Evaluation of microarray data normalization procedures using spike-in experiments

Background: Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spike-in experiments, it is possible to characterize the analyzed data and thereby enable comparisons of different analysis methods. Results: A spike-in experiment using eight in-house produced arrays was used to evaluate established and novel methods for filtration, background adjustment, scanning, channel adjustment, and censoring. The S-plus package EDMA, a stand-alone tool providing characterization of analyzed cDNA-microarray data obtained from spike-in experiments, was developed and used to evaluate 252 normalization methods. For all analyses, the sensitivities at low false positive rates were observed together with estimates of the overall bias and the standard deviation. In general, there was a trade-off between the ability of the analyses to identify differentially expressed genes (i.e. the analyses' sensitivities) and their ability to provide unbiased estimators of the desired ratios. Virtually all analysis underestimated the magnitude of the regulations; often less than 50% of the true regulations were observed. Moreover, the bias depended on the underlying mRNA-concentration; low concentration resulted in high bias. Many of the analyses had relatively low sensitivities, but analyses that used either the constrained model (i.e. a procedure that combines data from several scans) or partial filtration (a novel method for treating data from so-called not-found spots) had with few exceptions high sensitivities. These methods gave considerable higher sensitivities than some commonly used analysis methods. Conclusion: The use of spike-in experiments is a powerful approach for evaluating microarray preprocessing procedures. Analyzed data are characterized by properties of the observed log-ratios and the analysis' ability to detect differentially expressed genes. If bias is not a major problem; we recommend the use of either the CM-procedure or partial filtration.

Time-gated luminescence acquisition for biochemical sensing: miRNA detection*Relacionar en OpeAire*

Luminescence emission is a multidimensional phenomenon comprising a time-domain layer defined by its excited-state kinetics and corresponding lifetime, which is specific to each luminophore and depends on environmental conditions. This feature allows for the discrimination of luminescence signals from species with a similar spectral profile but different lifetimes by time-gating (TG) the acquisition of luminescence. This approach represents an efficient tool for removing unwanted, usually short-lived, signals from scattered light and fluorescence interferents using luminophores with a long lifetime. Due to the emergence of time-resolved techniques using rapid excitation and acquisition methods (i.e., pulsed lasers and single-photon timing acquisition) and new long-lifetime luminophores (i.e., acridones, lanthanide complexes, nanoparticles, etc.), TG analyses can be easily applied to relevant chemical and biochemical issues. The successful application of TG to important biomedical topics has attracted the attention of the R&D industry due to its potential in the development and patenting of new probes, methods and techniques for drug discovery, immunoassays, biomarker discovery and biomolecular interactions, etc. Here, we review the technological efforts of innovative companies in the application of TG-based techniques. Among the many currently available biomarkers, circulating microRNAs (miRNAs) have received attention since they are highly specific and sensitive to different pathological stages of numerous diseases and easily accessible from biological fluids. qPCR is a powerful and routine technique used for the detection and quantification of miRNAs, but qPCR may introduce numerous artefacts and low reproducibility during the amplification process, particularly using complex samples. Thus, due to the efficiency of TG in separating short- lived sources of fluorescence common in biological fluids, TG is an ideal approach for the direct detection of miRNAs in liquid biopsies. Recently, great efforts in the use of TG have been achieved. Our contribution is the proposal of a direct detection approach using TG- imagining with single nucleobase resolution.European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 690866 (miRNA-DisEASY)Proyecto CTQ2017-85658-R. Ministerio de Economía y Competitividad/Agencia Estatal deInvestigación/Fondo Europeo de Desarrollo Regional (FEDER