CLASTR: The Cellosaurus STR similarity search tool ‐ A precious help for cell line authentication

• Published in: International journal of cancer 2020-03, Vol.146 (5), p.1299-1306
• Main Authors: Robin, Thibault, Capes‐Davis, Amanda, Bairoch, Amos
• Format: Article
• Language: English
• Subjects: Animals; authentication; Biomarkers - analysis; Cancer; cell culture; Cell Line; Cell Line Authentication - methods; Cell lines; Contamination; Data Mining - methods; Databases, Factual; DNA Fingerprinting; Dogs; Humans; Medical research; Mice; Microsatellite Repeats - genetics; misidentification; Researchers; Software; STR profiling
• ISSN: 0020-7136; 1097-0215
• DOI: 10.1002/ijc.32639

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 July 31, 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. What's new? Despite increased awareness, cell line cross‐contamination and misidentification remain a major source of erroneous experimental results in biomedical research. Nowadays, researchers performing experiments on cell lines are thus expected to ensure their authenticity using short‐tandem repeat (STR) profiling. The Cellosaurus, which compiles all publicly available STR profiles, has become a valuable knowledge resource for this purpose. However, the database lacked a dedicated tool allowing a similarity search for a query STR profile. Here, the authors present CLASTR, the Cellosaurus STR similarity search tool that aims to facilitate the authentication process and the detection of potentially cross‐contaminated or misidentified cell lines.