Project update from the Steering Committee meeting in Budapest
NMD-chip is a scientific project funded by the European Union under its Seventh Framework Programme (FP7). Its aim is to design, develop and validate new sensitive high-throughput DNA microarrays ("gene chips") to diagnose patients affected by neuromuscular disorders.
Within the project, chips are being designed for the diagnosis of Duchenne / Becker muscular dystrophies (DMD/BMD), limb girdle muscular dystrophies (LGMD), congenital muscular dystrophies (CMD), and hereditary motor-sensory neuropathies or Charcot-Marie-Tooth neuropathies (CMT).
Additionally, "candidate gene chips" are being developed to look for mutations in patients who have a neuromuscular disorder where the disease-causing mutation has not yet been discovered.
NMD-chip was launched in 2008 and the project is now entering its final phase, with its official end date being 31 September 2010. At the penultimate Steering Committee meeting held in Budapest in March, project partners gathered for a progress update and an analysis of the final stage of the project and the next steps to be taken to advance cutting-edge neuromuscular diagnostics in 2012 and beyond.
Partners provided detailed updates on the individual "workpackages" that make up the project, in particular the experiments taking place to refine and validate the chips. Work on the design of the "known gene" chips officially finished in January 2011. A second comparative genomic hybridization (CGH) array design for LGMD/CMD has been performed, and sequence capture (SC) array design has been initiated and tests are ongoing. Chips for the 50 known LGMD/DMD/CMD genes are being manufactured, and the CMT gene chip is also underway.
Extensive testing and technical validation using control DNA is essential to refine the chip design and validate its reliability, and robust methods of data analysis have to be implemented in order to assess the quality of each experiment. Development and testing of software to enable analysis of the vast amounts of data created by every single experiment, and setting criteria for this analysis, is a crucial part of the project.
For the candidate gene chips, lists of candidate genes were established for LGMD/CMD/CMT, with the same candidate lists used for both CGH and sequence capture chips. Both types of chip have been ordered and tested. Due to rapid technological advances during the lifetime of the project, it was felt that "in solution" capture might be a preferable method to "on array" capture – the initial chip designs used “on array” capture but comparison with a new design using "in solution" capture is now ongoing.
Collecting all the variant data obtained in the different labs using the chips by means of a reference materials database is a major part of the work, as it is essential to build up a database of variants that can be analysed and compared to assess pathogenicity. Additionally, recent successes with exomes generate a vast number of variants to assess, and thus it is very important to use consistent software and thresholds and to share all findings from the start to sort interesting/recurrent variants.
Overall, the NMD-chip project has been an excellent opportunity to advance the field of neuromuscular diagnostics. It has provided a platform for international collaboration across Europe and improved links with US specialist groups working in the same area. However, the speed of evolution of the technology has exceeded the estimates prior to the start of the project, and this has necessitated modifications to chip design and changes in the project’s focus. The formal end of the EU project in September will by no means be the end of the work, and the project partners will continue to work together to optimise the chips and build on the technological advances that have taken place, making use of further grant opportunities where possible.
Running costs for next-generation sequencing are still high. Not all labs can afford platforms/equipment for next-generation sequencing, but prices are falling and academic/private partnerships toward installation of next-generation sequencing machines for diagnostics are occurring in some places. The new tools will most likely continue to evolve very fast, given the speed of the technological improvements arising in whole genome exploration techniques (in-solution and next-generation-sequencing-only techniques). The key questions for the future of molecular genetic diagnostics include validation, data versus result, the need for bio-informatics tools that can cope with the data analysis tasks, and the ethical issues surrounding the collection of variants and possible unexpected findings. The final Steering Committee meeting in London at the end of September will formally conclude the project but has to be regarded as another step towards further work in this rapidly developing field.
