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High Throughput Systematic Single Cell Genomics using Micro/Nano-Fluidic Chips for Extracting, Pre-analysing, Selecting and Preparing Sequence-ready DNA

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.

Field of science

  • /natural sciences/biological sciences/genetics and heredity/genome
  • /natural sciences/biological sciences/genetics and heredity/dna

Call for proposal

FP7-HEALTH-2011-two-stage
See other projects for this call

Funding Scheme

CP-FP - Small or medium-scale focused research project

Coordinator

DANMARKS TEKNISKE UNIVERSITET
Address
Anker Engelundsvej 1 Bygning 101 A
2800 Kgs Lyngby
Denmark
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 1 710 434,56
Administrative Contact
Majken Lerche Møller (Ms.)

Participants (13)

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
United Kingdom
EU contribution
€ 588 183,40
Address
Wellington Square University Offices
OX1 2JD Oxford
Activity type
Higher or Secondary Education Establishments
Administrative Contact
Stephen Conway (Dr.)
PHILIPS ELECTRONICS NEDERLAND BV
Netherlands
EU contribution
€ 273 604
Address
High Tech Campus 52
5656 AG Eindhoven
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Patrick Keur (Mr.)
ROCHE DIAGNOSTICS GMBH

Participation ended

Germany
EU contribution
€ 12 295,85
Address
Sandhofer Strasse 116
68305 Mannheim
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Reiner Babiel (Dr.)
GENOTYPE2PHENOTYPE LTD

Participation ended

United Kingdom
EU contribution
€ 333 382,92
Address
St Judes Chambers 103A Manningham Lane
BD1 3BN Bradford
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Kalim Mir (Dr.)
DIAGENODE
Belgium
EU contribution
€ 481 730,17
Address
Rue Du Bois Saint Jean 3 Liege Park Science
4102 Seraing
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Didier Allaer (Dr.)
OXFORD NANOPORE TECHNOLOGIES LTD

Participation ended

United Kingdom
Address
Robert Robinson Avenue - Oxford Science Park 4
OX4 4GA Oxford
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Spike Willcocks (Dr.)
NIL TECHNOLOGY APS
Denmark
EU contribution
€ 526 379,59
Address
Haldor Topsoes Alle 1
2800 Kongens Lyngby
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Theodor Kamp Nielsen (Mr.)
BIOCOMPUTING PLATFORMS LTD OY
Finland
EU contribution
€ 278 200
Address
Innopoli 3 Vaisalantie 6
02130 Espoo
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Anita Eliasson (Ms.)
FLUIGENT SA
France
EU contribution
€ 227 237,01
Address
57-77 Avenue De Fontainebleau
94270 Le Kremlin-bicetre
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Jérémie Weber (Dr.)
FASTERIS SA
Switzerland
EU contribution
€ 670 600
Address
Chemin Du Pont Du Centenaire 109
1228 Plan Les Ouates
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Laurent Farinelli (Dr.)
DNA ELECTRONICS LTD

Participation ended

United Kingdom
Address
John Street 10
WCIN 2EB London
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Patrick Stephansen (Mr.)
PHILIPS BIOCELL AS
Denmark
EU contribution
€ 681 010
Address
Gydevang 42
3450 Allerod
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Tommy Berg (Mr.)
GENOTYPE2PHENOTYPE LLC
United States
EU contribution
€ 215 730,50
Address
30 Elmwood Ave
02138 Cambridge
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Administrative Contact
Kalim Mir (Dr.)