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The misidentification and contamination of CCLs are serious problems, leading to unreliable results and waste of resources. Current methods for CCL authentication are mainly based on the CCL-specific genetic polymorphism, whereas no method is available for CCL authentication using gene expression profiles. Here, we developed a novel method and homonymic web server (CCLA, Cancer Cell Line Authentication, http:\/\/bioinfo.life.hust.edu.cn\/web\/CCLA\/) to authenticate 1291 human CCLs of 28 tissues using gene expression profiles. CCLA showed an excellent speed advantage and high accuracy for CCL authentication, a top 1 accuracy of 96.58 or 92.15% (top 3 accuracy of 100 or 95.11%) for microarray or RNA-Seq validation data (719 samples, 461 CCLs), respectively. To the best of our knowledge, CCLA is the first approach to authenticate CCLs using gene expression data. Users can freely and conveniently authenticate CCLs using gene expression profiles or NCBI GEO accession on CCLA website.<\/jats:p>","DOI":"10.1093\/bib\/bbaa093","type":"journal-article","created":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T07:19:14Z","timestamp":1589440754000},"source":"Crossref","is-referenced-by-count":9,"title":["CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles"],"prefix":"10.1093","volume":"22","author":[{"given":"Qiong","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0183-2373","authenticated-orcid":false,"given":"Mei","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chun-Jie","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,6,8]]},"reference":[{"key":"2021052109500298900_ref1","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1242\/dmm.028274","article-title":"In vivo models in breast cancer research: progress, challenges and future directions","volume":"10","author":"Holen","year":"2017","journal-title":"Dis Model Mech"},{"key":"2021052109500298900_ref2","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The cancer cell line encyclopedia enables predictive modeling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2021052109500298900_ref3","doi-asserted-by":"crossref","first-page":"D955","DOI":"10.1093\/nar\/gks1111","article-title":"Genomics of drug sensitivity in cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells","volume":"41","author":"Yang","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2021052109500298900_ref4","doi-asserted-by":"crossref","first-page":"e1002477","DOI":"10.1371\/journal.pbio.1002477","article-title":"Authentication: a standard problem or a problem of standards?","volume":"14","author":"Capes-Davis","year":"2016","journal-title":"PLoS Biol"},{"key":"2021052109500298900_ref5","doi-asserted-by":"crossref","first-page":"e0186281","DOI":"10.1371\/journal.pone.0186281","article-title":"The ghosts of HeLa: how cell line misidentification contaminates the scientific literature","volume":"12","author":"Horbach","year":"2017","journal-title":"PLOS One"},{"key":"2021052109500298900_ref6","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1038\/nrc2852","article-title":"Cell line misidentification: the beginning of the end","volume":"10","author":"Development Organization Workgroup Asn-0002 ATCCS","year":"2010","journal-title":"Nat Rev Cancer"},{"key":"2021052109500298900_ref7","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1126\/science.1259110","article-title":"Fixing problems with cell lines","volume":"346","author":"Lorsch","year":"2014","journal-title":"Science"},{"key":"2021052109500298900_ref8","doi-asserted-by":"crossref","first-page":"e2001438","DOI":"10.1371\/journal.pbio.2001438","article-title":"The need for a worldwide consensus for cell line authentication: experience implementing a mandatory requirement at the international journal of cancer","volume":"15","author":"Fusenig","year":"2017","journal-title":"PLoS Biol"},{"key":"2021052109500298900_ref9","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1038\/bjc.2014.166","article-title":"Guidelines for the use of cell lines in biomedical research","volume":"111","author":"Geraghty","year":"2014","journal-title":"Br J Cancer"},{"key":"2021052109500298900_ref10","first-page":"35","article-title":"Authentication of scientific human cell lines: easy-to-use DNA fingerprinting","volume":"290","author":"Dirks","year":"2005","journal-title":"Methods Mol Biol Clifton NJ"},{"key":"2021052109500298900_ref11","doi-asserted-by":"crossref","first-page":"2446","DOI":"10.1093\/nar\/gkn089","article-title":"SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines","volume":"36","author":"Demichelis","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2021052109500298900_ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/ijc.25242","article-title":"Check your cultures! 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