Objective
We propose a technology that will sit at the front-end of sequencing pipelines, present and future, and will significantly enhance the quality and throughput of DNA sequencing.
Although much attention has been given to throughput/cost of the sequencing process itself, the same cannot be said for the preparation of samples. Identified bottlenecks are (1) sequencing technologies require days of upfront sample preparation which is further increased when sequencing selected parts of the genome; (2) genome assembly relies on computationally intensive comparisons to the reference genome because existing technologies produce short sequence reads; (3) it is difficult to begin with small amounts of sample material comprising micro-biopsies and single cells.
The CELL-O-MATIC project will synergize efforts from SMEs, academics and large companies to address these bottlenecks by developing chip-based systems that process DNA from individual cells, ready for next generation high-throughput sequencing.
Single cell analysis has numerous applications in systems biology but we will emphasize DNA isolation and sequencing from circulating tumor cells (CTC), which have a strong prognostic value in cancer management.
A second innovation will be to develop methods that enable up to whole chromosome lengths of DNA to be contiguously mapped using nanofluidics. The inclusion of nanofluidics makes the project particularly distinctive and introduces European SMEs to an area that so far has been the domain of US companies.
A modular prototype comprising, a chip, fluid and thermal control, sonication and optical detection will be developed. Samples prepared using CELL-O-MATIC technology will be benchmarked in a high throughput environment with samples prepared by existing methods. Finally, the information obtained from the CELL-O-MATIC processed sample material will be validated for its utility as an aid to clinical decision making.
Fields of science
Call for proposal
FP7-HEALTH-2011-two-stage
See other projects for this call
Funding Scheme
CP-FP - Small or medium-scale focused research projectCoordinator
2800 Kongens Lyngby
Denmark
See on map
Participants (13)
OX1 2JD Oxford
See on map
5656 AG Eindhoven
See on map
Participation ended
68305 Mannheim
See on map
Participation ended
BD1 3BN BRADFORD
See on map
4102 Seraing
See on map
Participation ended
OX4 4GA Oxford
See on map
2800 Kongens Lyngby
See on map
02130 Espoo
See on map
94270 Le Kremlin-Bicetre
See on map
1228 PLAN LES OUATES
See on map
Participation ended
WCIN 2EB LONDON
See on map
3450 ALLEROD
See on map
02138 CAMBRIDGE
See on map