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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.

Field of science

  • /natural sciences/biological sciences/genetics and heredity/mutation
  • /natural sciences/computer and information sciences/software
  • /medical and health sciences/clinical medicine/oncology/cancer
  • /medical and health sciences/basic medicine/pharmacology and pharmacy/drug resistance/antibiotic resistance
  • /natural sciences/computer and information sciences/data science/data analysis

Call for proposal

H2020-PHC-2014-two-stage
See other projects for this call

Funding Scheme

RIA - Research and Innovation action

Coordinator

TEL AVIV UNIVERSITY
Address
Ramat Aviv
69978 Tel Aviv
Israel
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 1 147 250

Participants (7)

CHALMERS TEKNISKA HOEGSKOLA AB
Sweden
EU contribution
€ 840 361,25
Address
-
41296 Goeteborg
Activity type
Higher or Secondary Education Establishments
LUNDS UNIVERSITET
Sweden
EU contribution
€ 799 863,75
Address
Paradisgatan 5C
22100 Lund
Activity type
Higher or Secondary Education Establishments
TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY
Israel
EU contribution
€ 844 475
Address
Senate Building Technion City
32000 Haifa
Activity type
Higher or Secondary Education Establishments
KATHOLIEKE UNIVERSITEIT LEUVEN
Belgium
EU contribution
€ 778 312,49
Address
Oude Markt 13
3000 Leuven
Activity type
Higher or Secondary Education Establishments
GENOMIC VISION SA
France
EU contribution
€ 674 497,50
Address
80/84 Rue Des Meuniers
92220 Bagneux
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)
THE UNIVERSITY OF BIRMINGHAM
United Kingdom
EU contribution
€ 703 578,75
Address
Edgbaston
B15 2TT Birmingham
Activity type
Higher or Secondary Education Establishments
IMPASARA LIMITED
United Kingdom
EU contribution
€ 245 687,35
Address
43-45 Dorset Street 2Nd Floor
W1U 7NA London
Activity type
Private for-profit entities (excluding Higher or Secondary Education Establishments)