New developments at the Genome Center Maastricht (GCM)2006
The Genome Center is pleased to announce a number of important new developments that will significantly increase our capabilities to support genomics researchers of the UM and azM. Furthermore, due to new investments and increasing demand (package deals) we are able to bring down the costs for most of our activities considerably.

Alma-Grid:A virtual Lab for the Euregio

As cofounder of the Interreg Alma-GRID project (www.alma-grid.eu) the Genome Center will further extend and optimize its infrastructure and stimulate collaborations with sister universities in the Euregion Meuse-Rhine. The alma-grid project aims at establishing a virtual lab and scientific community in this Euregion in order to use expensive, complementary infrastructure and expertise more efficiently and to provide services in the field of genomics, proteomics and bioinfomatics. Investments are being carried out as part of the project in a computer GRID and in software (LIMS). This LIMS of Labvantage (www.labvantage.com) will be the backbone of the project and will facilitate exchanges within the Euregional scientific community. Investigators or laboratories interested to join this initiative or the LIMS application, please feel free to contact us, as we aim to make the scientific community as big and lively as possible.

Sequencing and resequencing
The purchase of a new ABI3730 sequencer due to the joint efforts of university and hospital has increased the sequencing capacity and reduced costs and prices considerably. We are currently automating the entire sequencing pipeline and implementing DNA isolation and pipetting robots to increase sequencing throughput. New software tools, like Mutation Surveyor, for sequence and MLPA analysis allow a much easier and faster interpretation of data.

A major breakthrough has been the implementation of Affymetrix resequencing CHIPs for the mitochondrial DNA (mtDNA). We are currently negotiating to analyze this year about 600 mtDNA CHIPs of €170 each for clinical service and collaborative research.

Protein assays – 96-well luminometer
The GCM has with the support of the research institutes GROW and CARIM purchased a 96-well luminometer to measure bioluminescence (mainly luciferase). The major advantage of a luminometer is its superior sensitivity. A logic extension of transcription profiling work using microarrays includes the functional characterization of promoters that coordinately respond to the particular perturbations that were the focus of the microarray experiment. In such settings it is clear that a higher throughput will spare time and reagents. A medium throughput experiment involving the effect of 500 siRNAs would require less that an hour of measurement time enabling these kind of experiments.

GCM steps into the proteomics field with PamChip kinase profiling
The Genome Center Maastricht has at its disposal a PamStation™ 4, a fully automated 4-array system designed for processing PamChip® 4 Arrays. It is ideal for low to medium sample throughput applications and assay development. The ‘heart’ of PamChip technology is the use of sheets of a micro porous material as the solid support for manufacturing microarrays.   This material contains millions of 0.2 x 60 micron pores in parallel orientation connecting the top and bottom surfaces. Peptides or antibodies or other proteins are pre-coupled to the large internal surfaces of these pores. Samples containing proteins (or nucleic acid target molecules) are actively “pulsed” backwards and forwards through these pores where they interact by modifying or binding the immobilized peptides or proteins. Such “pulsing”, combined with minimization of diffusion distances, means that equilibration of binding is significantly speeded up. The result is that binding is reduced from hours to minutes depending on the application. In general, monitoring of this binding is possible in real-time, which means that kinetic information is gained for each interaction in question. It is possible to generate up to 400 kinetic curves for each array/sample in parallel.  There are two “of the shelve” PamChip kinase profiling arrays available, one with peptide substrates derived from genuine tyrosine phosphorylated proteins and one for serine/threonine phosphorylated proteins. The tyrosine kinase array contains 144 peptide substrates for tyrosine kinases that can be interrogated independently for their phosphorylation status. Samples of pure kinases or extracts containing tyrosine-kinase activity are actively “pulsed” backwards and forwards through the pores of the arrays. These samples, in presence of ATP, phosphorylate the immobilized  peptide substrates. Furthermore, the effect of varying additional parameters (temperature, salt, presence of inhibitory or competing ligands, etc.) can be interrogated in real-time. This enabling technology has several applications in proteomics: both protein profiling (detection of the presence of members of a sub-proteome in a complex mixture) and functional proteomics.

Genotyping- ABI7900HT Taqman for SNP genotyping
The Genome Center has expanded the Genotyping Unit with an ABI7900HT Taqman. This 384-well Real-Time PCR system is suitable for singleplex SNP-assays in 5µl reaction volumes, which leads to a significant reduction of the cost per sample compared to 96-well based systems. The costs of a typical assay is currently estimated at about €0.30 - €0.35 per SNP genotype. Furthermore, over 2 million SNP assays are already available through the website of Applied Biosystems (Taqman SNP Assays). The Taqman assays are designed and produced by Applied Biosystems and contain 2 PCR primers and 2 allele specific probes. Normally, the assays can be delivered within 2 weeks after ordering. Applied Biosystems will give a refund if assays are not functional. The small scale assay contains enough material for about 1500 samples. The ABI7900HT is therefore suited for projects in which a few hundred to thousands of samples have to be genotyped for a limited number of SNPs.

Affymetrix Targeted Genotyping (Megallele)- system
As the only Affymetrix corelab in the Netherlands, the GCM has recently upgraded the Affymetrix platform (http://www.affymetrix.com/) to a Megallele system. This has a large number of advantages. We can now scan 5 µm features, enabling us to analyse the newest generation of GeneChips like the 500.000 SNP chip for whole genome association studies or CGH, the tiling arrays for detailed unbiased chromosomal analysis and the all exon chips (containing all confirmed and predicted exons in the human genome). Furthermore, this upgrade makes it now possible to run and analyse custom SNP-chips (3K, 5K, 10K and 20K) with the Megallele MIP assays developed by Parallele (Targeted Genotyping). It should be clear that this upgrade significantly improves our 'genomics-toolbox' but also, the use of smaller features will lead to reduced costs per data point.


Bioinformatics
Planning a new study or writing a grant, and in need of help for designing your experiment or with statistical issues? Do not hesitate to contact us for advise to insure that you shall be collecting all the proper information to analyze and answer your questions of interest. We are also pleased to collaborate with you if you need any assistance in analyzing the data you have collected.