The goal of the TECHGENE project is to incorporate the novel MPS technology in routine diagnostic laboratories for the improved diagnosis of genetically heterogeneous diseases. To meet this goal, key criteria have to be met: accuracy; throughput; completeness and low cost per nucleotide. Also, the novel MPS technology needs to be validated by data obtained with standard Sanger- sequencing based equipment. The following approach is therefore used in the project:
In WPs 1 to 4, we will in each WP focus on a particular technical or qualitative aspect of the medical resequencing approach, i.e. in WP1 the crucial enrichment step by long range PCR will be developed, in WP2 the model for validation will be developed, in WP3 enrichment by array technology will be developed, and in WP4 the development of read-out and data analysis systems will be addressed. Information and developed tools will be exchanged between the participants of the different WPs. In WPs 1 to 4 medical resequencing for a particular model disease with increasing genetic complexity will be developed, making use of the obtained knowledge and tools from the other WPs.
Cost effectiveness and economic health issues, ethical and societal issues and dissemination/training activities will be dealt with in separate WPs (WP 5-7), respectively.
The outline of the work plan in the different work packages is as follows:
Identification of novel mutations in patient samples using existing technologies (WP1-4)
Design of mini-genomes to be analyzed per model disease (WP1-4)
The list of genes to be included in the initial design for the different clinical entities and model diseases is summarized in the WP descriptions. For all genes to be analysed we will screen the entire coding sequence, as well as the promoter region and other regulatory non-coding regions.
Optimisation of enrichment steps for the different MPS platforms (WP1, WP3)
- Enrichment based on long-range PCR, more suitable for smaller regions (max 10 genes), or
- Enrichment based on recently described selector or collector approaches
- Enrichment using customized microarrays, suitable for a wide range of genomic regions.
Validations for the different clinical applications (WP2)
Diagnostic validations will be performed for the different model diseases, to determine clinical sensitivity and specificity.
Development of a read-out and data analysis tool (WP4)
The first goal is the development of a readout and data analysis software package for the medical resequencing approach to be developed in this proposal. This tool has to support other genomics oriented applications from the same central module and has to contain an intuitive user interface, so that users do not need to learn new software for each new method. The second goal is to create a central server that will actually allow the exchange and storage of data in a uniform way. The third and final goal is to develop an automated and integrated tool for interpretation of the possible pathogenic effect of identified DNA sequence variants.