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Cellosaurus SK-NEP-1 (CVCL_0631)

[Text version]
Cell line name SK-NEP-1
Synonyms SKNEP-1; SKNEP1; SKNEP
Accession CVCL_0631
Resource Identification Initiative To cite this cell line use: SK-NEP-1 (RRID:CVCL_0631)
Comments Problematic cell line: Misclassified. Originally thought to be a Wilm's tumor cell line but shown to be from an Ewing sarcoma (PubMed=17154184; PubMed=30924592).
Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Part of: MD Anderson Cell Lines Project.
From: Memorial Sloan Kettering Cancer Center; New York; USA.
Registration: Memorial Sloan Kettering Cancer Center Office of Technology Development; SK2008-052.
Population: Caucasian.
Microsatellite instability: Stable (MSS) (Sanger).
Omics: Deep exome analysis.
Omics: DNA methylation analysis.
Omics: Protein expression by reverse-phase protein arrays.
Omics: SNP array analysis.
Omics: Transcriptome analysis by microarray.
Omics: Transcriptome analysis by RNAseq.
Derived from site: Metastatic; Pleural effusion; UBERON=UBERON_0000175.
Sequence variations
  • Gene deletion; HGNC; 1787; CDKN2A; Zygosity=Homozygous (PubMed=25010205).
  • Gene fusion; HGNC; 3508; EWSR1 + HGNC; 3749; FLI1; Name(s)=EWSR1-FLI1, EWS-FLI1; Note=Type 2 fusion (Ex7/Ex5) (PubMed=17154184; PubMed=25010205; DepMap).
  • Mutation; HGNC; 11998; TP53; Simple; p.Gly245Ser (c.733G>A); ClinVar=VCV000012365; Zygosity=Homozygous (PubMed=25010205; DepMap).
Genome ancestry Source: PubMed=30894373

Origin% genome
African0
Native American0
East Asian, North0.75
East Asian, South0
South Asian1.81
European, North66.07
European, South31.37
Disease Ewing sarcoma (NCIt: C4817)
Ewing sarcoma (ORDO: Orphanet_319)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Sex of cell Female
Age at sampling 25Y
Category Cancer cell line
STR profile Source(s): ATCC; CLS; Cosmic-CLP; PubMed=25010205

Markers:
AmelogeninX
CSF1PO10
D2S133819,20
D3S135814,15
D5S81813
D7S8208,10
D8S117912
D13S31711
D16S53911
D18S5115,17
D19S43312,14
D21S1129,31
FGA24
Penta D11,12
Penta E7,18
TH018,9.3
TPOX8,11
vWA15,19

Run an STR similarity search on this cell line
Web pages https://www.mskcc.org/research-advantage/support/technology/tangible-material/sk-nep-1-human-ewing-sarcoma-cell-line
https://tcpaportal.org/mclp/
Publications

DOI=10.1007/978-1-4757-1647-4_5
Fogh J., Trempe G.L.
New human tumor cell lines.
(In) Human tumor cells in vitro; Fogh J. (eds.); pp.115-159; Springer; New York (1975)

PubMed=327080; DOI=10.1093/jnci/59.1.221
Fogh J., Fogh J.M., Orfeo T.
One hundred and twenty-seven cultured human tumor cell lines producing tumors in nude mice.
J. Natl. Cancer Inst. 59:221-226(1977)

PubMed=833871; DOI=10.1093/jnci/58.2.209
Fogh J., Wright W.C., Loveless J.D.
Absence of HeLa cell contamination in 169 cell lines derived from human tumors.
J. Natl. Cancer Inst. 58:209-214(1977)

PubMed=571047
Fogh J.
Cultivation, characterization, and identification of human tumor cells with emphasis on kidney, testis, and bladder tumors.
Natl. Cancer Inst. Monogr. 49:5-9(1978)

PubMed=6244232
Williams R.D.
Human urologic cancer cell lines.
Invest. Urol. 17:359-363(1980)

PubMed=7459858
Rousset M., Zweibaum A., Fogh J.
Presence of glycogen and growth-related variations in 58 cultured human tumor cell lines of various tissue origins.
Cancer Res. 41:1165-1170(1981)

PubMed=3518877; DOI=10.3109/07357908609038260
Fogh J.
Human tumor lines for cancer research.
Cancer Invest. 4:157-184(1986)

PubMed=17154184; DOI=10.1002/pbc.21099
Smith M.A., Morton C.L., Phelps D.A., Girtman K., Neale G., Houghton P.J.
SK-NEP-1 and Rh1 are Ewing family tumor lines.
Pediatr. Blood Cancer 50:703-706(2008)

PubMed=20164919; DOI=10.1038/nature08768
Bignell G.R., Greenman C.D., Davies H., Butler A.P., Edkins S., Andrews J.M., Buck G., Chen L., Beare D., Latimer C., Widaa S., Hinton J., Fahey C., Fu B.-Y., Swamy S., Dalgliesh G.L., Teh B.T., Deloukas P., Yang F.-T., Campbell P.J., Futreal P.A., Stratton M.R.
Signatures of mutation and selection in the cancer genome.
Nature 463:893-898(2010)

PubMed=20215515; DOI=10.1158/0008-5472.CAN-09-3458
Rothenberg S.M., Mohapatra G., Rivera M.N., Winokur D., Greninger P., Nitta M., Sadow P.M., Sooriyakumar G., Brannigan B.W., Ulman M.J., Perera R.M., Wang R., Tam A., Ma X.-J., Erlander M., Sgroi D.C., Rocco J.W., Lingen M.W., Cohen E.E.W., Louis D.N., Settleman J., Haber D.A.
A genome-wide screen for microdeletions reveals disruption of polarity complex genes in diverse human cancers.
Cancer Res. 70:2158-2164(2010)

PubMed=25010205; DOI=10.1371/journal.pgen.1004475
Brohl A.S., Solomon D.A., Chang W., Wang J.-J., Song Y., Sindiri S., Patidar R., Hurd L., Chen L., Shern J.F., Liao H.-L., Wen X.-Y., Gerard J., Kim J.-S., Lopez Guerrero J.A., Machado I., Wai D.H., Picci P., Triche T.J., Horvai A.E., Miettinen M.M., Wei J.S., Catchpoole D., Llombart-Bosch A., Waldman T., Khan J.
The genomic landscape of the Ewing sarcoma family of tumors reveals recurrent STAG2 mutation.
PLoS Genet. 10:E1004475-E1004475(2014)

PubMed=28196595; DOI=10.1016/j.ccell.2017.01.005
Li J., Zhao W., Akbani R., Liu W.-B., Ju Z.-L., Ling S.-Y., Vellano C.P., Roebuck P., Yu Q.-H., Eterovic A.K., Byers L.A., Davies M.A., Deng W.-L., Gopal Y.N.V., Chen G., von Euw E.M., Slamon D.J., Conklin D., Heymach J.V., Gazdar A.F., Minna J.D., Myers J.N., Lu Y.-L., Mills G.B., Liang H.
Characterization of human cancer cell lines by reverse-phase protein arrays.
Cancer Cell 31:225-239(2017)

PubMed=28489074; DOI=10.1038/ncomms15165
Sinha R., Winer A.G., Chevinsky M., Jakubowski C., Chen Y.-B., Dong Y.-Y., Tickoo S.K., Reuter V.E., Russo P., Coleman J.A., Sander C., Hsieh J.J.-D., Hakimi A.A.
Analysis of renal cancer cell lines from two major resources enables genomics-guided cell line selection.
Nat. Commun. 8:15165.1-15165.10(2017)

PubMed=30894373; DOI=10.1158/0008-5472.CAN-18-2747
Dutil J., Chen Z.-H., Monteiro A.N.A., Teer J.K., Eschrich S.A.
An interactive resource to probe genetic diversity and estimated ancestry in cancer cell lines.
Cancer Res. 79:1263-1273(2019)

PubMed=30924592; DOI=10.1002/pbc.27741
Pritchard-Jones K., Perotti D.
WARNING: G-401 and SK-NEP-1 cell lines are not Wilms tumor cell lines.
Pediatr. Blood Cancer 66:e27741.1-e27741.2(2019)

PubMed=31006967; DOI=10.1002/pbc.27769
Staege M.S.
Are EWSR1-FLI-positive cell lines from patients with other diagnoses than Ewing sarcoma really Ewing sarcoma cell lines?
Pediatr. Blood Cancer 66:e27769.1-e27769.2(2019)

PubMed=31068700; DOI=10.1038/s41586-019-1186-3
Ghandi M., Huang F.W., Jane-Valbuena J., Kryukov G.V., Lo C.C., McDonald E.R. III, Barretina J.G., Gelfand E.T., Bielski C.M., Li H.-X., Hu K., Andreev-Drakhlin A.Y., Kim J., Hess J.M., Haas B.J., Aguet F., Weir B.A., Rothberg M.V., Paolella B.R., Lawrence M.S., Akbani R., Lu Y.-L., Tiv H.L., Gokhale P.C., de Weck A., Mansour A.A., Oh C., Shih J., Hadi K., Rosen Y., Bistline J., Venkatesan K., Reddy A., Sonkin D., Liu M., Lehar J., Korn J.M., Porter D.A., Jones M.D., Golji J., Caponigro G., Taylor J.E., Dunning C.M., Creech A.L., Warren A.C., McFarland J.M., Zamanighomi M., Kauffmann A., Stransky N., Imielinski M., Maruvka Y.E., Cherniack A.D., Tsherniak A., Vazquez F., Jaffe J.D., Lane A.A., Weinstock D.M., Johannessen C.M., Morrissey M.P., Stegmeier F., Schlegel R., Hahn W.C., Getz G., Mills G.B., Boehm J.S., Golub T.R., Garraway L.A., Sellers W.R.
Next-generation characterization of the Cancer Cell Line Encyclopedia.
Nature 569:503-508(2019)

Cross-references
Cell line collections (Providers) ATCC; HTB-48
CLS; 300341
IZSLER; BS TCL 61
Cell line databases/resources CLO; CLO_0009055
CLDB; cl4353
cancercelllines; CVCL_0631
CCRID; 3101HUMTCHu164
Cell_Model_Passport; SIDM00027
Cosmic-CLP; 909730
DepMap; ACH-001192
IGRhCellID; SKNEP1
LINCS_LDP; LCL-1802
Biological sample resources BioSample; SAMN03472745
BioSample; SAMN10989620
Chemistry resources ChEMBL-Cells; CHEMBL3308141
ChEMBL-Targets; CHEMBL1075580
GDSC; 909730
PharmacoDB; SKNEP1_1410_2019
PubChem_Cell_line; CVCL_0631
Encyclopedic resources Wikidata; Q54954488
Experimental variables resources EFO; EFO_0002337
Gene expression databases ArrayExpress; E-MTAB-38
ArrayExpress; E-MTAB-783
ArrayExpress; E-MTAB-3610
GEO; GSM827180
GEO; GSM845556
GEO; GSM844692
GEO; GSM1670452
Polymorphism and mutation databases Cosmic; 688125
Cosmic; 909730
Cosmic; 1112129
Cosmic; 1196558
Cosmic; 2060801
Cosmic; 2228232
Cosmic; 2294587
IARC_TP53; 27243
Progenetix; CVCL_0631
Sequence databases EGA; EGAS00001000978
Entry history
Entry creation04-Apr-2012
Last entry update05-Oct-2023
Version number41