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Genomic diagnostics beyond the sequence

Objective

Cytogenetic diagnostic approaches provide information on the single-chromosome level but suffer from low resolution and throughput. In contrast, next generation sequencing (NGS) based diagnostics provides single base resolution and high throughput but suffer from short reads that prevent analysis of large genomic aberrations as well as being prone to PCR-amplification bias and erasure of epigenetic information. This proposal aims to bridge the gap between these domains by analyzing long individual DNA molecules without PCR-amplification via utilization of emerging optical DNA mapping technologies. We specifically address three types of challenges to current genomic based diagnostics:
1. Loss of relevant information such as DNA damage lesions, rare mutations or epigenetic markers following PCR amplification.
2. Limitations in resolving long-range variations in genomic layout and correlating them with single point mutations, preventing large scale screens.
3. Limitations imposed by the sample such as low sample amounts (micro biopsy, circulating tumor DNA) or inhomogeneous/highly variable samples (bacterial cultures).
We will develop a robust toolbox for integrated genetic and epigenetic profiling of single DNA molecules that will include automated sample preparation of native unamplified DNA as well as the hardware and software platforms and analysis tools for readout, extraction and quantification of medically relevant genomic information. This technology will be used to develop a set of specific, proof of principle diagnostic assays based on optical barcoding of individual DNA molecules. These assays will address:
-Bacterial infections and antibiotic resistance
-Diagnosis/prognosis tools for hematological malignancies
-Spinal Muscular Atrophy
-Early diagnosis of colorectal and lung cancer.
Ultimately our project will provide reagents, prototype DNA barcoding devices and data analysis software ready for large scale validation and early stage commercialization.

Call for proposal

H2020-PHC-2014-2015

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Sub call

H2020-PHC-2014-two-stage

Coordinator

TEL AVIV UNIVERSITY
Net EU contribution
€ 1 147 250,00
Address
Ramat Aviv
69978 Tel Aviv
Israel

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Activity type
Higher or Secondary Education Establishments
Other funding
€ 1 147 250,00

Participants (7)

CHALMERS TEKNISKA HOGSKOLA AB
Sweden
Net EU contribution
€ 840 361,25
Address
-
412 96 Goteborg

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Region
Södra Sverige Västsverige Västra Götalands län
Activity type
Higher or Secondary Education Establishments
Other funding
€ 840 361,25
LUNDS UNIVERSITET
Sweden
Net EU contribution
€ 799 863,75
Address
Paradisgatan 5c
22100 Lund

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Region
Södra Sverige Sydsverige Skåne län
Activity type
Higher or Secondary Education Establishments
Other funding
€ 799 863,75
TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Israel
Net EU contribution
€ 844 475,00
Address
Senate Building Technion City
32000 Haifa

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Activity type
Higher or Secondary Education Establishments
Other funding
€ 844 475,00
KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium
Net EU contribution
€ 778 312,49
Address
Oude Markt 13
3000 Leuven

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Region
Vlaams Gewest Prov. Vlaams-Brabant Arr. Leuven
Activity type
Higher or Secondary Education Establishments
Other funding
€ 778 312,49
GENOMIC VISION SA
France
Net EU contribution
€ 674 497,50
Address
80/84 Rue Des Meuniers
92220 Bagneux

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SME

The organization defined itself as SME (small and medium-sized enterprise) at the time the Grant Agreement was signed.

Yes
Region
Ile-de-France Ile-de-France Hauts-de-Seine
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Other funding
€ 674 497,50
THE UNIVERSITY OF BIRMINGHAM
United Kingdom
Net EU contribution
€ 703 578,75
Address
Edgbaston
B15 2TT Birmingham

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Region
West Midlands (England) West Midlands Birmingham
Activity type
Higher or Secondary Education Establishments
Other funding
€ 703 578,75
IMPASARA LIMITED
United Kingdom
Net EU contribution
€ 245 687,35
Address
43-45 Dorset Street 2nd Floor
W1U 7NA London

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SME

The organization defined itself as SME (small and medium-sized enterprise) at the time the Grant Agreement was signed.

Yes
Region
London Inner London — West Westminster
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
Other funding
€ 245 687,35