Informace o projektu
APERIM - Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy
(APERIM)
- Kód projektu
- 633592
- Období řešení
- 5/2015 - 4/2018
- Investor / Programový rámec / typ projektu
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Evropská unie
- Horizon 2020
- Health, demographic change and wellbeing (Societal Challenges)
- Fakulta / Pracoviště MU
- Středoevropský technologický institut
Cancer treatment platforms that involve the use of the adaptive immune system have demonstrated profound tumour regressions including complete cure. Importantly, technological advances in next-generation sequencing (NGS) allow for the first time the development of personalised cancer immunotherapies that target patient specific mutations. However, clinical application is currently hampered by specific bottlenecks in bioinformatics, which we aim to address in this proposal.
The overall objective of our trans-disciplinary network of leading experts in bioinformatics and cancer immunology is to develop an advanced bioinformatics platform for personalised cancer immunotherapy (APERIM). Specifically we aim to develop:
1) database for the integration of NGS data, images of whole tissue slides of tumour sections, and clinical data. To enhance the usability and the data sharing we will use semantic web technologies, and will provide standardised interfaces to a set of analytical tools.
2) tools for automated quantification of tumour-infiltrating lymphocytes using whole tissue slide images and NGS data for patient stratification.
3) analytical pipeline for NGS-guided individualised cancer vaccines including crucial NGS data analysis and epitope selections components for the selection of vaccination targets.
4) a method for deriving TCR sequences from NGS data and predicting TCR specificity.
[BioInfer] 2
We will achieve these aims using unique training and validation datasets available to the
consortium. We will develop user-friendly software modules as well as analytical standard
operating procedures for clinical use, and apply the bioinformatics platform in clinical settings. The
bioinformatics platform will considerably accelerate the clinical translation and maximise the
accessibility and utility of biomedical data in research and medicine.
Publikace
Počet publikací: 3
2017
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Antigen receptor repertoire profiling from RNA-seq data
Nature biotechnology, rok: 2017, ročník: 35, vydání: 10, DOI
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Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries
BMC Genomics, rok: 2017, ročník: 18, vydání: JUN, DOI
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MAGERI: Computational pipeline for molecular-barcoded targeted resequencing
PLoS Computational Biology, rok: 2017, ročník: 13, vydání: 5, DOI