New Technologies

Objectives, deliverables and milestones for Unit 5

Data analysis tools are critical in the process of a genetic diagnosis: they allow the lab to interpret large and complex data and to issue a diagnostic report. It is thus important to propose validation methods to the community for these tools. Our first objective is therefore to apply validation methods developed in Unit 2, in the first instance to sequence analysis tools.

Part of the data analysis process is the interpretation of the variants which are detected. This interpretation is most easily done when the variant has been found previously and its clinical impact has already been shown. In order to improve quality, laboratories are encouraged to look-up existing LSDBs as well as publish validated mutations for the diagnostics community. Automating the process of looking-up and publishing the mutations is foreseen to greatly improve compliance to this process. Automation requires standards to exchange this information, and their introduction is the second objective of this work package. This corresponds to Unit 5's objective of evaluating and supporting new technologies such as databases, their public interfaces, and tools to ensure a unified standard nomenclature of variants.

D5.4/3/5: Report on needs for standards to exchange mutation information for diagnostics and validation of mutation and proposal of standard
D5.4/3/6: Prototypes implementing the standard
D5.4/3/7: Report on tests in laboratories
D5.4/3/1: Report describing the assessment tool for sequencing software
D5.4/3/2: Report describing the assessment tool used on Phenosystems software
D5.4/3/3: Web tool detailing the assessment of sequencing software
D5.4/3/4: Report on the work on double vs single strand sequencing

General objective: Evaluate new and emerging technologies relevant to genetic testing
1. Update and maintain an inventory of (new) technologies relevant to genetic testing.
2. Prioritize new technologies in order of interest and in need for further evaluation by this Unit.
3. Beta testing and technology transfer issues, defining a master technical evaluation/implementation program for new technologies including draft protocols for beta testing.
4. Test the master program and the draft protocols in a pilot beta test project for a key exemplar.

D5.2/3/1: Updated technique database
D5.2/3/2: Evaluation report on the PamGene Flow through Arrays as read out for MLPA
D5.2/3/3: A new short list, of new technologies under evaluation and their level of importance to the testing labs
D5.2/3/4: 1st Evaluation report on the HR-MCA set up for BRCA1
D5.2/3/5: Evaluation of PAP technology

M5.2/3/1: Inventory on new technologies through literature/database search
M5.2/3/2: Negotiations with partners and companies for Beta testing/technical evaluation of new technology (eg. with Innogenetics)
M5.2/3/3: Round table with diagnostic industry representatives
M5.2/3/4: Beta tests ongoing in partner labs for two new technologies
M5.2/3/5: Second international workshop on new technologies in NICE June 2007
M5.2/3/6: Workshop on Flow through Arrays and/or HR-MCA in Leiden

D5.3/3/1: Support database of proprietary technologies and patents within the Network
D5.3/3/2: Report on claims in top-10 diagnostic gene patents in European and Network database
D5.3/3/3: Report on claims in top-20 diagnostic gene patents in European and Network database
D5.3/3/4: Report on claims in top-30 diagnostic gene patents in European and Network database

M5.3/3/1: Database of proprietary technologies and patents available within the Network
M5.3/3/2: Typology of claims in selected top-10 and 20 diagnostic gene patents in European and Network database

General objective: Validate different methods and technologies and generate SOPs.
1. Test the drafted standard program for analytical/technical validation in a pilot project, for example with respect to MLPA, DNA extractions, CSCE, HRMCA. Prepare SOPs and guidelines for these tests for future distribution.
2. Foster introduction of novel methods and technologies into the market.

D5.1/3/1: Publication of a generic SOP for MLPA, using the BRCA 1 gene as a model
D5.1/3/2: New call for technologies 2007 at the ESHG in Nice
D5.1/3/4: Publication of a generic SOP for HRMCA
D5.1/3/5: Publication of a report regarding validation of DNA extraction with Chemagen
D5.1/3/6: Publication of a paper regarding MLPA validation
D5.1/3/7: Publication of a report regarding HRMCA validation
D5.1/3/3: Publication of a generic SOP for automated DNA extraction with the Chemagen system

M5.1/3/1: Writing of a work plan for the validation of HRMCA
M5.1/3/2: Finalize technical validation of MLPA, followed by the collection and analysis of the data from the different laboratories
M5.1/3/3: Optimization of the Chemagen DNA extraction protocol
M5.1/3/4: Organization of meetings to create working groups for validation of CSCE and HRMCA and to discuss the setup
M5.1/3/5: Continue technical evaluation of the Chemagen, regarding concentration, yield, purity, quality, stability, repeatability, reproducibility
M5.1/3/6: Analytical validation and analysis of the data concerning CSCE and HRMCA