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1.  Ethical and Practical Guidelines for Reporting Genetic Research Results To Study Participants: Updated Guidelines from an NHLBI Working Group 
In January 2009 the National Heart, Lung, and Blood Institute (NHLBI) convened a 28-member multidisciplinary Working Group to update the recommendations of a 2004 NHLBI Working Group focused on Guidelines to the Return of Genetic Research Results. Changes in the genetic and societal landscape over the intervening five years raise multiple questions and challenges. The group noted the complex issues arising from the fact that the technologic and bioinformatic progress has made it possible to obtain considerable information on individuals which would not have been possible a decade ago. While unable to reach consensus on a number of issues, the Working Group produced five recommendations. The Working Group offers two recommendations addressing the criteria necessary to determine when genetic results should and may be returned to study participants, respectively. In addition, it suggests that a time limit be established to limit the duration of obligation of investigators to return genetic research results. The Group recommends the creation of a central body, or bodies, to provide guidance on when genetic research results are associated with sufficient risk and have established clinical utility to justify their return to study participants. The final Recommendation urges investigators to engage the broader community when dealing with identifiable communities to advise them on the return of aggregate and individual research results. Creation of an entity charged to provide guidance to IRBs, investigators, research institutions and research sponsors would provide rigorous review of available data, promote standardization of study policies regarding return of genetic research results, and enable investigators and study participants to clarify and share expectations for the handling of this increasingly valuable information with appropriate respect for the rights and needs of participants.
doi:10.1161/CIRCGENETICS.110.958827
PMCID: PMC3090664  PMID: 21156933
consent genetics; ethics; research genetics; risk rediction; single nucleotide polymorphism genetics
2.  Translation of Genetics Research to Clinical Medicine: the NHLBI Perspective 
The National Heart, Lung and Blood Institute (NHLBI) is firmly committed to advancing translational research, especially in the field of genetics. An evaluation of the NHLBI’s extramural research grants funded in FY2008 and FY2011 was conducted to establish a baseline from which to assess progress in translational research, to assess current commitments and initial progress, and to identify putative gaps, barriers, and opportunities in the Institute’s human genetics research portfolios.
A search of the category of Genetics using the NIH Research, Condition, and Disease Categorization (RCDC) system was conducted to identify human genetics research project grants in the NHLBI’s genetics research portfolio. The NHLBI genetics portfolios were evaluated using a multidisciplinary research framework continuum that comprises five categories: discovery (T0); characterization (T1); clinical utility (T2); implementation, dissemination and diffusion (T3); and population health impact (T4). The abstracts for the grants were evaluated independently by two reviewers with an adjudicator for discrepancies in coding. The majority of the grants in 2008 and 2011 were classified as T0 and T1 research, with only four grants classified as T2 and beyond.
The majority of genetics grants funded in 2008 and 2011 were in the T0 and T1 categories, although the proportion of grants in T0 actually increased in that period. NHLBI-initiated programs to address this inability to move beyond T1 translation research have yet to have an impact on grant-funded translational genetic research. Future genetics studies should be designed with an eye towards translation to help overcome this barrier.
doi:10.1161/CIRCGENETICS.113.000227
PMCID: PMC3957221  PMID: 24347619
genetics; translational medicine; NHLBI/NIH
3.  A QTL for genotype by sex interaction for anthropometric measurements in Alaskan Eskimos (GOCADAN study) on chromosome 19q12-13 
Obesity (Silver Spring, Md.)  2011;19(9):1840-1846.
Variation in anthropometric measurements due to sexual dimorphism can be the result of genotype by sex interactions (G×S). The purpose of this study was to examine the sex-specific genetic architecture in anthropometric measurements in Alaskan Eskimos from the Genetics of Coronary Artery Disease in Alaska Natives (GOCADAN) study. Maximum likelihood based variance components decomposition methods, implemented in SOLAR, were used for GxS analyses. Anthropometric measurements included BMI, waist circumference (WC), waist/height ratio, percent body fat (%BF) and subscapular and triceps skinfolds. Except for WC, mean values of all phenotypes were significantly different in men and women (p < 0.05). All anthropometric measures were significantly heritable (p< 0.001). In a preliminary analysis not allowing for G×S interaction, evidence of linkage was detected between markers D19S414 and D19S220 on chromosome 19 for WC (LOD = 3.5), %BF (LOD = 1.7), BMI (LOD = 2.4), WHtR (LOD = 2.5), subscapular (LOD = 2.1) and triceps skinfolds (LOD = 1.9). In subsequent analyses which allowed for G×S interaction, linkage was again found between these traits and the same two markers on chromosome 19 with significantly improved LOD scores for: WC (LOD = 4.5), %BF (LOD = 3.8), BMI (LOD = 3.5), waist/height ratio (LOD = 3.2), subscapular (LOD = 3.0) and triceps skinfolds (LOD = 2.9). These results support evidence of a G×S interaction in the expression of genetic effects resulting in sexual dimorphism in anthropometric phenotypes and identify the chromosome 19q12-13 region as important for adiposity-related traits in Alaskan Eskimos.
doi:10.1038/oby.2011.78
PMCID: PMC3525327  PMID: 21527897
Abdominal obesity; Adiposity; Body composition; Linkage
4.  Heart rate is associated with markers of fatty acid desaturation: the GOCADAN study 
Objectives
To determine if heart rate (HR) is associated with desaturation indexes as HR is associated with arrhythmia and sudden death.
Study design
A community based cross-sectional study of 1214 Alaskan Inuit.
Methods
Data of FA concentrations from plasma and red blood cell membranes from those ≥35 years of age (n = 819) were compared to basal HR at the time of examination. Multiple linear regression with backward stepwise selection was employed to analyze the effect of the desaturase indexes on HR, after adjustment for relevant covariates.
Results
The Δ5 desaturase index (Δ5-DI) measured in serum has recently been associated with a protective role for cardiovascular disease. This index measured here in plasma and red blood cells showed a negative correlation with HR. The plasma stearoyl-CoA-desaturase (SCD) index, previously determined to be related to cardiovascular disease (CVD) mortality, on the other hand, was positively associated with HR, while the Δ6 desaturase index (Δ6-DI) had no significant effect on HR.
Conclusion
Endogenous FA desaturation is associated with HR and thereby, in the case of SCD, possibly with arrhythmia and sudden death, which would at least partially explain the previously observed association between cardiovascular mortality and desaturase activity.
PMCID: PMC3387544  PMID: 22456045
Inuit; diet; fatty acid metabolism; CVD risk factors
5.  Variants in CPT1A, FADS1, and FADS2 are Associated with Higher Levels of Estimated Plasma and Erythrocyte Delta-5 Desaturases in Alaskan Eskimos 
The delta-5 and delta-6 desaturases (D5D and D6D), encoded by fatty acid desaturase 1 (FADS1) and 2 (FADS2) genes, respectively, are rate-limiting enzymes in the metabolism of ω-3 and ω-6 fatty acids. The objective of this study was to identify genes influencing variation in estimated D5D and D6D activities in plasma and erythrocytes in Alaskan Eskimos (n = 761) participating in the genetics of coronary artery disease in Alaska Natives (GOCADAN) study. Desaturase activity was estimated by product: precursor ratio of polyunsaturated fatty acids. We found evidence of linkage for estimated erythrocyte D5D (eD5D) on chromosome 11q12-q13 (logarithm of odds score = 3.5). The confidence interval contains candidate genes FADS1, FADS2, 7-dehydrocholesterol reductase (DHCR7), and carnitine palmitoyl transferase 1A, liver (CPT1A). Measured genotype analysis found association between CPT1A, FADS1, and FADS2 single-nucleotide polymorphisms (SNPs) and estimated eD5D activity (p-values between 10−28 and 10−5). A Bayesian quantitative trait nucleotide analysis showed that rs3019594 in CPT1A, rs174541 in FADS1, and rs174568 in FADS2 had posterior probabilities > 0.8, thereby demonstrating significant statistical support for a functional effect on eD5D activity. Highly significant associations of FADS1, FADS2, and CPT1A transcripts with their respective SNPs (p-values between 10−75 and 10−7) in Mexican Americans of the San Antonio Family Heart Study corroborated our results. These findings strongly suggest a functional role for FADS1, FADS2, and CPT1A SNPs in the variation in eD5D activity.
doi:10.3389/fgene.2012.00086
PMCID: PMC3371589  PMID: 22701466
essential fatty acids; single-nucleotide polymorphisms; bayesian quantitative trait nucleotide analysis
6.  Coffee consumption and the incidence of type 2 diabetes in men and women with normal glucose tolerance: The Strong Heart Study 
Background and aims
It was reported that high coffee consumption was related to decreased diabetes risk. The aim of this study is to examine the association between coffee consumption and the incidence of type 2 diabetes in persons with normal glucose tolerance in a population with a high incidence and prevalence of diabetes.
Methods and results
In a prospective cohort study, information about daily coffee consumption was collected at the baseline examination (1989-1992) in a population-based sample of American Indian men and women 45-74 years of age. Participants with normal glucose tolerance (N=1141) at the baseline examination were followed for an average of 7.6 years. The incidence of diabetes was compared across the categories of daily coffee consumption. The hazard ratios of diabetes related to coffee consumption were calculated using Cox proportional hazards models, adjusted for potential confounders.
Levels of coffee consumption were positively related to levels of current smoking and inversely related to body mass index, waist circumference, female gender, and hypertension. Compared to those who did not drink coffee, participants who drank 12 or more cups of coffee daily had 67% less risk of developing diabetes during the follow-up (hazard ratio: 0.33, 95% confidence interval: 0.13, 0.81).
Conclusion
In this population, a high level of coffee consumption was associated with a reduced risk of deterioration of glucose metabolism over an average 7.6 years of follow-up. More work is needed to understand whether there is a plausible biological mechanism for this observation.
doi:10.1016/j.numecd.2009.10.020
PMCID: PMC2888983  PMID: 20171062
coffee; Diabetes Mellitus; type 2; Indians; North American
7.  Individual saturated fatty acids are associated with different components of insulin resistance and glucose metabolism: the GOCADAN study 
Objectives
Type 2 diabetes and the consumption of saturated fatty acids (FAs) are on the rise among Alaska Inuits. This analysis, based on a cross-sectional study, explores the possible associations of saturated FA content in red blood cells (RBCs) and parameters of glucose metabolism in a sample of Alaska Natives.
Study design and methods
The sample included 343 women and 282 men aged 35–74. Statistical analyses explored the associations of selected RBC (myristic, palmitic and stearic acids) FAs with fasting glucose (plasma), fasting insulin (plasma), 2h glucose (2-hour glucose tolerance test), 2h insulin and homeostasis model assessment (HOMA) index. The models included sex and glucose metabolism status as fixed factors and age, body mass index (BMI), waist circumference, physical activity (METS) and FA content in RBCs as covariates. Measures of insulin, glucose and HOMA index were used as dependent variables.
Results
Myristic acid was positively associated with fasting insulin (β=0.47, p<0.001), 2h insulin (β=0.53, p=0.02) and HOMA index (β=0.455, p<0.001). Palmitic acid was associated with 2h glucose (β=2.3×10-2, p<0.001) and 2h insulin (β=5.6×10-2, p=0.002) and stearic acid was associated with fasting glucose (β=4.8×10-3, p=0.006).
Conclusions
These results strongly support the hypothesis that saturated fatty acids are associated with insulin resistance and glucose intolerance and that saturated fatty acids are significant risk factors for type 2 diabetes.
PMCID: PMC3307791  PMID: 20719107
myristic acid; palmitic acid; stearic acid; Inuit; Alaska Natives; diabetes; saturated fat
8.  Fasting Plasma Glucose and Hemoglobin A1c in Identifying and Predicting Diabetes 
Diabetes Care  2011;34(2):363-368.
OBJECTIVE
To compare fasting plasma glucose (FPG) and HbA1c in identifying and predicting type 2 diabetes in a population with high rates of diabetes.
RESEARCH DESIGN AND METHODS
Diabetes was defined as an FPG level ≥126 mg/dL or an HbA1c level ≥6.5%. Data collected from the baseline and second exams (1989–1995) of the Strong Heart Study were used.
RESULTS
For cases of diabetes identified by FPG ≥126 mg/dL, using HbA1c ≥6.5% at the initial and 4-year follow-up diabetes screenings (or in identifying incident cases in 4 years) among undiagnosed participants left 46% and 59% of cases of diabetes undetected, respectively, whereas for cases identified by HbA1c ≥6.5%, using FPG ≥126 mg/dL left 11% and 59% unidentified, respectively. Age, waist circumference, urinary albumin-to-creatinine ratio, and baseline FPG and HbA1c levels were common significant risk factors for incident diabetes defined by either FPG or HbA1c; triglyceride levels were significant for diabetes defined by HbA1c alone, and blood pressure and sibling history of diabetes were significant for diabetes defined by FPG alone. Using both the baseline FPG and HbA1c in diabetes prediction identified more people at risk than using either measure alone.
CONCLUSIONS
Among undiagnosed participants, using HbA1c alone in initial diabetes screening identifies fewer cases of diabetes than FPG, and using either FPG or HbA1c alone cannot effectively identify diabetes in a 4-year periodic successive diabetes screening or incident cases of diabetes in 4 years. Using both criteria may identify more people at risk. The proposed models using the commonly available clinical measures can be applied to assessing the risk of incident diabetes using either criterion.
doi:10.2337/dc10-1680
PMCID: PMC3024350  PMID: 21270194
9.  Genetic Influences on Serum Bilirubin in American Indians: The Strong Heart Family Study 
Objective
To identify genetic variation influencing serum bilirubin levels in American Indians, we performed genome-wide screening and association analyses in the Strong Heart Family Study. Bilirubin is an endogenous antioxidant that has demonstrated an inverse relationship with cardiovascular disease. Genetic variation within the promoter region of uridine diphosphate glucuronosyltransferase (UGT1A1) on chromosome 2q has been associated with elevated serum bilirubin levels in European populations. However, no study has investigated the UGT1A1 promoter in American Indians.
Methods
Statistical analyses were carried out with 3,484 participants aged 14 to 93 years recruited from three geographic areas in the United States; Arizona, Oklahoma, and North and South Dakota.
Results
Variance components linkage analysis detected a quantitative trait locus (QTL) for bilirubin on chromosome 2q in the combined centers (LOD = 6.61, P = 4.24 × 10−6) and in Oklahoma (LOD = 5.65, P = 4.57 24 × 10−5). Genetic association of the UGT1A1 promoter polymorphism was significant for all geographic locations. After adjustment using conditional linkage for UGT1A1 promoter variance, the linkage signal dropped to 1.10 in the combined sample and to 3.32 (P = 0.02) in Oklahoma, indicating this polymorphism is not completely responsible for the linkage signal in American Indians. We also detected suggestive linkage signals in the Dakotas on chromosome 10p12 (LOD = 2.18) and in the combined centers (LOD = 2.24) on chromosome 10q21.
Conclusions
Replication of a serum bilirubin QTL on chromosome 2q in American Indians implicates UGT1A1 but further genotyping is warranted to identify additional causative polymorphisms. Evidence also supports a potential novel locus for bilirubin on chromosome 10. Am. J. Hum. Biol. 23:118–125, 2011.
doi:10.1002/ajhb.21114
PMCID: PMC3046552  PMID: 21080475
10.  Heart rate is associated with markers of fatty acid desaturation: the GOCADAN study 
International Journal of Circumpolar Health  2012;71:10.3402/ijch.v71i0.17343.
Objectives
To determine if heart rate (HR) is associated with desaturation indexes as HR is associated with arrhythmia and sudden death.
Study design
A community based cross-sectional study of 1214 Alaskan Inuit.
Methods
Data of FA concentrations from plasma and red blood cell membranes from those ≥35 years of age (n =819) were compared to basal HR at the time of examination. Multiple linear regression with backward stepwise selection was employed to analyze the effect of the desaturase indexes on HR, after adjustment for relevant covariates.
Results
The Δ5 desaturase index (Δ5-DI) measured in serum has recently been associated with a protective role for cardiovascular disease. This index measured here in plasma and red blood cells showed a negative correlation with HR. The plasma stearoyl-CoA-desaturase (SCD) index, previously determined to be related to cardiovascular disease (CVD) mortality, on the other hand, was positively associated with HR, while the Δ6 desaturase index (Δ6-DI) had no significant effect on HR.
Conclusion
Endogenous FA desaturation is associated with HR and thereby, in the case of SCD, possibly with arrhythmia and sudden death, which would at least partially explain the previously observed association between cardiovascular mortality and desaturase activity.
doi:10.3402/ijch.v71i0.17343
PMCID: PMC3387544  PMID: 22456045
Inuit; diet; fatty acid metabolism; CVD risk factors
11.  Heart Rate is Associated with Red Blood Cell Fatty Acid Concentration: the GOCADAN Study 
American heart journal  2010;159(6):1020-1025.
Background
Consumption of omega-3 fatty acids (FAs) is associated with a reduction in deaths from coronary heart disease, arrhythmia, and sudden death. Although these FAs were originally thought to be anti-atherosclerotic, recent evidence suggests that their benefits are related to reducing risk for ventricular arrhythmia, and that this may be mediated by a slowed heart rate (HR).
Methods
The study was conducted in Alaskan Eskimos participating in the Genetics of Coronary Artery Disease in Alaska Natives (GOCADAN) Study, a population experiencing a dietary shift from unsaturated to saturated fats. We compared HR with red blood cell (RBC) FA content in 316 men and 391 women ages 35–74 years.
Results
Multivariate linear regression analyses of individual FAs with HR as the dependent variable and specific FAs as covariates revealed negative associations between HR and docosahexaenoic acid (DHA; 22:6n-3; p= 0.004) and eicosapentaenoic acid (EPA; 20:5n-3; p=0.009) and positive associations between HR and palmitoleic acid (16:1n-7; p=0.021), eicosenoic acid (20:1n9; p=0.007), and dihomo-gamma-linolenic acid (DGLA; 20:3n-6; p=0.021). Factor analysis revealed that the omega-3 FAs were negatively associated with HR (p=0.003), while a cluster of other, non-omega-3 unsaturated FAs (16:1, 20:1, and 20:3) was positively associated.
Conclusions
Marine omega 3 FAs are associated with lower HR, whereas palmitoleic and DGLA, previously identified as associated with saturated FA consumption and directly related to cardiovascular mortality, are associated with higher HR. These relations may at least partially explain the relations between omega-3 FAs, ventricular arrhythmia, and sudden death.
doi:10.1016/j.ahj.2010.03.001
PMCID: PMC2897142  PMID: 20569715
12.  Cardiovascular Disease Prevalence and its Relation to Risk Factors in Alaska Eskimos 
Background and Aims
Although Eskimos were thought to be protected from cardiovascular disease (CVD), state health data show a large proportion of deaths from CVD, despite traditional lifestyles and high omega-3 fatty acid intake. This article explores CVD prevalence and its relation to risk factors in Alaska Eskimos.
Methods and Results
A population-based cohort of 499 Alaska Eskimos > age 45 from the Norton Sound region was examined in 2000-2004 for CVD and associated risk factors as part of the Genetics of Coronary Artery Disease in Alaska Natives study. CVD and atherosclerosis were evaluated and adjudicated using standardized methods. Average age was 58y; diabetes prevalence was low and high-density lipoprotein cholesterol (HDL-C) concentrations were high, but a large proportion smoked and had high pathogen burden. CVD was higher in men (12.6%) than in women (5.3%) (prevalence ratio 2.4, CI 1.3-4.4). Rates of stroke (6.1% in men, 1.8% in women) were similar to those for coronary heart disease (CHD) (6.1% men, 2.5% women). MI prevalence was low in both genders (1.9% and 0.7%). CVD was higher in men and in those >60 yrs. Hypertension, diabetes, high LDL-C, high apoB, and low HDL-C were all strong correlates (<.002) and albuminuria and CRP were also correlated with CVD (p<.05) after adjustment for age and gender. Carotid atherosclerosis was correlated with CVD (p=.0079) independent of other risk factors.
Conclusion
These data show high CHD and stroke prevalence in Alaska Eskimos, despite low average LDL-C and high HDL-C. Hypertension and high LDL-C were independent correlates; identifying these risk factors early and treating to target is recommended.
doi:10.1016/j.numecd.2009.04.010
PMCID: PMC2981096  PMID: 19800772
cardiovascular disease; risk factors; epidemiology; omega-3 fatty acid
13.  Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study 
Fox, Ervin R. | Young, J. Hunter | Li, Yali | Dreisbach, Albert W. | Keating, Brendan J. | Musani, Solomon K. | Liu, Kiang | Morrison, Alanna C. | Ganesh, Santhi | Kutlar, Abdullah | Ramachandran, Vasan S. | Polak, Josef F. | Fabsitz, Richard R. | Dries, Daniel L. | Farlow, Deborah N. | Redline, Susan | Adeyemo, Adebowale | Hirschorn, Joel N. | Sun, Yan V. | Wyatt, Sharon B. | Penman, Alan D. | Palmas, Walter | Rotter, Jerome I. | Townsend, Raymond R. | Doumatey, Ayo P. | Tayo, Bamidele O. | Mosley, Thomas H. | Lyon, Helen N. | Kang, Sun J. | Rotimi, Charles N. | Cooper, Richard S. | Franceschini, Nora | Curb, J. David | Martin, Lisa W. | Eaton, Charles B. | Kardia, Sharon L.R. | Taylor, Herman A. | Caulfield, Mark J. | Ehret, Georg B. | Johnson, Toby | Chakravarti, Aravinda | Zhu, Xiaofeng | Levy, Daniel | Munroe, Patricia B. | Rice, Kenneth M. | Bochud, Murielle | Johnson, Andrew D. | Chasman, Daniel I. | Smith, Albert V. | Tobin, Martin D. | Verwoert, Germaine C. | Hwang, Shih-Jen | Pihur, Vasyl | Vollenweider, Peter | O'Reilly, Paul F. | Amin, Najaf | Bragg-Gresham, Jennifer L. | Teumer, Alexander | Glazer, Nicole L. | Launer, Lenore | Zhao, Jing Hua | Aulchenko, Yurii | Heath, Simon | Sõber, Siim | Parsa, Afshin | Luan, Jian'an | Arora, Pankaj | Dehghan, Abbas | Zhang, Feng | Lucas, Gavin | Hicks, Andrew A. | Jackson, Anne U. | Peden, John F. | Tanaka, Toshiko | Wild, Sarah H. | Rudan, Igor | Igl, Wilmar | Milaneschi, Yuri | Parker, Alex N. | Fava, Cristiano | Chambers, John C. | Kumari, Meena | JinGo, Min | van der Harst, Pim | Kao, Wen Hong Linda | Sjögren, Marketa | Vinay, D.G. | Alexander, Myriam | Tabara, Yasuharu | Shaw-Hawkins, Sue | Whincup, Peter H. | Liu, Yongmei | Shi, Gang | Kuusisto, Johanna | Seielstad, Mark | Sim, Xueling | Nguyen, Khanh-Dung Hoang | Lehtimäki, Terho | Matullo, Giuseppe | Wu, Ying | Gaunt, Tom R. | Charlotte Onland-Moret, N. | Cooper, Matthew N. | Platou, Carl G.P. | Org, Elin | Hardy, Rebecca | Dahgam, Santosh | Palmen, Jutta | Vitart, Veronique | Braund, Peter S. | Kuznetsova, Tatiana | Uiterwaal, Cuno S.P.M. | Campbell, Harry | Ludwig, Barbara | Tomaszewski, Maciej | Tzoulaki, Ioanna | Palmer, Nicholette D. | Aspelund, Thor | Garcia, Melissa | Chang, Yen-Pei C. | O'Connell, Jeffrey R. | Steinle, Nanette I. | Grobbee, Diederick E. | Arking, Dan E. | Hernandez, Dena | Najjar, Samer | McArdle, Wendy L. | Hadley, David | Brown, Morris J. | Connell, John M. | Hingorani, Aroon D. | Day, Ian N.M. | Lawlor, Debbie A. | Beilby, John P. | Lawrence, Robert W. | Clarke, Robert | Collins, Rory | Hopewell, Jemma C. | Ongen, Halit | Bis, Joshua C. | Kähönen, Mika | Viikari, Jorma | Adair, Linda S. | Lee, Nanette R. | Chen, Ming-Huei | Olden, Matthias | Pattaro, Cristian | Hoffman Bolton, Judith A. | Köttgen, Anna | Bergmann, Sven | Mooser, Vincent | Chaturvedi, Nish | Frayling, Timothy M. | Islam, Muhammad | Jafar, Tazeen H. | Erdmann, Jeanette | Kulkarni, Smita R. | Bornstein, Stefan R. | Grässler, Jürgen | Groop, Leif | Voight, Benjamin F. | Kettunen, Johannes | Howard, Philip | Taylor, Andrew | Guarrera, Simonetta | Ricceri, Fulvio | Emilsson, Valur | Plump, Andrew | Barroso, Inês | Khaw, Kay-Tee | Weder, Alan B. | Hunt, Steven C. | Bergman, Richard N. | Collins, Francis S. | Bonnycastle, Lori L. | Scott, Laura J. | Stringham, Heather M. | Peltonen, Leena | Perola, Markus | Vartiainen, Erkki | Brand, Stefan-Martin | Staessen, Jan A. | Wang, Thomas J. | Burton, Paul R. | SolerArtigas, Maria | Dong, Yanbin | Snieder, Harold | Wang, Xiaoling | Zhu, Haidong | Lohman, Kurt K. | Rudock, Megan E. | Heckbert, Susan R. | Smith, Nicholas L. | Wiggins, Kerri L. | Shriner, Daniel | Veldre, Gudrun | Viigimaa, Margus | Kinra, Sanjay | Prabhakaran, Dorairajan | Tripathy, Vikal | Langefeld, Carl D. | Rosengren, Annika | Thelle, Dag S. | MariaCorsi, Anna | Singleton, Andrew | Forrester, Terrence | Hilton, Gina | McKenzie, Colin A. | Salako, Tunde | Iwai, Naoharu | Kita, Yoshikuni | Ogihara, Toshio | Ohkubo, Takayoshi | Okamura, Tomonori | Ueshima, Hirotsugu | Umemura, Satoshi | Eyheramendy, Susana | Meitinger, Thomas | Wichmann, H.-Erich | Cho, Yoon Shin | Kim, Hyung-Lae | Lee, Jong-Young | Scott, James | Sehmi, Joban S. | Zhang, Weihua | Hedblad, Bo | Nilsson, Peter | Smith, George Davey | Wong, Andrew | Narisu, Narisu | Stančáková, Alena | Raffel, Leslie J. | Yao, Jie | Kathiresan, Sekar | O'Donnell, Chris | Schwartz, Steven M. | Arfan Ikram, M. | Longstreth, Will T. | Seshadri, Sudha | Shrine, Nick R.G. | Wain, Louise V. | Morken, Mario A. | Swift, Amy J. | Laitinen, Jaana | Prokopenko, Inga | Zitting, Paavo | Cooper, Jackie A. | Humphries, Steve E. | Danesh, John | Rasheed, Asif | Goel, Anuj | Hamsten, Anders | Watkins, Hugh | Bakker, Stephan J.L. | van Gilst, Wiek H. | Janipalli, Charles S. | Radha Mani, K. | Yajnik, Chittaranjan S. | Hofman, Albert | Mattace-Raso, Francesco U.S. | Oostra, Ben A. | Demirkan, Ayse | Isaacs, Aaron | Rivadeneira, Fernando | Lakatta, Edward G. | Orru, Marco | Scuteri, Angelo | Ala-Korpela, Mika | Kangas, Antti J. | Lyytikäinen, Leo-Pekka | Soininen, Pasi | Tukiainen, Taru | Würz, Peter | Twee-Hee Ong, Rick | Dörr, Marcus | Kroemer, Heyo K. | Völker, Uwe | Völzke, Henry | Galan, Pilar | Hercberg, Serge | Lathrop, Mark | Zelenika, Diana | Deloukas, Panos | Mangino, Massimo | Spector, Tim D. | Zhai, Guangju | Meschia, James F. | Nalls, Michael A. | Sharma, Pankaj | Terzic, Janos | Kranthi Kumar, M.J. | Denniff, Matthew | Zukowska-Szczechowska, Ewa | Wagenknecht, Lynne E. | Fowkes, Gerald R. | Charchar, Fadi J. | Schwarz, Peter E.H. | Hayward, Caroline | Guo, Xiuqing | Bots, Michiel L. | Brand, Eva | Samani, Nilesh J. | Polasek, Ozren | Talmud, Philippa J. | Nyberg, Fredrik | Kuh, Diana | Laan, Maris | Hveem, Kristian | Palmer, Lyle J. | van der Schouw, Yvonne T. | Casas, Juan P. | Mohlke, Karen L. | Vineis, Paolo | Raitakari, Olli | Wong, Tien Y. | Shyong Tai, E. | Laakso, Markku | Rao, Dabeeru C. | Harris, Tamara B. | Morris, Richard W. | Dominiczak, Anna F. | Kivimaki, Mika | Marmot, Michael G. | Miki, Tetsuro | Saleheen, Danish | Chandak, Giriraj R. | Coresh, Josef | Navis, Gerjan | Salomaa, Veikko | Han, Bok-Ghee | Kooner, Jaspal S. | Melander, Olle | Ridker, Paul M. | Bandinelli, Stefania | Gyllensten, Ulf B. | Wright, Alan F. | Wilson, James F. | Ferrucci, Luigi | Farrall, Martin | Tuomilehto, Jaakko | Pramstaller, Peter P. | Elosua, Roberto | Soranzo, Nicole | Sijbrands, Eric J.G. | Altshuler, David | Loos, Ruth J.F. | Shuldiner, Alan R. | Gieger, Christian | Meneton, Pierre | Uitterlinden, Andre G. | Wareham, Nicholas J. | Gudnason, Vilmundur | Rettig, Rainer | Uda, Manuela | Strachan, David P. | Witteman, Jacqueline C.M. | Hartikainen, Anna-Liisa | Beckmann, Jacques S. | Boerwinkle, Eric | Boehnke, Michael | Larson, Martin G. | Järvelin, Marjo-Riitta | Psaty, Bruce M. | Abecasis, Gonçalo R. | Elliott, Paul | van Duijn , Cornelia M. | Newton-Cheh, Christopher
Human Molecular Genetics  2011;20(11):2273-2284.
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.
doi:10.1093/hmg/ddr092
PMCID: PMC3090190  PMID: 21378095
14.  Genetic Influence on Variation in Serum Uric Acid in American Indians: The Strong Heart Family Study 
Human genetics  2009;126(5):667-676.
Hyperuricemia is associated with the metabolic syndrome, gout, renal and cardiovascular disease (CVD). American Indians have high rates of CVD and 25 % of individuals in the Strong Heart Family Study (SHFS) have high serum uric acid levels. The aim of this study was to investigate the genetic determinants of serum uric acid variation in American Indian participants of the SHFS. A variance component decomposition approach (implemented in SOLAR) was used to conduct univariate genetic analyses in each of three study centers and the combined sample. Serum uric acid was adjusted for age, sex, age*sex, BMI, estimated glomerular filtration rate, alcohol intake, diabetic status and medications. Overall mean ± SD serum uric acid for all individuals was 5.14 ± 1.5 mg/dl. Serum uric acid was found to be significantly heritable (0.46 ± 0.03 in all centers, and 0.39 ± 0.07, 0.51 ± 0.05, 0.44 ± 0.06 in Arizona, Dakotas and Oklahoma, respectively). Multipoint linkage analysis showed significant evidence of linkage for serum uric acid on chromosome 11 in the Dakotas center (logarithm of odds score (LOD) = 3.02) and in the combined sample (LOD = 3.56) and on chromosome 1 (LOD = 3.51) in the combined sample. A strong positional candidate gene in the chromosome 11 region is solute carrier family22, member 12 (SLC22A12) that encodes a major uric acid transporter URAT1. These results show a significant genetic influence and a possible role for one or more genes on chromosomes 1 and 11 on the variation in serum uric acid in American Indian populations.
doi:10.1007/s00439-009-0716-8
PMCID: PMC2784272  PMID: 19590895
SLC22A12 gene; URAT1; variance component decomposition approach; chromosome
15.  GENOME-WIDE LINKAGE ANALYSIS OF PULSE PRESSURE IN AMERICAN INDIANS: THE STRONG HEART STUDY 
American journal of hypertension  2008;21(2):194-199.
Background
Pulse pressure, a measure of central arterial stiffness and a predictor of cardiovascular mortality, has known genetic components.
Methods
To localize the genetic effects of pulse pressure, we conducted a genome-wide linkage analysis of 1,892 American Indian participants of the Strong Heart Family Study. Blood pressure was measured three times and the average of the last two measures was used for analyses. Pulse pressure, the difference between systolic and diastolic blood pressures, was log-transformed and adjusted for the effects of age and sex within each study center. Variance component linkage analyses were performed using marker allele frequencies derived from all individuals and multipoint identity-by-descent matrices calculated in Loki.
Results
We identified a quantitative trait locus influencing pulse pressure on chromosome 7 at 37 cM (marker D7S493, LOD=3.3) and suggestive evidence of linkage on chromosome 19 at 92 cM (marker D19S888, LOD=1.8).
Conclusions
The signal on 7p15.3 overlaps positive findings for pulse pressure among Utah population samples, suggesting that this region may harbor gene variants for blood pressure related traits.
doi:10.1038/ajh.2007.34
PMCID: PMC2812893  PMID: 18188160
Genetics; pulse pressure; American Indian
16.  C-Reactive Protein, Insulin Resistance, and Metabolic Syndrome in a Population With a High Burden of Subclinical Infection 
Diabetes Care  2008;31(12):2312-2314.
OBJECTIVE—To explore relationships between C-reactive protein (CRP), subclinical infection, insulin resistance, and metabolic syndrome.
RESEARCH DESIGN AND METHODS—Data from 1,174 Eskimos, aged ≥18 years, from the Genetics of Coronary Artery Disease in Alaska Natives (GOCADAN) study were analyzed; 40 participants with diabetes were eliminated. Baseline assessment included interviews, physical exam, and blood and urine sampling. Metabolic syndrome was assessed using Adult Treatment Panel III criteria. CRP and antibodies to common pathogens were measured.
RESULTS—Although CRP was related in univariate analyses to insulin resistance and metabolic syndrome, relations were attenuated or eliminated after adjustment for relevant covariates. CRP was not higher among those with impaired fasting glucose (IFG), and pathogen burden was not related to insulin resistance, metabolic syndrome, or IFG.
CONCLUSIONS—Pathogen burden and inflammation do not seem to be related to insulin resistance, metabolic syndrome, or IFG in this population. The inflammatory process may reflect insulin resistance or its correlates but most likely is not causative.
doi:10.2337/dc08-0815
PMCID: PMC2584187  PMID: 18796618
17.  A Longitudinal Study of Risk Factors for Incident Albuminuria in Diabetic American Indians: The Strong Heart Study 
Background
There have been no studies that employ longitudinal data with more than two measurements and use methods of longitudinal data analysis to identify risk factors for incident albuminuria over time more effectively.
Study Design
Longitudinal study.
Settings & Participants
A subgroup of participants in the Strong Heart Study, a population-based sample of American Indians, in central Arizona, Oklahoma, and North and South Dakota. Diabetic participants without albuminuria were followed for a mean of four years.
Predictors
Age, sex, study center, high-density lipoprotein and low-density lipoprotein cholesterol, triglycerides, body mass index, systolic blood pressure, use of antihypertensive medication, smoking, hemoglobin A1c, fasting glucose, type of diabetes therapy, diabetes duration, plasma creatinine and urinary albumin/creatinine ratio (UACR).
Outcomes & Measurements
Albuminuria was defined as UACR ≥ 30 mg/g. Urine creatinine and albumin was measured by the picric acid method and a sensitive nephelometric technique, respectively.
Results
Among the 750 and 568 diabetic participants without albuminuria and with normal plasma creatinine at the 1st and 2nd examinations, 246 and 132 developed albuminuria by the 2nd and 3rd examinations, respectively. Incident albuminuria was predicted by baseline UACR, fasting glucose, systolic blood pressure, plasma creatinine, study center, current smoking, and use of angiotensin converting enzyme (ACE) inhibitors and antidiabetic medications. UACR of 10–30 mg/g increased the odds of developing albuminuria 2.7-fold compared with UACR < 5 mg/g.
Limitations
Single random morning urine specimen.
Conclusions
Many of risk factors identified for incident albuminuria can be modified. The control of blood pressure and glucose, smoking cessation, and use of ACE inhibitors may reduce the incidence of albuminuria.
doi:10.1053/j.ajkd.2007.11.010
PMCID: PMC2776644  PMID: 18295057
longitudinal analysis; risk factors; incidence; albuminuria; American Indians
18.  Linkage Analysis of Glomerular Filtration Rate in American Indians: The Strong Heart Family Study 
Kidney international  2008;74(9):1185-1191.
American Indians have a disproportionately high rate of kidney disease likely due to a combination of increased environmental and genetic risk factors. In an attempt to localize genes influencing kidney disease risk factors, we performed a genome wide scan of estimated glomerular filtration rate on participants of the Strong Heart Family Study. Over 3 600 men and women from 13 American Indian tribes were recruited from 3 centers (Arizona, North and South Dakota, Oklahoma). Using SOLAR 2.1.2, multipoint variance component linkage analysis was performed in each center as well as the entire cohort after controlling for center effects. Two modeling strategies were utilized: model 1 incorporated age, sex and interaction terms and model 2 additionally controlled for diabetic status, systolic and diastolic blood pressure, body mass index, low density lipoproteins, high density lipoproteins, triglycerides and smoking status. Significant evidence for linkage in Arizona lay on 12p12.2 at 39cM nearest marker D12S310 (LOD=3.5). Additional loci with suggestive evidence for linkage were detected at 1p36.31 (LOD=2.0–2.3), 2q33.3 (LOD=1.8) and 9q34.2 (LOD=2.4). No significant evidence for additive interaction with diabetes, hypertension or obesity was noted. In conclusion, we found evidence for linkage of a quantitative trait locus influencing estimated glomerular filtration rate to a region of chromosome 12p in a large cohort of American Indians.
doi:10.1038/ki.2008.410
PMCID: PMC2651086  PMID: 18854848
19.  Reporting Genetic Results in Research Studies: Summary and Recommendations of an NHLBI Working Group 
Prospective epidemiologic studies aid in identifying genetic variants associated with diseases, health risks, and physiologic traits. These genetic variants may eventually be measured clinically for purposes of diagnosis, prognosis, and treatment. As evidence of the potential clinical value of such information accrues, research studies face growing pressure to report these results to study participants or their physicians, even before sufficient evidence is available to support widespread screening of asymptomatic persons. There is thus a need to begin to develop consensus on whether and when genetic findings should be reported to participants in research studies. The National Heart, Lung, and Blood Institute (NHLBI) convened a Working Group on Reporting Genetic Results in Research Studies to discuss if, when, and how genetic information should be reported to study participants. The Working Group concluded that genetic test results should be reported to study participants when the associated risk for the disease is significant; the disease has important health implications such as premature death or substantial morbidity or has significant reproductive implications; and proven therapeutic or preventive interventions are available. Finally, the Working Group recommended procedures for reporting genetic research results and encouraged increased efforts to create uniform guidelines for this activity.
doi:10.1002/ajmg.a.31195
PMCID: PMC2556074  PMID: 16575896
research results; genetic testing; reporting research results
20.  Bivariate genetic association of KIAA1797 with heart rate in American Indians: the Strong Heart Family Study 
Human Molecular Genetics  2010;19(18):3662-3671.
Heart rate (HR) has been identified as a risk factor for cardiovascular disease (CVD), yet little is known regarding genetic factors influencing this phenotype. Previous research in American Indians (AIs) from the Strong Heart Family Study (SHFS) identified a significant quantitative trait locus (QTL) for HR on chromosome 9p21. Genetic association on HR was conducted in the SHFS. HR was measured from electrocardiogram (ECG) and echocardiograph (Echo) Doppler recordings. We examined 2248 single-nucleotide polymorphisms (SNPs) on chromosome 9p21 for association using a gene-centric statistical test. We replicated the aforementioned QTL [logarithm of odds (LOD) = 4.83; genome-wide P= 0.0003] on chromosome 9p21 in one SHFS population using joint linkage of ECG and Echo HR. After correcting for effective number of SNPs using a gene-centric test, six SNPs (rs7875153, rs7848524, rs4446809, rs10964759, rs1125488 and rs7853123) remained significant. We applied a novel bivariate association method, which was a joint test of association of a single locus to two traits using a standard additive genetic model. The SNP, rs7875153, provided the strongest evidence for association (P = 7.14 × 10−6). This SNP (rs7875153) is rare (minor allele frequency = 0.02) in AIs and is located within intron 9 of the gene KIAA1797. To support this association, we applied lymphocyte RNA expression data from the San Antonio Family Heart Study, a longitudinal study of CVD in Mexican Americans. Expression levels of KIAA1797 were significantly associated (P = 0.012) with HR. These findings in independent populations support that KIAA1797 genetic variation may be associated with HR but elucidation of a functional relationship requires additional study.
doi:10.1093/hmg/ddq274
PMCID: PMC2928129  PMID: 20601674
21.  Candidate Gene Association Resource (CARe): Design, Methods, and Proof of Concept 
Background
. The National Heart, Lung, and Blood Institute’s Candidate Gene Association Resource (CARe), a planned cross-cohort analysis of genetic variation in cardiovascular, pulmonary, hematological, and sleep-related traits, comprises more than 40,000 participants representing four ethnic groups in nine community-based cohorts. The goals of CARe include the discovery of new variants associated with traits using a candidate gene approach and the discovery of new variants using the genome-wide association mapping approach specifically in African Americans.
Methods and Results
. CARe has assembled DNA samples for more than 40,000 individuals self-identified as European-American, African-American, Hispanic, or Chinese-American, with accompanying data on hundreds of phenotypes that have been standardized and deposited in the CARe Phenotype Database. All participants were genotyped for seven single-nucleotide polymorphisms (SNPs) selected based on prior association evidence. We performed association analyses relating each of these SNPs to lipid traits, stratified by gender and ethnicity and adjusted for age and age2. In at least two of the ethnic groups, SNPs near CETP, LIPC, and LPL strongly replicated for association with high-density lipoprotein cholesterol concentrations, PCSK9 with low-density lipoprotein cholesterol levels, and LPL and APOA5 with serum triglycerides. Notably, some SNPs showed varying effect sizes and significance of association in different ethnic groups.
Conclusions
. The CARe Pilot Study validates the operational framework for phenotype collection, SNP genotyping, and analytical pipeline of the CARe project and validates the planned candidate gene study of ~2,000 biologic candidate loci in all participants and genome-wide association study in ~8,000 African-American participants. CARe will serve as a valuable resource for the scientific community.
doi:10.1161/CIRCGENETICS.109.882696
PMCID: PMC3048024  PMID: 20400780
Genetics; lipids; diabetes; blood pressure; epidemiology
22.  The association of the MYH9 gene and kidney outcomes in American Indians: the Strong Heart Family Study 
Human genetics  2010;127(3):295-301.
Chronic kidney disease (CKD) is an important public health problem in American Indian populations. Recent research has identified associations of polymorphisms in the myosin heavy chain type II isoform A (MYH9) gene with hypertensive CKD in African-Americans. Whether these associations are also present among American Indian individuals is unknown. To evaluate the role of genetic polymorphisms in the MYH9 gene on kidney disease in American Indians, we genotyped 25 SNPs in the MYH9 gene region in 1,119 comparatively unrelated individuals. Four SNPs failed, and one SNP was monomorphic. We inferred haplotypes using seven SNPs within the region of the previously described E haplotype using Phase v2.1. We studied the association between 20 MYH9 SNPs with kidney function (estimated glomerular filtration rate, eGFR) and CKD (eGFR < 60 ml/min/1.73 m2 or renal replacement therapy or kidney transplant) using age-, sex- and center-adjusted models and measured genotyped within the variance component models. MYH9 SNPs were not significantly associated with kidney traits in additive or recessive genetic adjusted models. MYH9 haplotypes were also not significantly associated with kidney outcomes. In conclusion, common variants in MYH9 polymorphisms may not confer an increased risk of CKD in American Indian populations. Identification of the actual functional genetic variation responsible for the associations seen in African-Americans will likely help to clarify the lack of replication of this gene in our population of American Indians.
doi:10.1007/s00439-009-0769-8
PMCID: PMC2930187  PMID: 19921264
23.  Prevalence of Diabetes and Impaired Fasting Glucose in Chinese Adults, China National Nutrition and Health Survey, 2002 
Preventing Chronic Disease  2010;8(1):A13.
Introduction
As a result of rapid economic development in China, the lifestyles and dietary habits of its people have been changing, and the rates of obesity, diabetes, and other chronic conditions have increased substantially. We report the prevalence of type 2 diabetes and impaired fasting glucose (IFG) and the association between diabetes and overweight and obesity in Chinese adults. We also compare the results with those from the US National Health and Nutrition Examination Survey, 1999-2002.
Methods
Data were from adults aged 20 years or older who participated in the China National Nutrition and Health Survey, 2002 (n = 47,729). Diabetes and IFG were defined by the American Diabetes Association 2009 criteria. We assessed the prevalence of diabetes, IFG, and overweight and obesity by sex, age, region of residence, and ethnicity.
Results
The prevalence of diabetes and IFG in Chinese adults was 2.7% and 4.9%, respectively. The prevalence of diabetes increased with age and body mass index. Men and women had a similar prevalence of diabetes, but men had a significantly higher prevalence of IFG. The prevalence of diabetes among Chinese who lived in urban areas was 2 to 3 times higher than the prevalence among those who lived in rural areas (3.9% for urban areas and 6.1% for large cities vs 1.9% for rural areas), and the prevalence of IFG was 1.5 to 2 times higher (6.1% and 8.1% vs 4.2%, respectively). The prevalence of diabetes among Chinese women and young (20-39 y) and middle-aged (40-59 y) adults who lived in large cities was similar to the prevalence of diabetes in the US population.
Conclusion
The prevalence of diabetes and IFG was much higher in urban than rural areas, particularly in the large cities of China. Prevention must be emphasized among adults to reduce the future social and economic burden of diabetes in China.
PMCID: PMC3044024  PMID: 21159225
24.  Social- and Behavioral-Specific Genetic Effects on Blood Pressure Traits: The Strong Heart Family Study 
Background
Population studies have demonstrated an important role of social, behavioral, and environmental factors in blood pressure levels. Accounting for the genetic interaction of these factors may help to identify common blood pressure susceptibility alleles.
Methods and Results
We studied the interaction of additive genetic effects and behavioral (physical activity, smoking, alcohol use) and socioeconomic (education) factors on blood pressure in approximately 3,600 American Indians participants of the Strong Heart Family Study, using variance component models. The mean and standard deviation of resting systolic and diastolic blood pressures were 123 ± 17 and 76 ± 11 mm Hg, respectively. We detected evidence for distinct genetic effects on diastolic blood pressure among ever smokers compared to never smokers (P=0.01). For alcohol intake, we observed significant genotype-by-environment interactions on diastolic (ρg=0.10, P = 0.0003) and on systolic blood pressures (ρg= 0.59, P = 0.0008) among current drinkers compared to former or never drinkers. We also detected genotype-by-physical activity interactions on diastolic blood pressure (ρg=0.35, P = 0.0004). Lastly, there was evidence for distinct genetic effects on diastolic blood pressure among individuals with less than high school education compared to those with 12 or more years of education (ρg= 0.41, P = 0.02).
Conclusions
Our findings suggest that behavioral and socioeconomic factors can modify the genetic effects on blood pressure phenotypes. Accounting for context dependent factors may help us to better understand the complexities of the gene effects on blood pressure and other complex phenotypes with high levels of genetic heterogeneity.
doi:10.1161/CIRCGENETICS.109.853630
PMCID: PMC2742382  PMID: 20031612
epidemiology; genetics; blood pressure
25.  Concept, Design and Implementation of a Cardiovascular Gene-Centric 50 K SNP Array for Large-Scale Genomic Association Studies 
PLoS ONE  2008;3(10):e3583.
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a “cosmopolitan” tagging approach to capture the genetic diversity across ∼2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.
doi:10.1371/journal.pone.0003583
PMCID: PMC2571995  PMID: 18974833

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