Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-0

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p>aptured using SnagIt 7.0. The figure illustrates the appearance of the Statistic View panel and some of its features in the context of Contig View. It also demonstrates how the selection of a peak can enable the researcher to easily see where linkage data and other features such as potentially unstable tri-nucleotide repeats and gene expression data converge to suggest priority gene for association and sequence analysis

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-3

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-2

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p> (part B) of three data records that define plot coordinates along with other attributes. User databases are created to allow restricted access for uploading data

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-1

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p>age

The x-axis is in cM along with the location of genes on that chromosome

<p><b>Copyright information:</b></p><p>Taken from "Adjusting for covariates on a slippery slope: linkage analysis of change over time"</p><p>http://www.biomedcentral.com/1471-2156/4/s1/S50</p><p>BMC Genetics 2003;4(Suppl 1):S50-S50.</p><p>Published online 31 Dec 2003</p><p>PMCID:PMC1866487.</p><p></p> SOLAR curves are for the normalized SBP slopes. The SIBLINK curve shows the ASP LOD score for HBP

Case-Only Survival Analysis Reveals Unique Effects of Genotype, Sex, and Coronary Disease Severity on Survivorship

<div><p>Survival bias may unduly impact genetic association with complex diseases; gene-specific survival effects may further complicate such investigations. Coronary artery disease (CAD) is a complex phenotype for which little is understood about gene-specific survival effects; yet, such information can offer insight into refining genetic associations, improving replications, and can provide candidate genes for both mortality risk and improved survivorship in CAD. Building on our previous work, the purpose of this current study was to: evaluate <i>LSAMP</i> SNP-specific hazards for all-cause mortality post-catheterization in a larger cohort of our CAD cases; and, perform additional replication in an independent dataset. We examined two <i>LSAMP</i> SNPs—rs1462845 and rs6788787—using CAD case-only Cox proportional hazards regression for additive genetic effects, censored on time-to-all-cause mortality or last follow-up among Caucasian subjects from the Catheterization Genetics Study (CATHGEN; <i>n</i> = 2,224) and the Intermountain Heart Collaborative Study (IMHC; <i>n</i> = 3,008). Only after controlling for age, sex, body mass index, histories of smoking, type 2 diabetes, hyperlipidemia and hypertension (<i>HR</i> = 1.11, 95%<i>CI</i> = 1.01–1.22, <i>p</i> = 0.032), rs1462845 conferred significantly increased hazards of all-cause mortality among CAD cases. Even after controlling for multiple covariates, but in only the primary cohort, rs6788787 conferred significantly improved survival (<i>HR</i> = 0.80, 95% <i>CI</i> = 0.69–0.92, <i>p</i> = 0.002). Post-hoc analyses further stratifying by sex and disease severity revealed replicated effects for rs1462845: even after adjusting for aforementioned covariates and coronary interventional procedures, males with severe burden of CAD had significantly amplified hazards of death with the minor variant of rs1462845 in both cohorts (<i>HR</i> = 1.29, <i>95% CI</i> = 1.08–1.55, <i>p</i> = 0.00456; replication <i>HR</i> = 1.25, <i>95% CI</i> = 1.05–1.49, <i>p</i> = 0.013). Kaplan-Meier curves revealed unique cohort-specific genotype effects on survival. Additional analyses demonstrated that the homozygous risk genotype (‘A/A’) fully explained the increased hazard in both cohorts. None of the post-hoc analyses in control subjects were significant for any model. This suggests that genetic effects of rs1462845 on survival are unique to CAD presence. This represents formal, replicated evidence of genetic contribution of rs1462845 to increased risk for all-cause mortality; the contribution is unique to CAD case status and specific to males with severe burden of CAD.</p></div

Heritabilities of measured CVD biomarkers.

<p>Presented is the distribution of heritability and its corresponding p-value for all 18 biomarkers, with the heritability estimate on the X-axis and the –log base 10 of the associated p-value on the Y-axis. The 95% confidence interval is represented by a horizontal error bar. The threshold for significance is represented by a dashed line.</p

Kaplan–Meier survival curves for 5a) CATHGEN and 5b) IMHC Caucasian control subjects by genotype for LSAMP SNP rs1462845.

<p><i>X</i>-axis displays the number of days from index catheterization to death (all-cause mortality). <i>Y</i>-axis displays the Kaplan-Meier survival probability by genotype. G is the minor allele; AA, wild-type genotype (reference; black curve); AG, heterozygous genotype (blue curve); and GG, risk homozygous genotype (red curve). No significant differences were found in any statistical modeling (data not shown).</p

Hazards of Death by SNP (Additive) in Caucasian Males with Severe Burden of CAD.

<p>Hazards of Death by SNP (Additive) in Caucasian Males with Severe Burden of CAD.</p

<i>LSAMP</i> SNP Characteristics.

<p><i>LSAMP</i> SNP Characteristics.</p