Framingham Heart Study Papers

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On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal, Robust Analysis Approach and an Application to Four Genome-Wide Association Studies
(Public Library of Science, 2009-11-26) Won, Sungho; Wilk, Jemma B.; Mathias, Rasika A.; O'Donnell, Christopher J.; Silverman, Edwin K.; Barnes, Kathleen; O'Connor, George T.; Weiss, Scott T.; Lange, Christoph
For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1) in 4 genome-wide association studies. Author Summary In genome-wide association studies, the multiple testing problem and confounding due to population stratification have been intractable issues. Family-based designs have considered only the transmission of genotypes from founder to nonfounder to prevent sensitivity to the population stratification, which leads to the loss of information. Here we propose a novel analysis approach that combines mutually independent FBAT and screening statistics in a robust way. The proposed method is more powerful than any other, while it preserves the complete robustness of family-based association tests, which only achieves much smaller power level. Furthermore, the proposed method is virtually as powerful as population-based approaches/designs, even in the absence of population stratification. By nature of the proposed method, it is always robust as long as FBAT is valid, and the proposed method achieves the optimal efficiency if our linear model for screening test reasonably explains the observed data in terms of covariance structure and population admixture. We illustrate the practical relevance of the approach by an application in 4 genome-wide association studies.
The impact of complex informative missingness on the validity of the transmission/disequilibrium test (TDT)
(BioMed Central, 2007-12-18) Guo, Chao-Yu
The transmission/disequilibrium test was introduced to test for linkage and association between a marker and a putative disease locus using case-parent triads. Several extensions have been proposed to accommodate incomplete triads. Some strategies assumed that parental genotypes were missing completely at random and some methods allowed informative missingness for parental genotypes. However, the above tests assumed that offspring genotypes were missing completely at random and concluded that the transmission/disequilibrium test remained a valid test by excluding incomplete triads from the analysis. In this article, the conditional distribution of ascertained triads allowing informative missingness for offspring genotypes, as well as their parental genotypes, was derived and several tests under such scenarios were evaluated. In simulations, independent triads from the Genetic Analysis Workshop 15 simulated data (Problem 3) was ascertained. When offspring genotypes were missing informatively, simulation results revealed inflated type I error and/or reduced power for the transmission/disequilibrium test excluding incomplete triads.
Genome-wide association studies of serum magnesium, potassium, and sodium concentrations identify six loci influencing serum magnesium levels
(Public Library of Science, 2010-8-5) Meyer, Tamra E.; Verwoert, Germaine C.; Hwang, Shih-Jen; Glazer, Nicole L.; Smith, Albert V.; Van Rooij, Frank J. A.; Ehret, Georg B.; Boerwinkle, Eric; Felix, Janine F.; Leak, Tennille S.; Harris, Tamara B.; Yang, Qiong; Dehghan, Abbas; Aspelund, Thor; Katz, Ronit; Homuth, Georg; Kocher, Thomas; Rettig, Rainer; Ried, Janina S.; Gieger, Christian; Prucha, Hanna; Pfeufer, Arne; Meitinger, Thomas; Coresh, Josef; Hofman, Albert; Sarnak, Mark J.; Chen, Yii-Der Ida; Uitterlinden, André G.; Chakravarti, Aravinda; Psaty, Bruce M.; Van Duijn, Cornelia M.; Kao, W. H. Linda; Witteman, Jacqueline C. M.; Gudnason, Vilmundur; Siscovick, David S.; Fox, Caroline S.; Köttgen, Anna
Magnesium, potassium, and sodium, cations commonly measured in serum, are involved in many physiological processes including energy metabolism, nerve and muscle function, signal transduction, and fluid and blood pressure regulation. To evaluate the contribution of common genetic variation to normal physiologic variation in serum concentrations of these cations, we conducted genome-wide association studies of serum magnesium, potassium, and sodium concentrations using ∼2.5 million genotyped and imputed common single nucleotide polymorphisms (SNPs) in 15,366 participants of European descent from the international CHARGE Consortium. Study-specific results were combined using fixed-effects inverse-variance weighted meta-analysis. SNPs demonstrating genome-wide significant (p<5×10−8) or suggestive associations (p<4×10−7) were evaluated for replication in an additional 8,463 subjects of European descent. The association of common variants at six genomic regions (in or near MUC1, ATP2B1, DCDC5, TRPM6, SHROOM3, and MDS1) with serum magnesium levels was genome-wide significant when meta-analyzed with the replication dataset. All initially significant SNPs from the CHARGE Consortium showed nominal association with clinically defined hypomagnesemia, two showed association with kidney function, two with bone mineral density, and one of these also associated with fasting glucose levels. Common variants in CNNM2, a magnesium transporter studied only in model systems to date, as well as in CNNM3 and CNNM4, were also associated with magnesium concentrations in this study. We observed no associations with serum sodium or potassium levels exceeding p<4×10−7. Follow-up studies of newly implicated genomic loci may provide additional insights into the regulation and homeostasis of human serum magnesium levels. Author Summary Magnesium, potassium, and sodium are involved in important physiological processes. To better understand how common genetic variation may contribute to inter-individual differences in serum concentrations of these electrolytes, we evaluated single nucleotide polymorphisms (SNPs) across the genome in association with serum magnesium, potassium, and sodium levels in 15,366 participants of European descent from the CHARGE Consortium. We then verified the associations in an additional 8,463 study participants. Six different genomic regions contain variants that are reproducibly associated with serum magnesium levels, and only one of the regions had been previously known to influence serum magnesium concentrations in humans. The identified SNPs also show association with clinically defined hypomagnesemia, and some of them with traits that have been linked to serum magnesium levels, including kidney function, fasting glucose, and bone mineral density. We further provide evidence for a physiological role of magnesium transporters in humans which have previously only been studied in model systems. None of the SNPs evaluated in our study are significantly associated with serum levels of sodium or potassium. Additional studies are needed to investigate the underlying molecular mechanisms in order to help us understand the contribution of these newly identified regions to magnesium homeostasis.
Forty-Three Loci Associated with Plasma Lipoprotein Size, Concentration, and Cholesterol Content in Genome-Wide Analysis
(Public Library of Science, 2009-11-20) Chasman, Daniel I.; Paré, Guillaume; Mora, Samia; Hopewell, Jemma C.; Peloso, Gina; Clarke, Robert; Cupples, L. Adrienne; Hamsten, Anders; Kathiresan, Sekar; Mälarstig, Anders; Ordovas, José M.; Ripatti, Samuli; Parker, Alex N.; Miletich, Joseph P.; Ridker, Paul M.
While conventional LDL-C, HDL-C, and triglyceride measurements reflect aggregate properties of plasma lipoprotein fractions, NMR-based measurements more accurately reflect lipoprotein particle concentrations according to class (LDL, HDL, and VLDL) and particle size (small, medium, and large). The concentrations of these lipoprotein sub-fractions may be related to risk of cardiovascular disease and related metabolic disorders. We performed a genome-wide association study of 17 lipoprotein measures determined by NMR together with LDL-C, HDL-C, triglycerides, ApoA1, and ApoB in 17,296 women from the Women's Genome Health Study (WGHS). Among 36 loci with genome-wide significance (P<5×10−8) in primary and secondary analysis, ten (PCCB/STAG1 (3q22.3), GMPR/MYLIP (6p22.3), BTNL2 (6p21.32), KLF14 (7q32.2), 8p23.1, JMJD1C (10q21.3), SBF2 (11p15.4), 12q23.2, CCDC92/DNAH10/ZNF664 (12q24.31.B), and WIPI1 (17q24.2)) have not been reported in prior genome-wide association studies for plasma lipid concentration. Associations with mean lipoprotein particle size but not cholesterol content were found for LDL at four loci (7q11.23, LPL (8p21.3), 12q24.31.B, and LIPG (18q21.1)) and for HDL at one locus (GCKR (2p23.3)). In addition, genetic determinants of total IDL and total VLDL concentration were found at many loci, most strongly at LIPC (15q22.1) and APOC-APOE complex (19q13.32), respectively. Associations at seven more loci previously known for effects on conventional plasma lipid measures reveal additional genetic influences on lipoprotein profiles and bring the total number of loci to 43. Thus, genome-wide associations identified novel loci involved with lipoprotein metabolism—including loci that affect the NMR-based measures of concentration or size of LDL, HDL, and VLDL particles—all characteristics of lipoprotein profiles that may impact disease risk but are not available by conventional assay. Author Summary Genome-wide association studies (GWAS) of plasma lipoprotein fractions hold great promise for understanding lipid metabolism and its central role in cardiovascular disease and related disorders. Conventional assays for lipoprotein status determine total cholesterol content of low- or high-density lipoprotein particles (LDL-C or HDL-C, respectively) or total plasma triglyceride content (as an estimate of very-low density lipoprotein particle concentration [VLDL]). All three measures have been targets for recent GWAS. However, a more precise target for GWAS of lipoprotein metabolism would be the concentration of the individual lipoprotein particles according to class (LDL, HDL, VLDL) and size (small, medium, and large), all of which can be measured by NMR-based methods. In a population of 17,296 women of European ancestry from the Women's Genome Health Study, we have performed a GWAS for 22 lipoprotein measures derived from NMR-based and conventional assays. We find 43 genetic loci involved in lipoprotein metabolism, including 10 novel loci. The results offer a clearer picture of common genetic influences on lipoprotein metabolism than available previously, including genetic effects on the distribution of LDL, HDL, and VLDL particle size, as well as on IDL and VLDL particle concentration, neither of which can be assessed by conventional measures.
An integration of genome-wide association study and gene expression profiling to prioritize the discovery of novel susceptibility loci for osteoporosis-related traits
(Public Library of Science, 2010-6-10) Hsu, Yi-Hsiang; Zillikens, M. Carola; Wilson, Scott G.; Farber, Charles R.; Demissie, Serkalem; Soranzo, Nicole; Bianchi, Estelle N.; Grundberg, Elin; Liang, Liming; Richards, J. Brent; Estrada, Karol; Zhou, Yanhua; van Nas, Atila; Moffatt, Miriam F.; Zhai, Guangju; Hofman, Albert; van Meurs, Joyce B.; Pols, Huibert A. P.; Price, Roger I.; Nilsson, Olle; Pastinen, Tomi; Cupples, L. Adrienne; Lusis, Aldons J.; Schadt, Eric E.; Ferrari, Serge; Uitterlinden, André G.; Rivadeneira, Fernando; Spector, Timothy D.; Karasik, David; Kiel, Douglas P.
Osteoporosis is a complex disorder and commonly leads to fractures in elderly persons. Genome-wide association studies (GWAS) have become an unbiased approach to identify variations in the genome that potentially affect health. However, the genetic variants identified so far only explain a small proportion of the heritability for complex traits. Due to the modest genetic effect size and inadequate power, true association signals may not be revealed based on a stringent genome-wide significance threshold. Here, we take advantage of SNP and transcript arrays and integrate GWAS and expression signature profiling relevant to the skeletal system in cellular and animal models to prioritize the discovery of novel candidate genes for osteoporosis-related traits, including bone mineral density (BMD) at the lumbar spine (LS) and femoral neck (FN), as well as geometric indices of the hip (femoral neck-shaft angle, NSA; femoral neck length, NL; and narrow-neck width, NW). A two-stage meta-analysis of GWAS from 7,633 Caucasian women and 3,657 men, revealed three novel loci associated with osteoporosis-related traits, including chromosome 1p13.2 (RAP1A, p = 3.6×10−8), 2q11.2 (TBC1D8), and 18q11.2 (OSBPL1A), and confirmed a previously reported region near TNFRSF11B/OPG gene. We also prioritized 16 suggestive genome-wide significant candidate genes based on their potential involvement in skeletal metabolism. Among them, 3 candidate genes were associated with BMD in women. Notably, 2 out of these 3 genes (GPR177, p = 2.6×10−13; SOX6, p = 6.4×10−10) associated with BMD in women have been successfully replicated in a large-scale meta-analysis of BMD, but none of the non-prioritized candidates (associated with BMD) did. Our results support the concept of our prioritization strategy. In the absence of direct biological support for identified genes, we highlighted the efficiency of subsequent functional characterization using publicly available expression profiling relevant to the skeletal system in cellular or whole animal models to prioritize candidate genes for further functional validation. Author Summary BMD and hip geometry are two major predictors of osteoporotic fractures, the most severe consequence of osteoporosis in elderly persons. We performed sex-specific genome-wide association studies (GWAS) for BMD at the lumbar spine and femor neck skeletal sites as well as hip geometric indices (NSA, NL, and NW) in the Framingham Osteoporosis Study and then replicated the top findings in two independent studies. Three novel loci were significant: in women, including chromosome 1p13.2 (RAP1A) for NW; in men, 2q11.2 (TBC1D8) for NSA and 18q11.2 (OSBPL1A) for NW. We confirmed a previously reported region on 8q24.12 (TNFRSF11B/OPG) for lumbar spine BMD in women. In addition, we integrated GWAS signals with eQTL in several tissues and publicly available expression signature profiling in cellular and whole-animal models, and prioritized 16 candidate genes/loci based on their potential involvement in skeletal metabolism. Among three prioritized loci (GPR177, SOX6, and CASR genes) associated with BMD in women, GPR177 and SOX6 have been successfully replicated later in a large-scale meta-analysis, but none of the non-prioritized candidates (associated with BMD) did. Our results support the concept of using expression profiling to support the candidacy of suggestive GWAS signals that may contain important genes of interest.
Offspring's Leukocyte Telomere Length, Paternal Age, and Telomere Elongation in Sperm
(Public Library of Science, 2008-2-15) Kimura, Masayuki; Cherkas, Lynn F.; Kato, Bernet S.; Demissie, Serkalem; Hjelmborg, Jacob B.; Brimacombe, Michael; Cupples, Adrienne; Hunkin, Janice L.; Gardner, Jefferey P.; Lu, Xiaobin; Cao, Xiaojian; Sastrasinh, Malinee; Province, Michael A.; Hunt, Steven C.; Christensen, Kaare; Levy, Daniel; Spector, Tim D.; Aviv, Abraham
Leukocyte telomere length (LTL) is a complex genetic trait. It shortens with age and is associated with a host of aging-related disorders. Recent studies have observed that offspring of older fathers have longer LTLs. We explored the relation between paternal age and offspring's LTLs in 4 different cohorts. Moreover, we examined the potential cause of the paternal age on offspring's LTL by delineating telomere parameters in sperm donors. We measured LTL by Southern blots in Caucasian men and women (n=3365), aged 18–94 years, from the Offspring of the Framingham Heart Study (Framingham Offspring), the NHLBI Family Heart Study (NHLBI-Heart), the Longitudinal Study of Aging Danish Twins (Danish Twins), and the UK Adult Twin Registry (UK Twins). Using Southern blots, Q-FISH, and flow-FISH, we also measured telomere parameters in sperm from 46 young (>30 years) and older (<50 years) donors. Paternal age had an independent effect, expressed by a longer LTL in males of the Framingham Offspring and Danish Twins, males and females of the NHLBI-Heart, and females of UK Twins. For every additional year of paternal age, LTL in offspring increased at a magnitude ranging from half to more than twice of the annual attrition in LTL with age. Moreover, sperm telomere length analyses were compatible with the emergence in older men of a subset of sperm with elongated telomeres. Paternal age exerts a considerable effect on the offspring's LTL, a phenomenon which might relate to telomere elongation in sperm from older men. The implications of this effect deserve detailed study. Author Summary. Leukocyte telomere length becomes shorter with age and is apparently a biomarker of aging and a forecaster of longevity in humans. Leukocyte telomere length is heritable, longer in women than in men, and is relatively shorter in persons who suffer from aging-related diseases, cardiovascular diseases in particular. This study found in four different populations that leukocyte telomere length in adult offspring was positively correlated with paternal age at the time of birth of the offspring. Analysis of telomeres in sperm of young (>30 years) and older (<50 years) donors revealed the emergence in the older donors of a subset of sperm with elongated telomeres. The mechanisms behind this enigmatic, age-dependent elongation in telomere length of sperm are unknown but may relate to epigenetic factors or the survival of a subset of germ-line stem cells, resilient against aging. It is also unknown how older fathers endow their offspring with longer telomeres in their leukocytes. The potential impact of paternal age on leukocyte telomere length and, conceivably, aging-related diseases and longevity in the offspring is of relevance because offspring of older fathers comprise an increasing proportion of society.
Incorporating Biological Knowledge in the Search for Gene × Gene Interaction in Genome-Wide Association Studies
(BioMed Central, 2009-12-15) Manning, Alisa K.; Ngwa, Julius Suh; Hendricks, Audrey E.; Liu, Ching-Ti; Johnson, Andrew D.; Dupuis, Josée; Cupples, L. Adrienne
We sought to find significant gene × gene interaction in a genome-wide association analysis of rheumatoid arthritis (RA) by performing pair-wise tests of interaction among collections of single-nucleotide polymorphisms (SNPs) obtained by one of two methods. The first method involved screening the results of the genome-wide association analysis for main effects p-values < 1 × 10-4. The second method used biological databases such as the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes to define gene collections that each contained one of four genes with known associations with RA: PTPN22, STAT4, TRAF1, and C5. We used a permutation approach to determine whether any of these SNP sets had empirical enrichment of significant interaction effects. We found that the SNP set obtained by the first method was significantly enriched with significant interaction effects (empirical p = 0.003). Additionally, we found that the "protein complex assembly" collection of genes from the Gene Ontology collection containing the TRAF1 gene was significantly enriched with interaction effects with p-values < 1 × 10-8 (empirical p = 0.012).
Genetics Analysis Workshop 16 Problem 2: tTe Framingham Heart Study Data
(BioMed Central, 2009-12-15) Cupples, L. Adrienne; Heard-Costa, Nancy; Lee, Monica; Atwood, Larry D.
Genetic Analysis Workshop 16 (GAW16) Problem 2 presented data from the Framingham Heart Study (FHS), an observational, prospective study of risk factors for cardiovascular disease begun in 1948. Data have been collected in three generations of family participants in the study and the data presented for GAW16 included phenotype data from all three generations, with four examinations of data collected repeatedly for the first two generations. The trait data consisted of information on blood pressure, hypertension treatment, lipid levels, diabetes and blood glucose, smoking, alcohol consumed, weight, and coronary heart disease incidence. Additionally, genotype data obtained through a genome-wide scan (FHS SHARe) of 550,000 single-nucleotide polymorphisms from Affymetrix chips were included with the GAW16 data. The genotype data were also used for GAW16 Problem 3, where simulated phenotypes were generated using the actual FHS genotypes. These data served to provide investigators with a rich resource to study the behavior of genome-wide scans with longitudinally collected family data and to develop and apply new procedures.
Genetic Analysis Workshop 16: Strategies for Genome-Wide Association Study Analyses
(BioMed Central, 2009-12-15) Cupples, L. Adrienne; Beyene, Joseph; Bickeböller, Heike; Daw, E. Warwick; Fallin, M. Daniele; Gauderman, W. James; Ghosh, Saurabh; Goode, Ellen L.; Hauser, Elizabeth R.; Hinrichs, Anthony; Kent, Jack W.; Martin, Lisa J.; Martinez, Maria; Neuman, Rosalind J.; Province, Michael; Szymczak, Silke; Wilcox, Marsha A.; Ziegler, Andreas; MacCluer, Jean W.; Almasy, Laura
Consistency of Linkage Results across Exams and Methods in the Framingham Heart Study
(BioMed Central, 2003-12-31) Atwood, Larry D.; Heard-Costa, Nancy L.; Cupples, L. Adrienne; Levy, Daniel
BACKGROUND. The repeated measures in the Framingham Heart Study in the Genetic Analysis Workshop 13 data set allow us to test for consistency of linkage results within a study across time. We compared regression-based linkage to variance components linkage across time for six quantitative traits in the real data. RESULTS. The variance components approach found 11 significant linkages, the regression-based approach found 4. There was only one region that overlapped. Consistency between exams generally decreased as the time interval between exams increased. The regression-based approach showed higher consistency in linkage results across exams. CONCLUSION. The low consistency between exams and between methods may help explain the lack of replication between studies in this field.
Description of the Framingham Heart Study Data for Genetic Analysis Workshop 13
(BioMed Central, 2003-12-31) Cupples, L. Adrienne; Yang, Qiong; Demissie, Serkalem; Copenhafer, Donna; Levy, Daniel
A Three-Stage Approach for Genome-Wide Association Studies with Family Data for Quantitative Traits
(BioMed Central, 2010-5-14) Chen, Ming-Huei; Larson, Martin G.; Hsu, Yi-Hsiang; Peloso, Gina M.; Guo, Chao-Yu; Fox, Caroline S.; Atwood, Larry D.; Yang, Qiong
BACKGROUND. Genome-wide association (GWA) studies that use population-based association approaches may identify spurious associations in the presence of population admixture. In this paper, we propose a novel three-stage approach that is computationally efficient and robust to population admixture and more powerful than the family-based association test (FBAT) for GWA studies with family data. We propose a three-stage approach for GWA studies with family data. The first stage is to perform linear regression ignoring phenotypic correlations among family members. SNPs with a first stage p-value below a liberal cut-off (e.g. 0.1) are then analyzed in the second stage that employs a linear mixed effects (LME) model that accounts for within family correlations. Next, SNPs that reach genome-wide significance (e.g. 10-6 for 34,625 genotyped SNPs in this paper) are analyzed in the third stage using FBAT, with correction of multiple testing only for SNPs that enter the third stage. Simulations are performed to evaluate type I error and power of the proposed method compared to LME adjusting for 10 principal components (PC) of the genotype data. We also apply the three-stage approach to the GWA analyses of uric acid in Framingham Heart Study's SNP Health Association Resource (SHARe) project. RESULTS. Our simulations show that whether or not population admixture is present, the three-stage approach has no inflated type I error. In terms of power, using LME adjusting PC is only slightly more powerful than the three-stage approach. When applied to the GWA analyses of uric acid in the SHARe project of FHS, the three-stage approach successfully identified and confirmed three SNPs previously reported as genome-wide significant signals. CONCLUSIONS. For GWA analyses of quantitative traits with family data, our three-stage approach provides another appealing solution to population admixture, in addition to LME adjusting for genetic PC.
Evaluation of association of HNF1B variants with diverse cancers: collaborative analysis of data from 19 genome-wide association studies
(Public Library of Science, 2010-5-28) Elliott, Katherine S.; Zeggini, Eleftheria; McCarthy, Mark I.; Gudmundsson, Julius; Sulem, Patrick; Stacey, Simon N.; Thorlacius, Steinunn; Amundadottir, Laufey; Grönberg, Henrik; Xu, Jianfeng; Gaborieau, Valerie; Eeles, Rosalind A.; Neal, David E.; Donovan, Jenny L.; Hamdy, Freddie C.; Muir, Kenneth; Hwang, Shih-Jen; Spitz, Margaret R.; Zanke, Brent; Carvajal-Carmona, Luis; Brown, Kevin M.; Mann, Graham J.; Hayward, Nicholas K.; Macgregor, Stuart; Tomlinson, Ian P.M.; Lemire, Mathieu; Amos, Christopher I.; Murabito, Joanne M.; Isaacs, William B.; Easton, Douglas F.; Brennan, Paul; Barkardottir, Rosa B.; Gudbjartsson, Daniel F.; Rafnar, Thorunn; Hunter, David J.; Chanock, Stephen J.; Stefansson, Kari; Ioannidis, John P.A.; Hopper, John L.; Aitken, Joanne F.; Kefford, Richard F.; Giles, Graham G.; Armstrong, Bruce K.
BACKGROUND. Genome-wide association studies have found type 2 diabetes-associated variants in the HNF1B gene to exhibit reciprocal associations with prostate cancer risk. We aimed to identify whether these variants may have an effect on cancer risk in general versus a specific effect on prostate cancer only. METHODOLOGY/PRINCIPAL FINDINGS. In a collaborative analysis, we collected data from GWAS of cancer phenotypes for the frequently reported variants of HNF1B, rs4430796 and rs7501939, which are in linkage disequilibrium (r2=0.76, HapMap CEU). Overall, the analysis included 16 datasets on rs4430796 with 19,640 cancer cases and 21,929 controls; and 21 datasets on rs7501939 with 26,923 cases and 49,085 controls. Malignancies other than prostate cancer included colorectal, breast, lung and pancreatic cancers, and melanoma. Meta-analysis showed large between-dataset heterogeneity that was driven by different effects in prostate cancer and other cancers. The per-T2D-risk-allele odds ratios (95% confidence intervals) for rs4430796 were 0.79 (0.76, 0.83)] per G allele for prostate cancer (p<10-15 for both); and 1.03 (0.99, 1.07) for all other cancers. Similarly for rs7501939 the per-T2D-risk-allele odds ratios (95% confidence intervals) were 0.80 (0.77, 0.83) per T allele for prostate cancer (p<10-15 for both); and 1.00 (0.97, 1.04) for all other cancers. No malignancy other than prostate cancer had a nominally statistically significant association. CONCLUSIONS/SIGNIFICANCE. The examined HNF1B variants have a highly specific effect on prostate cancer risk with no apparent association with any of the other studied cancer types.
NRXN3 Is a Novel Locus for Waist Circumference: A Genome-Wide Association Study from the CHARGE Consortium
(Public Library of Science, 2009-6-26) Heard-Costa, Nancy L.; Zillikens, M. Carola; Monda, Keri L.; Johansson, Åsa; Harris, Tamara B.; Fu, Mao; Haritunians, Talin; Feitosa, Mary F.; Aspelund, Thor; Eiriksdottir, Gudny; Garcia, Melissa; Launer, Lenore J.; Smith, Albert V.; Mitchell, Braxton D.; McArdle, Patrick F.; Shuldiner, Alan R.; Bielinski, Suzette J.; Boerwinkle, Eric; Brancati, Fred; Demerath, Ellen W.; Pankow, James S.; Arnold, Alice M.; Chen, Yii-Der Ida; Glazer, Nicole L.; McKnight, Barbara; Psaty, Bruce M.; Rotter, Jerome I.; Amin, Najaf; Campbell, Harry; Gyllensten, Ulf; Pattaro, Cristian; Pramstaller, Peter P.; Rudan, Igor; Struchalin, Maksim; Vitart, Veronique; Gao, Xiaoyi; Kraja, Aldi; Province, Michael A.; Zhang, Qunyuan; Atwood, Larry D.; Dupuis, Josée; Hirschhorn, Joel N.; Jaquish, Cashell E.; O'Donnell, Christopher J.; Vasan, Ramachandran S.; White, Charles C.; Aulchenko, Yurii S.; Estrada, Karol; Hofman, Albert; Rivadeneira, Fernando; Uitterlinden, André G.; Witteman, Jacqueline C. M.; Oostra, Ben A.; Kaplan, Robert C.; Gudnason, Vilmundur; O'Connell, Jeffrey R.; Borecki, Ingrid B.; Van Duijn, Cornelia M.; Cupples, L. Adrienne; Fox, Caroline S.; North, Kari E.
Central abdominal fat is a strong risk factor for diabetes and cardiovascular disease. To identify common variants influencing central abdominal fat, we conducted a two-stage genome-wide association analysis for waist circumference (WC). In total, three loci reached genome-wide significance. In stage 1, 31,373 individuals of Caucasian descent from eight cohort studies confirmed the role of FTO and MC4R and identified one novel locus associated with WC in the neurexin 3 gene [NRXN3 (rs10146997, p = 6.4×10−7)]. The association with NRXN3 was confirmed in stage 2 by combining stage 1 results with those from 38,641 participants in the GIANT consortium (p = 0.009 in GIANT only, p = 5.3×10−8 for combined analysis, n = 70,014). Mean WC increase per copy of the G allele was 0.0498 z-score units (0.65 cm). This SNP was also associated with body mass index (BMI) [p = 7.4×10−6, 0.024 z-score units (0.10 kg/m2) per copy of the G allele] and the risk of obesity (odds ratio 1.13, 95% CI 1.07–1.19; p = 3.2×10−5 per copy of the G allele). The NRXN3 gene has been previously implicated in addiction and reward behavior, lending further evidence that common forms of obesity may be a central nervous system-mediated disorder. Our findings establish that common variants in NRXN3 are associated with WC, BMI, and obesity. Author Summary Obesity is a major health concern worldwide. In the past two years, genome-wide association studies of DNA markers known as SNPs (single nucleotide polymorphisms) have identified two novel genetic factors that may help scientists better understand why some people may be more susceptible to obesity. Similarly, this paper describes results from a large scale genome-wide association analysis for obesity susceptibility genes that includes 31,373 individuals from 8 separate studies. We uncovered a new gene influencing waist circumference, the neurexin 3 gene (NRXN3), which has been previously implicated in studies of addiction and reward behavior. These findings lend further evidence that our genes may influence our desire and consumption of food and, in turn, our susceptibility to obesity.
A Genome-Wide Association Study of Pulmonary Function Measures in the Framingham Heart Study
(Public Library of Science, 2009-3-20) Wilk, Jemma B.; Chen, Ting-hsu; Gottlieb, Daniel J.; Walter, Robert E.; Nagle, Michael W.; Brandler, Brian J.; Myers, Richard H.; Borecki, Ingrid B.; Silverman, Edwin K.; Weiss, Scott T.; O'Connor, George T.
The ratio of forced expiratory volume in one second to forced vital capacity (FEV1/FVC) is a measure used to diagnose airflow obstruction and is highly heritable. We performed a genome-wide association study in 7,691 Framingham Heart Study participants to identify single-nucleotide polymorphisms (SNPs) associated with the FEV1/FVC ratio, analyzed as a percent of the predicted value. Identified SNPs were examined in an independent set of 835 Family Heart Study participants enriched for airflow obstruction. Four SNPs in tight linkage disequilibrium on chromosome 4q31 were associated with the percent predicted FEV1/FVC ratio with p-values of genome-wide significance in the Framingham sample (best p-value = 3.6e-09). One of the four chromosome 4q31 SNPs (rs13147758; p-value 2.3e-08 in Framingham) was genotyped in the Family Heart Study and produced evidence of association with the same phenotype, percent predicted FEV1/FVC (p-value = 2.0e-04). The effect estimates for association in the Framingham and Family Heart studies were in the same direction, with the minor allele (G) associated with higher FEV1/FVC ratio levels. Results from the Family Heart Study demonstrated that the association extended to FEV1 and dichotomous airflow obstruction phenotypes, particularly among smokers. The SNP rs13147758 was associated with the percent predicted FEV1/FVC ratio in independent samples from the Framingham and Family Heart Studies producing a combined p-value of 8.3e-11, and this region of chromosome 4 around 145.68 megabases was associated with COPD in three additional populations reported in the accompanying manuscript. The associated SNPs do not lie within a gene transcript but are near the hedgehog-interacting protein (HHIP) gene and several expressed sequence tags cloned from fetal lung. Though it is unclear what gene or regulatory effect explains the association, the region warrants further investigation. Author Summary Cigarette smoking is the primary risk factor for impaired lung function, yet only 20% of smokers develop chronic obstructive pulmonary disease (COPD). This observation, along with family studies of lung function and COPD, suggests that genetic factors influence susceptibility to cigarette smoke. We examined the relationship between common genetic variants and measures of lung function in a sample of 7,691 participants from the Framingham Heart Study and confirmed our observations in 835 participants from the Family Heart Study selected to include cases of airflow obstruction. We identified a variant on chromosome 4 that was strongly associated with FEV1/FVC in the Framingham Study and confirmed the association in the Family Heart Study. The accompanying manuscript identified the same region to be associated with COPD. Several interesting genes are present in the region that we identified, including a gene (HHIP) interacting with a biological pathway involved in lung development, but it is not yet clear which gene in the region explains the association. Our results identified a region of chromosome 4 that warrants further study to understand the genetic effects influencing lung function.
Interpreting Metabolomic Profiles using Unbiased Pathway Models
(Public Library of Science, 2010-2-26) Deo, Rahul C.; Hunter, Luke; Lewis, Gregory D.; Pare, Guillaume; Vasan, Ramachandran S.; Chasman, Daniel I.; Wang, Thomas J.; Gerszten, Robert E.; Roth, Frederick P.
Human disease is heterogeneous, with similar disease phenotypes resulting from distinct combinations of genetic and environmental factors. Small-molecule profiling can address disease heterogeneity by evaluating the underlying biologic state of individuals through non-invasive interrogation of plasma metabolite levels. We analyzed metabolite profiles from an oral glucose tolerance test (OGTT) in 50 individuals, 25 with normal (NGT) and 25 with impaired glucose tolerance (IGT). Our focus was to elucidate underlying biologic processes. Although we initially found little overlap between changed metabolites and preconceived definitions of metabolic pathways, the use of unbiased network approaches identified significant concerted changes. Specifically, we derived a metabolic network with edges drawn between reactant and product nodes in individual reactions and between all substrates of individual enzymes and transporters. We searched for "active modules"—regions of the metabolic network enriched for changes in metabolite levels. Active modules identified relationships among changed metabolites and highlighted the importance of specific solute carriers in metabolite profiles. Furthermore, hierarchical clustering and principal component analysis demonstrated that changed metabolites in OGTT naturally grouped according to the activities of the System A and L amino acid transporters, the osmolyte carrier SLC6A12, and the mitochondrial aspartate-glutamate transporter SLC25A13. Comparison between NGT and IGT groups supported blunted glucose- and/or insulin-stimulated activities in the IGT group. Using unbiased pathway models, we offer evidence supporting the important role of solute carriers in the physiologic response to glucose challenge and conclude that carrier activities are reflected in individual metabolite profiles of perturbation experiments. Given the involvement of transporters in human disease, metabolite profiling may contribute to improved disease classification via the interrogation of specific transporter activities. Author Summary Human disease is complex, arising from the interaction of many genetic and environmental factors. Efforts to personalize treatment have been thwarted by "phenotypic heterogeneity", the apparent similarity of disease states with diverse underlying causes. One approach to resolve this heterogeneity is to redefine diseases on the basis of abnormal physiologic activities, which should allow grouping patients into categories with similar treatment response and prognosis. Physiologic activities can be identified and assessed through quantitative measurements of biomolecules—proteins, mRNAs, metabolites—in individual patient samples. The field of metabolomics involves the analysis of a broad array of metabolite levels from clinical fluid samples such as blood or urine and can be used to evaluate disease states. Because metabolic profiles are complex, we have taken an integrative network-based approach to understand them in terms of abnormal activities of enzymes and small molecule transporters. We have focused on the oral glucose tolerance test, used to diagnose diabetes, and have found that multiple transporters play an important role in the normal response to ingesting sugar. Many of these transporter activities are abnormal in individuals with impaired glucose tolerance and differing activities among them may reflect the diverse underlying causes and variable clinical courses of such patients.
Metabolic Profiling of the Human Response to a Glucose Challenge Reveals Distinct Axes of Insulin Sensitivity
(Nature Publishing Group, 2008-08-05) Shaham, Oded; Wei, Ru; Wang, Thomas J.; Ricciardi, Catherine; Lewis, Gregory D.; Vasan, Ramachandran S.; Carr, Steven A.; Thadhani, Ravi; Gerszten, Robert E.; Mootha, Vamsi K.
Glucose ingestion after an overnight fast triggers an insulin-dependent, homeostatic program that is altered in diabetes. The full spectrum of biochemical changes associated with this transition is currently unknown. We have developed a mass spectrometry-based strategy to simultaneously measure 191 metabolites following glucose ingestion. In two groups of healthy individuals (n=22 and 25), 18 plasma metabolites changed reproducibly, including bile acids, urea cycle intermediates, and purine degradation products, none of which were previously linked to glucose homeostasis. The metabolite dynamics also revealed insulin's known actions along four key axes—proteolysis, lipolysis, ketogenesis, and glycolysis—reflecting a switch from catabolism to anabolism. In pre-diabetics (n=25), we observed a blunted response in all four axes that correlated with insulin resistance. Multivariate analysis revealed that declines in glycerol and leucine/isoleucine (markers of lipolysis and proteolysis, respectively) jointly provide the strongest predictor of insulin sensitivity. This observation indicates that some humans are selectively resistant to insulin's suppression of proteolysis, whereas others, to insulin's suppression of lipolysis. Our findings lay the groundwork for using metabolic profiling to define an individual's 'insulin response profile', which could have value in predicting diabetes, its complications, and in guiding therapy.
Impact of Non-Ignorable Missingness on Genetic Tests of Linkage and/or Association Using Case-Parent Trios
(BioMed Central, 2005-12-30) Guo, Chao-Yu; Cui, Jing; Cupples, L. Adrienne
The transmission/disequilibrium test was introduced to test for linkage disequilibrium between a marker and a putative disease locus using case-parent trios. However, parental genotypes may be incomplete in such a study. When parental information is non-randomly missing, due, for example, to death from the disease under study, the impact on type I error and power under dominant and recessive disease models has been reported. In this paper, we examine non-ignorable missingness by assigning missing values to the genotypes of affected parents. We used unrelated case-parent trios in the Genetic Analysis Workshop 14 simulated data for the Danacaa population. Our computer simulations revealed that the type I error of these tests using incomplete trios was not inflated over the nominal level under either recessive or dominant disease models. However, the power of these tests appears to be inflated over the complete information case due to an excess of heterozygous parents in dyads.
Efficacy of Dietary Behavior Modification for Preserving Cardiovascular Health and Longevity
(SAGE-Hindawi Access to Research, 2010-12-28) Pryde, Moira McAllister; Kannel, William Bernard
Cardiovascular disease (CVD) and its predisposing risk factors are major lifestyle and behavioral determinants of longevity. Dietary lifestyle choices such as a heart healthy diet, regular exercise, a lean weight, moderate alcohol consumption, and smoking cessation have been shown to substantially reduce CVD and increase longevity. Recent research has shown that men and women who adhere to this lifestyle can substantially reduce their risk of coronary heart disease (CHD). The preventive benefits of maintaining a healthy lifestyle exceed those reported for using medication and procedures. Among the modifiable preventive measures, diet is of paramount importance, and recent data suggest some misconceptions and uncertainties that require reconsideration. These include commonly accepted recommendations about polyunsaturated fat intake, processed meat consumption, fish choices and preparation, transfatty acids, low carbohydrate diets, egg consumption, coffee, added sugar, soft drink beverages, glycemic load, chocolate, orange juice, nut consumption, vitamin D supplements, food portion size, and alcohol.
Cross-Sectional Associations Bet ween Abdominal and Thoracic Adipose Tissue Compartments and Adiponectin and Resistin in the Framingham Heart Study
(American Diabetes Association, 2009-2-17) Jain, Shilpa H.; Massaro, Joseph M.; Hoffmann, Udo; Rosito, Guido A.; Vasan, Ramachandran S.; Raji, Annaswamy; O'Donnell, Christopher J.; Meigs, James B.; Fox, Caroline S.
OBJECTIVE: To test the association of regional fat depots with circulating adiponectin and resistin concentrations and to assess the potential mediating effect of adipokines on associations between abdominal fat depots and cardiometabolic risk factors. RESEARCH DESIGN AND METHODS: Participants from the Framingham Heart Study offspring cohort (n = 916, 55% women; mean age 59 years) free of cardiovascular disease underwent computed tomography measurement of visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), pericardial fat, and intrathoracic fat volumes and assays of circulating adiponectin and resistin. RESULTS: VAT, SAT, pericardial fat, and intrathoracic fat were negatively correlated with adiponectin (r = −0.19 to −0.34, P < 0.001 [women]; r = −0.15 to −0.26, P < 0.01 [men] except SAT) and positively correlated with resistin (r = 0.16–0.21, P < 0.001 [women]; r = 0.11–0.14, P < 0.05 [men] except VAT). VAT increased the multivariable model R2 for adiponectin from 2–4% to 10–13% and for resistin from 3–4% to 3–6%. Adjustment for adipokines did not fully attenuate associations between VAT, SAT, and cardiometabolic risk factors. CONCLUSIONS: Adiponectin and resistin are correlated with fat depots cross-sectionally, but none of the adipokines can serve as surrogates for the fat depots. Relations between VAT, SAT, and cardiometabolic risk factors were not fully explained by adiponectin or resistin concentrations.

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