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1.  Hypertension in Pregnancy is a Risk Factor for Peripheral Arterial Disease Decades after Pregnancy 
Atherosclerosis  2013;229(1):212-216.
An ankle-brachial index (ABI) (the ratio of ankle to brachial artery systolic blood pressure) value ≤0.9 identifies patients with peripheral arterial disease (PAD) and elevated cardiovascular event risk. This study examined whether women with a history of hypertension in pregnancy are more likely to have an ABI ≤0.9 decades after pregnancy.
Methods and Results
ABI was measured in nulliparous women (n=144), and women with a history of normotensive (n=1,272) or hypertensive (n=281) pregnancies who participated in the Genetic Epidemiology Network of Arteriopathy (GENOA) study [non-Hispanic white (39%) and black (61%) women, 60 (mean) ± 10 (SD) years of age]. Relationships between PAD and pregnancy history were examined by logistic regression. Compared to women with a history of normotensive pregnancy, women with a history of hypertensive pregnancy had greater odds of PAD (1.61 (odds ratio); 1.04–2.49 (95% confidence interval), p=0.03, adjusted for age, race, height and heart rate). Additional adjustment for ever smoking, hypertension, diabetes, dyslipidemia, a family history of hypertension or coronary heart disease, body mass index and education did not attenuate this relationship (1.63; 1.02–2.62, p=0.04). PAD risk did not differ between women with a history of normotensive pregnancy and nulliparous women (1.06; 0.52–2.14, p=0.87).
Hypertension in pregnancy is an independent risk factor for PAD decades after pregnancy after adjusting for race, age, height, heart rate, ever smoking, hypertension, diabetes, dyslipidemia, a family history of hypertension or coronary heart disease, body mass index and education.
PMCID: PMC3694211  PMID: 23659871
hypertension in pregnancy; peripheral vascular disease; ankle-brachial index
2.  Public Preferences Regarding Informed Consent Models for Participation in Population-based Genomic Research 
Some large population biobanks that house biospecimens and health information for research seek broad consent from participants, while others re-consent for specific new studies. Understanding research participants’ attitudes and preferences about broad and narrow consent may improve recruitment, retention, and public support.
An online survey was conducted among a representative sample of 4,659 US adults to examine relationships between consent preferences and demographic factors, beliefs about privacy, the value of research, and the perceived trustworthiness of researchers.
Participants preferred broad consent (52%) over study-by-study consent models (48%). Higher preferences for study-by-study consent observed among Black non-Hispanic respondents, and respondents with lower income and education were explained by differences in the prevalence of one or more beliefs about the study. Respondents with fears about research and those that would feel respected if asked for permission for each research use preferred study-by-study consent. Preference for broad consent was related to the desire not to be bothered with multiple requests and the belief that the study could lead to improved treatments, cures, and lives saved.
These data suggest that support for broad consent is contingent on sufficient information about data use. Work with research participants and community leaders to understand, respond to, and influence opinions about a given, ongoing study may improve uptake of broad consent.
PMCID: PMC3904287  PMID: 23660530
Informed consent; large population studies; biobank; broad consent; public engagement
3.  Community perspectives on public health biobanking: an analysis of community meetings on the Michigan BioTrust for Health 
Journal of Community Genetics  2013;5(2):125-138.
Biobanks raise challenges for developing ethically sound and practicable consent policies. Biobanks comprised of dried bloodspots (DBS) left over from newborn screening, maintained for long-term storage, and potential secondary research applications are no exception. Michigan has been a leader in transforming its DBS collection, marketing its biobank of de-identified samples for health research use. The Michigan BioTrust for Health includes approximately 4 million unconsented retrospective samples collected as early as 1984 and prospective samples added since the fall of 2010 with blanket parental consent. We engaged Michigan citizens to ascertain public attitudes, knowledge, and beliefs about the BioTrust and informed consent. A convenience sampling of 393 participants from communities around the state of Michigan (oversampling for minority populations) participated in meetings addressing newborn screening, the BioTrust and informed consent, yielding quantitative and qualitative survey and discussion data. Participants affirmed the principle of voluntary informed participation in research and advocated for greater public awareness of the existence of the BioTrust. Most expressed support for the use of DBS for research and a desire for greater involvement in granting permission for research use. Opinions varied as to which specific research uses were acceptable. Participants indicated a desire for greater engagement, public awareness, and more active decision making on the part of biobank participants and parents. Diversity of opinion over which research areas were deemed acceptable problematizes the blanket consent model that currently applies to the BioTrust’s prospective DBS collection and that could become the new norm for research using de-identified data under proposed changes to the Common Rule.
Electronic supplementary material
The online version of this article (doi:10.1007/s12687-013-0162-0) contains supplementary material, which is available to authorized users.
PMCID: PMC3955459  PMID: 23893769
Biobank; Public health; Informed consent; Newborn screening; Community engagement
4.  SNP Set Association Analysis for Familial Data 
Genetic epidemiology  2012;10.1002/gepi.21676.
Genome-wide association studies (GWAS) are a popular approach for identifying common genetic variants and epistatic effects associated with a disease phenotype. The traditional statistical analysis of such GWAS attempts to assess the association between each individual Single Nucleotide Polymorphism (SNP) and the observed phenotype. Recently, kernel machine-based tests for association between a SNP set (e.g., SNPs in a gene) and the disease phenotype have been proposed as a useful alternative to the traditional individual SNP approach, and allow for flexible modeling of the potentially complicated joint SNP effects in a SNP set while adjusting for covariates. We extend the kernel machine framework to accommodate related subjects from multiple independent families, and provide a score-based variance component test for assessing the association of a given SNP set with a continuous phenotype, while adjusting for additional covariates and accounting for within-family correlation. We illustrate the proposed method using simulation studies and an application to genetic data from the Genetic Epidemiology Network of Arteriopathy (GENOA) study.
PMCID: PMC3683469  PMID: 22968922
Family association studies; Kernel machine; Linear mixed model; Multi-locus test; Score statistics; Variance component test; Within family correlation
5.  A Matrix Gla Protein Gene Polymorphism is Associated with Increased Coronary Artery Calcification Progression 
Matrix gla protein (MGP) inhibits arterial and cartilaginous calcification. A Threonine to Alanine (Thr83Ala) polymorphism (codon 83) in MGP is associated with myocardial infarction (MI) and femoral artery calcification. We examined the association of the MGP Thr83Ala polymorphism with quantity and progression of coronary artery calcification (CAC), a non-invasive measure of subclinical coronary atherosclerosis.
Methods and Results
In 605 Epidemiology of Coronary Artery Calcification Study participants, generalized linear mixed models were fit to determine the association of MGP Thr83Ala with CAC quantity and progression. There was a significant additive relationship between MGP Thr83Ala and CAC progression (P=0.001). In the fully-adjusted model, every one Ala83 allele increase was associated with an estimated 1.9% (95% CI: 0.7%, 3.0%) per one-year since baseline larger increase in CAC quantity. A proxy SNP for MGP Thr83Ala (rs6488724) was similarly associated with CAC progression in an independent cohort from the Genetic Epidemiology Network of Arteriopathy (GENOA) Study.
Increased risk of MI associated with MGP ThrAla83 genotype observed elsewhere may be related to faster progression of subclinical coronary atherosclerosis. MGP genotype could be a potential candidate for identifying individuals at increased risk of atherosclerotic disease who would benefit from aggressive primary prevention strategies.
PMCID: PMC3586431  PMID: 23307874
Population; Genetics; Atherosclerosis; Calcium; Imaging
6.  Genome-Wide Association Study of Cardiac Structure and Systolic Function in African Americans: The Candidate Gene Association Resource (CARe) Study 
Using data from four community-based cohorts of African Americans (AA), we tested the association between genome-wide markers (SNPs) and cardiac phenotypes in the Candidate-gene Association REsource (CARe) study.
Methods and Results
Among 6,765 AA, we related age, sex, height and weight-adjusted residuals for nine cardiac phenotypes (assessed by echocardiogram or MRI) to 2.5 million SNPs genotyped using Genome-Wide Affymetrix Human SNP Array 6.0 (Affy6.0) and the remainder imputed. Within cohort genome-wide association analysis was conducted followed by meta-analysis across cohorts using inverse variance weights (genome-wide significance threshold=4.0 ×10−07). Supplementary pathway analysis was performed. We attempted replication in 3 smaller cohorts of African ancestry and tested look-ups in one consortium of European ancestry (EchoGEN). Across the 9 phenotypes, variants in 4 genetic loci reached genome-wide significance: rs4552931 in UBE2V2 (p=1.43 × 10−07) for left ventricular mass (LVM); rs7213314 in WIPI1 (p=1.68 × 10−07) for LV internal diastolic diameter (LVIDD); rs1571099 in PPAPDC1A (p= 2.57 × 10−08) for interventricular septal wall thickness (IVST); and rs9530176 in KLF5 (p=4.02 × 10−07) for ejection fraction (EF). Associated variants were enriched in three signaling pathways involved in cardiac remodeling. None of the 4 loci replicated in cohorts of African ancestry were confirmed in look-ups in EchoGEN.
In the largest GWAS of cardiac structure and function to date in AA, we identified 4 genetic loci related to LVM, IVST, LVIDD and EF that reached genome-wide significance. Replication results suggest that these loci may represent unique to individuals of African ancestry. Additional large-scale studies are warranted for these complex phenotypes.
PMCID: PMC3591479  PMID: 23275298
echocardiography; ethnic; genome-wide association studies; Left atrium genetics; left ventricular mass genetics
7.  Epigenetic Markers of Renal Function in African Americans 
Nursing Research and Practice  2013;2013:687519.
Chronic kidney disease (CKD) is an increasing concern in the United States due to its rapidly rising prevalence, particularly among African Americans. Epigenetic DNA methylation markers are becoming important biomarkers of chronic diseases such as CKD. To better understand how these methylation markers play a role in kidney function, we measured 26,428 DNA methylation sites in 972 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. We then evaluated (1) whether epigenetic markers are associated with estimated glomerular filtration rate (eGFR), (2) whether the significantly associated markers are also associated with traditional risk factors and/or novel biomarkers for eGFR, and (3) how much additional variation in eGFR is explained by epigenetic markers beyond established risk factors and biomarkers. The majority of methylation markers most significantly associated with eGFR (24 out of the top 30) appeared to function, at least in part, through pathways related to aging, inflammation, or cholesterol. However, six epigenetic markers were still able to significantly predict eGFR after adjustment for other risk factors. This work shows that epigenetic markers may offer valuable new insight into the complex pathophysiology of CKD in African Americans.
PMCID: PMC3874945  PMID: 24396594
8.  Exploring the Public Understanding of Basic Genetic Concepts 
Journal of genetic counseling  2004;13(4):305-320.
It is predicted that the rapid acquisition of new genetic knowledge and related applications during the next decade will have significant implications for virtually all members of society. Currently, most people get exposed to information about genes and genetics only through stories publicized in the media. We sought to understand how individuals in the general population used and understood the concepts of ‘genetics’ and ‘genes.’ During in-depth one-on-one telephone interviews with adults in the U.S., we asked questions exploring their basic understanding of these terms, as well as their belief as to the location of genes in the human body. A wide-range of responses was received. Despite conversational familiarity with genetic terminology, many noted frustration or were hesitant when trying to answer these questions. In addition, some responses reflected a lack of understanding about basic genetic science that may have significant implications for broader public education measures in genetic literacy, genetic counseling, public health practices, and even routine health care.
PMCID: PMC3832055  PMID: 19736696
genetic counseling; genetic education; genetic literacy; public understanding of genetics
9.  Genome-Wide Association Study of Gene by Smoking Interactions in Coronary Artery Calcification 
PLoS ONE  2013;8(10):e74642.
Many GWAS have identified novel loci associated with common diseases, but have focused only on main effects of individual genetic variants rather than interactions with environmental factors (GxE). Identification of GxE interactions is particularly important for coronary heart disease (CHD), a major preventable source of morbidity and mortality with strong non-genetic risk factors. Atherosclerosis is the major cause of CHD, and coronary artery calcification (CAC) is directly correlated with quantity of coronary atherosclerotic plaque. In the current study, we tested for genetic variants influencing extent of CAC via interaction with smoking (GxS), by conducting a GxS discovery GWAS in Genetic Epidemiology Network of Arteriopathy (GENOA) sibships (N = 915 European Americans) followed by replication in Framingham Heart Study (FHS) sibships (N = 1025 European Americans). Generalized estimating equations accounted for the correlation within sibships in strata-specific groups of smokers and nonsmokers, as well as GxS interaction. Primary analysis found SNPs that showed suggestive associations (p≤10−5) in GENOA GWAS, but these index SNPs did not replicate in FHS. However, secondary analysis was able to replicate candidate gene regions in FHS using other SNPs (+/−250 kb of GENOA index SNP). In smoker and nonsmoker groups, replicated genes included TCF7L2 (p = 6.0×10−5) and WWOX (p = 4.5×10−6); and TNFRSF8 (p = 7.8×10−5), respectively. For GxS interactions, replicated genes included TBC1D4 (p = 6.9×10−5) and ADAMTS9 (P = 7.1×10−5). Interestingly, these genes are involved in inflammatory pathways mediated by the NF-κB axis. Since smoking is known to induce chronic and systemic inflammation, association of these genes likely reflects roles in CAC development via inflammatory pathways. Furthermore, the NF-κB axis regulates bone remodeling, a key physiological process in CAC development. In conclusion, GxS GWAS has yielded evidence for novel loci that are associated with CAC via interaction with smoking, providing promising new targets for future population-based and functional studies of CAC development.
PMCID: PMC3789744  PMID: 24098343
10.  Gene-Specific DNA Methylation Association with Serum Levels of C-Reactive Protein in African Americans 
PLoS ONE  2013;8(8):e73480.
A more thorough understanding of the differences in DNA methylation (DNAm) profiles in populations may hold promise for identifying molecular mechanisms through which genetic and environmental factors jointly contribute to human diseases. Inflammation is a key molecular mechanism underlying several chronic diseases including cardiovascular disease, and it affects DNAm profile on both global and locus-specific levels. To understand the impact of inflammation on the DNAm of the human genome, we investigated DNAm profiles of peripheral blood leukocytes from 966 African American participants in the Genetic Epidemiology Network of Arteriopathy (GENOA) study. By testing the association of DNAm sites on CpG islands of over 14,000 genes with C-reactive protein (CRP), an inflammatory biomarker of cardiovascular disease, we identified 257 DNAm sites in 240 genes significantly associated with serum levels of CRP adjusted for age, sex, body mass index and smoking status, and corrected for multiple testing. Of the significantly associated DNAm sites, 80.5% were hypomethylated with higher CRP levels. The most significant Gene Ontology terms enriched in the genes associated with the CRP levels were immune system process, immune response, defense response, response to stimulus, and response to stress, which are all linked to the functions of leukocytes. While the CRP-associated DNAm may be cell-type specific, understanding the DNAm association with CRP in peripheral blood leukocytes of multi-ethnic populations can assist in unveiling the molecular mechanism of how the process of inflammation affects the risks of developing common disease through epigenetic modifications.
PMCID: PMC3747126  PMID: 23977389
11.  Copy number variations associated with obesity related traits in African Americans: a joint analysis between GENOA and HyperGEN 
Obesity (Silver Spring, Md.)  2012;20(12):2431-2437.
Obesity is a highly heritable trait and a growing public health problem. African Americans are a genetically diverse, yet understudied population with a high prevalence of obesity (body mass index (BMI) greater than 30 kg/m2). Recent studies based upon single nucleotide polymorphisms (SNPs) have identified genetic markers associated with obesity. However, a large proportion of the heritability of obesity remains unexplained. Copy number variation (CNV) has been cited as a possible source of missing heritability in common diseases such as obesity. We conducted a CNV genome-wide association study of BMI in two African American cohorts from GENOA and HyperGEN. We performed independent and identical association analyses in each study, then combined the results in a meta-analysis. We identified three CNVs associated with BMI, obesity, and other obesity-related traits after adjusting for multiple testing. These CNVs overlap the PARK2, GYPA and SGCZ genes. Our results suggest that CNV may play a role in the etiology of obesity in African Americans.
PMCID: PMC3484176  PMID: 22836685
Obesity; CNVs; Meta-analysis; BMI; African Americans
12.  Risk factor profile for chronic kidney disease is similar to risk factor profile for small artery disease 
Journal of hypertension  2011;29(9):1796-1801.
Background and method
We investigated whether chronic kidney disease detected by increased serum creatinine (SCr) or urine albumin-to-creatinine ratio (UACR) may reflect arteriosclerosis involving the kidneys. The sample consisted of 1585 members of sibships (804 non-Hispanic whites and 781 non-Hispanic blacks) in which at least two siblings had primary hypertension. We first evaluated the correlations of increased SCr and UACR with the presence of cerebral small vessel arteriosclerosis, which was determined by increased subcortical white matter hyperintensity (WMH) volume on brain magnetic resonance imaging; and with peripheral large vessel arteriosclerosis, which was determined by decreased ankle-brachial index (ABI). After age adjustment, increased SCr and UACR correlated with increased WMH volume (0.54 and 0.52, respectively) and with decreased ABI (0.50 and 0.54, respectively; all P < 0.001). We then used logistic regression to evaluate the dependency of each measure of disease on conventional risk factors for arteriosclerosis to assess whether the risk factors’ effects were proportional across different measures of disease.
Age, race, sex, hypertension, diabetes, total cholesterol, and smoking made similar overall contributions to the prediction of each measure of disease, as judged by the model C-statistics, which varied in a narrow range from 0.84 to 0.85 (all P < 0.001). However, the relative contributions that the modifiable risk factors, including hypertension, diabetes, total cholesterol, and smoking made to prediction of increased SCr and UACR were disproportionate to their relative contributions to prediction of decreased ABI (P < 0.0001).
The findings support the view that chronic kidney disease detected by increased SCr or UACR primarily reflects small vessel arteriosclerosis involving the kidneys.
PMCID: PMC3651813  PMID: 21720267
albuminuria; ankle-brachial blood pressure index; arteriosclerosis; blood pressure; glomerular filtration rate; hypertension; subcortical white matter hyperintensity
13.  Genome-wide Association Study for Coronary Artery Calcification with Follow-up in Myocardial Infarction 
Circulation  2011;124(25):2855-2864.
Coronary artery calcification (CAC) detected by computed tomography is a non-invasive measure of coronary atherosclerosis, that underlies most cases of myocardial infarction (MI). We aimed to identify common genetic variants associated with CAC and further investigate their associations with MI.
Methods and Results
Computed tomography was used to assess quantity of CAC. A meta-analysis of genome-wide association studies for CAC was carried out in 9,961 men and women from five independent community-based cohorts, with replication in three additional independent cohorts (n=6,032). We examined the top single nucleotide polymorphisms (SNPs) associated with CAC quantity for association with MI in multiple large genome-wide association studies of MI. Genome-wide significant associations with CAC for SNPs on chromosome 9p21 near CDKN2A and CDKN2B (top SNP: rs1333049, P=7.58×10−19) and 6p24 (top SNP: rs9349379, within the PHACTR1 gene, P=2.65×10−11) replicated for CAC and for MI. Additionally, there is evidence for concordance of SNP associations with both CAC and with MI at a number of other loci, including 3q22 (MRAS gene), 13q34 (COL4A1/COL4A2 genes), and 1p13 (SORT1 gene).
SNPs in the 9p21 and PHACTR1 gene loci were strongly associated with CAC and MI, and there are suggestive associations with both CAC and MI of SNPs in additional loci. Multiple genetic loci are associated with development of both underlying coronary atherosclerosis and clinical events.
PMCID: PMC3397173  PMID: 22144573
cardiac computed tomography; coronary artery calcification; coronary atherosclerosis; genome-wide association studies; myocardial infarction
14.  Joint relationship between renal function and proteinuria on mortality of patients with type 2 diabetes: The Taichung Diabetes Study 
Estimated glomerular filtration rate (eGFR) is a powerful predictor of mortality in diabetic patients with limited proteinuria data. In this study, we tested whether concomitant proteinuria increases the risk of mortality among patients with type 2 diabetes.
Participants included 6523 patients > 30 years with type 2 diabetes who were enrolled in a management program of a medical center before 2007. Renal function was assessed by eGFR according to the Modification of Diet in Renal Disease Study equation for Chinese. Proteinuria was assessed by urine dipstick.
A total of 573 patients (8.8%) died over a median follow-up time of 4.91 years (ranging from 0.01 year to 6.42 years). The adjusted expanded cardiovascular disease (CVD)-related mortality rates among patients with proteinuria were more than three folds higher for those with an eGFR of 60 mL/min/1.73 m2 or less compared with those with an eGFR of 90 mL/min/1.73 m2 or greater [hazard ratio, HR, 3.15 (95% confidence interval, CI, 2.0–5.1)]. The magnitude of adjusted HR was smaller in patients without proteinuria [1.98 (95% CI, 1.1–3.7)]. An eGFR of 60 mL/min/1.73 m2 to 89 mL/min/1.73 m2 significantly affected all-cause mortality and mortality from expanded CVD-related causes only in patients with proteinuria. Similarly, proteinuria affected all outcomes only in patients with an eGFR of <60 mL/min/1.73 m2.
The risks of all-cause mortality, as well as expanded and non-expanded mortality from CVD-related causes associated with proteinuria or an eGFR of 90 mL/min/1.73 m2 or greater are independently increased. Therefore, the use of proteinuria measurements with eGFR increases the precision of risk stratification for mortality.
PMCID: PMC3515506  PMID: 23083001
Renal function; Mortality; Type 2 diabetes
15.  Evaluating the Influence of Quality Control Decisions and Software Algorithms on SNP Calling for the Affymetrix 6.0 SNP Array Platform 
Human Heredity  2011;71(4):221-233.
Our goal was to evaluate the influence of quality control (QC) decisions using two genotype calling algorithms, CRLMM and Birdseed, designed for the Affymetrix SNP Array 6.0.
Various QC options were tried using the two algorithms and comparisons were made on subject and call rate and on association results using two data sets.
For Birdseed, we recommend using the contrast QC instead of QC call rate for sample QC. For CRLMM, we recommend using the signal-to-noise rate ≥4 for sample QC and a posterior probability of 90% for genotype accuracy. For both algorithms, we recommend calling the genotype separately for each plate, and dropping SNPs with a lower call rate (<95%) before evaluating samples with lower call rates. To investigate whether the genotype calls from the two algorithms impacted the genome-wide association results, we performed association analysis using data from the GENOA cohort; we observed that the number of significant SNPs were similar using either CRLMM or Birdseed.
Using our suggested workflow both algorithms performed similarly; however, fewer samples were removed and CRLMM took half the time to run our 854 study samples (4.2 h) compared to Birdseed (8.4 h).
PMCID: PMC3136375  PMID: 21734406
Genotype call; Birdseed; CRLMM; Quality control decisions; Association
16.  Gene-Environment Effects of SLC4A5 and Skin Color on Blood Pressure among African American Women 
Ethnicity & disease  2012;22(2):155-161.
To determine the relationship between genetic polymorphisms and environmental factors (skin color) on blood pressure among African American women.
A descriptive study, consisting of 137 African American women from a Midwestern, metropolitan area was conducted. Blood pressure was measured using a digital blood pressure monitor. Self-reporting methods were utilized to obtain information on skin color. Buccal swab saliva samples were obtained for genotyping.
Of the four single nucleotide polymorphisms (SNPs) on the sodium bicarbonate co-transporter gene (SLC4A5) examined in this study, only one SNP (rs10177833) and skin color interaction was found to be associated with systolic blood pressure. The additive effect of rs10177833 on systolic blood pressure is statistically different between women with dark skin color and women with medium skin color (P=.0153). No SNP and skin color interaction was found to be associated with blood pressure readings in other SNPs tested (rs8179526, rs6726450 and rs6731545).
These findings of genetic and skin color relatedness to blood pressure is important when considering appropriate diagnostic and treatment plans for African American women with hypertension. African American women with darker skin color may require further assessment for risk factors such as discrimination related stress when being seen by health professionals for hypertension. (Ethn Dis. 2012;22(2):155-161)
PMCID: PMC3391738  PMID: 22764636
Blood Pressure; Genetic; African American; Skin Color
17.  Combined admixture mapping and association analysis identifies a novel blood pressure genetic locus on 5p13: contributions from the CARe consortium 
Human Molecular Genetics  2011;20(11):2285-2295.
Admixture mapping based on recently admixed populations is a powerful method to detect disease variants with substantial allele frequency differences in ancestral populations. We performed admixture mapping analysis for systolic blood pressure (SBP) and diastolic blood pressure (DBP), followed by trait-marker association analysis, in 6303 unrelated African-American participants of the Candidate Gene Association Resource (CARe) consortium. We identified five genomic regions (P< 0.001) harboring genetic variants contributing to inter-individual BP variation. In follow-up association analyses, correcting for all tests performed in this study, three loci were significantly associated with SBP and one significantly associated with DBP (P< 10−5). Further analyses suggested that six independent single-nucleotide polymorphisms (SNPs) contributed to the phenotypic variation observed in the admixture mapping analysis. These six SNPs were examined for replication in multiple, large, independent studies of African-Americans [Women's Health Initiative (WHI), Maywood, Genetic Epidemiology Network of Arteriopathy (GENOA) and Howard University Family Study (HUFS)] as well as one native African sample (Nigerian study), with a total replication sample size of 11 882. Meta-analysis of the replication set identified a novel variant (rs7726475) on chromosome 5 between the SUB1 and NPR3 genes, as being associated with SBP and DBP (P< 0.0015 for both); in meta-analyses combining the CARe samples with the replication data, we observed P-values of 4.45 × 10−7 for SBP and 7.52 × 10−7 for DBP for rs7726475 that were significant after accounting for all the tests performed. Our study highlights that admixture mapping analysis can help identify genetic variants missed by genome-wide association studies because of drastically reduced number of tests in the whole genome.
PMCID: PMC3090198  PMID: 21422096
18.  Genetic polymorphisms and obesity influence estradiol decline during the menopause 
Clinical Endocrinology  2011;74(5):618-623.
Obesity and genetic variation in aromatase and type 1 17-β hydroxysteroid dehydrogenase (HSD) could influence the E2 trajectory of decline during the menopause transition.
Design and participants
E2 trajectories during the menopause transition (phenotype) were identified using 5934 data points acquired annually from 681 women in Study of Women’s Health across the Nation (SWAN), a multiethnic study of the mid-life. E2 trajectories were related to CYP19 and type I 17-βHSD single-nucleotide polymorphisms (SNPs) and obesity.
logE2 trajectories began to decline precipitously 2 years before the final menstrual period (FMP). The trajectory of the logE2 decline varied with genotypes and obesity. logE2 rates of decline were greater in nonobese women than in obese women, P < 0.05. Women with the CYP19rs936306 CT variant had logE2 rate of decline that was 54% as rapid as the rate of decline of women with the TT variant, P < 0.05. logE2 rate of decline in women with the CYP19rs749292 GG variant was two-thirds the rate of logE2 decline in women with the AG variant, P < 0.05. logRates of E2 decline with 17-βHSD SNPs (rs2830, rs592389, and rs615942) varied according to genotype within obesity groups. Within each obesity group, logE2 rate of decline was greater in heterozygous variants and much less in homozygotes (P < 0.05). Obese women with selected CYP19 and 17-β HSD gene variants had remarkably different E2 trajectories around the FMP, resulting in different postmenopausal E2 levels. The rate of the E2 decline and the subsequent postmenopausal E2 levels may be relevant to oestrogen-sensitive chronic diseases including cancers.
PMCID: PMC3357071  PMID: 21198743
19.  Association between SLC2A9 transporter gene variants and uric acid phenotypes in African American and white families 
Rheumatology (Oxford, England)  2010;50(5):871-878.
Objectives. SLC2A9 gene variants associate with serum uric acid in white populations, but little is known about African American populations. Since SLC2A9 is a transporter, gene variants may be expected to associate more closely with the fractional excretion of urate, a measure of renal tubular transport, than with serum uric acid, which is influenced by production and extrarenal clearance.
Methods. Genotypes of single nucleotide polymorphisms (SNPs) distributed across the SLC2A9 gene were obtained in the Genetic Epidemiology Network of Arteriopathy cohorts. The associations of SNPs with serum uric acid, fractional excretion of urate and urine urate-to-creatinine ratio were assessed with adjustments for age, sex, diuretic use, BMI, homocysteine and triglycerides.
Results. We identified SLC2A9 gene variants that were associated with serum uric acid in 1155 African American subjects (53 SNPs) and 1132 white subjects (63 SNPs). The most statistically significant SNPs in African American subjects (rs13113918) and white subjects (rs11723439) were in the latter half of the gene and explained 2.7 and 2.8% of the variation in serum uric acid, respectively. After adjustment for this SNP in African Americans, 0.9% of the variation in serum uric acid was explained by an SNP (rs1568318) in the first half of the gene. Unexpectedly, SLC2A9 gene variants had stronger associations with serum uric acid than with fractional excretion of urate.
Conclusions. These findings support two different loci by which SLC2A9 variants affect uric acid levels in African Americans and suggest SLC2A9 variants affect serum uric acid level via renal and extrarenal clearance.
PMCID: PMC3077913  PMID: 21186168
Uric acid; Fractional excretion of urate; SLC2A9; Race; Genetic epidemiology
20.  Genetic variation in NCAM1 contributes to left ventricular wall thickness in hypertensive families 
Circulation Research  2011;108(3):279-283.
Left ventricular (LV) mass and related phenotypes are heritable, important predictors of cardiovascular disease, particularly in hypertensive individuals.
Identify genetic predictors of echocardiographic phenotypes in hypertensive families.
Methods & Results
A multi-stage genome-wide association study (GWAS) was conducted in hypertensive-ascertained African American families (HyperGEN, Stage I; GENOA, Stage II); findings were replicated in HyperGEN Caucasian families (Stage III). Echocardiograms were collected using a common protocol, and participants were genotyped with the Affymetrix Genome-Wide Human SNP 6.0 Array. In Stages I and II, 1258 and 989 African Americans, and Stage III 1316 Caucasians, were analyzed using mixed models adjusted for ancestry. Phenotypes included LV mass, LV internal dimension (LVID), wall thicknesses (posterior (PWT) and intraventricular septum (IVST)), and relative wall thickness (RWT). In Stage I, 5 single nucleotide polymorphisms (SNP) had P≤10−6. In Stage II, one SNP (rs1436109; NCAM1 intron 1) replicated with the same phenotype (PWT, P=0.025) in addition to RWT (P=0.032). In Stage III, rs1436109 was associated with RWT (P=5.47×10−4) and LVID (P=1.86×10−4). Fisher’s combined P-value for all stages was RWT=3.80×10−9, PWT=3.12×10−7, IVST=8.69×10−7, LV mass=2.52×10−3, and LVID=4.80×10−4.
This GWAS conducted in hypertensive families identified a variant in NCAM1 associated with LV wall thickness and RWT. NCAM is upregulated during the remodeling period of hypertrophy to heart failure in Dahl salt-sensitive rats. Our initial screening in hypertensive African-Americans may have provided the context for this novel locus.
PMCID: PMC3328104  PMID: 21212386
GWAS; NCAM1; hypertrophy; genomics
21.  A Bivariate Genome-Wide Approach to Metabolic Syndrome 
Diabetes  2011;60(4):1329-1339.
The metabolic syndrome (MetS) is defined as concomitant disorders of lipid and glucose metabolism, central obesity, and high blood pressure, with an increased risk of type 2 diabetes and cardiovascular disease. This study tests whether common genetic variants with pleiotropic effects account for some of the correlated architecture among five metabolic phenotypes that define MetS.
Seven studies of the STAMPEED consortium, comprising 22,161 participants of European ancestry, underwent genome-wide association analyses of metabolic traits using a panel of ∼2.5 million imputed single nucleotide polymorphisms (SNPs). Phenotypes were defined by the National Cholesterol Education Program (NCEP) criteria for MetS in pairwise combinations. Individuals exceeding the NCEP thresholds for both traits of a pair were considered affected.
Twenty-nine common variants were associated with MetS or a pair of traits. Variants in the genes LPL, CETP, APOA5 (and its cluster), GCKR (and its cluster), LIPC, TRIB1, LOC100128354/MTNR1B, ABCB11, and LOC100129150 were further tested for their association with individual qualitative and quantitative traits. None of the 16 top SNPs (one per gene) associated simultaneously with more than two individual traits. Of them 11 variants showed nominal associations with MetS per se. The effects of 16 top SNPs on the quantitative traits were relatively small, together explaining from ∼9% of the variance in triglycerides, 5.8% of high-density lipoprotein cholesterol, 3.6% of fasting glucose, and 1.4% of systolic blood pressure.
Qualitative and quantitative pleiotropic tests on pairs of traits indicate that a small portion of the covariation in these traits can be explained by the reported common genetic variants.
PMCID: PMC3064107  PMID: 21386085
22.  Association of the vitamin D metabolism gene CYP24A1 with coronary artery calcification 
The Vitamin D endocrine system is essential for calcium homeostasis, and low levels of vitamin D metabolites have been associated with cardiovascular disease risk. We hypothesized that DNA sequence variation in genes regulating vitamin D metabolism and signaling pathways might influence variation in coronary artery calcification (CAC).
Methods and Results
We genotyped single nucleotide polymorphisms (SNPs) in GC, CYP27B1, CYP24A1, and VDR and tested their association with CAC quantity, as measured by electron beam computed tomography. Initial association studies were carried out in a discovery sample comprised of 697 Amish subjects and SNPs nominally associated with CAC quantity (4 SNPs in CYP24A1, P = 0.008-0.00003) were then tested for association with CAC quantity in two independent cohorts of subjects of European Caucasian ancestry (Genetic Epidemiology Network of Arteriopathy (GENOA) Study (n = 916) and The Penn Coronary Artery Calcification (PennCAC) sample (n = 2,061)). One of the four SNPs, rs2762939, was associated with CAC quantity in both GENOA (P = 0.007) and PennCAC (P = 0.01). In all three populations the rs2762939 C allele was associated with lower CAC quantity. Meta-analysis for the association of this SNP with CAC quantity across all three studies yielded a P value of 2.9 × 10-6.
A common SNP in the CYP24A1 gene was associated with CAC quantity in three independent populations. This result suggests a role for vitamin D metabolism in the development of CAC quantity.
PMCID: PMC2988112  PMID: 20847308
23.  Identification of genes associated with complex traits by testing the genetic dissimilarity between individuals 
BMC Proceedings  2011;5(Suppl 9):S120.
Using the exome sequencing data from 697 unrelated individuals and their simulated disease phenotypes from Genetic Analysis Workshop 17, we develop and apply a gene-based method to identify the relationship between a gene with multiple rare genetic variants and a phenotype. The method is based on the Mantel test, which assesses the correlation between two distance matrices using a permutation procedure. Using up to 100,000 permutations to estimate the statistical significance in 200 replicate data sets, we found that the method had 5.1% type I error at an α level of 0.05 and had various power to detect genes with simulated genetic associations. FLT1 and KDR had the most significant correlations with Q1 and were replicated 170 and 24 times, respectively, in 200 simulated data sets using a Bonferroni corrected p-value of 0.05 as a threshold. These results suggest that the distance correlation method can be used to identify genotype-phenotype association when multiple rare genetic variants in a gene are involved.
PMCID: PMC3287845  PMID: 22373401
24.  Identification of epistatic effects using a protein–protein interaction database 
Human Molecular Genetics  2010;19(22):4345-4352.
Epistasis (i.e. gene–gene interaction) has long been recognized as an important mechanism underlying the complexity of the genetic architecture of human traits. Definitions of epistasis range from the purely molecular to the traditional statistical measures of interaction. The statistical detection of epistasis usually does not map onto or easily relate to the biological interactions between genetic variations through their combined influence on gene expression or through their interactions at the gene product (i.e. protein) or DNA level. Recently, greater high-dimensional data on protein–protein interaction (PPI) and gene expression profiles have been collected that enumerates sets of biological interactions. To better align statistical and molecular models of epistasis, we present an example of how to incorporate the PPI information into the statistical analysis of interactions between copy number variations (CNVs). Among the 23 640 pairs of known human PPIs and the 1141 common CNVs detected among HapMap samples, we identified 37 pairs of CNVs overlapping with both genes of a PPI pair. Two CNV pairs provided sufficient genotype variation to search for epistatic effects on gene expression. Using 47 294 probe-specific gene expression levels as the outcomes, five epistatic effects were identified with P-value less than 10−6. We found a CNV–CNV interaction significantly associated with gene expression of TP53TG3 (P-value of 2 × 10−20). The proteins associated with the CNV pair also bind TP53 which regulates the transcription of TP53TG3. This study demonstrates that using PPI data can assist in targeting statistical hypothesis testing to biological plausible epistatic interaction that reflects molecular mechanisms.
PMCID: PMC2957319  PMID: 20736252
25.  Metabolic syndrome is associated with change in subclinical arterial stiffness - A community-based Taichung Community Health Study 
BMC Public Health  2011;11:808.
The aim of this study was to evaluate the effect of MetS on arterial stiffness in a longitudinal study.
Brachial-ankle pulse wave velocity (baPWV), a measurement interpreted as arterial stiffness, was measured in 1518 community-dwelling persons at baseline and re-examined within a mean follow-up period of 3 years. Multivariate linear regression with generalized estimating equations (GEE) were used to examine the longitudinal relationship between MetS and its individual components and baPWV, while multivariate logistic regression with GEE was used to examine the longitudinal relationship between MetS and its individual components and the high risk group with arterial stiffness.
Subjects with MetS showed significantly greater baPWV at the end point than those without MetS, after adjusting for age, gender, education, hypertension medication and mean arterial pressure (MAP). MetS was associated with the top quartile of baPWV (the high-risk group of arterial stiffness, adjusted odds ratio [95% confidence interval] 1.52 [1.21-1.90]), and a significant linear trend of risk for the number of components of MetS was found (p for trend < 0.05). In further considering the individual MetS component, elevated blood pressure and fasting glucose significantly predicted a high risk of arterial stiffness (adjusted OR [95% CI] 3.72 [2.81-4.93] and 1.35 [1.08-1.68], respectively).
MetS affects the subject's progression to arterial stiffness. Arterial stiffness increased as the number of MetS components increased. Management of MetS is important for preventing the progression to advanced arterial stiffness.
PMCID: PMC3213226  PMID: 21999611
metabolic syndrome; pulse wave velocity; arterial stiffness

Results 1-25 (59)