation

Biallelic rare pathogenic loss-of-function (LOF) variants in lipoprotein lipase (LPL) cause familial chylomicronemia syndrome (FCS). Heterozygosity for these same variants is associated with a highly variable plasma triglyceride (TG) phenotype ranging from normal to severe hypertriglyceridemia (HTG), with longitudinal variation in phenotype severity seen often in a given carrier. Here, we provide an updated overview of genetic variation in LPL in the context of HTG, with a focus on disease-causing and/or disease-associated variants. We provide a curated list of 300 disease-causing variants discovered in LPL, as well as an exon-by-exon breakdown of the LPL gene and protein, highlighting the impact of variants and the various functional residues of domains of the LPL protein. We also provide a curated list of variants of unknown or uncertain significance, many of which may be upgraded to pathogenic/likely pathogenic classification should an additional case and/or segregation data be reported. Finally, we also review the association between benign/likely benign variants in LPL, many of which are common polymorphisms, and the TG phenotype.

Universal genome-wide association studies: Powerful joint ancestry and association testing

The vast majority of human populations and individuals have mixed ancestry. Consequently, adjustment for locus-specific ancestry is essential for genetic association studies. To empower association studies for all populations, it is necessary to integrate effects of locus-specific ancestry and genotype. We developed a joint test of ancestry and association that can be performed with summary statistics, is independent of study design, can take advantage of locus-specific ancestry effects to boost power in association testing, and can utilize association effects to fine map admixture peaks. We illustrate the test using the association between serum triglycerides and LPL. By combining data from African Americans, European Americans, and West Africans, we identify three conditionally independent variants with varying amounts of ancestrally differentiated allele frequencies. Using out-of-sample data, we demonstrate improved prediction achievable by accounting for multiple causal variants and locus-specific ancestry effects at a single locus.

Tale of two systems: the intertwining duality of fibrinolysis and lipoprotein metabolism

Fibrinolysis is an enzymatic process that breaks down fibrin clots, while dyslipidemia refers to abnormal levels of lipids and lipoproteins in the blood. Both fibrinolysis and lipoprotein metabolism are critical mechanisms that regulate a myriad of functions in the body, and the imbalance of these mechanisms is linked to the development of pathologic conditions, such as thrombotic complications in atherosclerotic cardiovascular diseases. Accumulated evidence indicates the close relationship between the 2 seemingly distinct and complicated systems-fibrinolysis and lipoprotein metabolism. Observational studies in humans found that dyslipidemia, characterized by increased blood apoB-lipoprotein and decreased high-density lipoprotein, is associated with lower fibrinolytic potential. Genetic variants of some fibrinolytic regulators are associated with blood lipid levels, supporting a causal relationship between these regulators and lipoprotein metabolism. Mechanistic studies have elucidated many pathways that link the fibrinolytic system and lipoprotein metabolism. Moreover, profibrinolytic therapies improve lipid panels toward an overall cardiometabolic healthier phenotype, while some lipid-lowering treatments increase fibrinolytic potential. The complex relationship between lipoprotein and fibrinolysis warrants further research to improve our understanding of the bidirectional regulation between the mediators of fibrinolysis and lipoprotein metabolism.

Intracellular tPA-PAI-1 interaction determines VLDL assembly in hepatocytes

Apolipoprotein B (apoB)-lipoproteins initiate and promote atherosclerotic cardiovascular disease. Plasma tissue plasminogen activator (tPA) activity is negatively associated with atherogenic apoB-lipoprotein cholesterol levels in humans, but the mechanisms are unknown. We found that tPA, partially through the lysine-binding site on its Kringle 2 domain, binds to the N terminus of apoB, blocking the interaction between apoB and microsomal triglyceride transfer protein (MTP) in hepatocytes, thereby reducing very-low-density lipoprotein (VLDL) assembly and plasma apoB-lipoprotein cholesterol levels. Plasminogen activator inhibitor 1 (PAI-1) sequesters tPA away from apoB and increases VLDL assembly. Humans with PAI-1 deficiency have smaller VLDL particles and lower plasma levels of apoB-lipoprotein cholesterol. These results suggest a mechanism that fine-tunes VLDL assembly by intracellular interactions among tPA, PAI-1, and apoB in hepatocytes.

Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals

Individuals of admixed ancestries (for example, African Americans) inherit a mosaic of ancestry segments (local ancestry) originating from multiple continental ancestral populations. This offers the unique opportunity of investigating the similarity of genetic effects on traits across ancestries within the same population. Here we introduce an approach to estimate correlation of causal genetic effects (radmix) across local ancestries and analyze 38 complex traits in African-European admixed individuals (N = 53,001) to observe very high correlations (meta-analysis radmix = 0.95, 95% credible interval 0.93-0.97), much higher than correlation of causal effects across continental ancestries. We replicate our results using regression-based methods from marginal genome-wide association study summary statistics. We also report realistic scenarios where regression-based methods yield inflated heterogeneity-by-ancestry due to ancestry-specific tagging of causal effects, and/or polygenicity. Our results motivate genetic analyses that assume minimal heterogeneity in causal effects by ancestry, with implications for the inclusion of ancestry-diverse individuals in studies.

Association Between Dietary and Serum Cholesterol and Cognitive Function Among the U.S. Elderly from NHANES 2011-2014

BACKGROUND

The association between dietary or serum cholesterol and cognitive performance in older adults has not been well-established.

OBJECTIVE

This study aimed to investigate the potential association between dietary or serum cholesterol and cognitive performance in the elderly population.

METHODS

A cross-sectional analysis was conducted using data from the National Health and Nutrition Examination Survey (NHANES) 2011-2012 and 2013-2014. Diet and supplement cholesterol was estimated based on two non-consecutive 24-hour dietary recalls. Cognitive function was assessed using various statistical tests. Poor cognitive performance was defined as scores below the lowest quartile within age groups. Regression models were adjusted for demographic factors, and subgroup analyses were performed for non-Hispanic White (NHW) and non-Hispanic Black (NHB) individuals.

RESULTS

Among 759 participants aged 60 years and above, dietary cholesterol was only associated with dietary saturated fatty acids and serum high-density lipoprotein cholesterol. There was no evidence of an association between dietary cholesterol and cognitive function, except for NHB individuals, where dietary cholesterol showed a positive correlation with cognitive function. In the overall sample and NHW participants, there were consistent positive associations between serum total cholesterol and cognitive performance across statistical tests, while such associations were rare among NHB individuals. Although not statistically significant, NHB individuals had higher dietary/supplementary/total cholesterol intake compared with NHW individuals.

CONCLUSION

Within the normal range, increasing serum cholesterol may be a potential factor to prevent or relieve cognitive dysfunction. However, ethnic differences should be taken into account when considering the association between cholesterol and cognitive performance.

Prevalence of High HDL Cholesterol and Its Associated Factors Among Tunisian Women of Childbearing Age: A Cross-Sectional Study

The protective role of high high-density lipoprotein cholesterol (HDL-C) against cardiovascular risk has been questioned recently. Due to the increasing trend of cardiovascular diseases (CVD) in Tunisia, this study aimed to determine the prevalence of high HDL-C and its associated factors in Tunisian women of childbearing age. A cross-sectional survey was conducted among a subsample of 1689 women, aged 20 to 49 years, in the Great Tunis region. Data on socio-demographic and lifestyle factors were collected by a questionnaire. Overall adiposity was assessed by body mass index (BMI). All biological variables were assayed in blood samples coated with anticoagulant ethylene diamine tetra acetic acid (EDTA) by enzymatic methods. Stata software (2015) was used for data management and statistical analysis. High HDL-C values were recorded in 26.6% of selected women. After adjustment for all socio-demographic and lifestyle factors, age, hypertension, and smoking were negatively associated with high HDL-C levels, while family history of cancer was positively associated with high HDL-C in women. An additional investigation on the relationship between high HDL-C and cancer risk should be performed due to controversial results.

Residual Cardiovascular Risk at Low LDL: Remnants, Lipoprotein(a), and Inflammation

BACKGROUND

Current guidelines target low-density lipoprotein cholesterol (LDL-C) concentrations to reduce atherosclerotic cardiovascular disease (ASCVD) risk, and yet clinical trials demonstrate persistent residual ASCVD risk despite aggressive LDL-C lowering.

CONTENT

Non-LDL-C lipid parameters, most notably triglycerides, triglyceride-rich lipoproteins (TGRLs), and lipoprotein(a), and C-reactive protein as a measure of inflammation are increasingly recognized as associated with residual risk after LDL-C lowering. Eicosapentaenoic acid in statin-treated patients with high triglycerides reduced both triglycerides and ASCVD events. Reducing TGRLs is believed to have beneficial effects on inflammation and atherosclerosis. High lipoprotein(a) concentrations increase ASCVD risk even in individuals with LDL-C < 70 mg/dL. Although statins do not generally lower lipoprotein(a), proprotein convertase subtilisin/kexin type 9 inhibitors reduce lipoprotein(a) and cardiovascular outcomes, and newer approaches are in development. Persistent increases in C-reactive protein after intensive lipid therapy have been consistently associated with increased risk for ASCVD events.

SUMMARY

We review the evidence that biochemical assays to measure TGRLs, lipoprotein(a), and C-reactive protein are associated with residual risk in patients treated to low concentrations of LDL-C. Growing evidence supports a causal role for TGRLs, lipoprotein(a), and inflammation in ASCVD; novel therapies that target TGRLs, lipoprotein(a), and inflammation are in development to reduce residual ASCVD risk.

Candidate Gene Analysis Reveals Strong Association of CETP Variants With High Density Lipoprotein Cholesterol and PCSK9 Variants With Low Density Lipoprotein Cholesterol in Ghanaian Adults: An AWI-Gen Sub-Study

Variations in lipid levels are attributed partly to genetic factors. Genome-wide association studies (GWASs) mainly performed in European, African American and Asian cohorts have identified variants associated with LDL-C, HDL-C, total cholesterol (TC) and triglycerides (TG), but few studies have been performed in sub-Saharan Africans. This study evaluated the effect of single nucleotide variants (SNVs) in eight candidate loci (ABCA1, LCAT, LPL, PON1, CETP, PCSK9, MVK, and MMAB) on lipid levels among 1855 Ghanaian adults. All lipid levels were measured directly using an automated analyser. DNA was extracted and genotyped using the H3Africa SNV array. Linear regression models were used to test the association between SNVs and log-transformed lipid levels, adjusting for sex, age and waist circumference. In addition Bonferroni correction was performed to account for multiple testing. Several variants of CETP, LCAT, PCSK9, and PON1 (MAF > 0.05) were associated with HDL-C, LDL-C and TC levels at p < 0.05. The lead variants for association with HDL-C were rs17231520 in CETP (β = 0.139, p < 0.0001) and rs1109166 in LCAT (β = −0.044, p = 0.028). Lower LDL-C levels were associated with an intronic variant in PCSK9 (rs11806638 [β = −0.055, p = 0.027]) and increased TC was associated with a variant in PON1 (rs854558 [β = 0.040, p = 0.020]). In silico functional analyses indicated that these variants likely influence gene function through their effect on gene transcription. We replicated a strong association between CETP variants and HDL-C and between PCSK9 variant and LDL-C in West Africans, with two potentially functional variants and identified three novel variants in linkage disequilibrium in PON1 which were associated with increasing TC levels in Ghanaians.

Association between lipoprotein lipase gene polymorphisms and cardiovascular disease risk factors in European adolescents: The Healthy Lifestyle in Europe by Nutrition in Adolescence study

OBJECTIVES

To examine the association of lipoprotein lipase (LPL) polymorphisms with cardiovascular disease (CVD) risk factors in European adolescents, along with the influence of physical activity on these associations.

METHODS

A total of 13 LPL polymorphisms were genotyped in 1.057 European adolescents (12-18 years old) from the Healthy Lifestyle in Europe by Nutrition in Adolescence Cross-Sectional Study. Serum lipids, glucose, insulin, and leptin (LEP) levels were measured and a CVD risk score was computed. We also measured body weight and height, waist and hip circumferences, and triceps and subscapular skinfold thickness. Physical activity was objectively measured by accelerometry for 7 days.

RESULTS

The rs1534649, rs258, rs320, and rs328 polymorphisms were associated with several CVD risk factors (ie, body mass index, triglycerides [TG], LEP, and cholesterol/high-density lipoprotein [HDL], low-density lipoprotein [LDL]/HDL, TG/HDL ratios). TG and TG/HDL were associated with haplotype blocks 3 (rs282, rs285 polymorphisms) and 4 (rs3126, rs320, rs328, rs10099160 polymorphisms), being the latter also associated with the CVD risk score. Physical activity modulated the association of adiposity with rs1534649 and rs258 polymorphisms.

CONCLUSIONS

Polymorphisms rs1534649, rs258, rs320 and rs328, and two haplotypes of LPL were significantly associated with CVD risk factors in European adolescents. Higher levels of moderate to vigorous physical activity may attenuate the effects of rs1534649 and rs258 polymorphisms on adiposity.

Triglyceride Paradox Is Related to Lipoprotein Size, Visceral Adiposity and Stearoyl-CoA Desaturase Activity in Black Versus White Women

RATIONALE

In black women, triglycerides are paradoxically normal in the presence of insulin resistance. This relationship may be explained by race-related differences in central adiposity and SCD (stearoyl-CoA desaturase)-1 enzyme activity index.

OBJECTIVE

In a cross-sectional study, to compare fasting and postprandial triglyceride-rich lipoprotein particle (TRLP) concentrations and size in black compared with white pre- and postmenopausal women and determine the relationship between TRLP subfractions and whole-body insulin sensitivity, hepatic and visceral fat, and SCD-1 levels.

METHODS AND RESULTS

In 122 federally employed women without diabetes mellitus, 73 black (58 African American and 15 African immigrant) and 49 white; age, 44±10 (mean±SD) years; body mass index, 30.0±5.6 kg/m², we measured lipoprotein subfractions using nuclear magnetic resonance. Hepatic fat was measured by proton magnetic resonance spectroscopy, insulin sensitivity index calculated by minimal modeling from a frequently sampled intravenous glucose test, and red blood cell fatty acid profiles were measured by gas chromatography and were used to estimate SCD-1 indices. Hepatic fat, insulin sensitivity index, and SCD-1 were similar in black women and lower than in whites, regardless of menopausal status. Fasting and postprandial large, medium, and small TRLPs, but not very small TRLPs, were lower in black women. Fasting large, medium, and very small TRLPs negatively correlated with insulin sensitivity index and positively correlated with visceral and hepatic fat and SCD-1 activity in both groups. In multivariate models, visceral fat and SCD-1 were associated with total fasting TRLP concentrations (adjR2, 0.39; P=0.001). Black women had smaller postprandial changes in large (P=0.005) and medium TRLPs (P=0.007).

CONCLUSIONS

Lower visceral fat and SCD-1 activity may contribute to the paradoxical association of lower fasting and postprandial TRLP subfractions despite insulin resistance in black compared with white pre- and postmenopausal women. Similar concentrations of very small TRLPs are related to insulin resistance and could be important mediators of cardiometabolic disease risk in women.

CLINICAL TRIAL REGISTRATION

URL: http://www.clinicaltrials.gov. Unique identifier: NCT01809288.

Genetic association of LPL rs1121923 and rs258 with plasma TG and VLDL levels

Lipoprotein lipase (LPL) is a rate-limiting enzyme for the hydrolysis of triglycerides (TG). Hundreds of genetic variants including single nucleotide polymorphisms have been identified across the 30Kb gene locus on chromosome 8q22. Several of these variants have been demonstrated to have genetic association with lipid level variation but many remain unresolved. Controversial reports on the genetic association of variants among different populations pose a challenge to which variants are informative. This study aimed to investigate "common" LPL variants (rs1121923, rs258, rs328, rs13702) and their possible role in plasma lipid level. Genotyping was performed using Realtime PCR. Based on the observed genotypes, the minor allele frequencies were A: 0.065 for rs1121923; C: 0.379 for rs258; G: 0.087 for rs328 and C: 0.337 for rs13702. Using linear regression, a lowering effect of rs1121923 (p = 0.024) on TG levels (-0.14 B coefficient: CI: -0.27--0.019) and rs258 (p = 0.013) on VLDL levels (B: -0.046; CI: -0.082--0.009) was observed indicating a "protective" role for the two variants. Moreover, the findings indicate the potential for including rs1121923 and rs258 in diagnostic panels for use as an estimator of "risk" scores for dyslipidemia.

Genetic control of the mouse HDL proteome defines HDL traits, function, and heterogeneity

HDLs are nanoparticles with more than 80 associated proteins, phospholipids, cholesterol, and cholesteryl esters. The potential inverse relation of HDL to coronary artery disease (CAD) and the effects of HDL on myriad other inflammatory conditions warrant a better understanding of the genetic basis of the HDL proteome. We conducted a comprehensive genetic analysis of the regulation of the proteome of HDL isolated from a panel of 100 diverse inbred strains of mice (the hybrid mouse diversity panel) and examined protein composition and efflux capacity to identify novel factors that affect the HDL proteome. Genetic analysis revealed widely varied HDL protein levels across the strains. Some of this variation was explained by local cis-acting regulation, termed cis-protein quantitative trait loci (QTLs). Variations in apoA-II and apoC-3 affected the abundance of multiple HDL proteins, indicating a coordinated regulation. We identified modules of covarying proteins and defined a protein-protein interaction network that describes the protein composition of the naturally occurring subspecies of HDL in mice. Sterol efflux capacity varied up to 3-fold across the strains, and HDL proteins displayed distinct correlation patterns with macrophage and ABCA1-specific cholesterol efflux capacity and cholesterol exchange, suggesting that subspecies of HDL participate in discrete functions. The baseline and stimulated sterol efflux capacity phenotypes were associated with distinct QTLs with smaller effect size, suggesting a multigenetic regulation. Our results highlight the complexity of HDL particles by revealing the high degree of heterogeneity and intercorrelation, some of which is associated with functional variation, and support the concept that HDL-cholesterol alone is not an accurate measure of HDL’s properties, such as protection against CAD.

The burden of dyslipidaemia and factors associated with lipid levels among adults in rural northern Ghana: An AWI-Gen sub-study

Dyslipidaemia is a primary risk factor for cardiometabolic disease, causing over 17 million deaths globally in 2015. However, the burden of dyslipidaemia and factors associated with lipid levels remain unknown in many rural African populations. Therefore, this study evaluated the association of socio-demographic, anthropometric and behavioural factors with lipid levels in rural Ghana. The prevalence of hypercholesterolaemia, hypertriglyceridaemia and elevated LDL-C in the total population of 1839 (846 men and 993 women) was 4.02%, 2.12%, and 5.55% respectively and did not differ between genders. The prevalence of low HDL-C levels was 60.30% and differed (p = 0.005) between men (56.86%) and women (63.24%). Subcutaneous abdominal fat was associated with TC (β = 0.067, p = 0.015) and TG (β = 0.137, p<0.001) among women and LDL-C (β = 0.139, p = 0.006) and TC (β = 0.071, p = 0.048) among men. Body mass index was associated with TC (β = 0.010, p = 0.043) among men while waist circumference was associated with LDL-C (β = 0.116, p<0.001) and TG (β = 0.094, p<0.001) among women. Hip circumference was negatively associated (β = -0.053, p = 0.043) while visceral fat was positively associated with TG (β = 0.033, p = 0.022) among women. Socioeconomic status, education, being unmarried and employment were associated with HDL-C (β = 0.081, p = 0.004), LDL-C (β = 0.095, p = 0.004) and TG (β = 0.095, p = 0.001) all among women, and TC (β = 0.070, p = 0.010) among men, respectively. Nankana women had lower TC (β = -0.069, p = 0.001), and men lower TG levels (β = -0.084, p = 0.008) than the other ethnic groups. Tobacco smoking (β = 0.066, p = 0.024) and alcohol intake (β = 0.084, p = 0.001) were associated with HDL-C levels among men and women respectively. Further studies are required to investigate whether high prevalence of low HDL-C levels in this population presents with any adverse cardiovascular disease outcomes. Associations of education, employment and adiposity with lipid levels suggest that future societal advances and increases in the prevalence of obesity may lead to associated adverse health consequences. Monitoring and interventions are required to limit these effects.

Remnant-Like Particle Cholesterol, Low-Density Lipoprotein Triglycerides, and Incident Cardiovascular Disease

BACKGROUND

Hypertriglyceridemia is associated with increased remnant-like particle cholesterol (RLP-C) and triglycerides in low-density lipoprotein (LDL-TG). Recent studies have focused on atherogenicity of RLP-C, with few data on LDL-TG.

OBJECTIVES

The aim of this study was to examine associations of RLP-C and LDL-TG with incident cardiovascular disease (CVD) events and genetic variants in the ARIC (Atherosclerosis Risk In Communities) study.

METHODS

Fasting plasma RLP-C and LDL-TG levels were measured in 9,334 men and women without prevalent CVD. Participants were followed for incident CVD events (coronary heart disease and ischemic stroke) for up to 16 years. Associations between LDL-TG and RLP-C levels and genetic variants were assessed by whole-exome sequencing using single-variant analysis for common variants and gene-based burden tests for rare variants; both an unbiased and a candidate gene approach were explored.

RESULTS

RLP-C and LDL-TG levels were correlated with triglyceride levels (r = 0.85 and r = 0.64, p < 0.0001). In minimally adjusted analyses, RLP-C and LDL-TG were associated with CVD risk, but in models adjusted for traditional risk factors including lipids, only LDL-TG was associated with incident CHD (hazard ratio: 1.28; 95% confidence interval: 1.10 to 1.50) and stroke (hazard ratio: 1.47; 95% confidence interval: 1.13 to 1.92). A common APOE variant, rs7412, had the strongest association with LDL-TG and RLP-C (p < 5 × 10-8).

CONCLUSIONS

RLP-C and LDL-TG levels were predictive of CVD and associated with APOE variants. LDL-TG may represent a marker of dysfunctional remnant lipoprotein metabolism associated with increased CVD risk. Further research is needed to determine whether LDL-TG plays a causal role in CVD and may be a target for therapy.

A novel LPL intronic variant: g.18704C>A identified by re-sequencing Kuwaiti Arab samples is associated with high-density lipoprotein, very low-density lipoprotein and triglyceride lipid levels

The role interethnic genetic differences play in plasma lipid level variation across populations is a global health concern. Several genes involved in lipid metabolism and transport are strong candidates for the genetic association with lipid level variation especially lipoprotein lipase (LPL). The objective of this study was to re-sequence the full LPL gene in Kuwaiti Arabs, analyse the sequence variation and identify variants that could attribute to variation in plasma lipid levels for further genetic association. Samples (n = 100) of an Arab ethnic group from Kuwait were analysed for sequence variation by Sanger sequencing across the 30 Kb LPL gene and its flanking sequences. A total of 293 variants including 252 single nucleotide polymorphisms (SNPs) and 39 insertions/deletions (InDels) were identified among which 47 variants (32 SNPs and 15 InDels) were novel to Kuwaiti Arabs. This study is the first to report sequence data and analysis of frequencies of variants at the LPL gene locus in an Arab ethnic group with a novel “rare” variant (LPL:g.18704C>A) significantly associated to HDL (B = -0.181; 95% CI (-0.357, -0.006); p = 0.043), TG (B = 0.134; 95% CI (0.004–0.263); p = 0.044) and VLDL (B = 0.131; 95% CI (-0.001–0.263); p = 0.043) levels. Sequence variation in Kuwaiti Arabs was compared to other populations and was found to be similar with regards to the number of SNPs, InDels and distribution of the number of variants across the LPL gene locus and minor allele frequency (MAF). Moreover, comparison of the identified variants and their MAF with other reports provided a list of 46 potential variants across the LPL gene to be considered for future genetic association studies. The findings warrant further investigation into the association of g.18704C>A with lipid levels in other ethnic groups and with clinical manifestations of dyslipidemia.

The genomic landscape of African populations in health and disease

A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.

Interethnic Differences in Serum Lipids and Implications for Cardiometabolic Disease Risk in African Ancestry Populations

African Americans generally have a healthier lipid profile (lower triglycerides and higher high-density lipoprotein cholesterol concentration) compared with those of other ethnicities. Paradoxically, African Americans do not experience a decreased risk of the cardiometabolic diseases that serum lipids are expected to predict. This review explores this mismatch between biomarker and disease among African ancestry individuals by investigating the presence of interethnic differences in the biological relationships underlying the serum lipids-disease association. This review also discusses the physiologic and genomic factors underlying these interethnic differences. Additionally, because of the importance of serum lipids in assessing disease risk, interethnic differences in serum lipids have implications for identifying African ancestry individuals at risk of cardiometabolic disease. Where possible, data from Africa is included, to further elucidate these ancestral differences in the context of a different environmental background.

The African diaspora: history, adaptation and health

The trans-Atlantic slave trade brought millions of Africans to the New World. Advances in genomics are providing novel insights into the history and health of Africans and the diasporan populations. Recent examples reviewed here include the unraveling of substantial hunter-gatherer and 'Eurasian' admixtures across sub-Saharan Africa, expanding our understanding of ancestral African genetics; the global ubiquity of mixed ancestry; the revealing of African ancestry in Latin Americans that likely derived from the slave trade; and understanding of the ancestral backgrounds of APOL1 and LPL found to influence kidney disease and lipid levels, respectively, providing specific insights into disease etiology and health disparities.

Social Determinants of Racial Disparities in CKD

Significant disparities in CKD rates and outcomes exist between black and white Americans. Health disparities are defined as health differences that adversely affect disadvantaged populations, on the basis of one or more health outcomes. CKD is the complex result of genetic and environmental factors, reflecting the balance of nature and nurture. Social determinants of health have an important role as environmental components, especially for black populations, who are disproportionately disadvantaged. Understanding the social determinants of health and appreciating the underlying differences associated with meaningful clinical outcomes may help nephrologists treat all their patients with CKD in an optimal manner. Altering the social determinants of health, although difficult, may embody important policy and research efforts, with the ultimate goal of improving outcomes for patients with kidney diseases, and minimizing the disparities between groups.

Trimethylamine N-Oxide and Cardiovascular Events in Hemodialysis Patients

Cardiovascular disease causes over 50% of the deaths in dialysis patients, and the risk of death is higher in white than in black patients. The underlying mechanisms for these findings are unknown. We determined the association of the proatherogenic metabolite trimethylamine N-oxide (TMAO) with cardiovascular outcomes in hemodialysis patients and assessed whether this association differs by race. We measured TMAO in stored serum samples obtained 3-6 months after randomization from a total of 1232 white and black patients of the Hemodialysis Study, and analyzed the association of TMAO with cardiovascular outcomes using Cox models adjusted for potential confounders (demographics, clinical characteristics, comorbidities, albumin, and residual kidney function). Mean age of the patients was 58 years; 35% of patients were white. TMAO concentration did not differ between whites and blacks. In whites, 2-fold higher TMAO associated with higher risk (hazard ratio [95% confidence interval]) of cardiac death (1.45 [1.24 to 1.69]), sudden cardiac death [1.70 (1.34 to 2.15)], first cardiovascular event (1.15 [1.01 to 1.32]), and any-cause death (1.22 [1.09 to 1.36]). In blacks, the association was nonlinear and significant only for cardiac death among patients with TMAO concentrations below the median (1.58 [1.03 to 2.44]). Compared with blacks in the same quintile, whites in the highest quintile for TMAO (≥135 μM) had a 4-fold higher risk of cardiac or sudden cardiac death and a 2-fold higher risk of any-cause death. We conclude that TMAO concentration associates with cardiovascular events in hemodialysis patients but the effects differ by race.

Association between Polymorphisms and Haplotype in the ABCA1 Gene and Overweight/Obesity Patients in the Uyghur Population of China

OBJECTIVE

This study aimed to detect the association between polymorphisms and haplotype in the ATP-binding cassette transporter A1 (ABCA1) gene and overweight/obese Uyghur patients in China.

METHODS

A total of 259 overweight/obese patients and 276 normal weight subjects, which were randomly selected from among 3049 adult Uyghurs, were matched for age. We genotyped ABCA1 single nucleotide polymorphisms of rs2515602, rs3890182, rs2275542, rs2230806, rs1800976, and rs4149313.

RESULTS

(1) The genotypic and allelic frequencies of rs2515602 and rs4149313 differed between the control group and case group. The genotypic frequency of rs2275542 also differed between the control group and case group (p < 0.05); (2) rs2515602, rs2230806, and rs4149313 polymorphisms were significantly related to risk of overweight/obese; (3) a significant linkage disequilibrium (LD) was observed between the ABCA1 gene rs2275542 with rs3890182 and rs2515602 with rs4149313. (4) the C-C-C-A-G-G, T-C-G-A-G-G, and T-T-G-G-G-A haplotypes were significant in normal weight and overweight/obese subjects (p < 0.05); (5) the levels of HDL-C (rs2515602, rs2275542, rs4149313) in normal weight subjects were different among the genotypes (p < 0.05); the levels of TC, LDL-C and TG (rs1800976) in overweight/obese subjects were different among the genotypes (p < 0.05).

CONCLUSIONS

The rs2515602, rs4149313, and rs2275542 polymorphisms were associated with overweight/obese conditions among Uyghurs. Strong LD was noted between rs2275542 with rs3890182 and rs2515602 with rs4149313. The C-C-C-A-G-G and T-C-G-A-G-G haplotypes may serve as risk factors of overweight/obesity among Uyghurs. The T-T-G-G-G-A haplotype may serve as a protective factor of overweight/obesity among Uyghurs. Rs2515602, rs2275542, rs4149313, and rs1800976 polymorphisms in the ABCA1 gene may influence lipid profiles.

Interactions of Six SNPs in ABCA1gene and Obesity in Low HDL-C Disease in Kazakh of China

OBJECTIVE

To detect the interactions between six functional polymorphisms in ABCA1 and obesity in Kazakhs with low HDL-C levels.

METHODS

A total of 204 patients with low HDL-C and 207 health control subjects, which were randomly selected from among 5692 adult Kazakhs, were matched for age and sex. We genotyped ABCA1 single nucleotide polymorphisms of rs2515602, rs3890182, rs2275542, rs2230806, rs1800976, and rs4149313.

RESULTS

(1) The genotypic and allelic frequencies of rs2515602, rs2230806 and rs4149313 were different between normal HDL-C and low HDL-C subjects, the genotypic frequency of rs2275542 was also different between normal HDL-C and low HDL-C subjects (p < 0.05); (2) the level of HDL-C (rs2515602 and rs2275542) in normal HDL-C subjects were different among the genotypes (p < 0.05); the levels of TC, LDL-C (rs2515602, rs4149313); TG (rs2515602, rs1800976, rs4149313) in low HDL-C patients were different among the genotypes (p < 0.05); (3) interactions between the rs3890182, rs2275542, rs180096, and rs4149313 polymorphisms in ABCA1 gene and obesity may be associated with low HDL-C disease; (4) the C-C-C-A-A-G, T-C-C-A-A-A, T-C-C-A-A-G, C-C-C-A-A-A, C-T-G-G-A-A, and T-T-C-G-A-A haplotypes were significant between the subjects with normal HDL-C and low HDL-C level (p < 0.05).

CONCLUSIONS

The differences in serum lipid levels between normal HDL-C and low HDL-C subjects among Kazakhs might partly result from ABCA1 gene polymorphisms; ABCA1 gene polymorphisms may be associated with low HDL-C disease; the low HDL-C disease might partly result from interactions between ABCA1 gene polymorphisms and obesity; the C-C-C-A-A-G, T-C-C-A-A-A, and T-C-C-A-A-G haplotypes may serve as risk factors of low HDL-C disease among Kazakhs, the C-C-C-A-A-A, C-T-G-G-A-A, and T-T-C-G-A-A haplotypes may serve as protective factor of low HDL-C disease among Kazakhs.

Dissecting ancestry genomic background in substance dependence genome-wide association studies

AIMS

To understand the role of ancestral genomic background in substance dependence (SD) genome-wide association studies (GWAS), we analyzed population diversity at genetic loci associated with SD traits and evaluated its effect on GWAS outcomes.

MATERIALS & METHODS

We investigated 24 genes with variants associated with SD by GWAS; and 82 loci with putative subordinate roles with respect to SD-associated genes.

RESULTS

We observed high ancestry-related frequency differences in common functional alleles in GWAS relevant genes and their interactive partners. Common functional alleles with high frequency differences demonstrated significant effects on the GWAS outcomes.

CONCLUSION

Population differences in SD GWAS outcomes seem not to be influenced by general variation across the genome, but by ancestry-related local haplotype structures at SD-associated loci.

Genetics of celiac disease

New insights into the underlying molecular pathophysiology of celiac disease (CeD) over the last few years have been guided by major advances in the fields of genetics and genomics. The development and use of the Immunochip genotyping platform paved the way for the discovery of 39 non-HLA loci associated to CeD, and for follow-up functional genomics studies that pinpointed new disease genes, biological pathways and regulatory elements. By combining information from genetics with gene expression data, it has become clear that CeD is a disease with a dysregulated immune response, which can probably occur in a variety of immune cells. This type of information is crucial for our understanding of the disease and for providing leads for developing alternative therapies to the current gluten-free diet. In this review, we place these genetic findings in a wider context and suggest how they can assist the clinical care of CeD patients.

Trans-ethnic genome-wide association studies: advantages and challenges of mapping in diverse populations

Genome-wide association studies (GWASs) are the method most often used by geneticists to interrogate the human genome, and they provide a cost-effective way to identify the genetic variants underpinning complex traits and diseases. Most initial GWASs have focused on genetically homogeneous cohorts from European populations given the limited availability of ethnic minority samples and so as to limit population stratification effects. Transethnic studies have been invaluable in explaining the heritability of common quantitative traits, such as height, and in examining the genetic architecture of complex diseases, such as type 2 diabetes. They provide an opportunity for large-scale signal replication in independent populations and for cross-population meta-analyses to boost statistical power. In addition, transethnic GWASs enable prioritization of candidate genes, fine-mapping of functional variants, and potentially identification of SNPs associated with disease risk in admixed populations, by taking advantage of natural differences in genomic linkage disequilibrium across ethnically diverse populations. Recent efforts to assess the biological function of variants identified by GWAS have highlighted the need for large-scale replication, meta-analyses and fine-mapping across worldwide populations of ethnically diverse genetic ancestries. Here, we review recent advances and new approaches that are important to consider when performing, designing or interpreting transethnic GWASs, and we highlight existing challenges, such as the limited ability to handle heterogeneity in linkage disequilibrium across populations and limitations in dissecting complex architectures, such as those found in recently admixed populations.