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1.  Plasma Adiponectin, Clinical Factors, and Patient Outcomes during the Acute Respiratory Distress Syndrome 
PLoS ONE  2014;9(9):e108561.
Objective
Adiponectin (APN) is an anti-inflammatory hormone derived from adipose tissue that attenuates acute lung injury in rodents. In this study, we investigated the association between circulating APN and outcomes among patients with acute respiratory distress syndrome (ARDS).
Methods
We performed a retrospective cohort study using data and plasma samples from participants in the multicenter ARDS Network Fluid and Catheter Treatment Trial.
Results
Plasma APN concentrations were measured in 816 (81.6%) trial participants at baseline and in 568 (56.8%) subjects at both baseline and day 7 after enrollment. Clinical factors associated with baseline APN levels in multivariable-adjusted models included sex, body mass index, past medical history of cirrhosis, and central venous pressure (model R2 = 9.7%). We did not observe an association between baseline APN and either severity of illness (APACHE III) or extent of lung injury (Lung Injury Score). Among patients who received right heart catheterization (n = 384), baseline APN was inversely related to mean pulmonary artery pressure (β = −0.015, R2 1.5%, p = 0.02); however, this association did not persist in multivariable models (β = −0.009, R2 0.5%, p = 0.20). Neither baseline APN levels [HR per quartile1.04 (95% CI 0.91–1.18), p = 0.61], nor change in APN level from baseline to day 7 [HR 1.04 (95% CI 0.89–1.23), p = 0.62)] were associated with 60 day mortality in Cox proportional hazards regression models. However, subgroup analysis identified an association between APN and mortality among patients who developed ARDS from extra-pulmonary etiologies [HR per quartile 1.31 (95% CI 1.08–1.57)]. APN levels did not correlate with mortality among patients developing ARDS in association with direct pulmonary injury [HR 0.96 (95% CI 0.83–1.13)], pinteraction = 0.016.
Conclusions
Plasma APN levels did not correlate with disease severity or mortality in a large cohort of patients with ARDS. However, higher APN levels were associated with increased mortality among patients developing ARDS from extra-pulmonary etiologies.
doi:10.1371/journal.pone.0108561
PMCID: PMC4178176  PMID: 25259893
2.  Variations of CT-Based Trunk Muscle Attenuation by Age, Sex, and Specific Muscle 
Background.
Fat accumulation in muscle may contribute to age-related declines in muscle function and is indicated by reduced attenuation of x-rays by muscle tissue in computed tomography scans. Reduced trunk muscle attenuation is associated with poor physical function, low back pain, and increased hyperkyphosis in older adults. However, variations in trunk muscle attenuation with age, sex and between specific muscles have not been investigated.
Methods.
A cross-sectional examination of trunk muscle attenuation in computed tomography scans was performed in 60 younger (35–50 years) and 60 older (75–87 years) adults randomly selected from participants in the Framingham Heart Study Offspring and Third Generation Multidetector Computed Tomography Study. Computed tomography attenuation of 11 trunk muscles was measured at vertebral levels T8 and L3, and the effects of age, sex, and specific muscle on computed tomography attenuation of trunk muscles were determined.
Results.
Muscle attenuation varied by specific muscle (p < .001), was lower in older adults (p < .001), and was generally lower in women than in men (p < .001), although not in all muscles. Age-related differences in muscle attenuation varied with specific muscle (p < .001), with the largest age differences occurring in the paraspinal and abdominal muscles.
Conclusions.
Trunk muscle attenuation is lower in older adults than in younger adults in both women and men, but such age-related differences vary widely between muscle groups. The reasons that some muscles exhibit larger age-related differences in fat content than others should be further explored to better understand age-related changes in functional capacity and postural stability.
doi:10.1093/gerona/gls168
PMCID: PMC3605905  PMID: 22904095
3.  Assessment of Gene-by-Sex Interaction Effect on Bone Mineral Density 
Liu, Ching-Ti | Estrada, Karol | Yerges-Armstrong, Laura M. | Amin, Najaf | Evangelou, Evangelos | Li, Guo | Minster, Ryan L. | Carless, Melanie A. | Kammerer, Candace M. | Oei, Ling | Zhou, Yanhua | Alonso, Nerea | Dailiana, Zoe | Eriksson, Joel | García-Giralt, Natalia | Giroux, Sylvie | Husted, Lise Bjerre | Khusainova, Rita I. | Koromila, Theodora | Kung, Annie WaiChee | Lewis, Joshua R. | Masi, Laura | Mencej-Bedrac, Simona | Nogues, Xavier | Patel, Millan S. | Prezelj, Janez | Richards, J Brent | Sham, Pak Chung | Spector, Timothy | Vandenput, Liesbeth | Xiao, Su-Mei | Zheng, Hou-Feng | Zhu, Kun | Balcells, Susana | Brandi, Maria Luisa | Frost, Morten | Goltzman, David | González-Macías, Jesús | Karlsson, Magnus | Khusnutdinova, Elza K. | Kollia, Panagoula | Langdahl, Bente Lomholt | Ljunggren, Östen | Lorentzon, Mattias | Marc, Janja | Mellström, Dan | Ohlsson, Claes | Olmos, José M. | Ralston, Stuart H. | Riancho, José A. | Rousseau, François | Urreizti, Roser | Van Hul, Wim | Zarrabeitia, María T. | Castano-Betancourt, Martha | Demissie, Serkalem | Grundberg, Elin | Herrera, Lizbeth | Kwan, Tony | Medina-Gómez, Carolina | Pastinen, Tomi | Sigurdsson, Gunnar | Thorleifsson, Gudmar | vanMeurs, Joyce B.J. | Blangero, John | Hofman, Albert | Liu, Yongmei | Mitchell, Braxton D. | O’Connell, Jeffrey R. | Oostra, Ben A. | Rotter, Jerome I | Stefansson, Kari | Streeten, Elizabeth A. | Styrkarsdottir, Unnur | Thorsteinsdottir, Unnur | Tylavsky, Frances A. | Uitterlinden, Andre | Cauley, Jane A. | Harris, Tamara B. | Ioannidis, John P.A. | Psaty, Bruce M. | Robbins, John A | Zillikens, M. Carola | vanDuijn, Cornelia M. | Prince, Richard L. | Karasik, David | Rivadeneira, Fernando | Kiel, Douglas P. | Cupples, L. Adrienne | Hsu, Yi-Hsiang
Background
Sexual dimorphism in various bone phenotypes, including bone mineral density (BMD), is widely observed; however the extent to which genes explain these sex differences is unclear. To identify variants with different effects by sex, we examined gene-by-sex autosomal interactions genome-wide, and performed eQTL analysis and bioinformatics network analysis.
Methods
We conducted an autosomal genome-wide meta-analysis of gene-by-sex interaction on lumbar spine (LS-) and femoral neck (FN-) BMD, in 25,353 individuals from eight cohorts. In a second stage, we followed up the 12 top SNPs (P<1×10−5) in an additional set of 24,763 individuals. Gene-by-sex interaction and sex-specific effects were examined in these 12 SNPs.
Results
We detected one novel genome-wide significant interaction associated with LS-BMD at the Chr3p26.1-p25.1 locus, near the GRM7 gene (male effect = 0.02 & p-value = 3.0×10−5; female effect = −0.007 & p-value=3.3×10−2) and eleven suggestive loci associated with either FN- or LS-BMD in discovery cohorts. However, there was no evidence for genome-wide significant (P<5×10−8) gene-by-sex interaction in the joint analysis of discovery and replication cohorts.
Conclusion
Despite the large collaborative effort, no genome-wide significant evidence for gene-by-sex interaction was found influencing BMD variation in this screen of autosomal markers. If they exist, gene-by-sex interactions for BMD probably have weak effects, accounting for less than 0.08% of the variation in these traits per implicated SNP.
doi:10.1002/jbmr.1679
PMCID: PMC3447125  PMID: 22692763
gene-by-sex; interaction; BMD; association; aging
5.  Genetics of coronary artery calcification among African Americans, a meta-analysis 
BMC Medical Genetics  2013;14:75.
Background
Coronary heart disease (CHD) is the major cause of death in the United States. Coronary artery calcification (CAC) scores are independent predictors of CHD. African Americans (AA) have higher rates of CHD but are less well-studied in genomic studies. We assembled the largest AA data resource currently available with measured CAC to identify associated genetic variants.
Methods
We analyzed log transformed CAC quantity (ln(CAC + 1)), for association with ~2.5 million single nucleotide polymorphisms (SNPs) and performed an inverse-variance weighted meta-analysis on results for 5,823 AA from 8 studies. Heritability was calculated using family studies. The most significant SNPs among AAs were evaluated in European Ancestry (EA) CAC data; conversely, the significance of published SNPs for CAC/CHD in EA was queried within our AA meta-analysis.
Results
Heritability of CAC was lower in AA (~30%) than previously reported for EA (~50%). No SNP reached genome wide significance (p < 5E-08). Of 67 SNPs with p < 1E-05 in AA there was no evidence of association in EA CAC data. Four SNPs in regions previously implicated in CAC/CHD (at 9p21 and PHACTR1) in EA reached nominal significance for CAC in AA, with concordant direction. Among AA, rs16905644 (p = 4.08E-05) had the strongest association in the 9p21 region.
Conclusions
While we observed substantial heritability for CAC in AA, we failed to identify loci for CAC at genome-wide significant levels despite having adequate power to detect alleles with moderate to large effects. Although suggestive signals in AA were apparent at 9p21 and additional CAC and CAD EA loci, overall the data suggest that even larger samples and an ethnic specific focus will be required for GWAS discoveries for CAC in AA populations.
doi:10.1186/1471-2350-14-75
PMCID: PMC3733595  PMID: 23870195
Atherosclerosis; Coronary artery calcium; Genetics; Meta-analysis; African-American
6.  Genetic variation in TRPS1 may regulate hip geometry as well as bone mineral density 
Bone  2012;50(5):1188-1195.
Trps1 has been proposed as a candidate gene for a mouse bone mineral density (BMD) QTL on Chromosome (Chr) 15, but it remained unclear if this gene was associated with BMD in humans. We used newly available data and advanced bioinformatics techniques to confirm that Trps1 is the most likely candidate gene for the mouse QTL. In short, by combining the raw genetic mapping data from two F2 generation crosses of inbred strains of mice, we narrowed the 95% confidence interval of this QTL down to the Chr 15 region spanning from 6 to 24 cM. This region contains 131 annotated genes. Using block haplotyping, all other genes except Trps1 were eliminated as candidates for this QTL. We then examined associations of 208 SNPs within 10kb of TRPS1 with BMD and hip geometry, using human genome-wide association study (GWAS) data from the GEFOS consortium. After correction for multiple testing, six TRPS1 SNPs were significantly associated with femoral neck BMD (P=0.0015–0.0019; adjusted P=0.038–0.048). We also found that three SNPs were highly associated with femoral neck width in women (rs10505257, P = 8.6x10−5, adjusted P=2.15x10−3; rs7002384, P = 5.5x10−4, adjusted P=01.38x10−2). In conclusion, we demonstrated that combining association studies in humans with murine models provides an efficient strategy to identify new candidate genes for bone phenotypes.
doi:10.1016/j.bone.2012.01.011
PMCID: PMC3322322  PMID: 22306695
Trichorhinophalangeal syndrome I; mouse models; human genetic association study; bone mineral density
7.  A Polymorphism in a Gene Encoding Perilipin 4 Is Associated with Height but not with Bone Measures in Individuals from the Framingham Osteoporosis Study 
Calcified tissue international  2011;90(2):96-107.
There is increasing interest in identifying new pathways and candidate genes that confer susceptibility to osteoporosis. There is evidence that adipogenesis and osteogenesis may be related, including a common bone marrow progenitor cell for both adipocytes and osteoblasts. Perilipin 1 (PLIN1) and Perilipin 4 (PLIN4) are members of the PATS family of genes and are involved in lipolysis of intracellular lipid deposits. A previous study reported gender-specific associations between one polymorphism of PLIN1 and bone mineral density (BMD) in a Japanese population. We hypothesized that polymorphisms in PLIN1 and PLIN4 would be associated with bone measures in adult Caucasian participants of the Framingham Osteoporosis Study (FOS). We genotyped 1,206 male and 1,445 female participants of the FOS for four single-nucleotide polymorphism (SNPs) in PLIN1 and seven SNPs in PLIN4 and tested for associations with measures of BMD, bone ultrasound, hip geometry, and height. We found several gender-specific significant associations with the measured traits. The association of PLIN4 SNP rs8887, G>A with height in females trended toward significance after simulation testing (adjusted P = 0.07) and remained significant after simulation testing in the combined-sex model (adjusted P = 0.033). In a large study sample of men and women, we found a significant association between one SNP in PLIN4 and height but not with bone traits, suggesting that PATS family genes are not important in the regulation of bone. Identification of genes that influence human height may lead to a better understanding of the processes involved in growth and development.
doi:10.1007/s00223-011-9552-7
PMCID: PMC3628693  PMID: 22210160
Perilipin 1; Perilipin 4; Bone mineral density; Bone geometry; Framingham Osteoporosis Study
8.  Heritability of Prevalent Vertebral Fracture and Volumetric Bone Mineral Density and Geometry at the Lumbar Spine in Three Generations of the Framingham Study 
Genetic factors likely contribute to the risk for vertebral fractures; however, there are few studies on the genetic contributions to vertebral fracture (VFrx), vertebral volumetric bone mineral density (vBMD) and geometry. Also the heritability (h2) for VFrx and its genetic correlation with phenotypes contributing to VFrx risk have not been established. This study aims to estimate the h2 of vertebral fracture, vBMD and cross-sectional-area (CSA) derived from quantitative computed tomography (QCT) scans, and to estimate the extent to which they share common genetic association in adults of European ancestry from three generations of Framingham Heart Study (FHS) families. Members of the FHS families were assessed for VFrx by lateral radiographs or QCT lateral scout views at 13 vertebral levels (T4-L4) using Genant’s semi-quantitative (SQ) scale (grades 0–3). Vertebral fracture was defined as having at least 25% reduction in height of any vertebra. We also analyzed QCT scans at the L3 level for integral (In.BMD) and trabecular (Tb.BMD) vBMD and cross-sectional area (CSA). Heritability estimates were calculated, and bivariate genetic correlation analysis was performed, adjusting for various covariates. For VFrx, we analyzed 4,099 individuals (148 VFrx cases) including 2,082 women and 2,017 men from 3 generations. Estimates of crude and multivariable-adjusted h2 were 0.43 to 0.69 (P< 1.1×10−2). 3,333 individuals including 1,737 men and 1,596 women from 2 generations had VFrx status and QCT-derived vBMD and CSA information. Estimates of crude and multivariable-adjusted h2 for vBMD and CSA ranged from 0.27 to 0.51. In a bivariate analysis, there was a moderate genetic correlation between VFrx and multivariable-adjusted In.BMD (−0.22) and Tb.BMD (−0.29). Our study suggests vertebral fracture, vertebral vBMD and CSA in adults of European ancestry are heritable, underscoring the importance of further work to identify the specific variants underlying genetic susceptibility to vertebral fracture, bone density and geometry.
doi:10.1002/jbmr.1537
PMCID: PMC3375687  PMID: 22222934
vertebral fracture; bone mineral density; heritability; QCT
9.  Bias due to 2-stage residual-outcome regression analysis in genetic association studies 
Genetic epidemiology  2011;35(7):592-596.
Association studies of risk factors and complex diseases require careful assessment of potential confounding factors. Two-stage regression analysis, sometimes referred to as residual- or adjusted-outcome analysis, has been increasingly used in association studies of single nucleotide polymorphisms (SNPs) and quantitative traits. In this analysis, first, a residual-outcome is calculated from a regression of the outcome variable on covariates and then the relationship between the adjusted-outcome and the SNP is evaluated by a simple linear regression of the adjusted-outcome on the SNP. In this paper, we examine the performance of this 2-stage analysis as compared with multiple linear regression (MLR) analysis. Our findings show that when a SNP and a covariate are correlated, the 2-stage approach results in biased genotypic effect and loss of power. Bias is always toward the null and increases with the squared-correlation between the SNP and the covariate (ρSC2). For example, for ρSC2=0.0, 0.1 and 0.5, 2-stage analysis results in, respectively, 0%, 10% and 50% attenuation in the SNP effect. As expected, MLR was always unbiased. Since individual SNPs often show little or no correlation with covariates, a 2-stage analysis is expected to perform as well as MLR in many genetic studies; however, it produces considerably different results from MLR and may lead to incorrect conclusions when independent variables are highly correlated. While a useful alternative to MLR under ρSC2=0.0, the 2-stage approach has serious limitations. Its use as a simple substitute for MLR should be avoided.
doi:10.1002/gepi.20607
PMCID: PMC3201714  PMID: 21769934
confounding; conditional analysis; covariate; 2-stage regression; adjusted-outcome; adjusted-genotype
10.  Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study 
Voight, Benjamin F | Peloso, Gina M | Orho-Melander, Marju | Frikke-Schmidt, Ruth | Barbalic, Maja | Jensen, Majken K | Hindy, George | Hólm, Hilma | Ding, Eric L | Johnson, Toby | Schunkert, Heribert | Samani, Nilesh J | Clarke, Robert | Hopewell, Jemma C | Thompson, John F | Li, Mingyao | Thorleifsson, Gudmar | Newton-Cheh, Christopher | Musunuru, Kiran | Pirruccello, James P | Saleheen, Danish | Chen, Li | Stewart, Alexandre FR | Schillert, Arne | Thorsteinsdottir, Unnur | Thorgeirsson, Gudmundur | Anand, Sonia | Engert, James C | Morgan, Thomas | Spertus, John | Stoll, Monika | Berger, Klaus | Martinelli, Nicola | Girelli, Domenico | McKeown, Pascal P | Patterson, Christopher C | Epstein, Stephen E | Devaney, Joseph | Burnett, Mary-Susan | Mooser, Vincent | Ripatti, Samuli | Surakka, Ida | Nieminen, Markku S | Sinisalo, Juha | Lokki, Marja-Liisa | Perola, Markus | Havulinna, Aki | de Faire, Ulf | Gigante, Bruna | Ingelsson, Erik | Zeller, Tanja | Wild, Philipp | de Bakker, Paul I W | Klungel, Olaf H | Maitland-van der Zee, Anke-Hilse | Peters, Bas J M | de Boer, Anthonius | Grobbee, Diederick E | Kamphuisen, Pieter W | Deneer, Vera H M | Elbers, Clara C | Onland-Moret, N Charlotte | Hofker, Marten H | Wijmenga, Cisca | Verschuren, WM Monique | Boer, Jolanda MA | van der Schouw, Yvonne T | Rasheed, Asif | Frossard, Philippe | Demissie, Serkalem | Willer, Cristen | Do, Ron | Ordovas, Jose M | Abecasis, Gonçalo R | Boehnke, Michael | Mohlke, Karen L | Daly, Mark J | Guiducci, Candace | Burtt, Noël P | Surti, Aarti | Gonzalez, Elena | Purcell, Shaun | Gabriel, Stacey | Marrugat, Jaume | Peden, John | Erdmann, Jeanette | Diemert, Patrick | Willenborg, Christina | König, Inke R | Fischer, Marcus | Hengstenberg, Christian | Ziegler, Andreas | Buysschaert, Ian | Lambrechts, Diether | Van de Werf, Frans | Fox, Keith A | El Mokhtari, Nour Eddine | Rubin, Diana | Schrezenmeir, Jürgen | Schreiber, Stefan | Schäfer, Arne | Danesh, John | Blankenberg, Stefan | Roberts, Robert | McPherson, Ruth | Watkins, Hugh | Hall, Alistair S | Overvad, Kim | Rimm, Eric | Boerwinkle, Eric | Tybjaerg-Hansen, Anne | Cupples, L Adrienne | Reilly, Muredach P | Melander, Olle | Mannucci, Pier M | Ardissino, Diego | Siscovick, David | Elosua, Roberto | Stefansson, Kari | O'Donnell, Christopher J | Salomaa, Veikko | Rader, Daniel J | Peltonen, Leena | Schwartz, Stephen M | Altshuler, David | Kathiresan, Sekar
Lancet  2012;380(9841):572-580.
Summary
Background
High plasma HDL cholesterol is associated with reduced risk of myocardial infarction, but whether this association is causal is unclear. Exploiting the fact that genotypes are randomly assigned at meiosis, are independent of non-genetic confounding, and are unmodified by disease processes, mendelian randomisation can be used to test the hypothesis that the association of a plasma biomarker with disease is causal.
Methods
We performed two mendelian randomisation analyses. First, we used as an instrument a single nucleotide polymorphism (SNP) in the endothelial lipase gene (LIPG Asn396Ser) and tested this SNP in 20 studies (20 913 myocardial infarction cases, 95 407 controls). Second, we used as an instrument a genetic score consisting of 14 common SNPs that exclusively associate with HDL cholesterol and tested this score in up to 12 482 cases of myocardial infarction and 41 331 controls. As a positive control, we also tested a genetic score of 13 common SNPs exclusively associated with LDL cholesterol.
Findings
Carriers of the LIPG 396Ser allele (2·6% frequency) had higher HDL cholesterol (0·14 mmol/L higher, p=8×10−13) but similar levels of other lipid and non-lipid risk factors for myocardial infarction compared with non-carriers. This difference in HDL cholesterol is expected to decrease risk of myocardial infarction by 13% (odds ratio [OR] 0·87, 95% CI 0·84–0·91). However, we noted that the 396Ser allele was not associated with risk of myocardial infarction (OR 0·99, 95% CI 0·88–1·11, p=0·85). From observational epidemiology, an increase of 1 SD in HDL cholesterol was associated with reduced risk of myocardial infarction (OR 0·62, 95% CI 0·58–0·66). However, a 1 SD increase in HDL cholesterol due to genetic score was not associated with risk of myocardial infarction (OR 0·93, 95% CI 0·68–1·26, p=0·63). For LDL cholesterol, the estimate from observational epidemiology (a 1 SD increase in LDL cholesterol associated with OR 1·54, 95% CI 1·45–1·63) was concordant with that from genetic score (OR 2·13, 95% CI 1·69–2·69, p=2×10−10).
Interpretation
Some genetic mechanisms that raise plasma HDL cholesterol do not seem to lower risk of myocardial infarction. These data challenge the concept that raising of plasma HDL cholesterol will uniformly translate into reductions in risk of myocardial infarction.
Funding
US National Institutes of Health, The Wellcome Trust, European Union, British Heart Foundation, and the German Federal Ministry of Education and Research.
doi:10.1016/S0140-6736(12)60312-2
PMCID: PMC3419820  PMID: 22607825
11.  A Genome-wide Association Study Identifies LIPA as a Susceptibility Gene for Coronary Artery Disease 
Wild, Philipp S | Zeller, Tanja | Schillert, Arne | Szymczak, Silke | Sinning, Christoph R | Deiseroth, Arne | Schnabel, Renate B | Lubos, Edith | Keller, Till | Eleftheriadis, Medea S | Bickel, Christoph | Rupprecht, Hans J | Wilde, Sandra | Rossmann, Heidi | Diemert, Patrick | Cupples, L Adrienne | Perret, Claire | Erdmann, Jeanette | Stark, Klaus | Kleber, Marcus E | Epstein, Stephen E | Voight, Benjamin F | Kuulasmaa, Kari | Li, Mingyao | Schäfer, Arne S | Klopp, Norman | Braund, Peter S | Sager, Hendrik B | Demissie, Serkalem | Proust, Carole | König, Inke R | Wichmann, Heinz-Erich | Reinhard, Wibke | Hoffmann, Michael M | Virtamo, Jarmo | Burnett, Mary Susan | Siscovick, David | Wiklund, Per Gunnar | Qu, Liming | El Mokthari, Nour Eddine | Thompson, John R | Peters, Annette | Smith, Albert V | Yon, Emmanuelle | Baumert, Jens | Hengstenberg, Christian | März, Winfried | Amouyel, Philippe | Devaney, Joseph | Schwartz, Stephen M | Saarela, Olli | Mehta, Nehal N | Rubin, Diana | Silander, Kaisa | Hall, Alistair S | Ferrieres, Jean | Harris, Tamara B | Melander, Olle | Kee, Frank | Hakonarson, Hakon | Schrezenmeir, Juergen | Gudnason, Vilmundur | Elosua, Roberto | Arveiler, Dominique | Evans, Alun | Rader, Daniel J | Illig, Thomas | Schreiber, Stefan | Bis, Joshua C | Altshuler, David | Kavousi, Maryam | Witteman, Jaqueline CM | Uitterlinden, Andre G | Hofman, Albert | Folsom, Aaron R | Barbalic, Maja | Boerwinkle, Eric | Kathiresan, Sekar | Reilly, Muredach P | O'Donnell, Christopher J | Samani, Nilesh J | Schunkert, Heribert | Cambien, Francois | Lackner, Karl J | Tiret, Laurence | Salomaa, Veikko | Munzel, Thomas | Ziegler, Andreas | Blankenberg, Stefan
Background
eQTL analyses are important to improve the understanding of genetic association results. Here, we performed a genome-wide association and global gene expression study to identify functionally relevant variants affecting the risk of coronary artery disease (CAD).
Methods and Results
In a genome-wide association analysis of 2,078 CAD cases and 2,953 controls, we identified 950 single nucleotide polymorphisms (SNPs) that were associated with CAD at P<10-3. Subsequent in silico and wet-lab replication stages and a final meta-analysis of 21,428 CAD cases and 38,361 controls revealed a novel association signal at chromosome 10q23.31 within the LIPA (Lysosomal Acid Lipase A) gene (P=3.7×10-8; OR 1.1; 95% CI: 1.07-1.14). The association of this locus with global gene expression was assessed by genome-wide expression analyses in the monocyte transcriptome of 1,494 individuals. The results showed a strong association of this locus with expression of the LIPA transcript (P=1.3×10-96). An assessment of LIPA SNPs and transcript with cardiovascular phenotypes revealed an association of LIPA transcript levels with impaired endothelial function (P=4.4×10-3).
Conclusions
The use of data on genetic variants and the addition of data on global monocytic gene expression led to the identification of the novel functional CAD susceptibility locus LIPA, located on chromosome 10q23.31. The respective eSNPs associated with CAD strongly affect LIPA gene expression level, which itself was related to endothelial dysfunction, a precursor of CAD.
doi:10.1161/CIRCGENETICS.110.958728
PMCID: PMC3157552  PMID: 21606135
coronary artery disease; genome-wide association studies; gene expression; genetic variation; genomics; eQTL; eSNP; LIPA
12.  Meta-analysis of genome-wide association studies from the CHARGE consortium identifies common variants associated with carotid intima media thickness and plaque 
Bis, Joshua C. | Kavousi, Maryam | Franceschini, Nora | Isaacs, Aaron | Abecasis, Gonçalo R | Schminke, Ulf | Post, Wendy | Smith, Albert V. | Cupples, L. Adrienne | Markus, Hugh S | Schmidt, Reinhold | Huffman, Jennifer E. | Lehtimäki, Terho | Baumert, Jens | Münzel, Thomas | Heckbert, Susan R. | Dehghan, Abbas | North, Kari | Oostra, Ben | Bevan, Steve | Stoegerer, Eva-Maria | Hayward, Caroline | Raitakari, Olli | Meisinger, Christa | Schillert, Arne | Sanna, Serena | Völzke, Henry | Cheng, Yu-Ching | Thorsson, Bolli | Fox, Caroline S. | Rice, Kenneth | Rivadeneira, Fernando | Nambi, Vijay | Halperin, Eran | Petrovic, Katja E. | Peltonen, Leena | Wichmann, H. Erich | Schnabel, Renate B. | Dörr, Marcus | Parsa, Afshin | Aspelund, Thor | Demissie, Serkalem | Kathiresan, Sekar | Reilly, Muredach P. | Uitterlinden, Andre | Couper, David J. | Sitzer, Matthias | Kähönen, Mika | Illig, Thomas | Wild, Philipp S. | Orru, Marco | Lüdemann, Jan | Shuldiner, Alan R. | Eiriksdottir, Gudny | White, Charles C. | Rotter, Jerome I. | Hofman, Albert | Seissler, Jochen | Zeller, Tanja | Usala, Gianluca | Ernst, Florian | Launer, Lenore J. | D'Agostino, Ralph B. | O'Leary, Daniel H. | Ballantyne, Christie | Thiery, Joachim | Ziegler, Andreas | Lakatta, Edward G. | Chilukoti, Ravi Kumar | Harris, Tamara B. | Wolf, Philip A. | Psaty, Bruce M. | Polak, Joseph F | Li, Xia | Rathmann, Wolfgang | Uda, Manuela | Boerwinkle, Eric | Klopp, Norman | Schmidt, Helena | Wilson, James F | Viikari, Jorma | Koenig, Wolfgang | Blankenberg, Stefan | Newman, Anne B. | Witteman, Jacqueline | Heiss, Gerardo | van Duijn, Cornelia | Scuteri, Angelo | Homuth, Georg | Mitchell, Braxton D. | Gudnason, Vilmundur | O’Donnell, Christopher J.
Nature Genetics  2011;43(10):940-947.
doi:10.1038/ng.920
PMCID: PMC3257519  PMID: 21909108
genome-wide association study; genetic epidemiology; genetics; subclinical atherosclerosis; carotid intima media thickness; cardiovascular disease; cohort study; meta-analysis; risk
13.  Mining the LIPG Allelic Spectrum Reveals the Contribution of Rare and Common Regulatory Variants to HDL Cholesterol 
PLoS Genetics  2011;7(12):e1002393.
Genome-wide association studies (GWAS) have successfully identified loci associated with quantitative traits, such as blood lipids. Deep resequencing studies are being utilized to catalogue the allelic spectrum at GWAS loci. The goal of these studies is to identify causative variants and missing heritability, including heritability due to low frequency and rare alleles with large phenotypic impact. Whereas rare variant efforts have primarily focused on nonsynonymous coding variants, we hypothesized that noncoding variants in these loci are also functionally important. Using the HDL-C gene LIPG as an example, we explored the effect of regulatory variants identified through resequencing of subjects at HDL-C extremes on gene expression, protein levels, and phenotype. Resequencing a portion of the LIPG promoter and 5′ UTR in human subjects with extreme HDL-C, we identified several rare variants in individuals from both extremes. Luciferase reporter assays were used to measure the effect of these rare variants on LIPG expression. Variants conferring opposing effects on gene expression were enriched in opposite extremes of the phenotypic distribution. Minor alleles of a common regulatory haplotype and noncoding GWAS SNPs were associated with reduced plasma levels of the LIPG gene product endothelial lipase (EL), consistent with its role in HDL-C catabolism. Additionally, we found that a common nonfunctional coding variant associated with HDL-C (rs2000813) is in linkage disequilibrium with a 5′ UTR variant (rs34474737) that decreases LIPG promoter activity. We attribute the gene regulatory role of rs34474737 to the observed association of the coding variant with plasma EL levels and HDL-C. Taken together, the findings show that both rare and common noncoding regulatory variants are important contributors to the allelic spectrum in complex trait loci.
Author Summary
Genetic association studies have identified genomic regions that affect quantifiable traits such as lipid levels. When a gene and a trait are found to be associated with one another, the gene is often further studied to determine its role in affecting the trait. One approach is to sequence the gene in individuals at the extremes of the trait's distribution with the hope of finding rare mutations that directly contribute to the trait. Until now studies using this approach have focused on genetic variation in the protein coding sequence of these genes and have been largely successful in identifying functionally important mutations. However, other studies have found an abundance of noncoding variation in the genome that may also contribute to the heritability of these traits. Here we seek to determine the contribution of such noncoding mutations to high density lipoprotein cholesterol (HDL-C) levels in humans using the HDL-C candidate gene LIPG as an example. Through a sequencing study in individuals with high and low HDL-C levels, we demonstrate that both rare and common noncoding mutations are influential contributors to the allelic spectrum of such traits and should be further characterized after initial association with the trait.
doi:10.1371/journal.pgen.1002393
PMCID: PMC3234219  PMID: 22174694
14.  Large-scale association analyses identifies 13 new susceptibility loci for coronary artery disease 
Schunkert, Heribert | König, Inke R. | Kathiresan, Sekar | Reilly, Muredach P. | Assimes, Themistocles L. | Holm, Hilma | Preuss, Michael | Stewart, Alexandre F. R. | Barbalic, Maja | Gieger, Christian | Absher, Devin | Aherrahrou, Zouhair | Allayee, Hooman | Altshuler, David | Anand, Sonia S. | Andersen, Karl | Anderson, Jeffrey L. | Ardissino, Diego | Ball, Stephen G. | Balmforth, Anthony J. | Barnes, Timothy A. | Becker, Diane M. | Becker, Lewis C. | Berger, Klaus | Bis, Joshua C. | Boekholdt, S. Matthijs | Boerwinkle, Eric | Braund, Peter S. | Brown, Morris J. | Burnett, Mary Susan | Buysschaert, Ian | Carlquist, Cardiogenics, John F. | Chen, Li | Cichon, Sven | Codd, Veryan | Davies, Robert W. | Dedoussis, George | Dehghan, Abbas | Demissie, Serkalem | Devaney, Joseph M. | Do, Ron | Doering, Angela | Eifert, Sandra | El Mokhtari, Nour Eddine | Ellis, Stephen G. | Elosua, Roberto | Engert, James C. | Epstein, Stephen E. | Faire, Ulf de | Fischer, Marcus | Folsom, Aaron R. | Freyer, Jennifer | Gigante, Bruna | Girelli, Domenico | Gretarsdottir, Solveig | Gudnason, Vilmundur | Gulcher, Jeffrey R. | Halperin, Eran | Hammond, Naomi | Hazen, Stanley L. | Hofman, Albert | Horne, Benjamin D. | Illig, Thomas | Iribarren, Carlos | Jones, Gregory T. | Jukema, J.Wouter | Kaiser, Michael A. | Kaplan, Lee M. | Kastelein, John J.P. | Khaw, Kay-Tee | Knowles, Joshua W. | Kolovou, Genovefa | Kong, Augustine | Laaksonen, Reijo | Lambrechts, Diether | Leander, Karin | Lettre, Guillaume | Li, Mingyao | Lieb, Wolfgang | Linsel-Nitschke, Patrick | Loley, Christina | Lotery, Andrew J. | Mannucci, Pier M. | Maouche, Seraya | Martinelli, Nicola | McKeown, Pascal P. | Meisinger, Christa | Meitinger, Thomas | Melander, Olle | Merlini, Pier Angelica | Mooser, Vincent | Morgan, Thomas | Mühleisen, Thomas W. | Muhlestein, Joseph B. | Münzel, Thomas | Musunuru, Kiran | Nahrstaedt, Janja | Nelson, Christopher P. | Nöthen, Markus M. | Olivieri, Oliviero | Patel, Riyaz S. | Patterson, Chris C. | Peters, Annette | Peyvandi, Flora | Qu, Liming | Quyyumi, Arshed A. | Rader, Daniel J. | Rallidis, Loukianos S. | Rice, Catherine | Rosendaal, Frits R. | Rubin, Diana | Salomaa, Veikko | Sampietro, M. Lourdes | Sandhu, Manj S. | Schadt, Eric | Schäfer, Arne | Schillert, Arne | Schreiber, Stefan | Schrezenmeir, Jürgen | Schwartz, Stephen M. | Siscovick, David S. | Sivananthan, Mohan | Sivapalaratnam, Suthesh | Smith, Albert | Smith, Tamara B. | Snoep, Jaapjan D. | Soranzo, Nicole | Spertus, John A. | Stark, Klaus | Stirrups, Kathy | Stoll, Monika | Tang, W. H. Wilson | Tennstedt, Stephanie | Thorgeirsson, Gudmundur | Thorleifsson, Gudmar | Tomaszewski, Maciej | Uitterlinden, Andre G. | van Rij, Andre M. | Voight, Benjamin F. | Wareham, Nick J. | Wells, George A. | Wichmann, H.-Erich | Wild, Philipp S. | Willenborg, Christina | Witteman, Jaqueline C. M. | Wright, Benjamin J. | Ye, Shu | Zeller, Tanja | Ziegler, Andreas | Cambien, Francois | Goodall, Alison H. | Cupples, L. Adrienne | Quertermous, Thomas | März, Winfried | Hengstenberg, Christian | Blankenberg, Stefan | Ouwehand, Willem H. | Hall, Alistair S. | Deloukas, Panos | Thompson, John R. | Stefansson, Kari | Roberts, Robert | Thorsteinsdottir, Unnur | O’Donnell, Christopher J. | McPherson, Ruth | Erdmann, Jeanette | Samani, Nilesh J.
Nature genetics  2011;43(4):333-338.
We performed a meta-analysis of 14 genome-wide association studies of coronary artery disease (CAD) comprising 22,233 cases and 64,762 controls of European descent, followed by genotyping of top association signals in 60,738 additional individuals. This genomic analysis identified 13 novel loci harboring one or more SNPs that were associated with CAD at P<5×10−8 and confirmed the association of 10 of 12 previously reported CAD loci. The 13 novel loci displayed risk allele frequencies ranging from 0.13 to 0.91 and were associated with a 6 to 17 percent increase in the risk of CAD per allele. Notably, only three of the novel loci displayed significant association with traditional CAD risk factors, while the majority lie in gene regions not previously implicated in the pathogenesis of CAD. Finally, five of the novel CAD risk loci appear to have pleiotropic effects, showing strong association with various other human diseases or traits.
doi:10.1038/ng.784
PMCID: PMC3119261  PMID: 21378990
15.  Association of Leukocyte Telomere Length with Circulating Biomarkers of the Renin-Angiotensin-Aldosterone System: The Framingham Heart Study 
Circulation  2008;117(9):1138-1144.
Background
Leucocyte telomere length (LTL) chronicles the cumulative burden of oxidative stress and inflammation over a life course. Activation of the renin-angiotensin-aldosterone system (RAAS) is associated with increased oxidative stress and inflammation. Therefore, LTL may be related to circulating biomarkers of the RAAS.
Methods
We evaluated the cross-sectional relations of LTL (dependent variable) to circulating renin and aldosterone concentrations and the renin-aldosterone ratio (all logarithmically-transformed; independent variables) in 1203 Framingham Study participants (mean age 59 years, 51% women). We used multivariable linear regression and adjusted for age, blood pressure, hypertension treatment, smoking, diabetes, body mass index, hormone replacement therapy, serum creatinine and the urine sodium-creatinine ratio.
Results
Overall, multivariable-adjusted LTL was inversely related to renin (beta coefficient per unit increase [β]=-0.038; p= 0.036), directly related to aldosterone (β=0.099; p= 0.002), and inversely related to the renin-aldosterone ratio (β=-0.049; p= 0.003). Relations of LTL to biomarkers were stronger in those with hypertension, although a formal test of interaction was not statistically significant (p=0.20). Individuals with hypertension displayed significant associations of LTL with renin (β=-0.060; p= 0.005), aldosterone (β=0.134; p= 0.002) and renin-aldosterone ratio (β=-0.072; p<0.001). Participants with hypertension who were in the top tertile of the renin-aldosterone ratio had LTL that was 182 base pairs shorter relative to those in the lowest tertile.
Conclusions
In our community-based sample, LTL was shorter in individuals with a higher renin-aldosterone ratio, especially so in participants with hypertension. Additional investigations are warranted to confirm our observations.
doi:10.1161/CIRCULATIONAHA.107.731794
PMCID: PMC3142671  PMID: 18268147
Telomere; Renin; Aldosterone; Hypertension; Epidemiology; Association; Salt; Oxidative stress
16.  Genome-Wide Pleiotropy of Osteoporosis-Related Phenotypes: The Framingham Study 
Journal of Bone and Mineral Research  2010;25(7):1555-1563.
Genome-wide association studies offer an unbiased approach to identify new candidate genes for osteoporosis. We examined the Affymetrix 500K + 50K SNP GeneChip marker sets for associations with multiple osteoporosis-related traits at various skeletal sites, including bone mineral density (BMD, hip and spine), heel ultrasound, and hip geometric indices in the Framingham Osteoporosis Study. We evaluated 433,510 single-nucleotide polymorphisms (SNPs) in 2073 women (mean age 65 years), members of two-generational families. Variance components analysis was performed to estimate phenotypic, genetic, and environmental correlations (ρP, ρG, and ρE) among bone traits. Linear mixed-effects models were used to test associations between SNPs and multivariable-adjusted trait values. We evaluated the proportion of SNPs associated with pairs of the traits at a nominal significance threshold α = 0.01. We found substantial correlation between the proportion of associated SNPs and the ρP and ρG (r = 0.91 and 0.84, respectively) but much lower with ρE (r = 0.38). Thus, for example, hip and spine BMD had 6.8% associated SNPs in common, corresponding to ρP = 0.55 and ρG = 0.66 between them. Fewer SNPs were associated with both BMD and any of the hip geometric traits (eg, femoral neck and shaft width, section moduli, neck shaft angle, and neck length); ρG between BMD and geometric traits ranged from −0.24 to +0.40. In conclusion, we examined relationships between osteoporosis-related traits based on genome-wide associations. Most of the similarity between the quantitative bone phenotypes may be attributed to pleiotropic effects of genes. This knowledge may prove helpful in defining the best phenotypes to be used in genetic studies of osteoporosis. © 2010 American Society for Bone and Mineral Research.
doi:10.1002/jbmr.38
PMCID: PMC3153998  PMID: 20200953
bone mineral density; quantitative ultrasound; femoral geometry; genome-wide association; single-nucleotide polymorphisms; genetic correlations; pleiotropy
17.  Allostatic load is associated with chronic conditions in the Boston Puerto Rican Health Study 
Social science & medicine (1982)  2010;70(12):1988-1996.
Puerto Ricans living in the United States mainland present multiple disparities in prevalence of chronic diseases, relative to other racial and ethnic groups. Allostatic load (AL), or the cumulative wear and tear of physiological responses to stressors such as major life events, social and environmental burden, has been proposed as a possible mechanism for the inequalities observed in minority groups, but has not been studied in Puerto Ricans. The aim of this study was to determine the association of AL to six chronic diseases (abdominal obesity, hypertension, diabetes, and self-reported cardiovascular disease (CVD), arthritis and cancer) in Puerto Ricans, and to contrast AL to metabolic syndrome (MetS). Participants of the Boston Puerto Rican Health Study (n=1,116, ages 45–75 years) underwent a home-based interview, where questionnaires were completed and biological samples collected. A summary definition of AL was constructed using clinically-defined cutoffs and medication use for 10 physiological parameters in different body systems. Logistic regression models were run to determine associations between AL score and disease status, controlling for age, sex, smoking, alcohol use, physical activity, total fat intake and energy intake. Parallel models were also run with MetS score replacing AL. We found that increasing categories of AL score were significantly associated with abdominal obesity, hypertension, diabetes and self-reported cardiovascular disease (CVD) and arthritis, but not with self-reported cancer. The strength of associations of AL with all conditions, except diabetes and cancer, was similar to or larger than those of MetS score. In conclusion, Puerto Rican older adults experienced physiological dysregulation that was associated with increased odds of chronic conditions. AL was more strongly associated with most conditions, compared to MetS, suggesting that this cumulative measure may be a better predictor of disease. These results have prospective research implications for Puerto Ricans and other ethnic groups.
doi:10.1016/j.socscimed.2010.02.024
PMCID: PMC2907654  PMID: 20381934
allostatic load; health disparities; Puerto Ricans; chronic diseases; metabolic syndrome; USA
18.  The Association of Genome-Wide Variation with the Risk of Incident Heart Failure in Adults of European and African Ancestry: A Prospective Meta-Analysis from the CHARGE Consortium 
Background
Although genetic factors contribute to the onset of heart failure (HF), no large-scale genome-wide investigation of HF risk has been published to date. We investigated the association of 2,478,304 single nucleotide polymorphisms (SNPs) with incident HF by meta-analyzing data from 4 community-based prospective cohorts: the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study.
Methods and Results
Eligible participants for these analyses were of European or African ancestry and free of clinical HF at baseline. Each study independently conducted genome-wide scans and imputed data to the ~2.5 million SNPs in HapMap. Within each study, Cox proportional hazards regression models provided age- and sex-adjusted estimates of the association between each variant and time to incident HF. Fixed-effect meta-analyses combined results for each SNP from the 4 cohorts to produce an overall association estimate and p-value. A genome-wide significance p-value threshold was set a priori at 5.0×10−7. During a mean follow-up of 11.5 years, 2,526 incident HF events (12%) occurred in 20,926 European-ancestry participants. The meta-analysis identified a genome-wide significant locus at chromosomal position 15q22 (1.4×10−8), which was 58.8 kb from USP3. Among 2,895 African-ancestry participants, 466 incident HF events (16%) occurred during a mean follow-up of 13.7 years. One genome-wide significant locus was identified at 12q14 (6.7×10−8), which was 6.3 kb from LRIG3.
Conclusions
We identified 2 loci that were associated with incident HF and exceeded genome-wide significance. The findings merit replication in other community-based settings of incident HF.
doi:10.1161/CIRCGENETICS.109.895763
PMCID: PMC3025695  PMID: 20445134
epidemiology; genetics; heart failure; genome-wide variation; incidence
19.  Genomic variation associated with mortality among adults of European and African ancestry with heart failure: the CHARGE Consortium 
Background
Prognosis and survival are significant concerns for individuals with heart failure (HF). In order to better understand the pathophysiology of HF prognosis, the association between 2,366,858 single nucleotide polymorphisms (SNPs) and all-cause mortality was evaluated among individuals with incident HF from four community-based prospective cohorts: the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study.
Methods and Results
Participants were 2,526 individuals of European ancestry and 466 individuals of African ancestry who suffered an incident HF event during follow-up in the respective cohorts. Within each study, the association between genetic variants and time to mortality among individuals with HF was assessed by Cox proportional hazards models that included adjustment for sex and age at the time of the HF event. Prospective fixed-effect meta-analyses were conducted for the four study populations of European ancestry (N=1,645 deaths) and for the two populations of African ancestry (N=281 deaths). Genome-wide significance was set at P=5.0×10-7. Meta-analytic findings among individuals of European ancestry revealed one genome-wide significant locus on chromosome 3p22 in an intron of CKLF-like MARVEL transmembrane domain containing 7 (CMTM7, p = 3.2×10-7). Eight additional loci in individuals of European ancestry and four loci in individuals of African ancestry were identified by high-signal SNPs (p < 1.0×10-5), but did not meet genome-wide significance.
Conclusions
This study identified a novel locus associated with all-cause mortality among individuals of European ancestry with HF. This finding warrants additional investigation, including replication, in other studies of HF.
doi:10.1161/CIRCGENETICS.109.895995
PMCID: PMC3033765  PMID: 20400778
heart failure; all-cause mortality; genetics; genome-wide variation
20.  The PLIN4 Variant rs8887 Modulates Obesity Related Phenotypes in Humans through Creation of a Novel miR-522 Seed Site 
PLoS ONE  2011;6(4):e17944.
PLIN4 is a member of the PAT family of lipid storage droplet (LSD) proteins. Associations between seven single nucleotide polymorphisms (SNPs) at human PLIN4 with obesity related phenotypes were investigated using meta-analysis followed by a determination if these phenotypes are modulated by interactions between PLIN4 SNPs and dietary PUFA. Samples consisted of subjects from two populations of European ancestry. We demonstrated association of rs8887 with anthropometrics. Meta-analysis demonstrated significant interactions between the rs8887 minor allele with PUFA n3 modulating anthropometrics. rs884164 showed interaction with both n3 and n6 PUFA modulating anthropometric and lipid phenotypes. In silico analysis of the PLIN4 3′UTR sequence surrounding the rs8887 minor A allele predicted a seed site for the human microRNA-522 (miR-522), suggesting a functional mechanism. Our data showed that a PLIN4 3′UTR luciferase reporter carrying the A allele of rs8887 was reduced in response to miR-522 mimics compared to the G allele. These results suggest variation at the PLIN4 locus, and its interaction with PUFA as a modulator of obesity related phenotypes, acts in part through creation of a miR-522 regulatory site.
doi:10.1371/journal.pone.0017944
PMCID: PMC3080366  PMID: 21533135
21.  Refined QTLs of osteoporosis-related traits by linkage analysis with genome-wide SNPs: Framingham SHARe 
Bone  2010;46(4):1114-1121.
Genome-wide association studies (GWAS) using high-density array of single-nucleotide polymorphisms (SNPs) offer an unbiased strategy to identify new candidate genes for osteoporosis.
We used a subset of autosomal SNPs from the Affymetrix 500K+50K SNP GeneChip marker set to examine genetic linkage with multiple highly heritable osteoporosis-related traits, including BMD of the hip and spine, heel ultrasound (attenuation and speed of sound), and geometric indices of the hip, in two generations from the Framingham Osteoporosis Study. Variance component linkage analysis was performed using normalized residuals (adjusted for age, height, BMI, and estrogen status in women).
Multipoint linkage analyses produced LOD scores ≥ 3.0 for BMD on chromosomes (chr.) 9 and 11, and for ultrasound speed of sound on chr. 5. Hip geometric traits were linked with higher LOD scores, such as with Shaft Width on chr. 4 (LOD = 3.9) and chr. 16 (LOD = 3.8), and with Shaft section modulus on chr. 22 (LOD = 4.0). LOD score ≥ 5.0 was obtained for femoral Neck Width on chr. 7.
In conclusion, with a SNP-based linkage approach, we identified several novel potential QTLs and confirmed previously identified chromosomal regions linked to bone mass and geometry. Subsequent focus on the spectrum of genetic polymorphisms in these refined regions may contribute to finding variants predisposing to osteoporosis.
doi:10.1016/j.bone.2010.01.001
PMCID: PMC2842472  PMID: 20064633
quantitative trait loci; BMD; bone geometry; osteoporosis; SNP array
22.  Leukocyte Telomere Length and Carotid Artery Intimal Medial Thickness: The Framingham Heart Study 
Background
Leukocyte telomere length (LTL) is relatively short in individuals who have evidence of cardiovascular disease.
Objective
To examine the link between LTL and the predisposition to atherosclerosis, as determined by carotid artery intimal medial thickness (IMT) in participants of the Framingham Offspring Study.
Methods
LTL was assayed by the mean length of the terminal restriction fragments and carotid artery IMT by B-mode ultrasonography in 1062 individuals (496 men, 566 women) aged 33–86 years,
Results
In the whole sample, there was a significant association of age-and sex-adjusted LTL with internal carotid artery IMT (ICA-IMT)(r= −0.07, p= 0.02). In sex-stratified analysis, this association remained significant for men (r= −0.11, p= 0.02) but not for women (r= −0.04, p= 0.36). After further adjustment for cigarette smoking and BMI, a borderline significant association persisted in men (p= 0.06). In secondary analysis, the age-adjusted LTL was significantly (and negatively) associated with ICA-IMT (r= −0.28, p 0.0006) in obese (BMI > 30kg/m2) men but not in non-obese (BMI ≤ 30 kg/m2) men. In addition, age-adjusted LTL was significantly shorter in men (6.89 ± 0.02 kb) than women (7.02 ± 0.02 kb) (p< 0.0001) and in current cigarette smokers (6.87±0.05 kb) than never smokers (6.99±0.03 kb) (p = 0.02). Although there was no significant association of LTL with common carotid artery-IMT or with carotid artery stenosis, there was a significant inverse association of LTL with common carotid artery IMT in obese men.
Conclusion
In obese men, shortened LTL is a powerful marker of increased carotid IMT. Given the public health impact of atherosclerosis and in particular the current epidemic of obesity, the associations noted in obese men warrant further confirmation.
doi:10.1161/ATVBAHA.107.154849
PMCID: PMC3042248  PMID: 18388332
Telomeres; atherosclerosis; leukocytes; obesity; sex; smoking
23.  Biological, Clinical, and Population Relevance of 95 Loci for Blood Lipids 
Teslovich, Tanya M. | Musunuru, Kiran | Smith, Albert V. | Edmondson, Andrew C. | Stylianou, Ioannis M. | Koseki, Masahiro | Pirruccello, James P. | Ripatti, Samuli | Chasman, Daniel I. | Willer, Cristen J. | Johansen, Christopher T. | Fouchier, Sigrid W. | Isaacs, Aaron | Peloso, Gina M. | Barbalic, Maja | Ricketts, Sally L. | Bis, Joshua C. | Aulchenko, Yurii S. | Thorleifsson, Gudmar | Feitosa, Mary F. | Chambers, John | Orho-Melander, Marju | Melander, Olle | Johnson, Toby | Li, Xiaohui | Guo, Xiuqing | Li, Mingyao | Cho, Yoon Shin | Go, Min Jin | Kim, Young Jin | Lee, Jong-Young | Park, Taesung | Kim, Kyunga | Sim, Xueling | Ong, Rick Twee-Hee | Croteau-Chonka, Damien C. | Lange, Leslie A. | Smith, Joshua D. | Song, Kijoung | Zhao, Jing Hua | Yuan, Xin | Luan, Jian'an | Lamina, Claudia | Ziegler, Andreas | Zhang, Weihua | Zee, Robert Y.L. | Wright, Alan F. | Witteman, Jacqueline C.M. | Wilson, James F. | Willemsen, Gonneke | Wichmann, H-Erich | Whitfield, John B. | Waterworth, Dawn M. | Wareham, Nicholas J. | Waeber, Gérard | Vollenweider, Peter | Voight, Benjamin F. | Vitart, Veronique | Uitterlinden, Andre G. | Uda, Manuela | Tuomilehto, Jaakko | Thompson, John R. | Tanaka, Toshiko | Surakka, Ida | Stringham, Heather M. | Spector, Tim D. | Soranzo, Nicole | Smit, Johannes H. | Sinisalo, Juha | Silander, Kaisa | Sijbrands, Eric J.G. | Scuteri, Angelo | Scott, James | Schlessinger, David | Sanna, Serena | Salomaa, Veikko | Saharinen, Juha | Sabatti, Chiara | Ruokonen, Aimo | Rudan, Igor | Rose, Lynda M. | Roberts, Robert | Rieder, Mark | Psaty, Bruce M. | Pramstaller, Peter P. | Pichler, Irene | Perola, Markus | Penninx, Brenda W.J.H. | Pedersen, Nancy L. | Pattaro, Cristian | Parker, Alex N. | Pare, Guillaume | Oostra, Ben A. | O'Donnell, Christopher J. | Nieminen, Markku S. | Nickerson, Deborah A. | Montgomery, Grant W. | Meitinger, Thomas | McPherson, Ruth | McCarthy, Mark I. | McArdle, Wendy | Masson, David | Martin, Nicholas G. | Marroni, Fabio | Mangino, Massimo | Magnusson, Patrik K.E. | Lucas, Gavin | Luben, Robert | Loos, Ruth J. F. | Lokki, Maisa | Lettre, Guillaume | Langenberg, Claudia | Launer, Lenore J. | Lakatta, Edward G. | Laaksonen, Reijo | Kyvik, Kirsten O. | Kronenberg, Florian | König, Inke R. | Khaw, Kay-Tee | Kaprio, Jaakko | Kaplan, Lee M. | Johansson, Åsa | Jarvelin, Marjo-Riitta | Janssens, A. Cecile J.W. | Ingelsson, Erik | Igl, Wilmar | Hovingh, G. Kees | Hottenga, Jouke-Jan | Hofman, Albert | Hicks, Andrew A. | Hengstenberg, Christian | Heid, Iris M. | Hayward, Caroline | Havulinna, Aki S. | Hastie, Nicholas D. | Harris, Tamara B. | Haritunians, Talin | Hall, Alistair S. | Gyllensten, Ulf | Guiducci, Candace | Groop, Leif C. | Gonzalez, Elena | Gieger, Christian | Freimer, Nelson B. | Ferrucci, Luigi | Erdmann, Jeanette | Elliott, Paul | Ejebe, Kenechi G. | Döring, Angela | Dominiczak, Anna F. | Demissie, Serkalem | Deloukas, Panagiotis | de Geus, Eco J.C. | de Faire, Ulf | Crawford, Gabriel | Collins, Francis S. | Chen, Yii-der I. | Caulfield, Mark J. | Campbell, Harry | Burtt, Noel P. | Bonnycastle, Lori L. | Boomsma, Dorret I. | Boekholdt, S. Matthijs | Bergman, Richard N. | Barroso, Inês | Bandinelli, Stefania | Ballantyne, Christie M. | Assimes, Themistocles L. | Quertermous, Thomas | Altshuler, David | Seielstad, Mark | Wong, Tien Y. | Tai, E-Shyong | Feranil, Alan B. | Kuzawa, Christopher W. | Adair, Linda S. | Taylor, Herman A. | Borecki, Ingrid B. | Gabriel, Stacey B. | Wilson, James G. | Stefansson, Kari | Thorsteinsdottir, Unnur | Gudnason, Vilmundur | Krauss, Ronald M. | Mohlke, Karen L. | Ordovas, Jose M. | Munroe, Patricia B. | Kooner, Jaspal S. | Tall, Alan R. | Hegele, Robert A. | Kastelein, John J.P. | Schadt, Eric E. | Rotter, Jerome I. | Boerwinkle, Eric | Strachan, David P. | Mooser, Vincent | Holm, Hilma | Reilly, Muredach P. | Samani, Nilesh J | Schunkert, Heribert | Cupples, L. Adrienne | Sandhu, Manjinder S. | Ridker, Paul M | Rader, Daniel J. | van Duijn, Cornelia M. | Peltonen, Leena | Abecasis, Gonçalo R. | Boehnke, Michael | Kathiresan, Sekar
Nature  2010;466(7307):707-713.
Serum concentrations of total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with serum lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 × 10-8), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (e.g., CYP7A1, NPC1L1, and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and impact lipid traits in three non-European populations (East Asians, South Asians, and African Americans). Our results identify several novel loci associated with serum lipids that are also associated with CAD. Finally, we validated three of the novel genes—GALNT2, PPP1R3B, and TTC39B—with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.
doi:10.1038/nature09270
PMCID: PMC3039276  PMID: 20686565
24.  The Validity of Self-Reported Rheumatoid Arthritis in a Large Cohort: Results from the Black Women's Health Study 
Arthritis care & research  2010;62(2):235-241.
Objective
To evaluate the positive predictive value (PPV) of three case definitions of rheumatoid arthritis (RA) based on self-reported data on RA diagnosis and use of arthritis medications and to determine if a validated screening survey would increase the PPVs in the three groups.
Methods
Medical records and physician-checklists were reviewed for confirmation of a RA diagnosis among a sample of Black Women's Health Study participants who reported incident RA and were categorized according to reported medications: disease-modifying anti-rheumatic drugs (DMARDs) (N=102), non-steroidal anti-inflammatory drugs (NSAIDs) (N=100), and no arthritis medications (No Meds) (N=101). PPVs for confirmed RA were calculated for each of the medication groups, overall and according to results of the screening survey.
Results
The PPV of confirmed RA was 76%, 61%, and 29% in the DMARDs group, NSAIDs group, and No Meds group, respectively. After exclusion of women who reported other rheumatic conditions or who reported taking only prednisone, the PPV increased in the DMARDs group to 88%, but little improvement was seen in the other groups. The PPVs increased somewhat according to results of the screening survey for the DMARDs group (positive: 92% vs. negative screen: 85%, p=1.00), and increased substantially for the NSAIDs group (89% vs. 38%, p=0.03), but only 43% of participants completed the survey.
Conclusion
We found that self-report of RA, along with DMARDs is a useful case definition for identifying confirmed RA. The validated screening survey could be useful for identifying cases of confirmed RA in some, but not all medication groups.
doi:10.1002/acr.20073
PMCID: PMC2832927  PMID: 20191523
25.  APOA2, Dietary Fat and Body Mass Index: Replication of a Gene-Diet Interaction in Three Independent Populations 
Archives of internal medicine  2009;169(20):1897-1906.
Background
Nutrigenetics studies the role of genetic variation on interactions between diet and health aimed at providing more personalized dietary advice. However, replication has been very low. Our aim was to study the interaction between a functional APOA2 polymorphism, food intake and body mass index (BMI) in independent populations to replicate findings and to increase their evidence level.
Methods
Cross-sectional, follow-up (20 years) and case-control analyses were undertaken in three independent populations. We analyzed gene-diet interactions between the APOA2 -265T>C polymorphism and saturated fat (SATFAT) intake on BMI and obesity in 3,462 subjects from three American populations: Framingham (1,454 Whites), GOLDN (1,078 Whites) and Boston-Puerto Rican studies (930 Hispanics of Caribbean origin).
Results
Prevalence of CC subjects ranged from 11-15%. We identified statistically significant interactions between the APOA2 -265T>C and SATFAT on BMI in all three populations. Thus, the magnitude of the difference in BMI between the CC and TT+TC subjects differed by SATFAT. A mean increase of 6.2% BMI (ranging from 4.3%-7.9%; P<0.05), was observed between genotypes with high (>=22g/d), but not with low SATFAT intake in all studies. Likewise, the CC genotype was significantly associated with higher obesity prevalence in all populations only in the high-SATFAT stratum. Meta-analysis estimations of obesity for CC compared with TT+TC subjects were: OR=1.84, 95%CI:1.38-2.47; P<0.0001 in the high-SATFAT stratum, but no association was detected in the low-SATFAT stratum (OR=0.81, 95%CI:0.59-1.11;P=0.181).
Conclusions
For the first time, a gene-diet interaction influencing BMI and obesity has been strongly and consistently replicated in three independent populations.
doi:10.1001/archinternmed.2009.343
PMCID: PMC2874956  PMID: 19901143

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