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BACKGROUND: The burden of stroke in Africa is high. Understanding how age associates with major modifiable stroke risk factors could inform tailored demographic stroke prevention strategies. PURPOSE: To quantify the magnitude and direction of the effect sizes of key modifiable stroke risk factors according to three age groups: 65 years (elderly) in West Africa. METHODS: This was a case-control study involving 15 sites in Ghana and Nigeria. Cases included adults aged ≥18 years with CT/MRI scan-typed stroke. Controls were age-and gender-matched stroke-free adults. Detailed evaluations for vascular, lifestyle and psychosocial factors were performed. We estimated adjusted odds ratios (aOR) using conditional logistic regression and population attributable risk (PAR) with 95% Confidence Interval of vascular risk factors by age groups. RESULTS: Among 3553 stroke cases, 813 (22.9%) were young, 1441 (40.6%) were middle-aged and 1299 (36.6%) were elderly. Among the 5 co-shared risk factors, dyslipidemia with PAR and aOR (95%CI) of 62.20% (52.82–71.58) and 4.13 (2.64–6.46) was highest among the young age group; hypertension with PAR of 94.31% (91.82–96.80) and aOR of 28.93 (15.10–55.44) was highest among the middle-age group. Diabetes with PAR of 32.29% (27.52–37.05) and aOR of 3.49 (2.56–4.75); meat consumption with PAR of 42.34%(32.33–52.35) and aOR of 2.40 (1.76, 3.26); and non-consumption of green vegetables, PAR of 16.81%(12.02–21.60) and aOR of 2.23 (1.60–3.12) were highest among the elderly age group. However confidence intervals of risk estimates over-lapped across age groups. Additionally, among the young age group cigarette smoking, psychosocial stress and cardiac disease were independently associated with stroke. Furthermore, education, stress, physical inactivity and salt intake were associated with stroke in the middle-age group while cardiac disease was associated with stroke in the elderly age group. CONCLUSION: There is a differential influence of age on the associations of major risk factors with stroke in this West African cohort. Targeting modifiable factors predominant within an age group may be more effective as a stroke prevention strategy.

OBJECTIVE The aim of this study was to characterize environmental exposure from Deepwater Horizon oil spill among pre-K to fourth-grade children from six schools in Mobile County, Alabama. METHODS A mail-in survey administered 11 months post-oil spill to children's parents/caregivers elicited information on exposure-related activities. Descriptive and multivariable analyses were performed. RESULTS Overall, 180 children (coastal schools, 90; inland schools, 90) completed the survey. During the post-oil spill period, children in coastal schools were less likely to reduce their exposure-related activities, including fishing; eating and selling caught fish; visiting beaches; and parental participation in cleanup activities, than children in inland schools. Particularly, fishing and eating caught fish were significantly associated with the coastal group (odds ratio = 2.28; 95% confidence interval = 1.54 to 3.36). CONCLUSION Proximity to the shoreline may serve as an indicator for potential exposure in oil spills among vulnerable populations including children.

BACKGROUND: Trimethylamine-N-oxide (TMAO), an atherogenic metabolite species, has emerged as a possible new risk factor for cardiovascular disease. Animal studies have shown that circulating TMAO levels are regulated by genetic and environmental factors. However, large-scale human studies have failed to replicate the observed genetic associations, and epigenetic factors such as DNA methylation have never been examined in relation to TMAO levels. METHODS AND RESULTS: We used data from the family-based Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) to investigate the heritable determinants of plasma TMAO in humans. TMAO was not associated with other plasma markers of cardiovascular disease, e.g. lipids or inflammatory cytokines. We first estimated TMAO heritability at 27%, indicating a moderate genetic influence. We used 1000 Genomes imputed data (n=626) to estimate genome-wide associations with TMAO levels, adjusting for age, sex, family relationships, and study site. The genome-wide study yielded one significant hit at the genome-wide level, located in an intergenic region on chromosome 4. We subsequently quantified epigenome-wide DNA methylation using the Illumina Infinium array on CD4+ T-cells. We tested for association of methylation loci with circulating TMAO (n=847), adjusting for age, sex, family relationships, and study site as the genome-wide study plus principal components capturing CD4+ T-cell purity. Upon adjusting for multiple testing, none of the epigenetic findings were statistically significant. CONCLUSIONS: Our findings contribute to the growing body of evidence suggesting that neither genetic nor epigenetic factors play a critical role in establishing circulating TMAO levels in humans. This work was funded by the American Heart Association (14CRP18060003, PI: Aslibekyan) and the National Institutes of Health (R01HL104135, PI: Arnett). Sí

Age is the dominant risk factor for most chronic human diseases; yet the mechanisms by which aging confers this risk are largely unknown.1 Recently, the age-related acquisition of somatic mutations in regenerating hematopoietic stem cell populations was associated with both hematologic cancer incidence2–4 and coronary heart disease prevalence.5 Somatic mutations with leukemogenic potential may confer selective cellular advantages leading to clonal expansion, a phenomenon termed ‘Clonal Hematopoiesis of Indeterminate Potential’ (CHIP).6 Simultaneous germline and somatic whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze high-coverage whole genome sequences from 97,691 participants of diverse ancestries in the NHLBI TOPMed program and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid, and inflammatory traits specific to different CHIP genes. Association of a genome-wide set of germline genetic variants identified three genetic loci associated with CHIP status, including one locus at TET2 that was African ancestry specific. In silico-informed in vitro evaluation of the TET2 germline locus identified a causal variant that disrupts a TET2 distal enhancer. Aggregates of rare germline loss-of-function variants in CHEK2, a DNA damage repair gene, predisposed to CHIP acquisition. Overall, we observe that germline genetic variation altering hematopoietic stem cell function and the fidelity of DNA-damage repair increase the likelihood of somatic mutations leading to CHIP.

© 2020, The Author(s), under exclusive licence to Springer Nature Limited. Age is the dominant risk factor for most chronic human diseases, but the mechanisms through which ageing confers this risk are largely unknown1. The age-related acquisition of somatic mutations that lead to clonal expansion in regenerating haematopoietic stem cell populations has recently been associated with both haematological cancer2–4 and coronary heart disease5—this phenomenon is termed clonal haematopoiesis of indeterminate potential (CHIP)6. Simultaneous analyses of germline and somatic whole-genome sequences provide the opportunity to identify root causes of CHIP. Here we analyse high-coverage whole-genome sequences from 97,691 participants of diverse ancestries in the National Heart, Lung, and Blood Institute Trans-omics for Precision Medicine (TOPMed) programme, and identify 4,229 individuals with CHIP. We identify associations with blood cell, lipid and inflammatory traits that are specific to different CHIP driver genes. Association of a genome-wide set of germline genetic variants enabled the identification of three genetic loci associated with CHIP status, including one locus at TET2 that was specific to individuals of African ancestry. In silico-informed in vitro evaluation of the TET2 germline locus enabled the identification of a causal variant that disrupts a TET2 distal enhancer, resulting in increased self-renewal of haematopoietic stem cells. Overall, we observe that germline genetic variation shapes haematopoietic stem cell function, leading to CHIP through mechanisms that are specific to clonal haematopoiesis as well as shared mechanisms that lead to somatic mutations across tissues.

Background Left ventricular (LV) hypertrophy affects up to 43% of African Americans (AAs). Antihypertensive treatment reduces LV mass (LVM). However, interindividual variation in LV traits in response to antihypertensive treatments exists. We hypothesized that genetic variants may modify the association of antihypertensive treatment class with LV traits measured by echocardiography. Methods We evaluated the main effects of the three most common antihypertensive treatments for AAs as well as the single nucleotide polymorphism (SNP)‐by‐drug interaction on LVM and relative wall thickness (RWT) in 2,068 participants across five community‐based cohorts. Treatments included thiazide diuretics (TDs), angiotensin converting enzyme inhibitors (ACE‐Is), and dihydropyridine calcium channel blockers (dCCBs) and were compared in a pairwise manner. We performed fixed effects inverse variance weighted meta‐analyses of main effects of drugs and 2.5 million SNP‐by‐drug interaction estimates. Results We observed that dCCBs versus TDs were associated with higher LVM after adjusting for covariates (p = 0.001). We report three SNPs at a single locus on chromosome 20 that modified the association between RWT and treatment when comparing dCCBs to ACE‐Is with consistent effects across cohorts (smallest p = 4.7 × 10−8, minor allele frequency range 0.09–0.12). This locus has been linked to LV hypertrophy in a previous study. A marginally significant locus in BICD1 (rs326641) was validated in an external population. Conclusions Our study identified one locus having genome‐wide significant SNP‐by‐drug interaction effect on RWT among dCCB users in comparison to ACE‐I users. Upon additional validation in future studies, our findings can enhance the precision of medical approaches in hypertension treatment.

Most genome-wide association and fine-mapping studies to date have been conducted in individuals of European descent, and genetic studies of populations of Hispanic/Latino and African ancestry are limited. In addition, these populations have more complex linkage disequilibrium structure. In order to better define the genetic architecture of these understudied populations, we leveraged >100,000 phased sequences available from deep-coverage whole genome sequencing through the multi-ethnic NHLBI Trans-Omics for Precision Medicine (TOPMed) program to impute genotypes into admixed African and Hispanic/Latino samples with genome-wide genotyping array data. We demonstrated that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations, which subsequently enhanced gene-mapping power for complex traits. For rare variants with minor allele frequency (MAF) < 0.5%, we observed a 2.3- to 6.1-fold increase in the number of well-imputed variants, with 11–34% improvement in average imputation quality, compared to the state-of-the-art 1000 Genomes Project Phase 3 and Haplotype Reference Consortium reference panels. Impressively, even for extremely rare variants with minor allele count 86%. Subsequent association analyses of TOPMed reference panel-imputed genotype data with hematological traits (hemoglobin (HGB), hematocrit (HCT), and white blood cell count (WBC)) in ~21,600 African-ancestry and ~21,700 Hispanic/Latino individuals identified associations with two rare variants in the HBB gene (rs33930165 with higher WBC [p = 8.8x10-15] in African populations, rs11549407 with lower HGB [p = 1.5x10-12] and HCT [p = 8.8x10-10] in Hispanics/Latinos). By comparison, neither variant would have been genome-wide significant if either 1000 Genomes Project Phase 3 or Haplotype Reference Consortium reference panels had been used for imputation. Our findings highlight the utility of the TOPMed imputation reference panel for identification of novel rare variant associations not previously detected in similarly sized genome-wide studies of under-represented African and Hispanic/Latino populations., Author summary Admixed African and Hispanic/Latino populations remain understudied in genetic studies of complex diseases. These populations have more complex linkage disequilibrium (LD) structure that can impair mapping of variants. Genotype imputation represents an approach to improve genome coverage, especially for rare or ancestry-specific variation; however, these understudied populations also have smaller relevant imputation reference panels. In this study, we leveraged >100,000 phased sequences generated from the multi-ethnic NHLBI TOPMed project for imputation in ~21,600 individuals of African ancestry (AAs) and ~21,700 Hispanics/Latinos. We demonstrated substantially higher imputation quality for low frequency and rare variants in comparison to the 1000 Genomes Project and Haplotype Reference Consortium reference panels. Analysis of quantitative hematological traits led to the discovery of associations with two rare variants in the HBB gene; one of these variants was replicated in an independent sample, and the other is known to cause anemia in the homozygous state. By comparison, the same HBB variants would not have been genome-wide significant using current reference panels due to lower imputation quality. Our findings demonstrate the power of TOPMed whole genome sequencing data for imputation and subsequent association analysis in admixed African and Hispanic/Latino populations.

Background African Americans have the highest rates of Chlamydia trachomatis (CT) infection in the U.S., nearly six-fold higher than Caucasians. Even after controlling for sociodemographic factors, African American women have higher CT infection rates, suggesting immunogenetic factors could influence infection risk. The primary objective of this study is to develop a Bayesian model to predict CT reinfection in African American women. Methods We are using data from a study cohort of CT-infected women who were enrolled when they returned to a STD clinic in Birmingham, AL, USA, for treatment of a positive screening urogenital CT nucleic acid amplification test. They had repeat urogenital CT NAAT performed at enrollment and 3- and 6-month follow-up visits. We modeled the probability of CT reinfection within 6 months after treatment using conditional logistic regression in a Bayesian framework and weakly informative priors. Primary predictors of interest were immunogenetic risk factors specified by the presence of at least one HLA-DQB1*06 allele and absence of a CT-specific CD4+ IFN-γ response. Additional predictors evaluated include the modifying effects of unprotected sex and concomitant bacterial vaginosis (BV). Results To date, we have evaluated 75 participants for whom complete data were available. Modeling both HLA-DQB1*06 and a CT-specific CD4+ IFN-γ response performed best for expected predictive accuracy of CT reinfection within 6 months after treatment. Under this model, the probability of reinfection for those with a CT-specific CD4+ IFN-γ response and no HLA-DQB1*06 alleles was 23.1% (95% CI: 7.6%–47.5%), whereas probability of reinfection for those without a CT-specific CD4+ IFN-γ response and at least one HLA-DQB1*06 allele was 75.0% (95% CI: 52.5%–89.1%). Conclusion Our model evaluating immunogenetic factors predicting CT reinfection demonstrated that presence of an HLA-DQB1*06 allele and absence of a CT-specific CD4+ IFN-γ response may be a significant predictor in African American women. Disclosure No significant relationships.

Background Little is known about the relationship between echocardiographic abnormalities and outcome among patients with acute stroke. We investigated the pattern and association of baseline echocardiographic variables with 1‐month disability and mortality among patients with stroke in the SIREN (Stroke Investigative Research and Education Network) study. Methods and Results We enrolled and followed up consecutive 1020 adult patients with acute stroke with baseline transthoracic echocardiography from west Africa. To explore the relationship between echocardiographic variables and 1‐month disability (using modified Rankin scale >3) and fatality, regression models were fitted. Relative risks were computed with 95% CIs. The participants comprised 60% men with a mean age of 59.2±14.6 years. Ischemic stroke was associated with smaller aortic root diameter (30.2 versus 32.5, P =0.018) and septal (16.8 versus 19.1, P P =0.004). Over 90% of patients with stroke had abnormal left ventricular (LV) geometry with eccentric hypertrophy predominating (56.1%). Of 13 candidate variables investigated, only baseline abnormal LV geometry (concentric hypertrophy) was weakly associated with 1‐month disability (unadjusted relative risk, 1.80; 95% CI , 0.97–5.73). Severe LV systolic dysfunction was significantly associated with increased 1‐month mortality (unadjusted relative risk, 3.05; 95% CI , 1.36–6.83). Conclusions Nine of 10 patients with acute stroke had abnormal LV geometry and a third had systolic dysfunction. Severe LV systolic dysfunction was significantly associated with 1 month mortality. Larger studies are required to establish the independent effect and unravel predictive accuracy of this association.

Background: Associations of both common and rare genetic variants with fasting blood lipids have been extensively studied. However, most of the rare coding variants associated with lipids are population-specific, and exploration of genetic data from diverse population samples may enhance the identification of novel associations with rare variants. Results: We searched for novel coding genetic variants associated with fasting lipid levels in 894 samples from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) with exome-wide sequencing-based genotype data. In single variant tests, one variant (rs11171663 in ITGA7) was associated with fasting triglyceride levels (P = 7.66E-08), explaining approximately 3.2% of the total trait variance. In gene-based tests, we found statistically significant associations between ITGA7 (P = 1.77E-07) and SLCO2A1 (P = 7.18E-07) and triglycerides, as well as between POT1 (P = 3.00E-07) and low-density lipoprotein cholesterol. In another independent replication cohort consisting of 3,183 African American samples from Hypertension Genetic Epidemiology Network (HyperGEN) and the Genetic Epidemiology Network of Arteriopathy (GENOA), the top genes achieved P-values of 0.04 (ITGA7), 0.08 (SLCO2A1), and 0.02 (POT1). In GOLDN, gene transcript levels of ITGA7 and SLCO2A1 were associated with fasting triglycerides (P = 0.07 and P = 0.02), highlighting functional relevance of our findings. Conclusion: In this study, we present preliminary evidence of novel rare variant determinants of fasting lipids, and reveal potential underlying molecular mechanisms. Moreover, these results were replicated in an independent cohort. Our findings may inform novel biomarkers of disease risk and treatment targets. The GOLDN study has been funded by the National Institutes of Health (NIH)National Heart, Lung, and Blood Institute (NHLBI) Grants U01HL072524 and R01HL091357. SA is additionally funded by NHLBI K01 HL136700 and JO by the U.S. Department of Agriculture, under agreement Nos. 8050-51000-098-00D and USDA-AFRI 2017-67017-26719. HyperGEN and GENOA have been funded by NIH R01HL055673 and U01HL075572. The HAPI Heart Study was supported by NIH grants U01 HL072515 and P30 DK072488. Whole genome sequencing of Amish subjects was provided by the Trans-Omics for Precision Medicine program through the National Heart, Lung and Blood Institute (NHLBI) and funded by 3R01HL12100701S1, 3R01HL-117626-02S1, and 3R01HL-120393-02S1. XG and DZ are partially supported by Agriculture and Food Research Initiative Competitive Grant no. 2015-67015-22975 from the USDA National Institute of Food and Agriculture, and USDA Aquaculture Research Program Competitive Grant no. 2014-70007-22395. Sí

Age-related hair graying is caused by malfunction in the regenerative potential of the adult pigmentation system. The retention of hair color over the life of an organism is dependent on the ability of the melanocyte stem cells and their progeny to produce pigment each time a new hair grows. Age-related hair graying is variable in association with genetic background suggesting that quantitative trait loci influencing this trait can be identified. Identification of these quantitative trait loci may lead to the discovery of novel and interesting genes involved in stem cell biology and/or melanogenesis. With this in mind we developed previously a sensitized, mouse modifier screen and discovered that the DBA/1J background is particularly resistant to melanocyte stem cell differentiation in comparison to the C57BL/6J background. Melanocyte stem cell differentiation generally precedes hair graying and is observed in melanocyte stem cells with age. Using quantitative trait loci analysis, we have now identified three quantitative trait loci on mouse chromosomes 7, 13, and X that are associated with DBA/1J-mediated variability in melanocyte stem cell differentiation. Taking advantage of publicly-available mouse sequence and variant data, in silico protein prediction programs, and whole genome gene expression results we describe a short list of potential candidate genes that we anticipate to be involved in melanocyte stem cell biology in mice.

Background Bronchopulmonary dysplasia (BPD) portends lifelong organ impairment and death. Our ability to predict BPD in first days of life is limited, but could be enhance using novel biomarkers. Methods Using an available clinical and urine biomarker database obtained from a prospective 113 infant cohort (birth weight ≤1200 g and/or gestational age ≤31 weeks), we evaluated the independent association of 14 urine biomarkers with BPD/mortality. Results Two of the 14 urine biomarkers were independently associated with BPD/mortality after controlling for gestational age (GA), small for gestational age (SGA), and intubation status. The best performing protein was clusterin, a ubiquitously expressed protein and potential sensor of oxidative stress associated with lung function in asthma patients. When modeling for BPD/mortality, the independent odds ratio for maximum adjusted urine clusterin was 9.2 (95% CI 3.3 - 32.8, P

Metabolomics, a systems biology discipline representing analysis of known and unknown pathways of metabolism, has grown tremendously over the past 20 years. Because of its comprehensive nature, metabolomics requires careful consideration of the question(s) being asked, the scale needed to answer the question(s), collection and storage of the sample specimens, methods for extraction of the metabolites from biological matrices, the analytical method(s) to be employed and the quality control of the analyses, how collected data are correlated, the statistical methods to determine metabolites undergoing significant change, putative identification of metabolites and the use of stable isotopes to aid in verifying metabolite identity and establishing pathway connections and fluxes. This second part of a comprehensive description of the methods of metabolomics focuses on data analysis, emerging methods in metabolomics and the future of this discipline. Copyright © 2016 John Wiley & Sons, Ltd.

The understanding of the genetic basis of neurological disorders has grown rapidly in the last two decades. Despite the genomic heterogeneity within African populations, large-scale candidate gene or linkage and exome studies are lacking. However, current knowledge on neurogenetics in African populations is limited and geographically very uneven. Isolated reports indicate the existence of autosomal dominant or recessive conditions incorporating cerebrovascular, movement, neuromuscular, seizure and motor neuron disorders in Africans. In addition, few African families with neurodegenerative disorders associated with dementia have been characterized in North, West and South Africa. The current insurgency in genomic research triggered by among others the Human Health and Heredity (H3) Africa Initiative indicates that there are unique opportunities to advance our knowledge and understanding of the influence of genomic variation on the pattern, presentations and prognosis of neurological disorders in Africa. These have enormous potential to unmask novel genes and molecular pathways germane to the neurobiology of brain disorders. It would facilitate the development of novel diagnostics, preventative and targeted treatments in the new paradigm of precision medicine. Nevertheless, it is crucial to strike a balance between effective traditional public health strategies and personalized genome based care. The translational barriers can be overcome through robust stakeholder engagement and sustainable multilevel, multigenerational and multidisciplinary capacity building and infrastructural development for genomic medicine in Africa.

BACKGROUND Low blood vitamin D concentration is a concern for people living in circumpolar regions, where sunlight is insufficient for vitamin D synthesis in winter months and the consumption of traditional dietary sources of vitamin D is decreasing. OBJECTIVE The objective was to characterize the effects of diet, genetic variation, and season on serum 25-hydroxycholecalciferol [25(OH)D3] concentrations in Yup'ik Alaska Native people living in rural southwest Alaska. METHODS This study was a cross-sectional design that assessed the associations of traditional diet (via a biomarker, the RBC δ(15)N value), age, gender, body mass index (BMI), community location, and genotype of select single nucleotide polymorphisms (SNPs) in cytochrome P450 family 2, subfamily R, peptide 1 (CYP2R1), 7-dehydrocholesterol reductase (DHCR7), and vitamin D binding protein (GC) with serum 25(OH)D3 concentrations in 743 Yup'ik male and female participants, aged 14-93 y, recruited between September 2009 and December 2013. RESULTS Yup'ik participants, on average, had adequate concentrations of serum 25(OH)D3 (31.1 ± 1.0 ng/mL). Variations in diet, BMI, age, gender, season of sample collection, and inland or coastal community geography were all significantly associated with serum 25(OH)D3 concentration. In models not adjusting for other covariates, age, diet, and seasonal effects explained 33.7%, 20.7%, and 9.8%, respectively, of variability in serum 25(OH)D3 concentrations. Of the 8 SNPs interrogated in CYP2R1 and DHCR7, only rs11023374 in CYP2R1 was significantly associated with serum 25(OH)D3, explaining 1.5% of variability. The GC haplotype explained an additional 2.8% of variability. Together, age, diet, gender, season of sample collection, BMI, geography of the community, and genotype at rs11023374 explained 52.5% of the variability in serum 25(OH)D3 concentrations. CONCLUSIONS Lower consumption of the traditional diet was associated with lower serum concentrations of 25(OH)D3. Younger adults and youth in this community may be at increased risk of adverse outcomes associated with vitamin D insufficiency compared with older members of the community, especially during seasons of low sunlight exposure, because of lower consumption of dietary sources of vitamin D.

African Americans have the highest prevalence of hypertension in the United States. Blood-pressure control is important to reduce cardiovascular disease (CVD)-related morbidity and mortality in this ethnic group. Genetic variants have been found to be associated with BP response to treatment. Previous pharmacogenetic studies of blood-pressure response to treatment in African Americans suffer limitations of small sample size as well as a limited number of candidate genes, and often focused on one antihypertensive treatment. Using 1,131 African-American treatment naïve participants from the Genetics of Hypertension Associated Treatment (GenHAT) Study, we examined whether variants in 35 candidate genes might modulate blood-pressure response to four different antihypertensive medications, including an angiotensin converting enzyme (ACE) inhibitor (lisinopril), a calcium channel blocker (amlodipine), and an α-adrenergic blocker (doxazosin) as compared to a thiazide diuretic (chlorthalidone) after 6 months of follow-up. Several suggestive gene by treatment interactions were identified. For example, among participants with two minor alleles of REN rs6681776, diastolic blood-pressure response was much improved on doxazosin compared to chlorthalidone (on average −9.49 mmHg vs. −1.70 mmHg) (P=0.007). Although several suggestive loci were identified, none of the findings passed significance criteria after correction for multiple testing. Given the impact of hypertension and its sequelae in this population, this research highlights the potential for genetic factors to contribute to blood-pressure response to treatment. Continued concerted research efforts focused on genetics are needed to improve treatment response in this high risk group.

Background DNA methylation is an epigenetic mechanism that has been proposed as a possible link between genetic and environmental determinants of disease. Prior studies reported robust associations between the methylation of specific cytosine-phosphate-guanine (CpG) sites and plasma lipids, namely triglycerides (TGs) and high-density lipoprotein cholesterol (HDL-C). However, the causality of the observed association remains elusive, hampered by weak instrumental variables for methylation status. Aim We present a novel application of the elastic net approach to implement a bidirectional Mendelian randomization approach to inferring causal relationships between candidate CpGs and plasma lipids in GAW20 data. Methods We used DNA methylation, TGs, and HDL-C measured during the visit 2. Based on prior findings, we selected 5 methylation markers (cg00574958, cg07504977, cg06690548, cg19693031, and cg03717755) related to TGs, 2 markers (cg09572125 and cg02650017) related to HDL-C, and 2 markers (cg06500161 and cg11024682) related to both traits. We implemented an elastic net approach to improve the selection of the genetic instrument for the methylation markers, followed by bidirectional Mendelian randomization 2-stage least-squares regression. Results We observed causal effects of blood fasting TGs on the methylation levels of cg00574958 (CPT1A) and cg06690548 (SLC7A11). For cg00574958, our findings were also consistent with the reverse direction of association, that is, from CPT1A methylation to TGs. Conclusions Current evidence does not rule out either direction of association between the methylation of the cg00574958 CPT1A locus and plasma TGs, highlighting the complexity of lipid homeostasis. We also demonstrated a novel approach to improve instrument selection in DNA methylation studies.

Background Although highly heritable, few genes have been linked to spontaneous intracerebral hemorrhage (SICH), which does not currently have any evidence-based disease-modifying therapy. Individuals of African ancestry are especially susceptible to SICH, even more so for indigenous Africans. We systematically reviewed the genetic variants associated with SICH and examined opportunities for rapidly advancing SICH genomic research for precision medicine. Method We searched the National Human Genome Research Institute-European Bioinformatics Institute (NHGRI–EBI) Genome Wide Association Study (GWAS) catalog and PubMed for original research articles on genetic variants associated with SICH as of 15 June 2019 using the PRISMA guideline. Results Eight hundred and sixty-four articles were identified using pre-specified search criteria, of which 64 met the study inclusion criteria. Among eligible articles, only 9 utilized GWAS approach while the rest were candidate gene studies. Thirty-eight genetic loci were found to be variously associated with the risk of SICH, hematoma volume, functional outcome and mortality, out of which 8 were from GWAS including APOE, CR1, KCNK17, 1q22, CETP, STYK1, COL4A2 and 17p12. None of the studies included indigenous Africans. Conclusion Given this limited information on the genetic contributors to SICH, more genomic studies are needed to provide additional insights into the pathophysiology of SICH, and develop targeted preventive and therapeutic strategies. This call for additional investigation of the pathogenesis of SICH is likely to yield more discoveries in the unexplored indigenous African populations which also have a greater predilection.

Africa was previously insufficiently represented in the emerging discipline of biobanking despite commendable early efforts. However, with the Human, Heredity, and Health in Africa (H3Africa) initiative, biorepository science has been bolstered, regional biobanks are springing up, and awareness about biobanks is growing on the continent. The Stroke Investigative Research and Educational Network (SIREN) project is a transnational, multicenter, hospital and community-based study involving over 3000 cases and 3000 controls recruited from 16 sites in Ghana and Nigeria. SIREN aims to explore and unravel the genetic and environmental factors that interact to produce the peculiar phenotypic and clinical characteristics of stroke as seen in people of African ancestry and facilitate the development of new diagnostics, therapeutics, and preventative strategies. The aim of this article is to describe our experience with the development of the procedure for collection, processing, storage, and shipment of biological samples (blood, serum, plasma, buffy coat, red cell concentrates, and DNA) and brain imaging across coordinating and participating sites within the SIREN Project. The SIREN network was initiated in 2014 with support and funding from the H3Africa Initiative. The SIREN Biobank currently has 3015 brain images, 92,950 blood fractions (serum, plasma, red cell concentrates, and buffy coat) accrued from 8450 recruited subjects, and quantified and aliquoted good-quality DNA extracts from 6150 study subjects. This represents an invaluable resource for future research with expanding genomic and trans-omic technologies. This will facilitate the involvement of indigenous African samples in cutting-edge stroke genomics and trans-omics research. It is, however, critical to effectively engage African stroke patients and community members who have contributed precious biological materials to the SIREN Biobank to generate appropriate evidence base for dealing with ethical, legal, and social issues of privacy, autonomy, identifiability, biorights, governance issues, and public understanding of stroke biobanking in the context of unique African culture, language, and belief systems.

Mendelian randomization studies have become increasingly common due to the maturation of genome-wide association studies and its potential to ascertain causal relationships. With the increasing use of this method comes the need for medical practitioners and clinicians to develop an understanding of its rationale, limitations, and interpretation. Mendelian randomization attempts to ascertain a causal relationship between some risk factor of interest and some outcome or disease of interest. It exploits Mendel's law on the random assortment of genetic variants. This random assortment of genetic variants mimics the main principle of randomization used in clinical trials; with the genetic variant replacing the randomly allocated treatment. In this paper we provide a readable introduction to the rationale behind Mendelian randomization and its limitations. We also discuss and interpret several examples of Mendelian randomization analyses which pertain to neurological diseases.

Introduction: Life’s Simple 7 (LS7) comprises seven health factors and behaviors promoted by the American Heart Association to reduce cardiovascular morbidity and mortality. Despite compelling evidence of inverse association between LS7 adherence and a variety of adverse health outcomes, the epigenetic sequelae of healthy lifestyle have not been comprehensively characterized and may offer valuable insights into the underlying biological mechanisms. Hypothesis: We hypothesized that LS7 adherence is associated with an epigenetic signature that is consistent with the deceleration of the aging process. Methods: Using data from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n=853), we have estimated cross-sectional associations between epigenome-wide DNA methylation at 487,432 cytosine-phosphate-guanine (CpG) sites in CD4+ T-cells and the number of achieved LS7 goals as measured by study staff (blood pressure, body mass index, total cholesterol, and fasting glucose) or reported by the participant (diet, smoking, physical activity). The associations were tested using linear mixed models adjusted for age, sex, study site, technical artifacts (fixed effects), and family relatedness (random effect). Additionally, we tested associations between LS7 compliance and age acceleration, estimated from DNA methylation data and chronological age using two complementary validated algorithms (1: Horvath and 2: Hannum). These linear mixed models adjusted for chronological age, sex, study site, CD4+ T-cell subtype estimates (fixed effects), and family relatedness (random effect). Epigenome-wide association results were considered statistically significant if they fell under the Bonferroni corrected threshold (alpha=0.05/487,432= 1.03x10 -7 ). Results: Methylation of an intronic CpG site in CPT1A , cg00574958, was positively associated with the number of achieved LS7 goals at the epigenome-wide significance level (beta= 0.008, SE= 0.001, P= 4.7x10 -8 ). CPT1A encodes a key enzyme in the beta-oxidation process and has previously been linked to fasting triglycerides, body mass index, and adiponectin levels. Age acceleration was associated with LS7 adherence under the Hannum algorithm (beta=-0.01, SE= 0.006, P= 0.02) but not the Horvath algorithm (beta=-0.005, SE= 0.004, P= 0.18). Conclusions: Achievement of LS7 goals was significantly associated with methylation variation in CPT1A , a critical lipid metabolism gene, and was associated with age deceleration in the Hannum but not the Horvath models. Following independent replication, future studies should consider interrogating CPT1A methylation in relation to cardiovascular morbidity and mortality in a prospective setting.

Advancements in science, technology, and medicine have contributed to the economic growth of the United States. However, this requires individuals to be trained for careers in biostatistics, bioinformatics and other areas of science, technology, engineering, and mathematics (STEM). Despite efforts to improve student recruitment and retention in STEM fields, the proportion of STEM graduates at the undergraduate level remains low in the United States, and is the lowest among underrepresented minorities. Several initiatives by the National Science Foundation (NSF), American Statistical Association (ASA), and academic organizations have invested in training individuals by developing programs to address issues that may be contributing to low recruitment and retention rates. Some factors may include lack of mentoring received from parents and teachers on STEM careers and less opportunities to explore STEM career options. In this study, a subsample of the High School Longitudinal Study (2009–2013) dataset (HSLS:09) is analyzed. Regression models were applied to evaluate mathematics achievement and student enrollment in STEM major/careers based on their individual participation in STEM activities and mentorship. Differences based on sex, race/ethnicity, and socioeconomic status (SES) were investigated. In summary, the aim of this work was to assess the significance of these stated factors in order to give insight into STEM education policy efforts. Our hope is that this work would shed light on the roles of mentors and student participation in STEM activities to motivate future programs aimed to recruit and retain STEM students.

Left ventricular (LV) hypertrophy, highest in prevalence among African Americans, is an established risk factor heart failure. Several genome wide association studies have identified common variants associated with LV-related quantitative-traits in African Americans. To date, however, the effect of rare variants on these traits has not been extensively studied, especially in minority groups. We therefore investigated the association between rare variants and LV traits among 1,934 African Americans using exome chip data from the Hypertension Genetic Epidemiology Network (HyperGEN) study, with replication in 1,090 African American from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. We used single-variant analyses and gene-based tests to investigate the association between 86,927 variants and six structural and functional LV traits including LV mass, LV internal dimension-diastole, relative wall thickness, left atrial dimension (LAD), fractional shortening (FS), and the ratio of LV early-to-late transmitral velocity (E/A ratio). Only rare variants (MAF

Cost-effective identification of novel pharmacogenetic variants remains a pressing need in the field. Using data from the Genetics of Lipid Lowering Drugs and Diet Network, we identified genomic regions of relevance to fenofibrate response in a sample of 173 families. Our approach included a multipoint linkage scan, followed by selection of the families showing evidence of linkage. We identified a strong signal for changes in LDL-cholesterol (LDL-C) on chromosome 7 (peak logarithm of odds score = 4.76) in the full sample (n = 821). The signal for LDL-C response remained even after adjusting for baseline LDL-C. Restricting analyses only to the families contributing to the linkage signal for LDL-C (N = 19), we observed a peak logarithm of odds score of 5.17 for chromosome 7. Two genes under this peak (ABCB4 and CD36) were of biological interest. These results suggest that linked family analyses might be a useful approach to gene discovery in the presence of a complex (e.g. multigenic) phenotype.

The triglyceride (TG) response to a high-fat meal (postprandial lipemia, PPL) affects cardiovascular disease risk and is influenced by genes and environment. Genes involved in lipid metabolism have dominated genetic studies of PPL TG response. We sought to elucidate common genetic variants through a genome-wide association (GWA) study in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN).The GOLDN GWAS discovery sample consisted of 872 participants within families of European ancestry. Genotypes for 2,543,887 variants were measured or imputed from HapMap. Replication of our top results was performed in the Heredity and Phenotype Intervention (HAPI) Heart Study (n = 843). PPL TG response phenotypes were constructed from plasma TG measured at baseline (fasting, 0 hour), 3.5 and 6 hours after a high-fat meal, using a random coefficient regression model. Association analyses were adjusted for covariates and principal components, as necessary, in a linear mixed model using the kinship matrix; additional models further adjusted for fasting TG were also performed. Meta-analysis of the discovery and replication studies (n = 1715) was performed on the top SNPs from GOLDN.GOLDN revealed 111 suggestive (p1E-05) associations, with two SNPs meeting GWA significance level (p5E-08). Of the two significant SNPs, rs964184 demonstrated evidence of replication (p = 1.20E-03) in the HAPI Heart Study and in a joint analysis, was GWA significant (p = 1.26E-09). Rs964184 has been associated with fasting lipids (TG and HDL) and is near ZPR1 (formerly ZNF259), close to the APOA1/C3/A4/A5 cluster. This association was attenuated upon additional adjustment for fasting TG.This is the first report of a genome-wide significant association with replication for a novel phenotype, namely PPL TG response. Future investigation into response phenotypes is warranted using pathway analyses, or newer genetic technologies such as metabolomics.

Objective : Information on the current burden of stroke in Africa is limited. The aim of this review was to comprehensively examine the current and projected burden of stroke in Africa. Methods : We systematically reviewed the available literature (PubMed and AJOL) from January 1960 and June 2014 on stroke in Africa. Percentage change in age-adjusted stroke incidence, mortality and disability-adjusted life years (DALYs) for African countries between 1990 and 2010 were calculated from the Global Burden of Diseases (GBD) model-derived figures. Results : Community-based studies revealed an age-standardised annual stroke incidence rate of up to 316 per 100 000 population, and age-standardised prevalence rates of up to 981 per 100 000. Model-based estimates showed significant mean increases in age-standardised stroke incidence. The peculiar factors responsible for the substantial disparities in incidence velocity, ischaemic stroke proportion, mean age and case fatality compared to high-income countries remain unknown. Conclusions : While the available study data and evidence are limited, the burden of stroke in Africa appears to be increasing.

Objective: The kernel machine (KM) test reportedly performs well in the set-based association test of rare variants. Many studies have been conducted to measure phenotypes at multiple time points, but the standard KM methodology has only been available for phenotypes at a single time point. In addition, family-based designs have been widely used in genetic association studies; therefore, the data analysis method used must appropriately handle familial relatedness. A rare-variant test does not currently exist for longitudinal data from family samples. Therefore, in this paper, we aim to introduce an association test for rare variants, which includes multiple longitudinal phenotype measurements for either population or family samples. Methods: This approach uses KM regression based on the linear mixed model framework and is applicable to longitudinal data from either population (L-KM) or family samples (LF-KM). Results: In our population-based simulation studies, L-KM has good control of Type I error rate and increased power in all the scenarios we considered compared with other competing methods. Conversely, in the family-based simulation studies, we found an inflated Type I error rate when L-KM was applied directly to the family samples, whereas LF-KM retained the desired Type I error rate and had the best power performance overall. Finally, we illustrate the utility of our proposed LF-KM approach by analyzing data from an association study between rare variants and blood pressure from the Genetic Analysis Workshop 18 (GAW18). Conclusion: We propose a method for rare-variant association testing in population and family samples using phenotypes measured at multiple time points for each subject. The proposed method has the best power performance compared to competing approaches in our simulation study.

Background: As the second leading cause of death and the leading cause of adult-onset disability, stroke is a major public health concern particularly pertinent in Sub-Saharan Africa (SSA), where nearly 80% of all global stroke mortalities occur, and stroke burden is projected to increase in the coming decades. However, traditional and emerging risk factors for stroke in SSA have not been well characterized, thus limiting efforts at curbing its devastating toll. The Stroke Investigative Research and Education Network (SIREN) project is aimed at comprehensively evaluating the key environmental and genomic risk factors for stroke (and its subtypes) in SSA while simultaneously building capacities in phenomics, biobanking, genomics, biostatistics, and bioinformatics for brain research. Methods: SIREN is a transnational, multicentre, hospital and community-based study involving 3,000 cases and 3,000 controls recruited from 8 sites in Ghana and Nigeria. Cases will be hospital-based patients with first stroke within 10 days of onset in whom neurovascular imaging will be performed. Etiological and topographical stroke subtypes will be documented for all cases. Controls will be hospital- and community-based participants, matched to cases on the basis of gender, ethnicity, and age (±5 years). Information will be collected on known and proposed emerging risk factors for stroke. Study Significance: SIREN is the largest study of stroke in Africa to date. It is anticipated that it will shed light on the phenotypic characteristics and risk factors of stroke and ultimately provide evidence base for strategic interventions to curtail the burgeoning burden of stroke on the sub-continent.

Background We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science. Methods Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017. Results We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, Trans-Omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes. Conclusion Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke.

Objective Worldwide, the highest frequencies of APOL1-associated kidney variants are found in indigenous West Africans among whom small vessel disease (SVD) ischemic stroke is the most common stroke phenotype. The objective of this study was to investigate the association and effect sizes of 23 selected SNPs in 14 genes of relevance, including the APOL1 G1 variants, with the occurrence of SVD ischemic stroke among indigenous West African participants in the Stroke Investigative Research and Education Network (SIREN) Study. Materials and Methods Cases were consecutively recruited consenting adults (aged 18 years or older) with neuroimaging—confirmed first clinical stroke. Stroke-free controls were ascertained using a locally validated version of the Questionnaire for Verifying Stroke-Free Status (QVSFS). Logistic regression models adjusting for known vascular risk factors were fitted to assess the associations of the 23 SNPs in rigorously phenotyped cases (N = 154) of SVD ischemic stroke and stroke-free (N = 483) controls. Results Apolipoprotein L1 (APOL1) rs73885319 (OR = 1.52; CI: 1.09-2.13, P-value = .013), rs2383207 in CDKN2A/CDKN2B (OR = 3.08; CI: 1.15-8.26, P –value = .026) and rs2107595 (OR = 1.70; CI: 1.12-2.60, P-value = .014) and rs28688791 (OR = 1.52; CI: 1.03-2.26, P-value = .036) in HDAC9 gene were associated with SVD stroke at 0.05 significance level. Polymorphisms in other genes did not show significant associations. Conclusion This is the first report of a specific association of APOL1 with a stroke subtype. Further research is needed to confirm these initial findings and deepen understanding of the genetics of stroke in people of African ancestry with possible implications for other ancestries as all humans originated from Africa.

Background Recently, epigenetic age acceleration—or older epigenetic age in comparison to chronological age—has been robustly associated with mortality and various morbidities. However, accelerated epigenetic aging has not been widely investigated in relation to inflammatory or metabolic markers, including postprandial lipids. Methods We estimated measures of epigenetic age acceleration in 830 Caucasian participants from the Genetics Of Lipid Lowering Drugs and diet Network (GOLDN) considering two epigenetic age calculations based on differing sets of 5′-Cytosine-phosphate-guanine-3′ genomic site, derived from the Horvath and Hannum DNA methylation age calculators, respectively. GOLDN participants underwent a standardized high-fat meal challenge after fasting for at least 8 h followed by timed blood draws, the last being 6 h postmeal. We used adjusted linear mixed models to examine the association of the epigenetic age acceleration estimate with fasting and postprandial (0- and 6-h time points) low-density lipoprotein (LDL), high-density lipoprotein (HDL), and triglyceride (TG) levels as well as five fasting inflammatory markers plus adiponectin. Results Both DNA methylation age estimates were highly correlated with chronological age (r > 0.90). We found that the Horvath and Hannum measures of epigenetic age acceleration were moderately correlated (r = 0.50). The regression models revealed that the Horvath age acceleration measure exhibited marginal associations with increased postprandial HDL (p = 0.05), increased postprandial total cholesterol (p = 0.06), and decreased soluble interleukin 2 receptor subunit alpha (IL2sRα, p = 0.02). The Hannum measure of epigenetic age acceleration was inversely associated with fasting HDL (p = 0.02) and positively associated with postprandial TG (p = 0.02), interleukin-6 (IL6, p = 0.007), C-reactive protein (C-reactive protein, p = 0.0001), and tumor necrosis factor alpha (TNFα, p = 0.0001). Overall, the observed effect sizes were small and the association of the Hannum residual with inflammatory markers was attenuated by adjustment for estimated T cell type percentages. Conclusions Our study demonstrates that epigenetic age acceleration in blood relates to inflammatory biomarkers and certain lipid classes in Caucasian individuals of the GOLDN study. Future studies should consider epigenetic age acceleration in other tissues and extend the analysis to other ethnic groups.

Summary: Background: Sub-Saharan Africa has the highest incidence, prevalence, and fatality from stroke globally. Yet, only little information about context-specific risk factors for prioritising interventions to reduce the stroke burden in sub-Saharan Africa is available. We aimed to identify and characterise the effect of the top modifiable risk factors for stroke in sub-Saharan Africa. Methods: The Stroke Investigative Research and Educational Network (SIREN) study is a multicentre, case-control study done at 15 sites in Nigeria and Ghana. Cases were adults (aged ≥18 years) with stroke confirmed by CT or MRI. Controls were age-matched and gender-matched stroke-free adults (aged ≥18 years) recruited from the communities in catchment areas of cases. Comprehensive assessment for vascular, lifestyle, and psychosocial factors was done using standard instruments. We used conditional logistic regression to estimate odds ratios (ORs) and population-attributable risks (PARs) with 95% CIs. Findings: Between Aug 28, 2014, and June 15, 2017, we enrolled 2118 case-control pairs (1192 [56%] men) with mean ages of 59·0 years (SD 13·8) for cases and 57·8 years (13·7) for controls. 1430 (68%) had ischaemic stoke, 682 (32%) had haemorrhagic stroke, and six (

Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.

Food preferences and cognitive control influence dietary habits thus affecting compliance with dietary advice and the risk of chronic diseases. A complex mix of genetic and environmental, cultural ...

Background Colorectal adenocarcinomas are characterized by abnormal mitochondrial DNA (mtDNA) copy number and genomic instability, but a molecular interaction between mitochondrial and nuclear genome remains unknown. Here we report the discovery of increased copies of nuclear mtDNA (NUMT) in colorectal adenocarcinomas, which supports link between mtDNA and genomic instability in the nucleus. We name this phenomenon of nuclear occurrence of mitochondrial component as numtogenesis. We provide a description of NUMT abundance and distribution in tumor versus matched blood-derived normal genomes. Methods Whole-genome sequence data were obtained for colon adenocarcinoma and rectum adenocarcinoma patients participating in The Cancer Genome Atlas, via the Cancer Genomics Hub, using the GeneTorrent file acquisition tool. Data were analyzed to determine NUMT proportion and distribution on a genome-wide scale. A NUMT suppressor gene was identified by comparing numtogenesis in other organisms. Results Our study reveals that colorectal adenocarcinoma genomes, on average, contains up to 4.2-fold more somatic NUMTs than matched normal genomes. Women colorectal tumors contained more NUMT than men. NUMT abundance in tumor predicted parallel abundance in blood. NUMT abundance positively correlated with GC content and gene density. Increased numtogenesis was observed with higher mortality. We identified YME1L1, a human homolog of yeast YME1 (yeast mitochondrial DNA escape 1) to be frequently mutated in colorectal tumors. YME1L1 was also mutated in tumors derived from other tissues. We show that inactivation of YME1L1 results in increased transfer of mtDNA in the nuclear genome. Conclusions Our study demonstrates increased somatic transfer of mtDNA in colorectal tumors. Our study also reveals sex-based differences in frequency of NUMT occurrence and that NUMT in blood reflects NUMT in tumors, suggesting NUMT may be used as a biomarker for tumorigenesis. We identify YME1L1 as the first NUMT suppressor gene in human and demonstrate that inactivation of YME1L1 induces migration of mtDNA to the nuclear genome. Our study reveals that numtogenesis plays an important role in the development of cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0420-6) contains supplementary material, which is available to authorized users.

Background: Calculated ‘epigenetic age,’ a novel biomarker based on DNA methylation levels of 353 CpGs, has been demonstrated to accurately predict chronological age across a broad spectrum of tissues and cell types. Recently epigenetic age acceleration or older epigenetic age in comparison to chronological age has been robustly associated with all-cause mortality independent of chronological age in multiple human cohorts. However, accelerated epigenetic aging has not been associated with lipids levels, including postprandial lipid levels which are linked to prothrombotic and proinflammatory processes that may precipitate aging. In the current study we aimed to evaluate the association between epigenetic age acceleration and lipid levels. Methods: We used the Horvath DNA methylation age calculator to estimate epigenetic age in 988 Caucasian participants from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) using Illumina Infinium HumanMethylation450 BeadChip array data derived from CD4+ T-cell DNA. GOLDN participants did not take lipid lowering drugs for at least four weeks prior to enrollment and underwent a standardized high fat meal challenge after fasting for at least 8 hours followed by timed blood draws at 3.5 and 6 hours following the meal. Epigenetic age acceleration was calculated as the residual from regressing methylation age on chronological age. We used linear mixed models to examine the association of age acceleration quartiles with fasting and postrandial (3.5 and 6 hour time points) low density lipoprotein (LDL), high density lipoprotein (HDL) and triglyceride (TG) levels after adjusting for age, study site, sex, fasting lipid level (if applicable), deconvolution estimated T-cell type percentages and a random effect of family relationship. Results: The correlation between calculated methylation age and chronological age was 0.91. The difference between methylation age and chronological age (methylation age - chronological age) was on average -5.8 (5.9), -0.5 (4.7), 2.9 (4.3), and 7.8 (5.0) years for the first through fourth quartiles of age acceleration, respectively. After adjustment for covariates neither fasting nor postprandial lipids were associated with age acceleration quartile. Conclusions: Evidence from the current study suggests lipid levels in the fasting and postprandial state are not related to accelerated epigenetic aging, however given the association between epigenetic age acceleration and mortality observed in previous studies the relationship of other metabolic parameters with age acceleration may be worthy of investigation.

Background: Animal model studies reported robust associations between fructose intake, a known determinant of metabolic health across species, and DNA methylation/ gene expression patterns. To date, these associations have not been comprehensively investigated in humans. Methods: Using DNA methylation data on ~470,000 cytosine-phosphate-guanine (CpG) sites in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN, n=991) quantified in CD4+ T-cells, we have interrogated the cross-sectional relationships between fructose intake (ascertained using a validated food frequency questionnaire) and epigenome-wide methylation. We fit linear mixed models adjusted for age, sex, study site, technical covariates (fixed effects) and family relatedness (random effect). We have supplemented the methylation analyses with a transcriptome-wide scan on 98 unrelated GOLDN participants with available RNASeq data in whole blood. For the RNASeq data analysis, we used negative binomial models of read counts as a function of fructose intake, adjusted for age, sex, study site, technical covariates (including differential white blood cell counts). Results and Conclusions: The top loci differentially methylated with respect to fructose intake mapped to SNED1 (regression coefficient +/- SE= 0.002 +/- 0.0005, P=5x10-6) and FARSB (regression coefficient +/- SE= 0.002 +/- 0.0004, P=5x10-6) on chromosome 2. SNED1 is an insulin responsive transcription factor that has previously been shown to be downregulated in the setting of metabolic syndrome. FARSB encodes an aminoacyl-tRNA synethetase implicated in cell growth. Additionally, two genes reached transcriptome-wide significance in the RNASeq analysis: MTATP8P1 (P=1x10-7) and PDXDC1 (P=6x10-7). Sequence variation in PDXDC1 (pyridoxal-dependent decarboxylase isoform) has previously been linked to lipid metabolism, while MTATP8P1 is a pseudogene for a mitochondrially encoded ATP synthase. Upon future replication and functional validation, our preliminary findings offer promising insights into the link between fructose intake and metabolic health.

Introduction: The relative contributions of racial and environmental factors to the higher risk of stroke in people of African ancestry are not clear due to limited opportunities to evaluate stroke type and risk among indigenous Africans, in comparison with Africans in diaspora and their host populations. This knowledge could provide insights into avenues for similar vs. unique approaches to managing stroke risk in Africans. Objective: To compare the pattern of stroke and contribution of vascular risk factors to stroke among indigenous Africans, African Americans and European Americans. Methods: SIREN is a large multicenter case-control study involving several sites in West Africa, the ancestral home of 71% African Americans, whilst REGARDS is a cohort study including African and European Americans in the United States. Stroke diagnosis and type were confirmed using CT or MRI scan. Traditional vascular risk factors were assessed using history, physical examination and laboratory investigations. We compared data from acute stroke cases age≥55 years in SIREN and REGARDS in the distribution of key socio-demographic and clinical risk factors based on harmonized standard definitions. Results: There were 811 stroke subjects in the SIREN population (A) and 452 African Americans (B) and 665 European Americans (C) from the REGARDS study with a progressive increment in mean age of 68.0 ± 9.3, 73.0 ± 8.3 and 76.0 ± 8.3 years respectively, p Conclusion: Environmental risk factors such as cigarette smoking may contribute to the higher proportion of ischemic stroke in African-Americans compared to indigenous Africans, while racial factors may contribute to the higher proportion of hypertension among stroke subjects of African ancestry.

Background Inherited genetic variations offer a possible explanation for the observed peculiarities of stroke in sub - Saharan African populations. Interleukin–6 polymorphisms have been previously associated with ischemic stroke in some non-African populations. Aim Herein we investigated, for the first time, the association of genetic polymorphisms of IL-6, CDKN2A- CDKN2B and other genes with ischemic stroke among indigenous West African participants in the Stroke Investigative Research and Education Network (SIREN) Study. Methods Twenty-three previously identified single nucleotide polymorphisms (SNPs) in 14 genes of relevance to the neurobiology of ischemic stroke were investigated. Logistic regression models adjusting for known cardiovascular disease risk factors were constructed to assess the associations of the 23 SNPs in rigorously phenotyped cases (N = 429) of ischemic stroke (Men = 198; Women = 231) and stroke– free (N = 483) controls (Men = 236; Women = 247). Results Interleukin-6 (IL6) rs1800796 (C minor allele; frequency: West Africans = 8.6%) was significantly associated with ischemic stroke in men (OR = 2.006, 95% CI = [1.065, 3.777], p = 0.031) with hypertension in the model but not in women. In addition, rs2383207 in CDKN2A/CDKN2B (minor allele A with frequency: West Africans = 1.7%) was also associated with ischemic stroke in men (OR = 2.550, 95% CI = [1.027, 6.331], p = 0.044) with primary covariates in the model, but not in women. Polymorphisms in other genes did not show significant association with ischemic stroke. Conclusion Polymorphisms rs1800796 in IL6 gene and rs2383207 in CDKN2A/CDKN2B gene have significant associations with ischemic stroke in indigenous West African men. CDKN2A/CDKN2B SNP rs2383207 is independently associated with ischemic stroke in indigenous West African men. Further research should focus on the contributions of inflammatory genes and other genetic polymorphisms, as well as the influence of sex on the neurobiology of stroke in people of African ancestry.

Background: Africa has a growing burden of stroke with associated high morbidity and a 3-year fatality rate of 84%. Cardiac disease contributes to stroke occurrence and outcomes, but the precise relationship of abnormalities as noted on a cheap and widely available test, the electrocardiogram (ECG), and acute stroke outcomes have not been previously characterized in Africans.Objectives: The study assessed the prevalence and prognoses of various ECG abnormalities among African acute stroke patients encountered in a multisite, cross-national epidemiologic study.Methods: We included 890 patients from Nigeria and Ghana with acute stroke who had 12-lead ECG recording within first 24 h of admission and stroke classified based on brain computed tomography scan or magnetic resonance imaging. Stroke severity at baseline was assessed using the Stroke Levity Scale (SLS), whereas 1-month outcome was assessed using the modified Rankin Scale (mRS).Results: Patients’ mean age was 58.4 ± 13.4 years, 490 were men (55%) and 400 were women (45%), 65.5% had ischemic stroke, and 85.4% had at least 1 ECG abnormality. Women were significantly more likely to have atrial fibrillation, or left ventricular hypertrophy with or without strain pattern. Compared to ischemic stroke patients, hemorrhagic stroke patients were less likely to have atrial fibrillation (1.0% vs. 6.7%; p = 0.002), but more likely to have left ventricular hypertrophy (64.4% vs. 51.4%; p = 0.004). Odds of severe disability or death at 1 month were higher with severe stroke (AOR: 2.25; 95% confidence interval: 1.44 to 3.50), or atrial enlargement (AOR: 1.45; 95% confidence interval: 1.04 to 2.02).Conclusions: About 4 in 5 acute stroke patients in this African cohort had evidence of a baseline ECG abnormality, but presence of any atrial enlargement was the only independent ECG predictor of death or disability.Highlights4 in 5 acute stroke patients in this African cohort had at least 1 ECG abnormality.Atrial fibrillation was rare in the cohort, occurring in

Background— Genetic research regarding blood lipids has largely focused on DNA sequence variation; few studies have explored epigenetic effects. Genome-wide surveys of DNA methylation may uncover epigenetic factors influencing lipid metabolism. Methods and Results— To identify whether differential methylation of cytosine-(phosphate)-guanine dinucleotides (CpGs) correlated with lipid phenotypes, we isolated DNA from CD4+ T cells and quantified the proportion of sample methylation at >450 000 CpGs by using the Illumina Infinium HumanMethylation450 Beadchip in 991 participants of the Genetics of Lipid Lowering Drugs and Diet Network. We modeled the percentage of methylation at individual CpGs as a function of fasting very-low-density lipoprotein cholesterol and triglycerides (TGs) by using mixed linear regression adjusted for age, sex, study site, cell purity, and family structure. Four CpGs (cg00574958, cg17058475, cg01082498, and cg09737197) in intron 1 of carnitine palmitoyltransferase 1A ( CPT1A ) were strongly associated with very-low low-density lipoprotein cholesterol ( P =1.8×10 –21 to 1.6×10 –8 ) and TG ( P =1.6×10 –26 to 1.5×10 –9 ). Array findings were validated by bisulfite sequencing. We performed quantitative polymerase chain reaction experiments demonstrating that methylation of the top CpG (cg00574958) was correlated with CPT1A expression. The association of cg00574958 with TG and CPT1A expression were replicated in the Framingham Heart Study ( P =4.1×10 –14 and 3.1×10 –13 , respectively). DNA methylation at CPT1A cg00574958 explained 11.6% and 5.5% of the variation in TG in the discovery and replication cohorts, respectively. Conclusions— This genome-wide epigenomic study identified CPT1A methylation as strongly and robustly associated with fasting very-low low-density lipoprotein cholesterol and TG. Identifying novel epigenetic contributions to lipid traits may inform future efforts to identify new treatment targets and biomarkers of disease risk.

Lipoprotein subfractions help discriminate cardiometabolic disease risk. Genetic loci validated as associating with lipoprotein measures do not account for a large proportion of the individual variation in lipoprotein measures. We hypothesized that DNA methylation levels across the genome contribute to interindividual variation in lipoprotein measures. Using data from participants of the Genetics of Lipid Lowering Drugs and Diet Network (n = 663 for discovery and n = 331 for replication stages, respectively), we conducted the first systematic screen of the genome to determine associations between methylation status at ∼470,000 cytosine-guanine dinucleotide (CpG) sites in CD4(+) T cells and 14 lipoprotein subfraction measures. We modeled associations between methylation at each CpG site and each lipoprotein measure separately using linear mixed models, adjusted for age, sex, study site, cell purity, and family structure. We identified two CpGs, both in the carnitine palmitoyltransferase-1A (CPT1A) gene, which reached significant levels of association with VLDL and LDL subfraction parameters in both discovery and replication phases (P < 1.1 × 10(-7) in the discovery phase, P < .004 in the replication phase, and P < 1.1 × 10(-12) in the full sample). CPT1A is regulated by PPARα, a ligand for drugs used to reduce CVD. Our associations between methylation in CPT1A and lipoprotein measures highlight the epigenetic role of this gene in metabolic dysfunction.

Traditional genome-wide association studies (GWASs) usually focus on single-marker analysis, which only accesses marginal effects. Pathway analysis, on the other hand, considers biological pathway gene marker hierarchical structure and therefore provides additional insights into the genetic architecture underlining complex diseases. Recently, a number of methods for pathway analysis have been proposed to assess the significance of a biological pathway from a collection of single-nucleotide polymorphisms. In this study, we propose a novel approach for pathway analysis that assesses the effects of genes using the sequence kernel association test and the effects of pathways using an extended adaptive rank truncated product statistic. It has been increasingly recognized that complex diseases are caused by both common and rare variants. We propose a new weighting scheme for genetic variants across the whole allelic frequency spectrum to be analyzed together without any form of frequency cutoff for defining rare variants. The proposed approach is flexible. It is applicable to both binary and continuous traits, and incorporating covariates is easy. Furthermore, it can be readily applied to GWAS data, exome-sequencing data, and deep resequencing data. We evaluate the new approach on data simulated under comprehensive scenarios and show that it has the highest power in most of the scenarios while maintaining the correct type I error rate. We also apply our proposed methodology to data from a study of the association between bipolar disorder and candidate pathways from Wellcome Trust Case Control Consortium (WTCCC) to show its utility.

Background Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), mainly among individuals of European ancestry. In the present study, we examined the frequency of these SNPs and their association with T2D-related traits in an Alaska Native study population with a historically low prevalence of T2D. We also investigated whether dietary characteristics that may protect against T2D, such as n-3 polyunsaturated fatty acid (PUFA) intake, modify these associations. Methods In 1144 Yup'ik people, we examined 17 SNPs repeatedly identified in GWAS for individual and cumulative associations with T2D-related traits. Cumulative associations were evaluated using a genetic risk score (GRS) calculated by summing risk alleles. Associations were tested for interactions with sex, body mass index (BMI), and n-3 PUFA intake. Results The rs7754840 SNP in CDKAL1 is significantly associated with HbA1c (P = 0.00091). The rs5015480 SNP near HHEX is significantly associated (in opposite direction to that in Europeans) with a combined fasting glucose (FG) and HbA1c measure (P = 0.00046) and with homeostatic model assessment of β-cell function (HOMA-B; P = 0.0014). The GRS is significantly associated with FG and combined FG and HbA1c only when the HHEX SNP is dropped from the GRS. Associations are not modified by BMI or n-3 PUFA intake. Conclusion Our results highlight the potential importance of CDKAL1 and HHEX in glucose homeostasis in this Alaska Native population with a low prevalence of T2D, and suggest that these loci should be examined in greater detail in this population. 摘要 背景 全基因组相关性研究已经鉴别出与2型糖尿病有关的单核苷酸多态性（single nucleotide polymorphisms，SNPs），主要是在有欧洲血统的人群中进行研究。在本研究中，我们在一个历史上2型糖尿病患病率较低的阿拉斯加原住民人群中研究了这些SNPs的出现频率以及它们与2型糖尿病相关特征的关系。我们还调查了他们的饮食习惯是否能够预防2型糖尿病，例如n-3多不饱和脂肪酸（polyunsaturated fatty acid，PUFA）的摄入，并且修正了这些相关性。 方法 在1144名尤皮克人群中，我们再次调查了17个在全基因组相关性研究人群中鉴别出的SNPs及其与2型糖尿病相关特征有关的个体和累积相关性。使用遗传风险评分（genetic risk score，GRS）通过计算危险等位基因总分来评估累积相关性。相关性要经过与性别、体重指数（BMI）以及n-3 PUFA摄入量等因素的相互作用的检验。 结果 位于CDKAL1上的rs7754840 SNP与HbA1c显著相关（P = 0.00091）。接近HHEX的rs5015480 SNP（在欧洲人群的相反方向）与联合空腹血糖以及HbA1c测量值（P = 0.00046）显著相关，并且还与β细胞功能稳态模型评估值显著相关（HOMA-B；P = 0.0014）。只有将HHEX SNP从GRS中撤除后GRS才与空腹血糖、联合空腹血糖以及HbA1c显著相关。相关性没有经过BMI或n-3 PUFA摄入量的校正。 结论 我们研究的亮点是在这个T2D患病率较低的阿拉斯加原住民人群中发现了CDKAL1与HHEX对葡萄糖内稳态平衡的潜在重要性，我们建议对这个人群应该更详细地筛查这些位点。

The prevalence of type 2 diabetes (T2D) in Alaska Native communities has historically been lower than the general US population, although the specific genetic and environmental factors that underlie these statistics remain poorly characterized. Accumulating evidence suggests that elements of the traditional diet such as omega-3 polyunsaturated fatty acids (n-3 PUFA) and low carbohydrate content (Naylor et al., 2003) may contribute to the low T2D prevalence in these communities. More recently, Alaska Native people have experienced a more dramatic rise in T2D burden than other Native groups, with the age-adjusted prevalence increasing from 17.3/1,000 in 1985 to 47.6/1,000 (Narayanan et al., 2010). This increase may be attributed to increased awareness, improved access to healthcare, decreased overall mortality rates, a change in diagnostic criteria in 1997, as well as nutritional and lifestyle transitions (Naylor et al., 2003). Moreover, the effects of the changing diet on chronic metabolic disease risk may be mediated by genetic factors that are unique to isolated populations (Lemas et al., 2013). Current understanding of the genetics of metabolic traits among circumpolar populations is limited in comparison to other ethnic groups, highlighting the need for comprehensive scans to identify the major susceptibility loci. Two recent candidate gene studies, conducted among the Canadian Inuit (Rudkowska et al., 2013) and Yup’ik people living in Southwest Alaska (Lemas et al., 2012) suggested that consumption of marine-derived n-3 PUFA may influence lipid traits through interactions with common genetic variants implicated in metabolic pathways. However, few studies have comprehensively examined the role of genes or gene-diet interactions in the etiology of metabolic traits in communities with a historically low prevalence of T2D, despite ample evidence of their etiologic relevance in other populations (Ntzani and Kawoura, 2012; Franks et al., 2007; Cole et al., 2005). Rudkowska et al. showed that the minor allele frequency distribution of several metabolism-related genetic markers differs markedly between the Inuit and Caucasians, and other studies of complex traits (Hegele et al., 1997; Hegele et al., 1999) also suggest differences in susceptibility genes. To further elucidate these differences, the purpose of this study was to examine the genetic architecture of metabolic traits in a Yup’ik population using whole-genome linkage analysis, followed by targeted association testing for variants genotyped within the observed peaks. Additionally, this study investigated potential interactions of these loci with habitual intake of marine-derived n-3 PUFA.