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Development of a complete integrated SNP analysis system

Final Report Summary - SNIP2CHIP (Development of a complete integrated SNP analysis system)

The main goal of the research is the development of a novel integrated mutation detection system, in which each of its modules have innovative solutions for deoxyribonucleic acid (DNA) extraction, amplification, and DNA microarray-based detection with either optical or magnetic detection. The project has demonstrated working modules for all of the required building blocks, and integration was demonstrated with some of the modules as a proof of concept for a complete integrated system. The integrated genetic analysis system architecture provides the basis for a novel solution for near-patient genetic analysis. However, the different modules which were developed within the system are also highly innovative.

The next step was to facilitate the commercialisation of the SNIP2CHIP integrated system involves optimising the device and system architectures to facilitate high volume manufacturing while ensuring the level of accuracy and reproducibility required for clinical diagnostics is maintained. Due to the modular nature of the system, it is envisaged that commercialisation may involve taking the best solutions which have been generated within the SNIP2CHIP project and combining them with externally sourced optimised modules, to ensure that the best possible system can be available within the shortest timeframe. The key challenge remaining towards product development from the SNIP2CHIP outputs, is to complete the integration of the system as a low cost solution, both for the instrument (e.g. less than EUR 5 000) and the disposable cartridge for each patient sample (e.g. less than EUR 10).

Laboratories face a proliferation of demand for molecular genetic testing for a wider range of diseases. Following the completion of the first draft of the human genome sequence, the results have been translated into medical applications including diagnostics and therapy and promote new concepts in predictive medicine. Several hundred hereditary diseases have already been assigned to specific genes and their mutations. The number of diseases for which genetic tests are available will continue to increase in the coming years. Additionally, genetic testing for predisposition to numerous human malignancies and to multifactorial diseases is being considered, opening up the possibility of making personalised or targeted disease prevention a new paradigm of medicine.

Pharmacogenetics based on common genetic variants influencing effectiveness of pharmaceuticals and aimed at developing and prescribing the right medicine for the right patient signifies another line of future possible applications of single nucleotide polymorphism (SNP) detection in medicine. The core originality of this technology will be the integration of DNA sample preparation and multiple SNP analysis in a single automated system. Despite the growing demand for accurate SNP data for clinical diagnosis of monogenic diseases, no products currently exist which enables multiple SNPs to be screened directly from a blood sample within a fully integrated system.

The project has developed innovative solutions for DNA extraction, amplification and SNP detection (based on optical and magnetic sensing platforms), and the development of a novel integrated system which enables complete processing of all molecular steps necessary to deliver genotype outputs directly from a finger stick blood biopsy. Various potential innovations have been explored with one invention disclosure form (IDF) filed on the optical sensor platform. However, following an in-depth patent review, similar intellectual property (IP) preceding the SNIP2CHIP IDF date was discovered which greatly eroded the potential patentability of the invention.

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