Cancer_Cell_Line_Exome_Sequencing_

Genomic characterisation of a large series of cancer cell lines.

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

3 Datasets 24 Publications

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
EGAD00001001039	Genomic characterisation of a large series of cancer cell lines.	Illumina HiSeq 2000	1072
EGAD00001004201	Multiple signatures of somatic mutations have been identified in human cancer genomes. To investigate whether mutational signatures continue to be generated, and if so their temporal patterns of activity, subsets of cell lines were cultured in vitro for extended periods and subjected to single cell cloning and whole genome or exome sequencing or directly to single cell whole genome sequencing. As expected, signatures of past exogenous exposures, such as tobacco smoke and ultraviolet light, were not generated in vitro. In contrast, signatures of normal and defective DNA repair and replication continued to be generated at essentially constant mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing activity exhibited a distinctive pattern with substantial fluctuations in mutation rate over time and episodic bursts of mutations. The initiating factors for these bursts are unclear although retrotransposon mobilisation may play a role. This cell line set now constitutes a comprehensive resource of live experimental models of mutational processes of both known and unknown aetiologies potentially retaining the patterns of activity and regulatory influences operative in human cells in vivo.	Illumina HiSeq 2000 Illumina HiSeq 2500	75
EGAD00010000644	Affymetrix SNP6.0 cancer cell line exome sequencing data		1022

Publications	Citations
A Landscape of Pharmacogenomic Interactions in Cancer. Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, Aben N, Gonçalves E, Barthorpe S, Lightfoot H, Cokelaer T, Greninger P, van Dyk E, Chang H, de Silva H, Heyn H, Deng X, Egan RK, Liu Q, Mironenko T, Mitropoulos X, Richardson L, Wang J, Zhang T, Moran S, Sayols S, Soleimani M, Tamborero D, Lopez-Bigas N, Ross-Macdonald P, Esteller M, Gray NS, Haber DA, Stratton MR, Benes CH, Wessels LFA, Saez-Rodriguez J, McDermott U, Garnett MJ. Cell 166: 2016 740-754	1446
Assessment of pharmacogenomic agreement. Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. F1000Res 5: 2016 825	26
Revisiting inconsistency in large pharmacogenomic studies. Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. F1000Res 5: 2016 2333	61
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models. Ng SY, Yoshida N, Christie AL, Ghandi M, Dharia NV, Dempster J, Murakami M, Shigemori K, Morrow SN, Van Scoyk A, Cordero NA, Stevenson KE, Puligandla M, Haas B, Lo C, Meyers R, Gao G, Cherniack A, Louissaint A, Nardi V, Thorner AR, Long H, Qiu X, Morgan EA, Dorfman DM, Fiore D, Jang J, Epstein AL, Dogan A, Zhang Y, Horwitz SM, Jacobsen ED, Santiago S, Ren JG, Guerlavais V, Annis DA, Aivado M, Saleh MN, Mehta A, Tsherniak A, Root D, Vazquez F, Hahn WC, Inghirami G, Aster JC, Weinstock DM, Koch R. Nat Commun 9: 2018 2024	79
Genetic and transcriptional evolution alters cancer cell line drug response. Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. Nature 560: 2018 325-330	627
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. Iorio F, Behan FM, Gonçalves E, Bhosle SG, Chen E, Shepherd R, Beaver C, Ansari R, Pooley R, Wilkinson P, Harper S, Butler AP, Stronach EA, Saez-Rodriguez J, Yusa K, Garnett MJ. BMC Genomics 19: 2018 604	71
The germline genetic component of drug sensitivity in cancer cell lines. Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O. Nat Commun 9: 2018 3385	41
An RNAi screen in human cell lines reveals conserved DNA damage repair pathways that mitigate formaldehyde sensitivity. Juarez E, Chambwe N, Tang W, Mitchell AD, Owen N, Kumari A, Monnat RJ, McCullough AK. DNA Repair (Amst) 72: 2018 1-9	10
Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects. Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ. Genome Biol 20: 2019 27	34
Next-generation characterization of the Cancer Cell Line Encyclopedia. Ghandi M, Huang FW, Jané-Valbuena J, Kryukov GV, Lo CC, McDonald ER, Barretina J, Gelfand ET, Bielski CM, Li H, Hu K, Andreev-Drakhlin AY, Kim J, Hess JM, Haas BJ, Aguet F, Weir BA, Rothberg MV, Paolella BR, Lawrence MS, Akbani R, Lu Y, Tiv HL, Gokhale PC, de Weck A, Mansour AA, Oh C, Shih J, Hadi K, Rosen Y, Bistline J, Venkatesan K, Reddy A, Sonkin D, Liu M, Lehar J, Korn JM, Porter DA, Jones MD, Golji J, Caponigro G, Taylor JE, Dunning CM, Creech AL, Warren AC, McFarland JM, Zamanighomi M, Kauffmann A, Stransky N, Imielinski M, Maruvka YE, Cherniack AD, Tsherniak A, Vazquez F, Jaffe JD, Lane AA, Weinstock DM, Johannessen CM, Morrissey MP, Stegmeier F, Schlegel R, Hahn WC, Getz G, Mills GB, Boehm JS, Golub TR, Garraway LA, Sellers WR. Nature 569: 2019 503-508	2502
Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening. Picco G, Chen ED, Alonso LG, Behan FM, Gonçalves E, Bignell G, Matchan A, Fu B, Banerjee R, Anderson E, Butler A, Benes CH, McDermott U, Dow D, Iorio F, Stronach E, Yang F, Yusa K, Saez-Rodriguez J, Garnett MJ. Nat Commun 10: 2019 2198	92
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Nat Commun 10: 2019 2674	224
Copy number variation is highly correlated with differential gene expression: a pan-cancer study. Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D, Fan X. BMC Med Genet 20: 2019 175	208
Chromosome arm aneuploidies shape tumour evolution and drug response. Shukla A, Nguyen THM, Moka SB, Ellis JJ, Grady JP, Oey H, Cristino AS, Khanna KK, Kroese DP, Krause L, Dray E, Fink JL, Duijf PHG. Nat Commun 11: 2020 449	87
Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns. Salvadores M, Fuster-Tormo F, Supek F. Sci Adv 6: 2020 eaba1862	48
Identification of Intrinsic Drug Resistance and Its Biomarkers in High-Throughput Pharmacogenomic and CRISPR Screens. Ayestaran I, Galhoz A, Spiegel E, Sidders B, Dry JR, Dondelinger F, Bender A, McDermott U, Iorio F, Menden MP. Patterns (N Y) 1: 2020 100065	9
A first-generation pediatric cancer dependency map. Dharia NV, Kugener G, Guenther LM, Malone CF, Durbin AD, Hong AL, Howard TP, Bandopadhayay P, Wechsler CS, Fung I, Warren AC, Dempster JM, Krill-Burger JM, Paolella BR, Moh P, Jha N, Tang A, Montgomery P, Boehm JS, Hahn WC, Roberts CWM, McFarland JM, Tsherniak A, Golub TR, Vazquez F, Stegmaier K. Nat Genet 53: 2021 529-538	113
Integrated evaluation of telomerase activation and telomere maintenance across cancer cell lines. Hu K, Ghandi M, Huang FW. Elife 10: 2021 e66198	16
Inferred Ancestral Origin of Cancer Cell Lines Associates with Differential Drug Response. Nguyen PBH, Ohnmacht AJ, Sharifli S, Garnett MJ, Menden MP. Int J Mol Sci 22: 2021 10135	3
Palbociclib-based high-throughput combination drug screening identifies synergistic therapeutic options in HPV-negative head and neck squamous cell carcinoma. Gu Z, Shi C, Li J, Han Y, Sun B, Zhang W, Wu J, Zhou G, Ye W, Li J, Zhang Z, Zhou R. BMC Med 20: 2022 175	15
Mutational signatures are markers of drug sensitivity of cancer cells. Levatić J, Salvadores M, Fuster-Tormo F, Supek F. Nat Commun 13: 2022 2926	61
CNpare: matching DNA copy number profiles. Chaves-Urbano B, Hernando B, Garcia MJ, Macintyre G. Bioinformatics 38: 2022 3638-3641	4
A genetic basis for sex differences in Xp11 translocation renal cell carcinoma. Achom M, Sadagopan A, Bao C, McBride F, Li J, Konda P, Tourdot RW, Xu Q, Nakhoul M, Gallant DS, Ahmed UA, O'Toole J, Freeman D, Lee GM, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. Cell 187: 2024 5735-5752.e25	20
A semi-supervised weighted SPCA- and convolution KAN-based model for drug response prediction. Miao R, Zhong BJ, Mei XY, Dong X, Ou YD, Liang Y, Yu HY, Wang Y, Dong ZH. Front Genet 16: 2025 1532651	0