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Kira C Taylor, Cara L Carty,
Logan Dumitrescu,
Petra B Ková,
Shelley A Cole,
Lucia Hindorff,
Fred R Schumacher,
Lynne R Wilkens,
Ralph V Shohet,
P Miguel Quibrera, [......],
Kristin Brown-Gentry,
Garnet Anderson,
Jose Luis Ambite,
Christopher Haiman,
Loïc Le Marchand,
Charles Kooperberg,
Dana C Crawford,
Steven Buyske,
Kari E North,
Myriam Fornage
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ABSTRACT: BACKGROUND: High-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels are influenced by both genes and the environment. Genome-wide association studies (GWAS) have identified ~100 common genetic variants associated with HDL-C, LDL-C, and/or TG levels, mostly in populations of European descent, but little is known about the modifiers of these associations. Here, we investigated whether GWAS-identified SNPs for lipid traits exhibited heterogeneity by sex in the Population Architecture using Genomics and Epidemiology (PAGE) study. RESULTS: A sex-stratified meta-analysis was performed for 49 GWAS-identified SNPs for fasting HDL-C, LDL-C, and ln(TG) levels among adults self-identified as European American (25,013). Heterogeneity by sex was established when phet < 0.001. There was evidence for heterogeneity by sex for two SNPs for ln(TG) in the APOA1/C3/A4/A5/BUD13 gene cluster: rs28927680 (phet = 7.4x10-7) and rs3135506 (phet = 4.3x10-4), one SNP in PLTP for HDL levels (rs7679; phet = 9.9x10-4), and one in HMGCR for LDL levels (rs12654264; phet = 3.1x10-5). We replicated heterogeneity by sex in five of seventeen loci previously reported by genome-wide studies (binomial p = 0.0009). We also present results for other racial/ethnic groups in the supplementary materials, to provide a resource for future meta-analyses. CONCLUSIONS: We provide further evidence for sex-specific effects of SNPs in the APOA1/C3/A4/A5/BUD13 gene cluster, PLTP, and HMGCR on fasting triglyceride levels in European Americans from the PAGE study. Our findings emphasize the need for considering context-specific effects when interpreting genetic associations emerging from GWAS, and also highlight the difficulties in replicating interaction effects across studies and across racial/ethnic groups.
BMC Genetics 05/2013; 14(1):33. · 2.47 Impact Factor
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Ying Wu,
Lindsay L Waite,
Anne U Jackson,
Wayne H-H Sheu,
Steven Buyske,
Devin Absher,
Donna K Arnett,
Eric Boerwinkle,
Lori L Bonnycastle, Cara L Carty, [......],
Tzung-Dau Wang,
Michael Boehnke,
Christopher A Haiman,
Yii-Der I Chen,
Charles Kooperberg,
Themistocles L Assimes,
Dana C Crawford,
Chao A Hsiung,
Kari E North,
Karen L Mohlke
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ABSTRACT: Genome-wide association studies (GWAS) have identified ∼100 loci associated with blood lipid levels, but much of the trait heritability remains unexplained, and at most loci the identities of the trait-influencing variants remain unknown. We conducted a trans-ethnic fine-mapping study at 18, 22, and 18 GWAS loci on the Metabochip for their association with triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C), respectively, in individuals of African American (n = 6,832), East Asian (n = 9,449), and European (n = 10,829) ancestry. We aimed to identify the variants with strongest association at each locus, identify additional and population-specific signals, refine association signals, and assess the relative significance of previously described functional variants. Among the 58 loci, 33 exhibited evidence of association at P<1×10(-4) in at least one ancestry group. Sequential conditional analyses revealed that ten, nine, and four loci in African Americans, Europeans, and East Asians, respectively, exhibited two or more signals. At these loci, accounting for all signals led to a 1.3- to 1.8-fold increase in the explained phenotypic variance compared to the strongest signals. Distinct signals across ancestry groups were identified at PCSK9 and APOA5. Trans-ethnic analyses narrowed the signals to smaller sets of variants at GCKR, PPP1R3B, ABO, LCAT, and ABCA1. Of 27 variants reported previously to have functional effects, 74% exhibited the strongest association at the respective signal. In conclusion, trans-ethnic high-density genotyping and analysis confirm the presence of allelic heterogeneity, allow the identification of population-specific variants, and limit the number of candidate SNPs for functional studies.
PLoS Genetics 03/2013; 9(3):e1003379. · 8.69 Impact Factor
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Kylee L Spencer,
Jennifer Malinowski, Cara L Carty,
Nora Franceschini,
Lindsay Fernández-Rhodes,
Alicia Young,
Iona Cheng,
Marylyn D Ritchie,
Christopher A Haiman,
Lynne Wilkens,
Chunyuanwu,
Tara C Matise,
Christopher S Carlson,
Kathleen Brennan,
Amy Park,
Aleksandar Rajkovic,
Lucia A Hindorff,
Steven Buyske,
Dana C Crawford
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ABSTRACT: Age at menarche (AM) and age at natural menopause (ANM) define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs) in 4,159 and 1,860 African American women, respectively, in the Women's Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10(-08); KCNQ1 rs79972789, p = 1.9×10(-07); COL4A3BP rs181686584, p = 2.9×10(-07)). Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10(-06)). While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations.
PLoS ONE 01/2013; 8(2):e55258. · 4.09 Impact Factor
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Christy L Avery,
Praveen Sethupathy,
Steven Buyske,
Qianchuan He,
Dan-Yu Lin,
Dan E Arking, Cara L Carty,
David Duggan,
Megan D Fesinmeyer,
Lucia A Hindorff, [......],
Kristen K Patton,
Ulrike Peters,
Ralph V Shohet,
Nona Sotoodehnia,
Alicia M Young,
Charles Kooperberg,
Christopher A Haiman,
Karen L Mohlke,
Eric A Whitsel,
Kari E North
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ABSTRACT: The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10(-4)): ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10(-5)): one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation.
PLoS Genetics 08/2012; 8(8):e1002870. · 8.69 Impact Factor
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ABSTRACT: For many complex traits, including height, the majority of variants identified by genome-wide association studies (GWAS) have small effects, leaving a significant proportion of the heritable variation unexplained. Although many penalized multiple regression methodologies have been proposed to increase the power to detect associations for complex genetic architectures, they generally lack mechanisms for false-positive control and diagnostics for model over-fitting. Our methodology is the first penalized multiple regression approach that explicitly controls Type I error rates and provide model over-fitting diagnostics through a novel normally distributed statistic defined for every marker within the GWAS, based on results from a variational Bayes spike regression algorithm.
We compare the performance of our method to the lasso and single marker analysis on simulated data and demonstrate that our approach has superior performance in terms of power and Type I error control. In addition, using the Women's Health Initiative (WHI) SNP Health Association Resource (SHARe) GWAS of African-Americans, we show that our method has power to detect additional novel associations with body height. These findings replicate by reaching a stringent cutoff of marginal association in a larger cohort.
An R-package, including an implementation of our variational Bayes spike regression (vBsr) algorithm, is available at http://kooperberg.fhcrc.org/soft.html.
Bioinformatics 05/2012; 28(13):1738-44. · 5.47 Impact Factor
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Cara L Carty,
Petra Buzková,
Myriam Fornage,
Nora Franceschini,
Shelley Cole,
Gerardo Heiss,
Lucia A Hindorff,
Barbara V Howard,
Sue Mann,
Lisa W Martin,
Ying Zhang,
Tara C Matise,
Ross Prentice,
Alexander P Reiner,
Charles Kooperberg
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ABSTRACT: Genome-wide association studies (GWAS) have identified loci associated with ischemic stroke (IS) and cardiovascular disease (CVD) in European-descent individuals, but their replication in different populations has been largely unexplored.
Nine single nucleotide polymorphisms (SNPs) selected from GWAS and meta-analyses of stroke, and 86 SNPs previously associated with myocardial infarction and CVD risk factors, including blood lipids (high density lipoprotein [HDL], low density lipoprotein [LDL], and triglycerides), type 2 diabetes, and body mass index (BMI), were investigated for associations with incident IS in European Americans (EA) N=26 276, African-Americans (AA) N=8970, and American Indians (AI) N=3570 from the Population Architecture using Genomics and Epidemiology Study. Ancestry-specific fixed effects meta-analysis with inverse variance weighting was used to combine study-specific log hazard ratios from Cox proportional hazards models. Two of 9 stroke SNPs (rs783396 and rs1804689) were associated with increased IS hazard in AA; none were significant in this large EA cohort. Of 73 CVD risk factor SNPs tested in EA, 2 (HDL and triglycerides SNPs) were associated with IS. In AA, SNPs associated with LDL, HDL, and BMI were significantly associated with IS (3 of 86 SNPs tested). Out of 58 SNPs tested in AI, 1 LDL SNP was significantly associated with IS.
Our analyses showing lack of replication in spite of reasonable power for many stroke SNPs and differing results by ancestry highlight the need to follow up on GWAS findings and conduct genetic association studies in diverse populations. We found modest IS associations with BMI and lipids SNPs, though these findings require confirmation.
Circulation Cardiovascular Genetics 03/2012; 5(2):210-6. · 6.11 Impact Factor
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ABSTRACT: Height is a complex trait under strong genetic influence. To date, numerous genetic loci have been associated with height in individuals of European ancestry. However, few large-scale discovery genome-wide association studies (GWAS) of height in minority populations have been conducted and thus information about population-specific height regulation is limited. We conducted a GWA analysis of height in 8149 African-American (AA) women from the Women's Health Initiative. Genetic variants with P< 5 × 10(-5) (n = 169) were followed up in a replication data set (n = 20 809) and meta-analyzed in a total of 28 958 AAs and African-descent individuals. Twelve single-nucleotide polymorphisms (SNPs) representing 7 independent loci were significantly associated with height at P < 5 × 10(-8). We identified novel SNPs in 17q23 (TMEM100/PCTP) and Xp22.3 (ARSE) reflecting population-specific regulation of height in AAs and replicated five loci previously reported in European-descent populations [4p15/LCORL, 11q13/SERPINH1, 12q14/HMGA2, 17q23/MAP3K3 (mitogen-activated protein kinase3) and 18q21/DYM]. In addition, we performed an admixture mapping analysis of height which is both complementary and supportive to the GWA analysis and suggests potential associations between ancestry and height on chromosomes 4 (4q21), 15 (15q26) and 17 (17q23). Our findings provide insight into the genetic architecture of height and support the investigation of non-European-descent populations for identifying genetic factors associated with complex traits. Specifically, we identify new loci that may reflect population-specific regulation of height and report several known height loci that are important in determining height in African-descent populations.
Human Molecular Genetics 02/2012; 21(3):711-20. · 7.64 Impact Factor
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Steven Buyske,
Ying Wu, Cara L Carty,
Iona Cheng,
Themistocles L Assimes,
Logan Dumitrescu,
Lucia A Hindorff,
Sabrina Mitchell,
Jose Luis Ambite,
Eric Boerwinkle, [......],
Carlos Rodriguez,
Fredrick R Schumacher,
Benjamin F Voight,
Alicia Young,
Teri A Manolio,
Karen L Mohlke,
Christopher A Haiman,
Ulrike Peters,
Dana C Crawford,
Kari E North
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ABSTRACT: The Metabochip is a custom genotyping array designed for replication and fine mapping of metabolic, cardiovascular, and anthropometric trait loci and includes low frequency variation content identified from the 1000 Genomes Project. It has 196,725 SNPs concentrated in 257 genomic regions. We evaluated the Metabochip in 5,863 African Americans; 89% of all SNPs passed rigorous quality control with a call rate of 99.9%. Two examples illustrate the value of fine mapping with the Metabochip in African-ancestry populations. At CELSR2/PSRC1/SORT1, we found the strongest associated SNP for LDL-C to be rs12740374 (p = 3.5 × 10(-11)), a SNP indistinguishable from multiple SNPs in European ancestry samples due to high correlation. Its distinct signal supports functional studies elsewhere suggesting a causal role in LDL-C. At CETP we found rs17231520, with risk allele frequency 0.07 in African Americans, to be associated with HDL-C (p = 7.2 × 10(-36)). This variant is very rare in Europeans and not tagged in common GWAS arrays, but was identified as associated with HDL-C in African Americans in a single-gene study. Our results, one narrowing the risk interval and the other revealing an associated variant not found in Europeans, demonstrate the advantages of high-density genotyping of common and rare variation for fine mapping of trait loci in African American samples.
PLoS ONE 01/2012; 7(4):e35651. · 4.09 Impact Factor
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ABSTRACT: Genome-wide association studies (GWAS) have identified loci associated with risk of breast cancer. These studies have primarily been conducted in populations of European descent. To fully understand the impact of these loci, it is important to study groups with other genetic ancestries, including African American women.
We examined 22 single-nucleotide polymorphisms (SNP), previously identified in GWAS of breast cancer risk in European and Asian descent women (index SNPs), and SNPs in the surrounding regions in a study of 7,800 African American women (including 316 women with incident invasive breast cancer) from the Women's Health Initiative SNP Health Association Resource.
Two index SNPs were associated with breast cancer: rs3803662 at 16q12.2/TOX3 (Hazard ratio [HR] for the T allele = 0.79, 95% CI: 0.67-0.92, P = 0.003) and rs10941679 at 5p12 (HR for the G allele = 1.31, 95% CI: 1.06-1.63, P = 0.014). When we expanded to regions, the 3p24.1 region showed an association with breast cancer risk (permutation based P = 0.027) and three regions (10p15.1, 10q26.13/FGFR2, and 16q12.2/TOX3) showed a trend toward association.
Our findings provide evidence that some breast cancer GWAS regions may be associated with breast cancer in African American women. Larger, more comprehensive studies are needed to fully assess generalizability of published GWAS findings and to identify potential novel associations in African American populations.
Both replication and lack of replication of published GWAS findings in other ancestral groups provides important information of the genetic etiology of this disease and may impact translation of GWAS findings to clinical and public health settings.
Cancer Epidemiology Biomarkers & Prevention 08/2011; 20(9):1950-9. · 4.12 Impact Factor
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Logan Dumitrescu, Cara L Carty,
Kira Taylor,
Fredrick R Schumacher,
Lucia A Hindorff,
José L Ambite,
Garnet Anderson,
Lyle G Best,
Kristin Brown-Gentry,
Petra Bůžková, [......],
Sarah A Pendergrass,
Miguel Quibrera,
Ralph V Shohet,
Lynne R Wilkens,
Christopher A Haiman,
Loïc Le Marchand,
Steven Buyske,
Charles Kooperberg,
Kari E North,
Dana C Crawford
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ABSTRACT: For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (~20,000), African American (~9,000), American Indian (~6,000), Mexican American/Hispanic (~2,500), Japanese/East Asian (~690), and Pacific Islander/Native Hawaiian (~175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.
PLoS Genetics 06/2011; 7(6):e1002138. · 8.69 Impact Factor
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ABSTRACT: Little is known about the acute precipitants of ischemic stroke, although evidence suggests infections contribute to risk. We hypothesized that acute hospitalization for infection is associated with the short-term risk of stroke.
The case-crossover design was used to compare hospitalization for infection during case periods (90, 30, or 14 days before an incident ischemic stroke) and control periods (equivalent time periods exactly 1 or 2 years before stroke) in the Cardiovascular Health Study, a population-based cohort of 5888 elderly participants from 4 US sites. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated by conditional logistic regression. Confirmatory analyses assessed hazard ratios of stroke from Cox regression models, with hospitalization for infection as a time-varying exposure.
During a median follow-up of 12.2 years, 669 incident ischemic strokes were observed in participants without a baseline history of stroke. Hospitalization for infection was more likely during case than control time periods; for 90 days before stroke, OR=3.4 (95% CI, 1.8 to 6.5). The point estimates of risks were higher when we examined shorter intervals: for 30 days, OR=7.3 (95% CI, 1.9 to 40.9), and for 14 days, OR=8.0 (95% CI, 1.7 to 77.3). In survival analyses, risk of stroke was associated with hospitalization for infection in the preceding 90 days, adjusted hazard ratio=2.4 (95% CI, 1.6 to 3.4).
Hospitalization for infection is associated with a short-term increased risk of stroke, with higher risks observed for shorter intervals preceding stroke.
Stroke 05/2011; 42(7):1851-6. · 5.73 Impact Factor
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Cara L Carty,
Charles Kooperberg,
Marian L Neuhouser,
Lesley Tinker,
Barbara Howard,
Jean Wactawski-Wende,
Shirley A A Beresford,
Linda Snetselaar,
Mara Vitolins,
Matthew Allison,
Nicole Budrys,
Ross Prentice,
Ulrike Peters
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ABSTRACT: The Women's Health Initiative Dietary Modification (DM) Trial was a randomized controlled trial that compared the effects of a low-fat (≤20% of total energy) or a usual diet in relation to chronic disease risk in postmenopausal women.
We characterized long-term body-composition changes associated with the DM trial and potential modifiers of these associations.
In the DM trial, 48,835 women aged 50-79 y were randomly assigned to intervention (40%) or comparison (60%) groups. We studied a subset with whole-body dual-energy X-ray absorptiometry scans at baseline and during follow-up. Changes in fat mass (FM), lean mass (LM), and percentage body fat between the intervention (n = 1580) and comparison (n = 2731) groups at years 1, 3, and 6 were compared. By using generalized estimating equations, we calculated overall differences between groups and tested for interactions with age, diabetes, race-ethnicity (white, black, and Hispanic), body mass index (BMI), and hormone therapy (HT).
The intervention women experienced significantly greater reductions in percentage body fat, FM, and LM at years 1 and 3 than did women in the comparison group (all P < 0.05). At year 6, only the FM change was significantly different between groups. Overall, the intervention was associated with reductions in percentage body fat (-0.8%; 95% CI: -1.0%, -0.6%), FM (-1.1 kg; 95% CI: -1.3, -0.8 kg), and LM (-0.17 kg; 95% CI: -0.28, -0.06 kg) during follow-up (all P < 0.003). Intervention associations varied by race-ethnicity, BMI, diabetes, and HT and remained significant after adjustment for physical activity.
This intervention was associated with modest long-term body-composition changes; the findings were more robust in years 1 and 3. This trial was registered at clinicaltrials.gov as NCT00000611.
American Journal of Clinical Nutrition 03/2011; 93(3):516-24. · 6.67 Impact Factor
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ABSTRACT: The inflammatory cytokine interleukin-6 (IL-6) is a main regulator of fibrinogen synthesis, though its interaction with fibrinogen genes (FGA, FGB, FGG) and subsequent impact on cardiovascular disease (CVD) risk is not well-studied. We investigated joint associations of fibrinogen and IL6 tagSNPs with fibrinogen concentrations, carotid intima-media thickness, and myocardial infarction or ischemic stroke in 3900 European-American Cardiovascular Health Study participants. To identify combinations of genetic main effects and interactions associated with outcomes, we used logic regression. We also evaluated whether the relationship between fibrinogen SNPs and fibrinogen level varied by IL-6 level using linear regression models with multiplicative interaction terms. Combinations of fibrinogen and IL6 SNPs were significantly associated with fibrinogen level (p < 0.005), but not with other outcomes. Fibrinogen levels were higher in individuals having FGB1437 (rs1800790) and lacking FGA6534 (rs6050) minor alleles; these SNPs interacted with IL6 rs1800796 to influence fibrinogen level. Marginally significant (p= 0.03) interactions between IL-6 level and FGA and FGG promoter SNPs associated with fibrinogen levels were detected. We identified potential gene-gene interactions influencing fibrinogen levels. Although IL-6 responsive binding sites are present in fibrinogen gene promoter regions, we did not find strong evidence of interaction between fibrinogen SNPs and IL6 SNPs or levels influencing CVD.
Annals of Human Genetics 01/2010; 74(1):1-10. · 2.57 Impact Factor
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ABSTRACT: The inflammatory cytokine interleukin-6 (IL-6) is a main regulator of fibrinogen synthesis, though its interaction with fibrinogen genes (FGA, FGB, FGG) and subsequent impact on cardiovascular disease (CVD) risk is not well-studied.We investigated joint associations of fibrinogen and IL6 tagSNPs with fibrinogen concentrations, carotid intima-media thickness, and myocardial infarction or ischemic stroke in 3900 European-American Cardiovascular Health Study participants. To identify combinations of genetic main effects and interactions associated with outcomes, we used logic regression. We also evaluated whether the relationship between fibrinogen SNPs and fibrinogen level varied by IL-6 level using linear regression models with multiplicative interaction terms. Combinations of fibrinogen and IL6 SNPs were significantly associated with fibrinogen level (p < 0.005), but not with other outcomes. Fibrinogen levels were higher in individuals having FGB1437 (rs1800790) and lacking FGA6534 (rs6050) minor alleles; these SNPs interacted with IL6 rs1800796 to influence fibrinogen level. Marginally significant (p= 0.03) interactions between IL-6 level and FGA and FGG promoter SNPs associated with fibrinogen levels were detected.We identified potential gene-gene interactions influencing fibrinogen levels. Although IL-6 responsive binding sites are present in fibrinogen gene promoter regions, we did not find strong evidence of interaction between fibrinogen SNPs and IL6 SNPs or levels influencing CVD.
Annals of Human Genetics 12/2009; 74(1):1 - 10. · 2.57 Impact Factor
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Daniel A Enquobahrie,
Nicholas L Smith,
Joshua C Bis, Cara L Carty,
Kenneth M Rice,
Thomas Lumley,
Lucia A Hindorff,
Rozenn N Lemaitre,
Michelle A Williams,
David S Siscovick,
Susan R Heckbert,
Bruce M Psaty
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ABSTRACT: Variations in candidate genes participating in oxidative stress, inflammation, and their interactions are potentially associated with diseases of atherosclerotic origin. We investigated independent and joint associations of variations in cholesterol ester transfer protein (CETP), interleukin-8 (IL8), peroxisome proliferator activator receptor-alpha (PPARA), and Toll-like receptor 4 (TLR4) genes with incident nonfatal myocardial infarction (MI) or ischemic stroke. In a population-based case-control study, patients (848 with MI and 368 with ischemic stroke) and controls (2,682) were recruited from postmenopausal women and hypertensive men/women who were members of Group Health in western Washington State. Common tag single-nucleotide polymorphisms (SNPs; n=34) representing gene-wide variations were selected from gene sequencing data using pairwise linkage disequilibrium. Haplotypes were inferred using a modified expectation maximization algorithm. Multivariate logistic regression evaluated individual haplotype and SNP-disease associations in log-additive models. Global haplotype tests assessed overall gene-disease associations. Logic regression was used to evaluate gene-gene interactions. False discovery rates and permutation tests were used for multiple testing adjustment in evaluating independent associations and interactions, respectively. Overall, gene-wide variations in PPARA and TLR4 genes were associated with MI. The minor allele of the PPARA SNP, rs4253623, was associated with a higher risk of MI (odds ratio 1.25, 95% confidence interval 1.08 to 1.46), whereas the minor allele of the TLR4 SNP, rs1927911, was associated with a lower risk of MI (odds ratio 0.88, 95% confidence interval 0.77 to 0.99). No within-gene or gene-gene interaction was associated with MI or ischemic stroke risk. In conclusion, potential SNP-disease associations identified in the present study are novel and need further investigation.
The American Journal of Cardiology 07/2008; 101(12):1683-8. · 3.37 Impact Factor
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Alexander P Reiner,
Mark M Wurfel,
Leslie A Lange,
Christopher S Carlson,
Alex S Nord, Cara L Carty,
Mark J Rieder,
Cindy Desmarais,
Nancy S Jenny,
Carlos Iribarren,
Jeremy D Walston,
O Dale Williams,
Deborah A Nickerson,
Gail P Jarvik
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ABSTRACT: Circulating levels of acute phase reactant proteins such as plasma C-reactive protein (CRP) are likely influenced by multiple genes regulating the innate immune response.
We screened a set of 16 inflammation-related genes for association with CRP in a large population-based study of healthy young adults (n=1627). Results were validated in 2 independent studies (n=1208 and n=4310), including a pooled analysis of all 3 studies. In the pooled analysis, the minor allele of IL1RN 1018 (rs4251961) within the gene encoding interleukin (IL)-1 receptor antagonist (IL-1RA) was significantly associated with higher mean plasma log(CRP) level (P<1 x 10(-4)). The same IL1RN 1018 allele was associated with higher mean plasma log(IL-6) levels (P=0.004). In the pooled analysis, the minor allele of IL1RN 13888 (rs2232354) was associated with higher fibrinogen, (P=0.001). The IL1RN 1018 and 13888 variant alleles tag a clade of IL1RN haplotypes linked to allele 1 of an 86-bp VNTR polymorphism. We confirmed that the IL1RN 1018 variant (rs4251961) was associated with decreased cellular IL-1RA production ex vivo.
Common functional polymorphisms of the IL1RN gene are associated with several markers of systemic inflammation.
Arteriosclerosis Thrombosis and Vascular Biology 07/2008; 28(7):1407-12. · 6.37 Impact Factor
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Cara L Carty,
Mary Cushman,
Daniel Jones,
Leslie A Lange,
Lucia A Hindorff,
Kenneth Rice,
Nancy S Jenny,
J Peter Durda,
Jeremy Walston,
Christopher S Carlson,
Debbie Nickerson,
Russell P Tracy,
Alex P Reiner
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ABSTRACT: Elevated plasma fibrinogen is a risk factor for cardiovascular disease (CVD), but associations between fibrinogen single nucleotide polymorphisms (SNPs) and disease risk are inconsistent. We investigated whether common (> or = 5% minor allele frequency) variation in the fibrinogen genes (FGA, FGB, FGG) is associated with fibrinogen concentration, carotid artery intima-medial thickness (IMT) and risk of incident myocardial infarction (MI), ischemic stroke and CVD mortality in European- (EA) and African-descent (AA) adults (> or = 65 years) from the Cardiovascular Health Study. TagSNPs were genotyped in 3,969 EA and 719 AA free of MI or stroke at baseline. Race-specific models included multiple testing correction and adjustment for sex, age and site. Among EA, minor alleles of FGA3807, FGB1437 and FGG902 were associated with higher fibrinogen levels; whereas FGA251, FGA2224, FGA6534 and FGG10034 were associated with lower levels, p<0.004 for each. Strongest associations were seen for FGB1437; each additional copy of the minor allele was associated with 13 mg/dl (95%CI: 9-16) higher fibrinogen level. Similar trends in AA were not significant. Fibrinogen haplotypes were not significantly associated with internal or common carotid IMT. No associations with MI or CVD mortality were seen in EA, though FGB1038 and FGG902 were significantly associated with increased and decreased risk of stroke in men, respectively, as were related haplotypes. FGB1038 was also associated with CVD mortality in AA, HR = 1.9 (95%CI: 1.3-2.7). In conclusion, while fibrinogen genetic variation was strongly associated with fibrinogen levels, there was less evidence of association with the more complex outcomes of IMT and CVD events.
Thrombosis and Haemostasis 02/2008; 99(2):388-95. · 5.04 Impact Factor
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Cara L Carty,
Patrick Heagerty,
Karen Nakayama,
E Clair McClung,
Julieann Lewis,
Dawn Lum,
Erin Boespflug,
Carrie McCloud-Gehring,
Behrooz R Soleimani,
Jane Ranchalis,
Tamara J Bacus,
Clement E Furlong,
Gail P Jarvik
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ABSTRACT: Inflammatory markers are associated with vascular disease; however, variation in the acute phase response (APR) has not been evaluated. We evaluated whether the APR magnitude in men with severe carotid artery disease (CAAD) (>80% stenosis) differed from that of men without stenosis (<15% stenosis).
White males with (n=43) and without (n=61) severe CAAD receiving clinical influenza vaccinations were recruited. Their baseline and 24-hour after -vaccination blood samples were assayed for C-reactive protein (CRP), IL-6, and serum amyloid-a (SAA). In vivo APR to vaccination was measurable and varied among subjects. Adjusted for age, smoking, oral hypoglycemics, aspirin, and stain use, the relative 24-hour changes in levels of ln(CRP), ln(IL-6), and ln(SAA) were higher in men with CAAD than in men without, but only the SAA response was significant (P=0.02); the relative SAA response was 1.6 (95% confidence interval, 1.1 to 2.5) times higher in men with than without CAAD. The APR for all markers appeared to be independent of baseline levels.
Influenza vaccination results in a mild, but measurable, APR in men with and without CAAD. SAA APR variability may be a predictor of severe vascular disease that is independent of basal SAA level.
Arteriosclerosis Thrombosis and Vascular Biology 12/2006; 26(12):2738-44. · 6.37 Impact Factor
