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RNA sequencing and Illumina 2.5M SNP array data collected from 675 commonly used human cancer cell lines.

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels2–4, the transcriptome – which represents the active program of a cell – remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001000725 Illumina HiSeq 2000 675
EGAD00001001013 Illumina HiSeq 2000 30
EGAD00010000951 Illumina 2.5M 668
Publications Citations
A comprehensive transcriptional portrait of human cancer cell lines.
Nat Biotechnol 33: 2015 306-312
Human biosample authentication using the high-throughput, cost-effective SNPtrace(TM) system.
PLoS One 10: 2015 e0116218
Metabolite profiling stratifies pancreatic ductal adenocarcinomas into subtypes with distinct sensitivities to metabolic inhibitors.
Proc Natl Acad Sci U S A 112: 2015 E4410-7
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome Med 7: 2015 118
Modeling the integration of bacterial rRNA fragments into the human cancer genome.
BMC Bioinformatics 17: 2016 134
A gene expression signature of retinoblastoma loss-of-function is a predictive biomarker of resistance to palbociclib in breast cancer cell lines and is prognostic in patients with ER positive early breast cancer.
Oncotarget 7: 2016 68012-68022
Gene isoforms as expression-based biomarkers predictive of drug response in vitro.
Nat Commun 8: 2017 1126
Transcription Factor Activities Enhance Markers of Drug Sensitivity in Cancer.
Cancer Res 78: 2018 769-780
The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs.
Life Sci Alliance 2: 2019 e201900445
Network-based method for drug target discovery at the isoform level.
Sci Rep 9: 2019 13868
B cells extract antigens at Arp2/3-generated actin foci interspersed with linear filaments.
Elife 8: 2019 e48093
A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset.
Noncoding RNA Res 5: 2020 48-59
The cell line A-to-I RNA editing catalogue.
Nucleic Acids Res 48: 2020 5849-5858
LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients.
RNA Biol 18: 2021 1136-1151
Molecular and cellular characterization of two patient-derived ductal carcinoma in situ (DCIS) cell lines, ETCC-006 and ETCC-010.
BMC Cancer 21: 2021 790
BK Channel in the Physiology and in the Cancer of Pancreatic Duct: Impact and Reliability of BK Openers.
Front Pharmacol 13: 2022 906608
Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis.
Nat Commun 13: 2022 4913
An intrinsic purine metabolite AICAR blocks lung tumour growth by targeting oncoprotein mucin 1.
Br J Cancer 128: 2023 1647-1664
Investigating the suitability of <i>in vitro</i> cell lines as models for the major subtypes of epithelial ovarian cancer.
Front Cell Dev Biol 11: 2023 1104514
Non-canonical integrin signaling activates EGFR and RAS-MAPK-ERK signaling in small cell lung cancer.
Theranostics 13: 2023 2384-2407
Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation.
Nat Commun 14: 2023 5417