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John C Chambers,
Weihua Zhang,
Joban Sehmi,
Xinzhong Li,
Mark N Wass,
Pim Van der Harst,
Hilma Holm,
Serena Sanna,
Maryam Kavousi,
Sebastian E Baumeister, [......],
Caroline S Fox,
Mika Ala-Korpela,
Kari Stefansson,
Peter Vollenweider,
Henry Völzke,
Eric E Schadt,
James Scott,
Marjo-Riitta Järvelin,
Paul Elliott,
Jaspal S Kooner
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ABSTRACT: Concentrations of liver enzymes in plasma are widely used as indicators of liver disease. We carried out a genome-wide association study in 61,089 individuals, identifying 42 loci associated with concentrations of liver enzymes in plasma, of which 32 are new associations (P = 10(-8) to P = 10(-190)). We used functional genomic approaches including metabonomic profiling and gene expression analyses to identify probable candidate genes at these regions. We identified 69 candidate genes, including genes involved in biliary transport (ATP8B1 and ABCB11), glucose, carbohydrate and lipid metabolism (FADS1, FADS2, GCKR, JMJD1C, HNF1A, MLXIPL, PNPLA3, PPP1R3B, SLC2A2 and TRIB1), glycoprotein biosynthesis and cell surface glycobiology (ABO, ASGR1, FUT2, GPLD1 and ST3GAL4), inflammation and immunity (CD276, CDH6, GCKR, HNF1A, HPR, ITGA1, RORA and STAT4) and glutathione metabolism (GSTT1, GSTT2 and GGT), as well as several genes of uncertain or unknown function (including ABHD12, EFHD1, EFNA1, EPHA2, MICAL3 and ZNF827). Our results provide new insight into genetic mechanisms and pathways influencing markers of liver function.
Nature Genetics 11/2011; 43(11):1131-8. · 35.53 Impact Factor
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Xiong Cai,
Gustavo Pacheco-Rodriguez,
Qing-Yuan Fan,
Mary Haughey,
Leigh Samsel,
Souheil El-Chemaly,
Hai-Ping Wu,
J Philip McCoy,
Wendy K Steagall, Jing-Ping Lin,
Thomas N Darling,
Joel Moss
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ABSTRACT: Lymphangioleiomyomatosis (LAM), occurring sporadically (S-LAM) or in patients with tuberous sclerosis complex (TSC), results from abnormal proliferation of LAM cells exhibiting mutations or loss of heterozygosity (LOH) of the TSC genes, TSC1 or TSC2.
To identify molecular markers useful for isolating LAM cells from body fluids and determine the frequency of TSC1 or TSC2 LOH.
Candidate cell surface markers were identified using gene microarray analysis of human TSC2⁻(/)⁻ cells. Cells from bronchoalveolar lavage fluid (BALF), urine, chylous effusions, and blood were sorted based on reactivity with antibodies against these proteins (e.g., CD9, CD44v6) and analyzed for LOH using TSC1- and TSC2-related microsatellite markers and single nucleotide polymorphisms in the TSC2 gene.
CD44v6(+)CD9(+) cells from BALF, urine, and chyle showed TSC2 LOH in 80%, 69%, and 50% of patient samples, respectively. LAM cells with TSC2 LOH were detected in more than 90% of blood samples. LAM cells from different body fluids of the same patients showed, in most cases, identical LOH patterns, that is, loss of alleles at the same microsatellite loci. In a few patients with S-LAM, LAM cells from different body fluids differed in LOH patterns. No patients with S-LAM with TSC1 LOH were identified, suggesting that TSC2 abnormalities are responsible for the vast majority of S-LAM cases and that TSC1-disease may be subclinical.
Our data support a common genetic origin of LAM cells in most patients with S-LAM, consistent with a metastatic model. In some cases, however, there was evidence for genetic heterogeneity between LAM cells in different sites or within a site.
American Journal of Respiratory and Critical Care Medicine 12/2010; 182(11):1410-8. · 11.08 Impact Factor
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ABSTRACT: Serum bilirubin has been consistently shown to be inversely related to cardiovascular disease (CVD). Recent studies showed serum bilirubin to be associated with CVD-related factors such as diabetes, metabolic syndrome, and body mass index. Although the association of serum bilirubin with CVD has been found in both retrospective and prospective studies, less information is available on the role of genes that control bilirubin concentrations and their association with CVD.
In this review, we provide detailed information on the identity of the major genes that control bilirubin concentrations and their association with serum bilirubin concentrations and CVD risk. We also update the results of the major studies that have been performed on the association between serum bilirubin, CVD, and CVD-related diseases such as diabetes or metabolic syndrome. Studies consistently indicate that bilirubin concentrations are inversely associated with different types of CVD and CVD-related diseases. A conditional linkage study indicates that UGT1A1 is the major gene controlling serum bilirubin concentrations, and this finding has been confirmed in recent genomewide association studies. Studies also indicate that individuals homozygous for UGT1A1*28 have a significantly lower risk of developing CVD than carriers of the wild-type alleles.
Serum bilirubin has a protective effect on CVD and CVD-related diseases, and UGT1A1 is the major gene controlling serum bilirubin concentrations. Pharmacologic, nonpharmacologic, or genetic interventions that increase serum bilirubin concentrations could provide more direct evidence on the role of bilirubin in CVD prevention.
Clinical Chemistry 10/2010; 56(10):1535-43. · 7.91 Impact Factor
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ABSTRACT: Serum lactate dehydrogenase (LDH) is used in diagnosing many diseases and is significantly determined by genetic factors. Three genes coding for LDH isoenzymes were mapped to chromosome 11q15 and 12p12. We used 330 Framingham Heart Study largest families for microsatellite linkage scan and 100K SNPs association scan to determine quantitative trait loci of LDH level. We estimated the heritability at 41%. Our genome-wide linkage analysis yielded several chromosomal regions, other than 11q and 12p, with LOD scores between 1 and 2.5. None of the 100K SNPs with a P-value <10(-4) in our genome-wide association study was close to the chromosomal regions where the LDH genes reside. Our study demonstrated a strong genetic effect on the variation of LDH levels. There may not be a single gene with a large effect, instead may be several genes with small effects in controlling the variation of serum LDH. Those genes may be located on chromosomal regions that differ from where the genes encoding LDH isoenzymes reside.
Human Genomics and Proteomics 01/2010; 2010:905237.
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Santhi K Ganesh,
Neil A Zakai,
Frank J A van Rooij,
Nicole Soranzo,
Albert V Smith,
Michael A Nalls,
Ming-Huei Chen,
Anna Kottgen,
Nicole L Glazer,
Abbas Dehghan, [......],
Bruce M Psaty,
Luigi Ferrucci,
Aravinda Chakravarti,
Andreas Greinacher,
Christopher J O'Donnell,
Jacqueline C M Witteman,
Susan Furth,
Mary Cushman,
Tamara B Harris, Jing-Ping Lin
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ABSTRACT: Measurements of erythrocytes within the blood are important clinical traits and can indicate various hematological disorders. We report here genome-wide association studies (GWAS) for six erythrocyte traits, including hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC) and red blood cell count (RBC). We performed an initial GWAS in cohorts of the CHARGE Consortium totaling 24,167 individuals of European ancestry and replication in additional independent cohorts of the HaemGen Consortium totaling 9,456 individuals. We identified 23 loci significantly associated with these traits in a meta-analysis of the discovery and replication cohorts (combined P values ranging from 5 x 10(-8) to 7 x 10(-86)). Our findings include loci previously associated with these traits (HBS1L-MYB, HFE, TMPRSS6, TFR2, SPTA1) as well as new associations (EPO, TFRC, SH2B3 and 15 other loci). This study has identified new determinants of erythrocyte traits, offering insight into common variants underlying variation in erythrocyte measures.
Nature Genetics 11/2009; 41(11):1191-8. · 35.53 Impact Factor
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Andrew D Johnson,
Maryam Kavousi,
Albert V Smith,
Ming-Huei Chen,
Abbas Dehghan,
Thor Aspelund, Jing-Ping Lin,
Cornelia M van Duijn,
Tamara B Harris,
L Adrienne Cupples,
Andre G Uitterlinden,
Lenore Launer,
Albert Hofman,
Fernando Rivadeneira,
Bruno Stricker,
Qiong Yang,
Christopher J O'Donnell,
Vilmundur Gudnason,
Jacqueline C Witteman
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ABSTRACT: Variation in serum bilirubin is associated with altered cardiovascular disease risk and drug metabolism. We aimed to identify genetic contributors to variability in serum bilirubin levels by combining results from three genome-wide association studies (Framingham heart study, n = 3424; Rotterdam study, n = 3847; Age, Gene, Environment and Susceptibility-Reykjavik, n = 2193). Meta-analysis showed strong replication for a genetic influence on serum bilirubin levels of the UGT1A1 locus (P < 5 x 10(-324)) and a 12p12.2 locus. The peak signal in the 12p12.2 region was a non-synonymous SNP in SLCO1B1 (rs4149056, P = 6.7 x 10(-13)), which gives rise to a valine to alanine amino acid change leading to reduced activity for a hepatic transporter with known affinity for bilirubin. There were also suggestive associations with several other loci. The top variants in UGT1A1 and SLCO1B1 explain approximately 18.0 and approximately 1.0% of the variation in total serum bilirubin levels, respectively. In a conditional analysis adjusted for individual genotypes for the top UGT1A1 variant, the top SLCO1B1 variant remained highly significant (P = 7.3 x 10(-13)), but no other variants achieved genome-wide significance. In one of the largest genetic studies of bilirubin to date (n = 9464), we confirm the substantial genetic influence of UGT1A1 variants, consistent with past linkage and association studies, and additionally provide strong evidence of a role for allelic variation in SLCO1B1. Given the involvement of bilirubin in a number of physiological and disease processes, and the roles for UGT1A1 and SLCO1B1 in drug metabolism, these genetic findings have potential clinical importance. In analyses for association with gallbladder disease or gallstones, top bilirubin SNPs in UGT1A1 and SLCO1B1 were not associated.
Human Molecular Genetics 05/2009; 18(14):2700-10. · 7.64 Impact Factor
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ABSTRACT: Lymphangioleiomyomatosis (LAM) is a rare multisystem disorder affecting primarily women of child-bearing age, and characterized by cystic lung destruction, tumors of the kidney (angiomyolipomas [AMLs]), and involvement of the axial lymphatics (lymphangioleiomyomas). Patients with LAM experience loss of pulmonary function attributed to the proliferation of abnormal-appearing smooth muscle-like cells (LAM cells). It is possible to group the LAM population by the presence or absence of extrapulmonary involvement (eg, AMLs, lymphangioleiomyomas, chylous effusions). Serum vascular endothelial growth factor (VEGF)-D, a lymphangiogenic factor, is higher in LAM patients than in healthy volunteers and has been proposed as a tool in the differential diagnosis of cystic lung disease. We assessed serum VEGF-D concentrations in relationship to clinical phenotype in LAM patients.
Serum VEGF-D levels were quantified by enzyme immunosorbent assay for 111 patients with LAM and 40 healthy volunteers. VEGF-D levels in patients with pulmonary LAM, with or without extrapulmonary manifestations, were compared to those of healthy volunteers.
Serum VEGF-D levels were greater in patients with LAM compared to those of healthy volunteers (p < 0.001). However, when patient samples were grouped based on the extent of lymphatic extrapulmonary involvement (eg, lymphangioleiomyomas and adenopathy), the statistical difference was maintained only for patients with LAM with lymphatic involvement (p < 0.001), not for those patients whose disease was restricted to the lung. Serum VEGF-D levels are a good biomarker for lymphatic involvement (area under the curve [AUC], 0.845; p < 0.0001), and a fair predictor for LAM disease (AUC, 0.751; p < 0.0001). Serum levels correlated to CT scan grade (p = 0.033).
Serum VEGF-D concentration is a measure of lymphatic involvement in patients with LAM.
Chest 05/2009; 135(5):1293-300. · 5.25 Impact Factor
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ABSTRACT: Low bilirubin levels are significantly associated with cardiovascular diseases (CVD). In previous genome-wide linkage studies we identified a major locus on chromosome 2q harboring the candidate gene UDP-glucuronosyltransferase (UGT1A1). The activity of this enzyme is significantly influenced by a TA-repeat polymorphism in the promoter of the gene. In a prospective study individuals with genotype (TA)7/(TA)7 had significantly higher bilirubin levels and approximately one-third the risk of CVD as carriers of the wildtype (TA)6 allele. In the present study we performed a conditional linkage study to investigate whether this polymorphism explains the observed linkage peak and extended our analysis by a genome-wide association study on bilirubin levels in 1345 individuals.
After adjustment for the bilirubin variance explained by this polymorphism, the LOD score on chromosome 2q dropped from 3.8 to 0.4, demonstrating that this polymorphism explains the previous linkage result. For the genome-wide association study, the closest marker to UGT1A1 was in the top ranking SNPs. The association became even stronger when we considered the TA-repeat polymorphism in the analysis (p=2.68 x 10(-53)). Five other SNPs in other regions reached genome-wide significance without obvious connection to bilirubin metabolism.
Our studies suggest that UGT1A1 may be the major gene with strong effects on bilirubin levels and the TA-repeat polymorphism might be the key polymorphism within the gene controlling bilirubin levels. Since this polymorphism has a high frequency and a substantial impact on the development of CVD, the gene might be an important drug target.
Atherosclerosis 04/2009; 206(1):228-33. · 3.79 Impact Factor
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ABSTRACT: Lymphangioleiomyomatosis (LAM) is characterized by cystic lung destruction caused by LAM cells (smooth-muscle-like cells) that have mutations in the tumor suppressor genes tuberous sclerosis complex (TSC) 1 or 2 and have the capacity to metastasize. Since chemokines and their receptors function in chemotaxis of metastatic cells, we hypothesized that LAM cells may be recruited by chemokine(s) in the lung. Quantification of 25 chemokines in bronchoalveolar lavage fluid from LAM patients and healthy volunteers revealed that concentrations of CCL2, CXCL1, and CXCL5 were significantly higher in samples from LAM patients than those from healthy volunteers. In vitro, CCL2 or MCP-1 induced selective migration of cells, showing loss of heterozygosity of TSC2 from a heterogeneous population of cells grown from explanted LAM lungs. Additionally, the frequencies of single-nucleotide polymorphisms in the CCL2 gene promoter region differed significantly in LAM patients and healthy volunteers (p = 0.018), and one polymorphism was associated significantly more frequently with the decline of lung function. The presence (i.e., potential functionality) of chemokine receptors was evaluated using immunohistochemistry in lung sections from 30 LAM patients. Expression of chemokines and these receptors varied among LAM patients and differed from that seen in some cancers (e.g., breast cancer and melanoma cells). These observations are consistent with the notion that chemokines such as CCL2 may serve to determine mobility and specify the site of metastasis of the LAM cell.
The Journal of Immunology 03/2009; 182(3):1270-7. · 5.79 Impact Factor
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Liver international: official journal of the International Association for the Study of the Liver 02/2009; 29(5):776-7. · 3.82 Impact Factor
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ABSTRACT: In a genome-wide association study with more than 100, 000 (100K) to 1 million single nucleotide polymor-phisms (SNPs), the first step is usually a genome-wide scan to identify candidate chromosome regions for further anal-yses. The goal of the genome-wide scan is to rank all the SNPs based on their association tests or p-values and select the top SNPs. A good ranking procedure ranks the SNPs with true associations as near to the top as possible. This enhances the probability of selecting at least one SNP with a true association. However, if the disease-associated SNPs have moderate genetic effects, the probability that a large number of null SNPs will have extremely small p-values (or large test statistics) is high when screening more than 300K SNPs. Therefore, when selecting a small fraction of top SNPs (usually less than 5%), the probability of select-ing at least one SNP with a true association is usually less than 80% unless the sample size is large. Robust statistics have been proposed to rank all the SNPs (e.g., MAX3 and MIN2). In this article we consider genome-wide scans with a genetic model selection and compare this proposed method to the existing approaches. Results from simulation studies are presented.
Statistics and Its Interface Volume. 01/2009; 2:145-151.
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Liver International - LIVER INT. 01/2009; 29(5):776-777.
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ABSTRACT: Lymphangioleiomyomatosis, a multisystem disease affecting women, is characterized by proliferation of abnormal smooth muscle-like cells in the lungs, leading to cystic destruction of the parenchyma and recurrent pneumothoraces. Clinical characteristics of lymphangioleiomyomatosis patients were analyzed to determine the relationship of pneumothoraces to disease progression. Patients were genotyped for polymorphisms in genes of extracellular matrix proteins collagen, elastin, and matrix metalloproteinase-1 to assess their association with pneumothoraces. Clinical data and polymorphisms in the genes for types I and III collagen, elastin, and matrix metalloproteinase-1 were compared with the prevalence of pneumothorax. Of 227 patients, 57% reported having had at least one pneumothorax. Cyst size on high-resolution computed tomography scans was associated with pneumothorax; patients with a history of pneumothorax were more likely to have larger cysts than patients who had no pneumothoraces. In patients with mild disease, those with a history of pneumothorax had a faster rate of decline in forced expiratory volume in 1 s (FEV(1); P = 0.001, adjusted for age) than those without. Genotype frequencies differed between patients with and without pneumothorax for polymorphisms in the types I and III collagen and matrix metalloproteinase-1 genes. Larger cysts may predispose lymphangioleiomyomatosis patients to pneumothorax, which, in early stages of disease, correlates with a more rapid rate of decline in FEV(1). Polymorphisms in types I and III collagen and matrix metalloproteinase-1 genes may cause differences in lung extracellular matrix that result in greater susceptibility to pneumothorax.
AJP Lung Cellular and Molecular Physiology 10/2007; 293(3):L800-8. · 3.66 Impact Factor
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ABSTRACT: Red blood cell (RBC) count and size are major criteria for evaluating anemia and related hematology disease diagnoses. While environmental factors influence RBC count (RBCC) and size, mean corpuscular volume (MCV), and mean corpuscular hemoglobin (MCH), studies have indicated that each of these measures has a substantial genetic component. So far, no linkage analysis or genome scan has been reported. We carried out 10 cM genome-wide scans on RBCC, MCV, and MCH in a community-based Caucasian cohort, the Framingham Heart Study, using 325 pedigrees with 1,144 individuals genotyped and phenotyped. Using variance-component linkage methods, heritabilities were estimated as 56, 52, and 52% after covariate adjusted for RBCC, MCV, and MCH, respectively. For RBCC, we found a maximum LOD score of 3.2 on chromosome 19, 24 cM (7.0 Mbp). Near this region, there lie a few important candidate genes, including erythropoietin receptor and erythroid Krüppel-like factor. For linkage analyses for MCV and MCH, there were coinciding maximized LOD scores on chromosome 11, 9 cM (5.2 Mbp) with values of 3.8 and 3.6, respectively. Under the peak resides the hemoglobin beta cluster - several beta-like genes, which are important candidates for RBC size. In subsequent analyses, we excluded individuals with low MCV to assess the possible influence of beta-thalassemia carriers, and there continued to be evidence for linkage in the same region on chromosome 11p15 (LOD scores of 2.6 and 2.7 for MCV and MCH, respectively). For MCV, we also identified a new region on chromosome 6q24 with a LOD score of 2.9. These findings suggest that further studies are warranted to identify potential causal genetic variants for RBC size and count and related erythrocyte indices.
American Journal of Hematology 08/2007; 82(7):605-10. · 4.67 Impact Factor
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ABSTRACT: Cystic fibrosis (CF), an autosomal recessive disease affecting the lung, pancreas, gut, liver, and reproductive tract, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a cyclic adenosine 3', 5' monophosphate-regulated chloride channel. The variability of disease progression among patients with CF suggests effects of genetic modifiers of disease. Beta-2 adrenergic receptors (beta2AR), which are abundant in airway epithelial cells, accelerate the formation of cyclic adenosine 3', 5' monophosphate, which can modulate CFTR activity and affect smooth muscle contractility. We tested the hypothesis that genetic variants of the beta2AR gene, which have been shown to influence receptor desensitization, are more frequent in patients than in controls.
We genotyped 130 adult CF patients and 1 : 1 age-matched, sex-matched, and ethnicity-matched normal volunteers for GlyArg and GlnGlu beta2AR.
We found that CF patients were more likely than controls to be Gly homozygotes (48 and 32%, respectively) (P<0.01) and Glu homozygotes (29 and 10%, respectively) (P<0.01).
Our results, showing a higher frequency of Gly and Glu beta2AR alleles in adult CF patients than in the control population, contrast with data from children with CF, who are reported to have lower frequency of Gly and similar frequency of G1u, and with data from young adults with CF, who showed no differences in frequencies of beta2AR variants. The GlyGlu variant of beta2AR may have properties that lead to enhanced beta2AR function, resulting in the upregulation of CFTR activity and the improvement of CF disease.
Pharmacogenetics and Genomics 06/2007; 17(6):425-30. · 3.48 Impact Factor
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ABSTRACT: Surfactant protein B (SP-B) is an essential component of surfactant that promotes adsorption and spreading of surfactant phospholipids and stabilizes the phospholipid monolayer. SP-B is essential for respiratory function in newborn humans and mice; adult mice with levels of SP-B below 25% of wild-type develop fatal respiratory distress syndrome. A potential regulatory function of the C/A(-18) single nucleotide polymorphism (SNP) in the promoter of the SP-B gene was examined. Transcriptional analysis and ELISA on bronchoalveolar lavage fluid revealed that the presence of the C allele correlated with more SP-B promoter activity and protein. There was approximately threefold difference in amounts of SP-B in bronchoalveolar lavage fluid from CA(-18) and AA(-18) individuals. By EMSA, Sp1 bound more tightly to the C allele sequence than to the A allele sequence, perhaps accounting for the differences in transcription. Genotyping of a normal volunteer population showed approximately 31% of the population were AA homozygotes, suggesting that these individuals produce less SP-B. Differences in amounts of SP-B resulting from the promoter SNP could affect the clinical presentation of pulmonary disease.
AJP Lung Cellular and Molecular Physiology 03/2007; 292(2):L448-53. · 3.66 Impact Factor
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ABSTRACT: The goal of this analysis is to compare different test strategies for genetic association in case-control studies using related individuals. The first test is the trend test that is corrected for related individuals on the basis of identity-by-descent information. The second approach is to use generalized estimating equations to adjust for the correlation between relatives, and the third is the multiple outputation method. We compare the power of these test strategies in a simulation study, and apply these methods to a candidate gene dataset of Genetic Analysis Workshop 15 from the North American Rheumatoid Arthritis Consortium.
BMC proceedings 02/2007; 1 Suppl 1:S31.
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ABSTRACT: In whole-genome association studies, at the first stage, all markers are tested for association and their test statistics or p-values are ranked. At the second stage, some most significant markers are further analyzed by more powerful statistical methods. This helps reduce the number of hypotheses to be corrected for in multiple testing. Ranks of true associations in genome-wide scans using a single test statistic have been studied. In a case-control design for association, the trend test has been proposed. However, three different trend tests, optimal for the recessive, additive, and dominant models, respectively, are available for each marker. Because the true genetic model is unknown, we rank markers based on multiple test statistics or test statistics robust to model mis-specification. We studied this problem with application to Problem 3 of Genetic Analysis Workshop 15. An independent simulation study was also conducted to further evaluate the proposed procedure.
BMC proceedings 02/2007; 1 Suppl 1:S165.
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ABSTRACT: We present a new method for testing association when data from both case-parents trios and unrelated controls are available. Our method combines test statistics for case-parents trio and unrelated case-control studies by adjusting for the correlation that arises when the same set of cases is used for both tests. We further consider several analytical approaches for two-stage studies on a large number of markers, including methods based on the joint analysis. The performance of the proposed approaches is examined by analyzing the simulated data provided by the Genetic Analysis Workshop 15.
BMC proceedings 02/2007; 1 Suppl 1:S28.
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Emelia J Benjamin,
Josée Dupuis,
Martin G Larson,
Kathryn L Lunetta,
Sarah L Booth,
Diddahally R Govindaraju,
Sekar Kathiresan,
John F Keaney,
Michelle J Keyes, Jing-Ping Lin,
James B Meigs,
Sander J Robins,
Jian Rong,
Renate Schnabel,
Joseph A Vita,
Thomas J Wang,
Peter W F Wilson,
Philip A Wolf,
Ramachandran S Vasan
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ABSTRACT: Systemic biomarkers provide insights into disease pathogenesis, diagnosis, and risk stratification. Many systemic biomarker concentrations are heritable phenotypes. Genome-wide association studies (GWAS) provide mechanisms to investigate the genetic contributions to biomarker variability unconstrained by current knowledge of physiological relations.
We examined the association of Affymetrix 100K GeneChip single nucleotide polymorphisms (SNPs) to 22 systemic biomarker concentrations in 4 biological domains: inflammation/oxidative stress; natriuretic peptides; liver function; and vitamins. Related members of the Framingham Offspring cohort (n = 1012; mean age 59 +/- 10 years, 51% women) had both phenotype and genotype data (minimum-maximum per phenotype n = 507-1008). We used Generalized Estimating Equations (GEE), Family Based Association Tests (FBAT) and variance components linkage to relate SNPs to multivariable-adjusted biomarker residuals. Autosomal SNPs (n = 70,987) meeting the following criteria were studied: minor allele frequency > or = 10%, call rate > or = 80% and Hardy-Weinberg equilibrium p > or = 0.001.
With GEE, 58 SNPs had p < 10(-6): the top SNPs were rs2494250 (p = 1.00*10(-14)) and rs4128725 (p = 3.68*10(-12)) for monocyte chemoattractant protein-1 (MCP1), and rs2794520 (p = 2.83*10(-8)) and rs2808629 (p = 3.19*10(-8)) for C-reactive protein (CRP) averaged from 3 examinations (over about 20 years). With FBAT, 11 SNPs had p < 10(-6): the top SNPs were the same for MCP1 (rs4128725, p = 3.28*10(-8), and rs2494250, p = 3.55*10(-8)), and also included B-type natriuretic peptide (rs437021, p = 1.01*10(-6)) and Vitamin K percent undercarboxylated osteocalcin (rs2052028, p = 1.07*10(-6)). The peak LOD (logarithm of the odds) scores were for MCP1 (4.38, chromosome 1) and CRP (3.28, chromosome 1; previously described) concentrations; of note the 1.5 support interval included the MCP1 and CRP SNPs reported above (GEE model). Previous candidate SNP associations with circulating CRP concentrations were replicated at p < 0.05; the SNPs rs2794520 and rs2808629 are in linkage disequilibrium with previously reported SNPs. GEE, FBAT and linkage results are posted at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.
The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
BMC Medical Genetics 02/2007; 8 Suppl 1:S11. · 2.33 Impact Factor
