title: A novel RNA sequencing data analysis method for cell line authentication.
abstract: We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.
authors.affiliation: School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Fasterius
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Cinzia
authors.initials: C
authors.lastname: Raso
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Susan
authors.initials: S
authors.lastname: Kennedy
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Nora
authors.initials: N
authors.lastname: Rauch
authors.affiliation: Science for Life Laboratory, Dept of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
authors.forename: Pär
authors.initials: P
authors.lastname: Lundin
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland.|Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.|School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: Walter
authors.initials: W
authors.lastname: Kolch
authors.affiliation: School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.|Science for Life Laboratory, Stockholm, Sweden.
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.affiliation: School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Cristina
authors.identifier: http://orcid.org/0000-0001-6990-1905
authors.initials: C
authors.lastname: Al-Khalili Szigyarto
mesh_terms: D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics / Q000473:pathology; D004252:DNA Mutational Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D020022:Genetic Predisposition to Disease / Q000235:genetics; D045325:HCT116 Cells; D019073:HT29 Cells; D006801:Humans; D009154:Mutation; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: C117307:KRAS protein, human; D016283:Proto-Oncogene Proteins p21(ras)