Literature DB >> 29527544

Data on genetic associations of carotid atherosclerosis markers in Mexican American and European American rheumatoid arthritis subjects.

Rector Arya1,2, Agustin Escalante3, Vidya S Farook1,2, Jose F Restrepo3, Daniel F Battafarano4, Marcio Almeida1,2, Mark Z Kos1,2, Marcel J Fourcaudot5, Srinivas Mummidi1,2, Satish Kumar1,2, Joanne E Curran1,2, Christopher P Jenkinson1,2, John Blangero1,2, Ravindranath Duggirala1,2, Inmaculada Del Rincon3.   

Abstract

Carotid Intima-media thickness (CIMT) and plaque are well established markers of subclinical atherosclerosis and are widely used for identifying subclinical atherosclerotic disease. We performed association analyses using Metabochip array to identify genetic variants that influence variation in CIMT and plaque, measured using B-mode ultrasonography, in rheumatoid arthritis (RA) patients. Data on genetic associations of common variants associated with both CIMT and plaque in RA subjects involving Mexican Americans (MA) and European Americans (EA) populations are presented in this article. Strong associations were observed after adjusting for covariate effects including baseline clinical characteristics and statin use. Susceptibility loci and genes and/or nearest genes associated with CIMT in MAs and EAs with RA are presented. In addition, common susceptibility loci influencing CIMT and plaque in both MAs and EAs have been presented. Polygenic Risk Score (PRS) plots showing complementary evidence for the observed CIMT and plaque association signals are also shown in this article. For further interpretation and details, please see the research article titled "A Genetic Association Study of Carotid Intima-Media Thickness (CIMT) and Plaque in Mexican Americans and European Americans with Rheumatoid Arthritis" which is being published in Atherosclerosis (Arya et al., 2018) [1].(Arya et al., in press) Thus, common variants in several genes exhibited significant associations with CIMT and plaque in both MAs and EAs as presented in this article. These findings may help understand the genetic architecture of subclinical atherosclerosis in RA populations.

Entities:  

Year:  2018        PMID: 29527544      PMCID: PMC5842364          DOI: 10.1016/j.dib.2018.02.006

Source DB:  PubMed          Journal:  Data Brief        ISSN: 2352-3409


Specifications table Value of the data. Genetic association data for CIMT and plaque in subjects with rheumatoid arthritis are valuable to understand the genetic architecture of the carotid atherosclerosis markers in RA patients. Observed association signals for carotid atherosclerosis markers in both Mexican American and European American cohorts would give more insight into population differences as well as trait-specific and common genetic determinants. This data could also be potentially used for replication of genetic association findings for atherosclerosis markers in other populations.

Data

A comprehensive association results of the transformed CIMT after adjustment for covariate effects in MAs and EAs are shown in Table 1, Table 2, respectively. As presented in Arya et al. [1], a total of 24 SNPs from 11 chromosomes exhibited association with CIMT in MAs at p < 1 × 10−4, and the p values ranged from 9.95 × 10−5 to 3.80 × 10−6, while 12 SNPs from 7 chromosomes were associated with CIMT in EAs and the p values ranged from 9.45 × 10−5 to 5.11 × 10−6. The best associated SNPs are different in both populations.
Table 1

Susceptibility loci associated with carotid IMT in Mexican Americans.

Chr.SNPPosition, bpaGene/nearest geneLoc.A1bMAFBETASEPc
6rs1752672226,026,834SLC17A2IA0.10−0.83770.17973.80E-06
6rs3601412925,992,498SLC17A3 | SLC17A2IGA0.10−0.850.1844.63E-06
6rs1321253426,090,989TRIM38IA0.10−0.86070.18916.36E-06
6rs1321395725,894,205SLC17A1IC0.10−0.78060.17621.10E-05
6rs5591263025,974,914SLC17A3IC0.10−0.78060.17621.10E-05
6rs1319129625,792,585SCGNIT0.08−0.77710.1761.19E-05
2rs4894108180,112,792ZNF385BIG0.19−0.25010.057511.59E-05
6rs1321194725,972,797SLC17A3IT0.10−0.81790.1891.75E-05
6rs4126677926,129,851HIST1H3A | HIST1H4AIGT0.10−0.81780.18911.78E-05
17rs267290176,411,261KIAA1303IA0.32−0.19290.044892.00E-05
13rs11619113109,716,661COL4A1IG0.20−0.39180.091652.21E-05
13rs12873154109,718,853COL4A1IG0.20−0.39180.091652.21E-05
13rs11619038109,721,800COL4A1IT0.20−0.39180.091652.21E-05
6rs1320268826,101,448TRIM38 | HIST1H1AIGG0.10−0.75050.17622.37E-05
10rs6185052663,190,012C10orf107IT0.02−0.46240.11264.56E-05
6rs3404343125,983,063SLC17A3 | SLC17A2IGC0.10−0.70120.1735.68E-05
11rs7659970061,401,283FADS3IT0.26−0.73170.18146.17E-05
16rs1186052982,330,023CDH13IT0.080.41120.10287.06E-05
1rs17436982219,622,889HLX | DUSP10IGT0.220.28270.071738.98E-05
5rs25021650,317,115PARP8| LOC642366IGC0.070.23220.058999.20E-05
7rs1176146727,828,130TAX1BP1IT0.10−0.32440.082569.44E-05
13rs11620140109,730,512COL4A1IC0.11−0.36960.094179.62E-05
6rs1196601812,317,214HIVEP1 | EDN1IGC0.030.6910.17639.82E-05
15rs717707497,357,475LOC145814IA0.05−0.51380.13129.95E-05

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).

A1 = minor allele.

p values ranked from low to high.

Table 2

Susceptibility loci associated with carotid IMT in European Americans.

Chr.SNPPosition, bpaGene/nearest geneLoc.A1bMAFBETASEPc
15rs186714873,127,038PPCDCIC0.44−0.28040.060645.11E-06
15rs716363673,133,813PPCDC / C15orf39IGC0.48−0.27480.060537.51E-06
13rs323453104,232,379LOC728183 | DAOAIGG0.34−0.27240.063462.23E-05
15rs381294573,076,775SCAMPSIG0.450.26260.063462.23E-05
1rs4846566217,797,888LOC728510 | ZC3H11BIGT0.01−1.1860.27772.46E-05
2rs1298704238,518,674ARL6IP2|RPLPO-likeIGA0.36−0.26080.06193.13E-05
1rs17006057217,790,022LOC728510/ZC3H11BIGA0.01−1.2250.29153.29E-05
15rs649512272,912,698CPLX3 | ULK3IGA0.42−0.25250.061494.90E-05
1rs26450912,214,505SKIIT0.15−0.35110.087417.07E-05
16rs1782153252,504,199FTOIA0.05−0.70060.17517.58E-05
6rs7742814119,185,974C6orf204|ASF1AIGG0.360.25550.064629.09E-05
11rs43873805,824,023OR52E6|OR52E8IGC0.03−0.82260.20859.45E-05

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).

A1 = minor allele.

p values ranked from low to high.

Susceptibility loci associated with carotid IMT in Mexican Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36 (hg18). A1 = minor allele. p values ranked from low to high. Susceptibility loci associated with carotid IMT in European Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36 (hg18). A1 = minor allele. p values ranked from low to high. Top SNPs that are associated with CIMT and plaque were different in significance levels but exhibited associations with either phenotype at nominal significance levels (p < 0.05) as shown in Table 3, Table 4, Table 5, Table 6. It is well known that some variants exhibit unique associations with a given phenotype (CIMT or plaque) while other variants exhibit common associations with both phenotypes (CIMT and plaque). Despite the correlation between CIMT and plaque, different trait-specific genetic determinants can be expected due to their differing pathobiology and associated phenotypic severity of plaque as shown by our earlier study as well as other studies [2], [3]. In addition, genetic differences are expected between the populations of European background and admixed populations such as the Mexican Americans that have both European and Native American ancestries. Furthermore, results from previous studies also support our findings [4], [5].
Table 3

Common susceptibility loci associated with carotid IMT and plaque in Mexican Americans.

Chr.SNPPosition, bpaGene/nearest geneLoc.A1bMAFBETASEPcCIMTPcPlaque
6rs1752672226,026,834SLC17A2IA0.10−0.83770.17973.80E-060.04112
2rs4894108180,112,792ZNF385BIG0.19−0.25010.057511.59E-050.00823
17rs267290176,411,261KIAA1303IA0.32−0.19290.044892.00E-050.01672
13rs12873154109,718,853COL4A1IG0.20−0.39180.091652.21E-050.04923
10rs6185052663,190,012C10orf107IT0.02−0.46240.11264.56E-050.001367
11rs7659970061,401,283FADS3IT0.26−0.73170.18146.17E-050.08027
16rs1186052982,330,023CDH13IT0.080.41120.10287.06E-050.02431
1rs17436982219,622,889HLX | DUSP10IGT0.220.28270.071738.98E-050.006092
5rs25021650,317,115PARP8 | LOC642366IGC0.070.23220.058999.20E-050.0262
7rs1176146727,828,130TAX1BP1IT0.10−0.32440.082569.44E-050.01331
6rs1196601812,317,214HIVEP1 | EDN1IGC0.030.6910.17639.82E-050.009176
15rs717707497,357,475LOC145814IA0.05−0.51380.13129.95E-050.001647

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36/130 (hg18).

A1 = minor allele.

p values ranked from low to high.

Table 4

Common susceptibility loci associated with plaque and CIMT in Mexican Americans.

Chr.SNPPosition, bpaGene/nearest geneLocA1bMAFORSEPcPlaquePcCIMT
13rs496916109,649,015COL4A1IC0.410.5140.14283.15E-060.03256
15rs980675346,953,709SHC4 | EID1IGA0.261.7390.12296.71E-060.1274
6rs946311012,890,588PHACTR1IG0.441.6990.12221.45E-050.02229
22rs209217938,364,539CACNA1IIC0.250.58830.12893.85E-050.02903
9rs786950698,127,033SLC35D2IT0.261.6880.12965.41E-050.005388
1rs666786036,730,800CSF3R|GRIK3IGC0.481.6580.12989.76E-050.0002729

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio.

A1 = minor allele.

p values ranked from low to high.

Table 5

Common susceptibility loci associated with CIMT and plaque in European Americans.

Chr.SNPPosition, bpaGene/Nearest GeneLoc.A1bMAFBETASEPcCIMTPcplaque
15rs186714873,127,038PPCDCIC0.44−0.28040.060645.11E-060.01242
13rs323453104,232,379LOC728183 | DAOAIGG0.34−0.27240.063462.23E-050.2049
1rs4846566217,797,888LOC728510 | ZC3H11BIGT0.01−1.1860.27772.46E-050.0676
2rs1298704238,518,674ARL6IP2|RPLPO-likeIGA0.36−0.26080.06193.13E-050.0005153
15rs649512272,912,698CPLX3 | ULK3IGA0.42−0.25250.061494.90E-050.005717
1rs26450912,214,505SKIIT0.15−0.35110.087417.07E-050.03331
16rs1782153252,504,199FTOIA0.05−0.70060.17517.58E-050.03347
6rs7742814119,185,974C6orf204|ASF1AIGG0.360.25550.064629.09E-050.3764
11rs43873805,824,023OR52E6|OR52E8IGC0.03−0.82260.20859.45E-050.06833

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36 (hg18).

A1 = minor allele.

p values ranked from low to high.

Table 6

Common susceptibility loci associated with carotid plaque and CIMT in European Americans.

Chr.SNPPosition, bpaGeneLoc.A1bMAFORSEPcPlaquePcCIMT
12rs51529138,689,259SLC2A13IG0.320.49870.1673.09E-050.0007138
11rs1050139968,979,039MYEOV|CCND1IGT0.090.29380.29523.34E-050.001367
15rs69239039,274,282EXDL1IA0.190.41380.21574.30E-050.0001269
5rs6887230148,706,339GRPEL2IG0.302.020.17465.61E-050.009851
17rs207077659,361,230CD79BC (ns)T0.330.50330.17226.68E-050.02914
16rs37852337,607,511A2BP1IC0.160.4190.22299.49E-050.0001409
6rs1094857350,800,310TFAP2DIG0.372.0440.18349.68E-050.2071

Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency.

Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio.

A1 = minor allele.

p values ranked from low to high.

Common susceptibility loci associated with carotid IMT and plaque in Mexican Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36/130 (hg18). A1 = minor allele. p values ranked from low to high. Common susceptibility loci associated with plaque and CIMT in Mexican Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio. A1 = minor allele. p values ranked from low to high. Common susceptibility loci associated with CIMT and plaque in European Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36 (hg18). A1 = minor allele. p values ranked from low to high. Common susceptibility loci associated with carotid plaque and CIMT in European Americans. Chr. = chromosome; SNP = single nucleotide polymorphism; Loc = Location; I = Intron; IG = Intergenic; MAF = minor allele frequency. Based on National Center for Biotechnology Information (NCBI) Build36 (hg18); OR = Odds Ratio. A1 = minor allele. p values ranked from low to high. As shown in Fig. 1, Quantile-Quantile (Q-Q) plots of the transformed CIMT and plaque in both MAs and EAs have been generated using EPACTS. Q-Q plots exhibited a roughly straight line through the origin with a unit slope indicating almost no inflation.
Fig. 1

Q-Q plots for CIMT and plaque association p-values in MAs and EAs.

Q-Q plots for CIMT and plaque association p-values in MAs and EAs. To further investigate the genetic architecture of CIMT, PRS analysis was conducted, with scores representing summations of CIMT-, and plaque-associated alleles from the Metabochip array. A PRS is the sum of trait-associated alleles across many genetic loci, and was calculated in an independent population i.e., EA population, using the genome-wide association results from the MA population, a discovery population for a given trait (i.e., CIMT) to detect shared genetic etiology among traits, to establish the presence of a genetic signal in underpowered studies, and to infer the genetic architecture of a trait [6]. Scoring routines were determined from the association test results for the MA cohort, with risk alleles identified based on varying p-value thresholds (1,000 different p-value (Pts) thresholds, representing increments of p = 0.001), each weighted by their estimated effect sizes on CIMT or plaque. Scores were then computed in the independent EA cohort, and evaluated as predictors of CIMT or plaque via regression models (covariates age, sex, PCs 1 and 2, RA duration, statin use, and htn) as shown in Fig. 2 (A and B). This work was performed using PRSice v.1.23, a polygenic risk score software.
Fig. 2

High-resolution Polygenic Risk Score Model Fit in EA for CIMT (A) and Plaque (B) with theoretical expectations across a range of PT in MA. A. High-resolution Polygenic Risk Score Model Fit in EA for CIMT with theoretical expectations across a range of PT in MA. B. High-resolution Polygenic Risk Score Model Fit in EA for Plaque with theoretical expectations across a range of PT in MA.

High-resolution Polygenic Risk Score Model Fit in EA for CIMT (A) and Plaque (B) with theoretical expectations across a range of PT in MA. A. High-resolution Polygenic Risk Score Model Fit in EA for CIMT with theoretical expectations across a range of PT in MA. B. High-resolution Polygenic Risk Score Model Fit in EA for Plaque with theoretical expectations across a range of PT in MA.

Experimental design, subjects and methods

Subjects

We used existing samples/data from the ORALE (Outcome of Rheumatoid Arthritis Longitudinal Evaluation) study, involving 700 unrelated MAs and unrelated 415 EAs. From 1996 to 2009, we recruited consecutive patients who met the 1987 criteria for RA [7] from 11 private and public rheumatology outpatient clinics in San Antonio, Texas.

Phenotyping

CIMT and plaque were measured using carotid ultrasound. A single technician performed a duplex scan of the carotid arteries in all patients, following a standardized vascular protocol as implemented in an ATL HDI-3000 High Resolution Imaging machine with a L7-4 Transducer (Philips Medical Systems North America Company, Bothell, WA). For CIMT, we measured the end diastole at each of the near and far walls of the right and left common carotid arteries, and the anterior oblique, lateral and posterior oblique views of the internal carotid artery, for a total of 16 CIMT measurements per person. The maximal CIMT of the common and internal carotid arteries were obtained by averaging the maximal measurement from the near and far walls at each projection, from the right and left sides. Then the composite maximal CIMT was calculated by averaging the common and internal carotid maximal CIMT values. The result is one CIMT value per person, expressed in millimeters. Carotid plaque was identified as a discrete projection of 50% or more from the adjacent wall into the vessel lumen.

Genotyping

The Metabochip (Illumina) is a custom BeadChip targeting 196,725 genetic variants. Common and less common genetic variants were chosen from among the first iteration of the 1000 Genomes Project and represent index GWAS-identified variants regardless of disease or phenotype as of 2009 [8]. As previously described [8], it was primarily designed for fine mapping of metabolic and cardiovascular disease-related loci, and replication of susceptibility loci for specific GWAS-identified regions associated with cardio-metabolic disease and related phenotypes. Several studies have used this platform to successfully identify genetic risk factors influencing complex disease phenotypes [8], [9]. Briefly, Metabochip was a custom Illumina iSelect genotyping array designed to test ~200,000 SNPs identified through genome‐wide meta‐analyses for metabolic and atherosclerotic/ cardiovascular diseases and traits in a cost‐effective manner. It was designed by representatives of the following GWAS meta‐analysis Consortia: CARDIoGRAM (coronary artery disease), DIAGRAM (type 2 diabetes), GIANT (height and weight), MAGIC (glycemic traits), Lipids (lipids), ICBP‐GWAS (blood pressure), and QT‐IGC (QT interval). It supports genotyping of SNPs selected according to five sets of criteria: (1) individual SNPs displaying evidence for association in GWA meta‐analyses to diseases and traits relevant to metabolic and atherosclerotic‐cardiovascular endpoints, (2) detailed fine mapping of loci validated at genome‐wide significance from these meta‐analyses, (3) all SNPs associated at genome‐wide significance with any human trait, (4) "wildcards" selected by each meta‐analysis Consortium for Consortium‐specific purposes, and (5) other useful content, including SNPs that tag common CNPs, SNPs in the HLA region, SNPs marking the X and Y chromosomes and mtDNA, and for sample fingerprinting (common SNPs represented on major genome‐wide array products from both Illumina and Affymetrix) [8], [10]. After merging and pruning the lists (to remove redundant SNPs), a total of 217,697 SNPs representing 245,243 bead types was submitted to Illumina for manufacturing on August 19, 2009. The final chip consisted of genotypes of ~200,000 SNPs per sample. We performed the genotyping according to the Illumina protocol and initial data handling and analysis was performed using Genome Studio v1.7.4 (Illumina).

Sample and SNP quality control measures

Several quality control measures were applied to the genotypic data of each ethnic group, and only the autosomal SNPs that passed QC were considered for this study. Subjects with low call rates (< 0.95) were removed (MA = 13 and EA = 0). To identify and exclude highly related individuals or duplicate samples, we performed the relationship inference analytical procedure as implemented in the computer program KING [Kinship-based Inference for Genome-wide association studies, [11] and identified related individuals. Subsequently, using the program PLINK [12] and the identity-by-descent (IBD) analysis, closely related individuals up to 3rd degree relatives (IBD > 0.185) were removed (MA = 17 and EA = 3). To detect ethnic outliers, we used EIGENSTRAT c3.0 software package [13] to employ principal components analysis to a subset of autosomal SNPs in our data that were in low LD (r2 < 0.2) and the HapMap samples as reference for the ethnic groups. Plots were generated using the first two principal components (PCs) for visual inspection. Using our data by ethnic group, samples were identified as population outliers, defined by 4SD from the mean of each of the 2 PCs that explained the majority of variation in the data, and were subsequently removed (MA = 2 and EA = 0). SNPs with a genotyping call rate less than 95% were removed using PLINK [12]. In addition, SNPs with Hardy-Weinberg Equilibrium (HWE) values of p < 10−4 [(MA = 236 (CIMT) and 120 (plaque); and EA = 114 (CIMT), and 38 (plaque)] and with minor allele frequency (MAF) < 0.01 (MA = 57, 323 and EA = 60, 168) were removed from the analysis. After filtering and genotyping pruning, 122,549 SNPs from 668 MAs and 120,827 from 415 EAs were remained in the association analyses.

Quantile-quantile (Q-Q) plots

Q-Q plots are probability plots, which are useful to compare two probability distributions, sample quantile distribution of the observed chi-squared values (y –axis) versus the quantile distribution of expected (normal or theoretical) chi-squared values (x –axis) graphically by plotting their quantiles against each other. Q-Q plots were done using Efficient and Parallelizable Association Container Toolbox software [EPACTS, http://genome.sph.umich.edu/wiki/EPACTS]. Association p values were adjusted for multiple testing using the conservative Bonferroni correction: 4.08 × 10−7 for MA and 4.14 × 10−7 for EA.

Statistical genetic analyses

We performed association analyses between the transformed CIMT (as a quantitative trait) and plaque (as a discrete trait) and SNP genotypes in both MA and EA samples after QCs, using PLINK software version 1.07 [12]. Principal Components (PCs) were derived using EIGENSTRAT principal component analysis [13] to adjust for potential population stratification influences. A linear regression additive genetic model (SNPs coded as 0,1, or 2 based on the minor allele dosage) adjusted for the effects of covariates age, sex, RA duration, medication status (statin use, and hypertension, [htn, medication]), and the first two PC1 and PC2, was used for association testing of CIMT, a quantitative trait. Association statistics for plaque, a discrete trait, were calculated using logistic regression assuming an additive model.

Polygenic risk score (PRS)

PRS for an individual is a summation of their genotypes at variants genome-wide, weighted by effect sizes on a trait of interest i.e. CIMT. Although effect sizes are usually estimated from a GWAS study, we used our Mexican American cohort association results for weighting. Thus, a sum of trait-associated alleles across many genetic loci, has been calculated in an independent population i.e., European American population, using the genome-wide association results from the Mexican-American population, a discovery population for a given trait (i.e., CIMT) to detect shared genetic etiology among traits, to establish the presence of a genetic signal in underpowered studies, and to infer the genetic architecture of a trait [6]. Using the array-wide association results for the MA samples for CIMT (n = 122,549 SNPs), PRS routines were designed and computed in the EA cohort, revealing significant associations with the target phenotype. As shown in Fig. 1, Fig. 2, the PRS model for Pt < 0.054 yielded the best fit for CIMT in EAs, but 1000 different Pt thresholds were examined, representing increments of P = 0.001. The computed PRSs are then used as predictors of a targeted phenotype in an independent European data set using regression models (i.e., linear or logistic based on the target phenotype). Furthermore, SNPs in the association results for the Mexican-American samples were pruned using PLINK's clumping methodology based on linkage disequilibrium (LD), distance, and association P-values (see http://pngu.mgh.harvard.edu/~purcell/plink/clump.shtml). We used the standard settings (r2 = 0.1 and 250 Kb), which reduced the number of SNPs actually used in the scoring routines from 122,549 to 36,630. This work was performed using PRSice v.1.23, a polygenic risk score software [6].
Subject areaGenetics, Genomics and Molecular Biology
More specific subject areaCIMT and plaque Genetic Association Data in RA subjects
Type of dataTables, figures and text file
How data was acquiredORALE study data were collected from 11 private and public rheumatology outpatient clinics in San Antonio, Texas.
Data formatOriginal and analyzed data set
Experimental factorsRecruited patients who met the 1987 criteria for RA
Experimental featuresMetabochip array-based Association Analyses
Data source locationDivision of Rheumatology and Clinical Immunology, Department of Medicine, UTHSCSA, San Antonio, TX USA.
Data accessibilityData are available with this article and/or upon request
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6.  Lack of associations of ten candidate coronary heart disease risk genetic variants and subclinical atherosclerosis in four US populations: the Population Architecture using Genomics and Epidemiology (PAGE) study.

Authors:  Lili Zhang; Petra Buzkova; Christina L Wassel; Mary J Roman; Kari E North; Dana C Crawford; Jonathan Boston; Kristin D Brown-Gentry; Shelley A Cole; Ewa Deelman; Robert Goodloe; Sarah Wilson; Gerardo Heiss; Nancy S Jenny; Neal W Jorgensen; Tara C Matise; Bob E McClellan; Alejandro Q Nato; Marylyn D Ritchie; Nora Franceschini; W H Linda Kao
Journal:  Atherosclerosis       Date:  2013-03-13       Impact factor: 5.162

7.  A genetic association study of carotid intima-media thickness (CIMT) and plaque in Mexican Americans and European Americans with rheumatoid arthritis.

Authors:  Rector Arya; Agustin Escalante; Vidya S Farook; Jose F Restrepo; Daniel F Battafarano; Marcio Almeida; Mark Z Kos; Marcel J Fourcaudot; Srinivas Mummidi; Satish Kumar; Joanne E Curran; Christopher P Jenkinson; John Blangero; Ravindranath Duggirala; Inmaculada Del Rincon
Journal:  Atherosclerosis       Date:  2017-11-26       Impact factor: 5.162

8.  PRSice: Polygenic Risk Score software.

Authors:  Jack Euesden; Cathryn M Lewis; Paul F O'Reilly
Journal:  Bioinformatics       Date:  2014-12-29       Impact factor: 6.937

9.  Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study.

Authors:  Nora Franceschini; Yijuan Hu; Alex P Reiner; Steven Buyske; Mike Nalls; Lisa R Yanek; Yun Li; Lucia A Hindorff; Shelley A Cole; Barbara V Howard; Jeanette M Stafford; Cara L Carty; Praveen Sethupathy; Lisa W Martin; Dan-Yu Lin; Karen C Johnson; Lewis C Becker; Kari E North; Abbas Dehghan; Joshua C Bis; Yongmei Liu; Philip Greenland; JoAnn E Manson; Nobuyo Maeda; Melissa Garcia; Tamara B Harris; Diane M Becker; Christopher O'Donnell; Gerardo Heiss; Charles Kooperberg; Eric Boerwinkle
Journal:  PLoS One       Date:  2014-12-26       Impact factor: 3.240

10.  The metabochip, a custom genotyping array for genetic studies of metabolic, cardiovascular, and anthropometric traits.

Authors:  Benjamin F Voight; Hyun Min Kang; Jun Ding; Cameron D Palmer; Carlo Sidore; Peter S Chines; Noël P Burtt; Christian Fuchsberger; Yanming Li; Jeanette Erdmann; Timothy M Frayling; Iris M Heid; Anne U Jackson; Toby Johnson; Tuomas O Kilpeläinen; Cecilia M Lindgren; Andrew P Morris; Inga Prokopenko; Joshua C Randall; Richa Saxena; Nicole Soranzo; Elizabeth K Speliotes; Tanya M Teslovich; Eleanor Wheeler; Jared Maguire; Melissa Parkin; Simon Potter; N William Rayner; Neil Robertson; Kathleen Stirrups; Wendy Winckler; Serena Sanna; Antonella Mulas; Ramaiah Nagaraja; Francesco Cucca; Inês Barroso; Panos Deloukas; Ruth J F Loos; Sekar Kathiresan; Patricia B Munroe; Christopher Newton-Cheh; Arne Pfeufer; Nilesh J Samani; Heribert Schunkert; Joel N Hirschhorn; David Altshuler; Mark I McCarthy; Gonçalo R Abecasis; Michael Boehnke
Journal:  PLoS Genet       Date:  2012-08-02       Impact factor: 5.917

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