Quantifying the relationship between co-expression, co-regulation and gene function

BACKGROUND: It is thought that genes with similar patterns of mRNA expression and genes with similar functions are likely to be regulated via the same mechanisms. It has been difficult to quantitatively test these hypotheses on a large scale because there has been no general way of determining whether genes share a common regulatory mechanism. Here we use data from a recent genome wide binding analysis in combination with mRNA expression data and existing functional annotations to quantify the likelihood that genes with varying degrees of similarity in mRNA expression profile or function will be bound by a common transcription factor. RESULTS: Genes with strongly correlated mRNA expression profiles are more likely to have their promoter regions bound by a common transcription factor. This effect is present only at relatively high levels of expression similarity. In order for two genes to have a greater than 50% chance of sharing a common transcription factor binder, the correlation between their expression profiles (across the 611 microarrays used in our study) must be greater than 0.84. Genes with similar functional annotations are also more likely to be bound by a common transcription factor. Combining mRNA expression data with functional annotation results in a better predictive model than using either data source alone. CONCLUSIONS: We demonstrate how mRNA expression data and functional annotations can be used together to estimate the probability that genes share a common regulatory mechanism. Existing microarray data and known functional annotations are sufficient to identify only a relatively small percentage of co-regulated genes

A prospective evaluation of the safety and efficacy of the TAXUS Element paclitaxel-eluting coronary stent system for the treatment of de novo coronary artery lesions: Design and statistical methods of the PERSEUS clinical program

<p>Abstract</p> <p>Background</p> <p>Paclitaxel-eluting stents decrease angiographic and clinical restenosis following percutaneous coronary intervention compared to bare metal stents. TAXUS Element is a third-generation paclitaxel-eluting stent which incorporates a novel, thinner-strut, platinum-enriched metal alloy platform. The stent is intended to have enhanced radiopacity and improved deliverability compared to other paclitaxel-eluting stents. The safety and efficacy of the TAXUS Element stent are being evaluated in the pivotal PERSEUS clinical trials.</p> <p>Methods/Design</p> <p>The PERSEUS trials include two parallel studies of the TAXUS Element stent in single, de novo coronary atherosclerotic lesions. The PERSEUS Workhorse study is a prospective, randomized (3:1), single-blind, non-inferiority trial in subjects with lesion length ≤28 mm and vessel diameter ≥2.75 mm to ≤4.0 mm which compares TAXUS Element to the TAXUS Express²paclitaxel-eluting stent system. The Workhorse study employs a novel Bayesian statistical approach that uses prior information to limit the number of study subjects exposed to the investigational device and thus provide a safer and more efficient analysis of the TAXUS Element stent. PERSEUS Small Vessel is a prospective, single-arm, superiority trial in subjects with lesion length ≤20 mm and vessel diameter ≥2.25 mm to <2.75 mm that compares TAXUS Element with a matched historical bare metal Express stent control.</p> <p>Discussion</p> <p>The TAXUS PERSEUS clinical trial program uses a novel statistical approach to evaluate whether design and metal alloy iterations in the TAXUS Element stent platform provide comparable safety and improved procedural performance compared to the previous generation Express stent. PERSEUS trial enrollment is complete and primary endpoint data are expected in 2010. PERSEUS Workhorse and Small Vessel are registered at <url>http://www.clinicaltrials.gov</url>, identification numbers NCT00484315 and NCT00489541.</p

Predictors of Paravalvular Regurgitation Following Implantation of the Fully Repositionable and Retrievable Lotus Transcatheter Aortic Valve (From the REPRISE II Trial Extended Cohort)

Paravalvular leak (PVL) following transcatheter aortic valve replacement (TAVR) is associated with worse long-term outcomes. The Lotus Valve incorporates an innovative adaptive seal designed to minimize PVL. This analysis evaluated the incidence and predictors of PVL following implantation of the Lotus transcatheter aortic valve. The REPRISE II study with Extended Cohort enrolled 250 high-surgical risk patients with severe symptomatic aortic stenosis. Aortic regurgitation was assessed by echocardiography pre-procedure, at discharge and 30 days by an independent core lab. Baseline and procedural predictors of mild or greater PVL at 30 days (or at discharge if 30-day data were not available) were determined using a multivariate regression model (N=229). Among 229 patients, 197 (86%) had no/trace PVL, 30 had mild, and 2 had moderate PVL; no patient had severe PVL. Significant predictors of mild/moderate PVL included device:annulus area ratio (odds ratio [OR]: 0.87 (95% CI: 0.83-0.92); P&lt;0.001), LVOT calcium volume (OR:2.85;(1.44-5.63); P=0.003), and annulus area (OR:0.89(0.82-0.96); P=0.002). When the device:annulus area ratio was &lt;1, the rate of mild/moderate PVL was 53.1% (17/32). The rates of mild/moderate PVL with 0-5%, 5-10%, and &gt;10% annular oversizing by area were 17.5% (11/63), 2.9% (2/70), and 3.2% (2/63), respectively. Significant independent predictors of PVL included device:annulus area ratio and LVOT calcium volume. When the prosthetic valve was oversized by ≥5%, the rate of mild or greater PVL was only 3%. In conclusion, the overall rates of PVL with the Lotus Valve are low and predominantly related to device/annulus areas and calcium; these findings have implications for optimal device sizing

Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

<p>Abstract</p> <p>Background</p> <p>Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance.</p> <p>Results</p> <p>We used small numbers of randomly selected single nucleotide polymorphisms (SNPs) from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome.</p> <p>Conclusion</p> <p>Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily chosen SNPs to identify stratification in study subjects and avoid false positive genotype-phenotype associations. Our findings also demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance.</p

Rationale and design of the EVOLVE Short DAPT Study to assess 3-month dual antiplatelet therapy in subjects at high risk for bleeding undergoing percutaneous coronary intervention.

BACKGROUND While extended dual antiplatelet therapy (DAPT) with aspirin and a platelet (P2Y) inhibitor after percutaneous coronary intervention (PCI) reduces the risk of stent thrombosis (ST) and myocardial infarction (MI), it also increases bleeding. Newer generation drug-eluting stents with bioabsorbable polymer coatings may reduce thrombotic events and allow abbreviated DAPT in selected patients. The EVOLVE Short DAPT study is designed to evaluate the safety of 3-month DAPT in high bleeding risk subjects treated with the SYNERGY bioabsorbable polymer everolimus-eluting stent. TRIAL DESIGN EVOLVE Short DAPT is a prospective, single-arm, international study that enrolled 2009 high risk bleeding subjects (defined as age ≥75 years, chronic anticoagulation, major bleeding within 12 months, history of stroke, renal insufficiency/failure, or thrombocytopenia) who underwent PCI with the SYNERGY stent. Subjects presenting with acute MI or complex lesions were excluded. After 3 months treatment with DAPT (except those on anticoagulant in whom aspirin is optional), subjects free from stroke, MI, revascularization or ST will be eligible to discontinue P2Y inhibitor, but continue aspirin. Co-primary endpoints assessed between 3-15 months are: i) death/MI compared for non-inferiority with propensity-adjusted historical group receiving 12-month DAPT, and ii) definite/probable ST compared to a performance goal. The secondary endpoint is the rate of bleeding in subjects not receiving chronic anticoagulation compared for superiority against a propensity-adjusted historical control. CONCLUSION The EVOLVE Short DAPT study will prospectively define the safety of DAPT discontinuation at 3 months in high bleeding risk patients treated with the SYNERGY stent