CORDIS
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CORDIS

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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

Project information

Grant agreement ID: 278204

Status

Closed project

  • Start date

    1 January 2012

  • End date

    31 December 2015

Funded under:

FP7-HEALTH

  • Overall budget:

    € 8 434 176,51

  • EU contribution

    € 5 998 788

Coordinated by:

DANMARKS TEKNISKE UNIVERSITET

Denmark

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.

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

PHILIPS ELECTRONICS NEDERLAND BV

Netherlands

EU Contribution

€ 273 604

ROCHE DIAGNOSTICS GMBH

Germany

EU Contribution

€ 12 295,85

GENOTYPE2PHENOTYPE LTD

United Kingdom

EU Contribution

€ 333 382,92

DIAGENODE

Belgium

EU Contribution

€ 481 730,17

OXFORD NANOPORE TECHNOLOGIES LTD

United Kingdom

NIL TECHNOLOGY APS

Denmark

EU Contribution

€ 526 379,59

BIOCOMPUTING PLATFORMS LTD OY

Finland

EU Contribution

€ 278 200

FLUIGENT SA

France

EU Contribution

€ 227 237,01

FASTERIS SA

Switzerland

EU Contribution

€ 670 600

DNA ELECTRONICS LTD

United Kingdom

PHILIPS BIOCELL AS

Denmark

EU Contribution

€ 681 010

GENOTYPE2PHENOTYPE LLC

United States

EU Contribution

€ 215 730,50

Project information

Grant agreement ID: 278204

Status

Closed project

  • Start date

    1 January 2012

  • End date

    31 December 2015

Funded under:

FP7-HEALTH

  • Overall budget:

    € 8 434 176,51

  • EU contribution

    € 5 998 788

Coordinated by:

DANMARKS TEKNISKE UNIVERSITET

Denmark