{"doi":"10.3390/genes15101254","title":"Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long-Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease","abstract":"BACKGROUND/OBJECTIVES: The rat osteosarcoma cell line UMR-106 is widely used for the study of bone cancer biology but it has not been well characterized with modern genomic methods. METHODS: To better understand the biology of UMR-106 cells we used a combination of optical genome mapping (OGM), long-read sequencing nanopore sequencing and RNA sequencing.The UMR-106 genome was compared to a strain-matched Sprague-Dawley rat for variants associated with human osteosarcoma while expression data were contrasted with a public osteoblast dataset. RESULTS: Using the COSMIC database to identify the most affected genes in human osteosarcomas we found somatic mutations in Tp53 and H3f3a. OGM identified a relatively small number of differences between the cell line and a strain-matched control animal but did detect a ~45 Mb block of amplification that included Myc on chromosome 7 which was confirmed by long-read sequencing. The amplified region showed several blocks of non-contiguous rearranged sequence implying complex rearrangements during their formation and included 14 genes reported as biomarkers in human osteosarcoma, many of which also showed increased transcription. A comparison of 5mC methylation from the nanopore reads of tumor and control samples identified genes with distinct differences including the OS marker Cdkn2a. CONCLUSIONS: This dataset illustrates the value of long DNA methods for the characterization of cell lines and how inter-species analysis can inform us about the genetic nature underlying mutations that underpin specific tumor types. The data should be a valuable resource for investigators studying osteosarcoma, in general, and specifically the UMR-106 model.","journal":"Genes","year":2024,"id":503820,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8912,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":469637,"name":"David W. Mohr","orcid":"0000-0002-2198-3822","position":1,"is_corresponding":false},{"id":1338281,"name":"William A Littrell","orcid":null,"position":2,"is_corresponding":false},{"id":994253,"name":"Reshma Babu","orcid":"0000-0002-0847-4214","position":3,"is_corresponding":false},{"id":1211853,"name":"Michelle Kokosinski","orcid":null,"position":4,"is_corresponding":false},{"id":1337845,"name":"Victoria Stinnett","orcid":"0000-0003-0317-1385","position":5,"is_corresponding":false},{"id":1338282,"name":"Janvi Madhiwala","orcid":null,"position":6,"is_corresponding":false},{"id":1337846,"name":"John Anderson","orcid":"0000-0003-0840-9890","position":7,"is_corresponding":false},{"id":477618,"name":"Ying Zou","orcid":"0000-0003-2787-1917","position":8,"is_corresponding":false},{"id":484337,"name":"Kathleen L. Gabrielson","orcid":"0000-0003-3901-4357","position":9,"is_corresponding":false},{"id":36493,"name":"Alan F. Scott","orcid":"0000-0002-9706-7839","position":0,"is_corresponding":true}],"reference_count":77,"raw_metadata":null,"created_at":"2026-07-19T02:10:35.597333Z","pmid":"39457378","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}