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Int J Cancer. 2019 Aug 24. doi: 10.1002/ijc.32639. [Epub ahead of print]

CLASTR: the Cellosaurus STR Similarity Search Tool A Precious Help for Cell Line Authentication.

Author information

1
CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Rue Michel-Servet 1, Geneva, Switzerland.
2
Microbiology and Molecular Medicine Department, Faculty of Medicine, University of Geneva, Switzerland.
3
Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CMU, Rue Michel-Servet 1, Geneva, Switzerland.
4
Computer Science Department, Faculty of Sciences, University of Geneva, Switzerland.
5
CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.

Abstract

Despite an increased awareness of the problematic of cell line cross-contamination and misidentification, it remains nowadays a major source of erroneous experimental results in biomedical research. To prevent it, researchers are expected to frequently test the authenticity of the cell lines they are working on. STR profiling was selected as the international reference method to perform cell line authentication. While the experimental protocols and manipulations for generating a STR profile are well described, the available tools and workflows to analyze such data are lacking. The Cellosaurus knowledge resource aimed to improve the situation by compiling all the publicly available STR profiles from the literature and other databases. As a result, it grew to become the largest database in terms of human STR profiles, with 6,474 distinct cell lines having an associated STR profile (release 31, July 2019). Here we present CLASTR, the Cellosaurus STR similarity search tool enabling users to compare one or more STR profiles with those available in the Cellosaurus cell line knowledge resource. It aims to help researchers in the process of cell line authentication by providing numerous functionalities. The tool is publicly accessible on the SIB ExPASy server (https://web.expasy.org/cellosaurus-str-search) and its source code is available on GitHub under the GPL-3.0 license. This article is protected by copyright. All rights reserved.

KEYWORDS:

STR profiling; authentication; cell culture; cell lines; contamination; misidentification

PMID:
31444973
DOI:
10.1002/ijc.32639

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