Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells

<p>Abstract</p> <p>Background</p> <p>In this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. Five RNA samples for each type of cell were hybridized to the two platforms in parallel. In addition, a reference list of differentially expressed genes (DEG) was generated from a larger number of hybridizations (mRNA from 86 individuals) using the RNG/MRC two-color platform.</p> <p>Results</p> <p>Our results show an important overlap of the Illumina and Affymetrix DEG lists. In addition, more than 70% of the genes in these lists were also present in the reference list. Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant for the biology of monocytes and macrophages. Our results support the conclusion of the MicroArray Quality Control (MAQC) project that the criteria used to constitute the DEG lists strongly influence the degree of concordance among platforms. However the importance of prioritizing genes by magnitude of effect (fold change) rather than statistical significance (p-value) to enhance cross-platform reproducibility recommended by the MAQC authors was not supported by our data.</p> <p>Conclusion</p> <p>Functional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference list.</p

Revisiting the effects of omitting aspirin in combined antithrombotic therapies for atrial fibrillation and acute coronary syndromes or percutaneous coronary interventions: meta-analysis of pooled data from the PIONEER AF-PCI, RE-DUAL PCI, and AUGUSTUS trials

International audienceAIMS:Recently, three randomized trials reported that dual antithrombotic treatments (DATs) including non-vitamin K antagonist oral anticoagulants (NOACs) and a P2Y12 inhibitor without aspirin were associated with significantly less bleeding than vitamin K antagonist (VKA)-based triple antithrombotic therapy (TAT) in atrial fibrillation (AF) patients with acute coronary syndrome (ACS) or undergoing percutaneous coronary intervention (PCI). We conducted an analysis of pooled data from these trials.METHODS AND RESULTS:A meta-analysis of the PIONEER AF-PCI, RE-DUAL PCI, and AUGUSTUS trials considering major bleeding [International Society on Thrombosis and Haemostasis (ISTH) and Thrombolysis in Myocardial Infarction], clinically relevant non-major bleeding, all-cause/cardiovascular death, stroke, myocardial infarction (MI), and stent thrombosis. Treatment effect is reported as odds ratio (OR) and 95% confidence interval. Among 9463 patients (53% with ACS), DAT regimens were associated with significantly less bleeding than TAT (OR 0.598, 0.491 -0.727; P < 0.001 for ISTH major bleeding), as were NOAC-based vs. VKA-based regimens (OR 0.577, 0.477 -0.698; P < 0.001). Stroke and mortality rates were similar, but there was statistically non-significant trend towards greater risk of MI (OR 1.211, 0.955 -1.535; P = 0.115) and significantly higher risk for stent thrombosis (OR 1.672, 1.022 -2.733, P = 0.041) with DAT vs. TAT (but not NOAC- vs. VKA-based regimens). This was mainly driven by Dabigatran 110 mg; the trends were lower with full-dose NOAC or Rivaroxaban 15 mg-based DATs.CONCLUSION:Our findings support the use of full-dose NOAC (Apixaban 5 mg, Dabigatran 150 mg) or Rivaroxaban 15 mg-based treatments in most AF patients with ACS or undergoing PCI. Notwithstanding the better safety of DAT, an initial course of NOAC-based TAT may be desirable in most AF patients

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells-5

) of two different samples on Affymetrix (a) and Illumina (b) platforms. The blue line on each plot represents a regression line that best fits the plotted set of points. Both array types provide high inter-replicates reproducibility of the relative gene expression intensities.<p><b>Copyright information:</b></p><p>Taken from "Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells"</p><p>http://www.biomedcentral.com/1471-2164/9/302</p><p>BMC Genomics 2008;9():302-302.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2464609.</p><p></p

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells-0

) of two different samples on Affymetrix (a) and Illumina (b) platforms. The blue line on each plot represents a regression line that best fits the plotted set of points. Both array types provide high inter-replicates reproducibility of the relative gene expression intensities.<p><b>Copyright information:</b></p><p>Taken from "Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells"</p><p>http://www.biomedcentral.com/1471-2164/9/302</p><p>BMC Genomics 2008;9():302-302.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2464609.</p><p></p

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells-3

He list was constituted by selecting DEG (Pc < 0.05), then within this list genes were ranked according to decreasing fold change. The number of overlapping genes between lists was calculated for increasing list size. When the number of probes in the lists was approximately 3800, the number of overlapping genes reached a plateau. The "best 3800" set of probes was defined accordingly.<p><b>Copyright information:</b></p><p>Taken from "Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells"</p><p>http://www.biomedcentral.com/1471-2164/9/302</p><p>BMC Genomics 2008;9():302-302.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2464609.</p><p></p

Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells-4

Examined; Genes present in the top-left and bottom right quarters of each plots show changes in opposite direction. These genes are expected to overlap by chance.<p><b>Copyright information:</b></p><p>Taken from "Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells"</p><p>http://www.biomedcentral.com/1471-2164/9/302</p><p>BMC Genomics 2008;9():302-302.</p><p>Published online 25 Jun 2008</p><p>PMCID:PMC2464609.</p><p></p

Balloon-Expandable Versus Self-Expanding Transcatheter Aortic Valve Replacement: A Propensity-Matched Comparison From the FRANCE-TAVI Registry

International audienceBackground - No randomized study powered to compare balloon expandable (BE) with self expanding (SE) transcatheter heart valves (THVs) on individual end points after transcatheter aortic valve replacement has been conducted to date. Methods - From January 2013 to December 2015, the FRANCE-TAVI nationwide registry (Registry of Aortic Valve Bioprostheses Established by Catheter) included 12 141 patients undergoing BE-THV (Edwards, n=8038) or SE-THV (Medtronic, n=4103) for treatment of native aortic stenosis. Long term mortality status was available in all patients (median 20 months; interquartile range, 14 to 30). Patients treated with BE-THV (n=3910) were successfully matched 1:1 with 3910 patients treated with SE-THV by using propensity score (25 clinical, anatomical, and procedural variables) and by date of the procedure (within 3 months). The first coprimary outcome was ≥ moderate occurrence of paravalvular regurgitation or in-hospital mortality, or both. The second coprimary outcome was 2-year all-cause mortality. Results - In propensity-matched analyses, the incidence of the first coprimary outcome was higher with SE-THV (19.8%) compared with BE-THV (11.9%; relative risk, 1.68 [95% CI, 1.46-1.91]; <0.0001). Each component of the outcome was also higher in patients receiving SE-THV: ≥ moderate paravalvular regurgitation (15.5% versus 8.3%; relative risk, 1.90 [95% CI, 1.63-2.22]; <0.0001) and in hospital mortality (5.6% versus 4.2%; relative risk, 1.34 [95% CI, 1.07-1.66]; =0.01). During follow up, all cause mortality occurred in 899 patients treated with SE-THV (2-year mortality, 29.8%) and in 801 patients treated with BE-THV (2-year mortality, 26.6%; hazard ratio, 1.17 [95% CI, 1.06-1.29]; =0.003). Similar results were found using inverse probability of treatment weighting using propensity score analysis. Conclusion - The present study suggests that use of SE-THV was associated with a higher risk of paravalvular regurgitation and higher in-hospital and 2-year mortality compared with use of BE-THV. These data strongly support the need for a randomized trial sufficiently powered to compare the latest generation of SE-THV and BE-THV. Clinical trial registration - https://www.clinicaltrials.gov. Unique identifier: NCT01777828