|Profiling formalin-fixed, paraffin-embedded (FFPE) samples on three Agilent microarray platforms|
Grazyna Fedorowicz, Srinka Ghosh, Steve Guerrero, Thomas Wu, and Zora Modrusan
Thousands of formalin-fixed, paraffin-embedded (FFPE) samples from clinical archives are available for retrospective studies. Such samples could provide crucial information for drug target discovery and diagnostics of various diseases. Here we used FFPE samples and their matched fresh-frozen (FF) counterparts to examine their performance on three types of microarrays including whole genome expression, comparative genomic hybridization (CGH) and microRNA.
|Geneset-based cancer survival analysis: On the non-uniform distributiuon of p-values under the null hypothesis|
Esteban Czwan, Benedikt Brors, David Kipling
Although null p-values are assumed to be uniformly distributed in gene expression experiments, the actual distribution often deviates from the assumed distribution. This can incorrectly associate the biology of a geneset with cancer prognosis in geneset-based survival studies. To assess the implications of this, a geneset-based method was developed. This method empirically approximates the distribution of null p-values and tests whether predefined sets of biologically-related genes are associate
|Microfluidic assembly of magnetic gel particles|
C. H. Chen, A. R. Abate, D. Lee, E. M. Terentjev and D. A. Weitz
Monodisperse spherical magnetic gel particles containing asymmetric infrastructure were fabricated by a new microfluidics-based technique using double-emulsion droplet as templates. Double emulsions with functional cores and hydrogel shells were generated by the flow-focusing drop makers with special wettability patterning. Particles were made with a consistently anisotropic internal structure, which leads to their uniform anisotropy to perform the highly rotational controls by applying the magn
|Evaluation of a Novel Approach for the Measurement of RNA Quality|
Timothy Wilkes; Alison Devonshire; Carole Foy
The potential medical applications of microarrays have generated much interest, within the biomedical community. Numerous potential sources of variation have raised concerns regarding assay consistency and data quality. Previous studies have highlighted RNA integrity as having a major effect on data quality. We describe here a comparison of the performance characteristics of the Agilent (Bioanalyser) and Lab901 (Screen Tape System) platforms, and their capacity to determine sample RNA integrity.
|Fabrication and characterization of a fully integrated microdevice for in-vitro single cell assays|
C. Collini, E. Morganti, R. Cunaccia, L. Odorizzi, C. Ress, and L. Lorenzelli (1), A. De Toni, G. Marinaro (2), M. Borgo (3), M. Maschietto (4)
This work presents the microfabrication and preliminary characterization of a fully integrated microdevice for in-vitro single cell assays. This technological platform combines IDEs and MEA-based modules for cell addressed delivery of bio-functionalized nano/microparticles and single cell electroporation respectively.
|Intended transcriptional gene silencing with siRNA to the human Vascular Endothelial Growth Factor (VEGF) promoter results in VEGF repression through sequence-specific off-targeting|
Joshua Moses, Amber Goodchild and Laurent Rivory
SiRNA designed to target the human VEGF gene promoter revealed a putative candidate for transcriptional gene silencing. However, mutation or deletion of the target site demonstrated that the observed VEGF knockdown was the result of a sequence-specific off-target effect. Bioinformatic and microarray analyses of genes implicated in VEGF transcriptional control followed by knockdown and Western blotting experiments presented one candidate, GRB2, as an unintended target of the VEGF promoter-specifi
|Point-of-care testing for prostate cancer diagnosis |
Y. Uludag; I.E. Tothill
This presentation describes the potential of using a new fully automated QCM biosensor and a commercial SPR biosensor for the detection of PSA, a biomarker for prostate cancer. Initially a new buffer was formulated to eliminate 98% of the non-specific human serum protein binding to the sensors. Obtained results indicate that both instruments can be used for the fast and easy detection of PSA (0.29-150 ng/ml) in serum.
|A Web Interface for Automatic Microarray Analysis|
Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
DNA-Microarray technology provides a diagnostic tool for studying cancer and genetic diseases, allowing the experimenter to identify disease related genes and predict the tumour type for new cell samples. However, the statistical analysis of microarray data is a time-consuming and error-prone process. To address this problem we have developed a web interface for automatic DNA-microarray analysis, ArrayMining.net, which guides the user through the analysis process and performs automatic parameter
|A modular and stochastic approach to the study of gene circuits using P systems|
Romero-Campero FJ, Blakes J, Cao H, Camara M, Krasnogor N.
presented at Genomes to Systems Manchester, UK March 17-19 2008