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Genome Med. 2015 Nov 20;7:118. doi: 10.1186/s13073-015-0240-5.

TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.

Author information

1
TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany.
2
Present address: European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany.
3
TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University, Freiligrathstrasse 12, 55131, Mainz, Germany. boegels@uni-mainz.de.
4
University Medical Center of the Johannes Gutenberg-University Mainz, 55131, Mainz, Germany. boegels@uni-mainz.de.
5
University Medical Center of the Johannes Gutenberg-University Mainz, 55131, Mainz, Germany.
6
Biopharmaceutical New Technologies (BioNTech) Corporation, An der Goldgrube 12, 55131, Mainz, Germany.
7
Present address: Agenus and 4-Antibody AG, Hochbergerstrasse 60C, CH-4057, Basel, Switzerland.

Abstract

Human cancer cell lines are an important resource for research and drug development. However, the available annotations of cell lines are sparse, incomplete, and distributed in multiple repositories. Re-analyzing publicly available raw RNA-Seq data, we determined the human leukocyte antigen (HLA) type and abundance, identified expressed viruses and calculated gene expression of 1,082 cancer cell lines. Using the determined HLA types, public databases of cell line mutations, and existing HLA binding prediction algorithms, we predicted antigenic mutations in each cell line. We integrated the results into a comprehensive knowledgebase. Using the Django web framework, we provide an interactive user interface with advanced search capabilities to find and explore cell lines and an application programming interface to extract cell line information. The portal is available at http://celllines.tron-mainz.de.

PMID:
26589293
PMCID:
PMC4653878
DOI:
10.1186/s13073-015-0240-5
[Indexed for MEDLINE]
Free PMC Article

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