Project description
Understanding and predicting ploidy in pan-sarcomas
Sarcomas are rare cancers that arise from mesenchymal tissues and are marked by complex genetic profiles and widespread aneuploidy. Current methods for assessing tumour ploidy, primarily through sequencing, face limitations in accuracy, affordability, and accessibility. Supported by the Marie Skłodowska-Curie Actions programme, the SImPloidy project aims to develop a more accessible and accurate approach to predicting tumour ploidy using haematoxylin and eosin (H&E)-stained whole slide images. The project will optimise a model for segmenting sarcoma cell nuclei and predicting ploidy at the single-nucleus level, validating the method against existing standards. Drawing on a dataset of images from more than 40 sarcoma types, it will offer unprecedented insights into ploidy across a broad range of sarcomas.
Objective
Sarcomas are a diverse group of rare cancers that originate from mesenchymal tissues. The rarity and intrinsic genetic complexity of sarcoma have made it one of the most challenging tumours to diagnose and consequently, to treat. A key genetic characteristic of many sarcoma subtypes is aneuploidy. Aneuploidy is defined by losses and gains of chromosomes, and is a prognostic marker for a variety of sarcomas. Currently, tumour ploidy are most commonly estimated using copy number alteration calling software on whole-exome and whole-genome sequencing data. However, the unsatisfactory accuracy, economic costs, infrastructure requirements, lack of trained personnel in interpreting the results is still an impediment to global adoption of these techniques for routine use, particularly in less developed economies.
The goal of this research is to develop a more accessible and more accurate approach for predicting tumour ploidy based on Hematoxylin and Eosin (H&E) stained whole slide images. The specific aims of the project are to 1) optimise a nucleus segmentation model for annotating sarcoma nuclei in H&E images, and predict tumour ploidy at single-nucleus level, 2) thoroughly validate image ploidy and systemically compare it with existing ploidy estimation methods, 3) evaluate the diagnostic and prognostic value of the image ploidy, and investigate its underlying biological mechanisms in pan-sarcoma.
This work will be carried out at University College London and the Royal National Orthopaedic Hospital, under the supervision of Prof. Adrienne Flanagan and Dr. Nischalan Pillay. The host labs have collected and scanned whole slide images of more than 40 types of bone and soft tissue sarcomas from more than 8000 cases, of which 1,600 cases have paired WGS and transcriptome sequencing. The access to this unique dataset will give an unprecedented opportunity to study ploidy at single-nucleus level in pan-sarcoma.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences computer and information sciences software
- natural sciences biological sciences genetics RNA transcriptomes
- medical and health sciences clinical medicine oncology
- medical and health sciences basic medicine pathology
- natural sciences biological sciences genetics chromosomes
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
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Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.2 - Marie Skłodowska-Curie Actions (MSCA)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
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Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-TMA-MSCA-PF-EF - HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships
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Call for proposal
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(opens in new window) HORIZON-MSCA-2024-PF-01
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
WC1E 6BT LONDON
United Kingdom
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