Open Access Research article

Fine mapping of a linkage peak with integration of lipid traits identifies novel coronary artery disease genes on chromosome 5

Daniel K Nolan1, Beth Sutton1, Carol Haynes1, Jessica Johnson1, Jacqueline Sebek1, Elaine Dowdy1, David Crosslin1, David Crossman4, Michael H Sketch2, Christopher B Granger2, David Seo3, Pascal Goldschmidt-Clermont3, William E Kraus2, Simon G Gregory12, Elizabeth R Hauser12 and Svati H Shah12*

Author Affiliations

1 Center for Human Genetics, Duke University, 905 S. LaSalle Street, Duke Univeristy Medical Center, Durham NC, 27710, USA

2 Department of Medicine, Duke University, 2301 Erwin Road, Durham NC, 27710, USA

3 Miller School of Medicine, University of Miami, 1601 Northwest 12th Avenue, Miami FL, 33136, USA

4 University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK

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BMC Genetics 2012, 13:12  doi:10.1186/1471-2156-13-12

Published: 27 February 2012

Additional files

Additional file 1:

Genes associated with LDL cholesterol traits in the GENECARD study. This table displays minor allele frequencies (MAF), sample sizes, and p-values for the most significant SNPs associated with LDL cholesterol using the quantitative trait disequilibrium test (QTDT) in the GENECARD study. Note that the sample size is less than the overall GENECARD study sample size since not all families could be included due to lack of unaffecteds. SNPs within our four key candidate genes are in bold.

Format: DOCX Size: 15KB Download file

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Additional file 2:

Genes associated with LDL cholesterol traits in the CATHGEN cohort. Displayed are the results for association of SNPs with LDLP levels in the CATHGEN sample. The significant SNPs are shown followed by the genic location, base pair position, and the corresponding p-value. SNPs within our four key candidate genes are presented in bold.

Format: DOCX Size: 22KB Download file

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Additional file 3:

Associations of EBF1 SNPs with Leptin Levels. Six SNPs within and flanking EBF1 are listed with their Wilcoxon rank test p-values for association with leptin levels in CATHGEN in the total sample with available leptin levels, and stratified by race.

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Additional file 4:

Association of SNPs with CAD in the GENECARD cohort. Displayed are results of the qualitative analysis using APL in the GENECARD sample. All significant SNPs are shown followed by their genic location, base pair position, and their corresponding p-values. Results within our four key candidate genes are displayed in bold.

Format: DOCX Size: 21KB Download file

Open Data

Additional file 5:

Linkage results for SNPs with early-onset CAD in the GENECARD cohort. Displayed are linkage results for the GENECARD sample. All SNPs with two-point lod scores ≥ 1.5 are listed followed by their genic location, base pair position, individual lod score, and genetic model used.

Format: DOCX Size: 15KB Download file

Open Data

Additional file 6:

Association of SNPs with CAD in the CATHGEN Cohort. Displayed are all significant results for the case-control analysis of SNPs with CAD in the CATHGEN sample. Each significant SNP is listed followed by their genic location, base pair, p-value, odds ratio, and 95% confidence interval for the genotypic and allelic models, respectively.

Format: DOCX Size: 46KB Download file

Open Data

Additional file 7:

Association of SNPs with CAD for GENECARD proband vs. CATHGEN controls sample set. Displayed are the results of the GENECARD proband-CATHGEN control analysis, with all significant SNPs listed followed by their genic location, base pair position, p-value, odds ratio, and 95% confidence intervals for the genotypic and allelic models used.

Format: DOCX Size: 35KB Download file

Open Data

Additional file 8:

Association of SNPs with Degree of Atherosclerosis in the Aorta Samples. Displayed are results of association of SNPs with degree of atherosclerosis in the aorta samples, with each significant SNP listed followed by their genic position, base pair position, p-value, odds ratio, and 95% confidence interval for the genotypic and allelic models.

Format: DOCX Size: 46KB Download file

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Additional file 9:

Linkage disequilibrium patterns of select SNPs in PPP2R2B. LD pattern using Haploview, with r-squared values displayed within each box and the shading of the boxes corresponding do D' values.

Format: JPEG Size: 14KB Download file

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Additional file 10:

Linkage disequilibrium patterns of select SNPs in EBF1. LD pattern using Haploview, with r-squared values displayed within each box and the shading of the boxes corresponding do D' values.

Format: JPEG Size: 7KB Download file

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Additional file 11:

Linkage disequilibrium patterns of select SNPs in SPOCK1. LD pattern using Haploview, with r-squared values displayed within each box and the shading of the boxes corresponding do D' values.

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Additional file 12:

Linkage disequilibrium patterns of select SNPs in PRELID2. LD pattern using Haploview, with r-squared values displayed within each box and the shading of the boxes corresponding do D' values.

Format: JPEG Size: 13KB Download file

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