|EM Algorithm for Gene Copy Number Estimation Using TaqMan® Assays|
Catalin Barbacioru, Kelly Li, Caifu Chen and Raymond Samaha
Recently, TaqMan® assays have been developed for detection of genetic variation at gene level using primers and probes designed for genomic DNA sequences. The R package TaqGCN contains classes and methods that can be used for data reading and plotting, and for predicting gene copy number.
|EasyBeacons™ - new Probes Ideal for Realtime PCR Detection of Methylation Status of Single CpG Duplets and SNPs|
K. Skadhauge, C. Nielsen & U.B. Christensen
The EasyBeacons™ presented here are based on the novel technology Intercalating Nucleic Acid, INA®, linked to a fluorophore and a quencher. INA® is composed of normal DNA nucleotides and Intercalating Pseudo Nucleotides (IPNs). The fact that the EasyBeacons™ are mostly composed of normal DNA nucleotides means that in many respects EasyBeacons™ behave like DNA based probes, allowing use of standard buffers, primers and enzymes and hence reduces the optimisation efforts.
|Determination of the Autoantibody Repertoire in Autoimmune Diseases with Factor Protein Arrays – A new Approach to Personalized Therapies|
A. Lueking, C. Gutjahr, V. Trappe, M. Ciupke, A. Kowald, K. Schulte, S. Cleves, T. Niehues, S. Schimrigk, M. Schneider, H. E. Meyer, Stefan Müllner and Jens Beator
Recently, we have presented a strategy to identify new marker molecules characteristic for Alopecia areata by combining protein microarray technology with the use of large cDNA expression libraries (Lueking et al., 2005). This strategy is now applied to Juvenile idiopathic Arthritis (JIA), Rheumatoid Arthritis (RA) and Multiple Sclerosis (MS) in a BMBF-funded project.
|Real-Time Multiplex Rt-PCR on Circulating Tumor Cells|
Anieta M. Sieuwerts, Stefan Sleijfer, Jaco Kraan, Joan Bolt-de Vries, Jan-Willem Gratama, John WM Martens and John A. Foekens
Using the CTC kit (CellSearch™), cells that attached to anti-EpCAM Moab were immunomagnetically separated and used for analysis of a selected pilot set of 32 genes by real time RT-PCR. This study shows the feasibility of multiple gene expression analysis on RNA isolated from only one tumor cell. Most importantly, expression analysis of several tumor-specific genes in blood samples containing only 2 tumor cells is already possible.
|Novel Fluidics Microbead Trap/Flow Cell Enhances Speed/Sensitivity of Bead-Based Bioassays Up to 5-Fold|
RM Ozanich, CJ Bruckner-Lea, JW Grate, MG Warner, BP Dockendorff, KC Antolick, HC Edberg, LH Johnson, AN Easterday
Pacific Northwest National Laboratory (PNNL) has developed a micro/nano particle trap that allows surface-functionalized magnetic or non-magnetic particles to be trapped with subsequent perfusion of sample, reagents and wash solutions, yielding significant (up to 5-fold) improvements in assay speed and sensitivity, while significantly reducing sample matrix effects.
|Utilizing High Speed Photography to Optimize Low Volume Dispensing Conditions |
Mary Cornett, Mitch Gordon and Anca Rothe
In this study we use high-speed photography as a feedback mechanism for adjusting the Nanodrop instrument dispense settings to improve the positional dispense accuracy of low volume (nanoliter) drops. These same parameters can be investigated, with various fluid classes, to reduce deleterious effects on dispensing performance such as deflected streams, satellite formation, secondary pulses and drop deformation.
|Usage of Low-Density Oligonucleotide Microarrays for Prognosis Prediction of Colorectal Cancer Patients|
Slabý O., Garajová I., Svoboda M., Fabian P., Svoboda M., Šmerdová T. and Vyzula R.
This study aimed to find individual up/down-regulated genes associated with progression and metastatic potential of colorectal cancers using low-density oligonucleotide microarrays spotted with genes known to be involved in process of metastasis development. We suppose that focusing on a particular biological pathway may be more useful than genome-wide screening for our purposes.
|Diagnosis of Aortic Aneurysm from Gene Expression Profiling of Peripheral Blood|
Catalin Barbacioru,Yulei Wang, Dov Shiffman, Olga Iakoubova, Sriram Balasubramanian, Julie Blake, John Elefteriades and Raymond Samaha
We report in this study that gene expression profiles of peripheral blood cells may allow early detection and diagnosis of aortic aneurysm. Gene expression profiles of peripheral blood samples collected from 58 individuals diagnosed with thoracic aortic aneurysm (cases) and 36 normal individuals (controls) were analyzed using the Applied Biosystems Expression Array Systems and Human Genome Survey Microarrays.
|New Platforms and Systems for DNA Microarrays|
B. Henze, B. Saal, D. Drutschmann, K. Wellesen and P. Schüßler
Operon has designed probes of different lengths to various positions in the Open Reading Frames (ORFs) and the results clearly show that 70mers offer the optimal combination of specificity and sensitivity.