Additional file 2: Table S2. of Genetic linkage of hyperglycemia and dyslipidemia in an intercross between BALB/cJ and SM/J Apoe-deficient mouse strains

Haplotype for glucose QTL Bglu17 on chromosome 9. Analysis was performed in the same way as for Hdlq17 illustrated above. (PDF 82 kb

Additional file 1: Table S1. of Genetic linkage of hyperglycemia and dyslipidemia in an intercross between BALB/cJ and SM/J Apoe-deficient mouse strains

Haplotype analysis to prioritize candidate genes for HDL QTL Hdlq17 on chromosome 9. Sanger SNP database ( http://www.sanger.ac.uk/sanger/Mouse_SnpViewer/rel-1410 ) was used to prioritize candidate genes for this locus, which were mapped in 3 separate crosses derived from different inbred strains. A high allele strain is the one that displays a larger allelic effect on HDL level at the locus and a low allele strain is the one showing a smaller allelic effect on HDL at the locus. (PDF 86 kb

Power was computed using TDT Power Calculator [15] varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).

<p>Power was computed using TDT Power Calculator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Chen1" target="_blank">[15]</a> varying SNP minor allele frequency (MAF) and genetic relative risk (GRR).</p

Top SNPs from the Raine cohort GWAS that were genotyped in our GWAS of COME/ROM.

<p>We report our OR and allele frequency using the Risk Allele corresponding to the Risk Allele listed in the Raine cohort GWAS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104212#pone.0104212-Rye1" target="_blank">[9]</a>.</p><p>*Indicates SNP is intergenic and therefore reports the nearest gene.</p>∧<p>Indicates the SNP was a top genotyped SNP from a subset of Raine study participants with full covariate data.</p

Association of the Lipoprotein Receptor <i>SCARB1</i> Common Missense Variant rs4238001 with Incident Coronary Heart Disease

<div><p>Background</p><p>Previous studies in mice and humans have implicated the lipoprotein receptor <i>SCARB1</i> in association with atherosclerosis and lipid levels. In the current study, we sought to examine association of <i>SCARB1</i> missense single nucleotide polymorphism (SNP) rs4238001 with incident coronary heart disease (CHD).</p><p>Methods and Results</p><p>Genotypes for rs4238001 were imputed for 2,319 White, 1,570 African American, and 1,292 Hispanic-American MESA participants using the 1,000 Genomes reference set. Cox proportional hazards models were used to determine association of rs4238001 with incident CHD, with adjustments for age, sex, study site, principal components of ancestry, body mass index, diabetes status, serum creatinine, lipid levels, hypertension status, education and smoking exposure. Meta-analysis across race/ethnic groups within MESA showed statistically significant association of the T allele with higher risk of CHD under a consistent and formally adjudicated definition of CHD events in this contemporary cohort study (hazard ratio [HR]=1.49, 95% CI [1.04, 2.14], <i>P</i> = 0.028). Analyses combining MESA with additional population-based cohorts expanded our samples in Whites (total n = 11,957 with 871 CHD events) and African Americans (total n = 5,962 with 355 CHD events) and confirmed an increased risk of CHD overall (HR of 1.19 with 95% CI [1.04, 1.37], <i>P</i> = 0.013), in African Americans (HR of 1.49 with 95% CI [1.07, 2.06], <i>P</i> = 0.019), in males (HR of 1.29 with 95% CI [1.08, 1.54], <i>P</i> = 4.91x10^-3) and in White males (HR of 1.24 with 95% CI [1.03, 1.51], <i>P</i> = 0.026).</p><p>Conclusion</p><p><i>SCARB1</i> missense rs4238001 is statistically significantly associated with incident CHD across a large population of multiple race/ethnic groups.</p></div

Summary of genetic additive effects of rs4238001 allele T on HDL-C (log mg/dL), HDL particle number (nmol/L) and HDL particle size (log nm) under a basic model (Model 1).

<p>Analyses were conducted stratified by race/ethnic group and combined by meta-analysis, for all participants as well as stratified by sex (males or female).</p

Summary of estimated genetic additive effects of rs4238001 allele T on LDL-C (mg/dL), LDL particle number (nmol/L) and LDL particle size (log nm) under a basic regression model (Model 1).

<p>Analyses were conducted stratified by race/ethnic group and combined by meta-analysis, for all participants as well as stratified by sex (males or female).</p

Effect estimates (log hazard ratio of CHD for rs4238001 effect allele T) and corresponding 95% confidence intervals shown for Model 1 (basic), Model 2 (extended), Model 3 (Model 2 + lipid medication) and Model 4 (NMR lipids).

<p>Analyses were conducted stratified by race/ethnic group and combined by meta- analysis, for all participants as well as stratified by sex (males or female).</p

Characteristics of MESA participants across three ethnic groups.

<p>Data are presented as N (%) for binary measures or median [IQR] for continuous measure.</p><p>*Summary statistics are reported for the subset of individuals with data available for at least one of the clinical events.</p><p>†P-values are presented for statistical significance of the difference in values across race/ethnic groups according to a likelihood ratio test with 2 degrees of freedom.</p><p>Characteristics of MESA participants across three ethnic groups.</p

(top panel) Representative IVUS frame from a patient with the ancestral allele (left) and a patient with the risk allele (right).

<p>Light green represents fibrofatty plaque, dark green fibrous plaque, red necrotic core, and white calcium. (bottom panel) Representative QCA from a patient with the ancestral allele with a 28% stenosis (left) and a patient with the risk allele and stenosis of 73% (right). Automated edge detection is used to determine stenosis severity.</p