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Cellosaurus SKM-1 (CVCL_0098)

[Text version]
Cell line name SKM-1
Synonyms SKM1
Accession CVCL_0098
Resource Identification Initiative To cite this cell line use: SKM-1 (RRID:CVCL_0098)
Comments Part of: Cancer Dependency Map project (DepMap) (includes Cancer Cell Line Encyclopedia - CCLE).
Part of: COSMIC cell lines project.
Population: Japanese.
Doubling time: ~48 hours (PubMed=8136267); ~48 hours (DSMZ=ACC-547).
Microsatellite instability: Stable (MSS) (Sanger).
Omics: Deep exome analysis.
Omics: Deep quantitative proteome analysis.
Omics: DNA methylation analysis.
Omics: SNP array analysis.
Omics: Transcriptome analysis by microarray.
Omics: Transcriptome analysis by RNAseq.
Caution: TP53 mutation indicated incorrectly as being at p.Tyr327His (c.981T>C) in PubMed=8136267.
Derived from site: In situ; Peripheral blood; UBERON=UBERON_0000178.
Sequence variations
  • Mutation; HGNC; 18318; ASXL1; Simple; p.Tyr591Ter (c.1773C>A); ClinVar=VCV000451016; Zygosity=Homozygous (PubMed=27750403).
  • Mutation; HGNC; 25657; BCORL1; Simple; c.4619-1G>A; Zygosity=Homozygous; Note=Splice acceptor mutation (PubMed=21989985; PubMed=27750403; Cosmic-CLP=909722; DepMap=ACH-000373).
  • Mutation; HGNC; 3527; EZH2; Simple; p.Tyr646Cys (c.1937A>G); Zygosity=Heterozygous (Cosmic-CLP=909722; DepMap=ACH-000373).
  • Mutation; HGNC; 6407; KRAS; Simple; p.Lys117Asn (c.351A>C); ClinVar=VCV000375965; Zygosity=Homozygous (Cosmic-CLP=909722; DepMap=ACH-000373).
  • Mutation; HGNC; 11998; TP53; Simple; p.Arg248Gln (c.743G>A); ClinVar=VCV000012356; Zygosity=Homozygous (PubMed=27750403; Cosmic-CLP=909722; DepMap=ACH-000373).
HLA typing Source: PubMed=26589293
Class I
HLA-AA*02:07,33:03
HLA-BB*40:01,59:01
HLA-CC*01:02,03:04
Class II
HLA-DQDQA1*01:02,03:02
DQB1*04:02,06:01
HLA-DRDRB1*04:05,08:03
Genome ancestry Source: PubMed=30894373

Origin% genome
African0
Native American0.67
East Asian, North75.52
East Asian, South22.98
South Asian0
European, North0.33
European, South0.5
Disease Adult acute myeloid leukemia (NCIt: C9154)
Myelodysplastic syndrome (NCIt: C3247)
Acute myeloid leukemia (ORDO: Orphanet_519)
Species of origin Homo sapiens (Human) (NCBI Taxonomy: 9606)
Hierarchy Children:
CVCL_IM24 (SKM-1/HHT)
Sex of cell Male
Age at sampling 76Y
Category Cancer cell line
STR profile Source(s): Cosmic-CLP=909722; DSMZ=ACC-547; JCRB=JCRB0118; PubMed=25877200

Markers:
AmelogeninX (Cosmic-CLP=909722; JCRB=JCRB0118)
X,Y (DSMZ=ACC-547; PubMed=25877200)
CSF1PO10,12
D2S133819,23
D3S135818
D5S81810,12
D7S82010,11
D8S117911,13
D13S31711,13
D16S5399,11
D18S5114,15
D19S43314,15
D21S1131.2,32.2
FGA22,23
Penta D9,12
Penta E15,19 (DSMZ=ACC-547)
15,20 (PubMed=25877200)
TH017,9
TPOX8,11
vWA18

Run an STR similarity search on this cell line
Publications

PubMed=8136267; DOI=10.1111/j.1365-2141.1993.tb03334.x
Nakagawa T., Matozaki S., Murayama T., Nishimura R., Tsutsumi M., Kawaguchi R., Yokoyama Y., Hikiji K., Isobe T., Chihara K.
Establishment of a leukaemic cell line from a patient with acquisition of chromosomal abnormalities during disease progression in myelodysplastic syndrome.
Br. J. Haematol. 85:469-476(1993)

PubMed=8580805; DOI=10.3109/10428199509056841
Nakagawa T., Matozaki S.
The SKM-1 leukemic cell line established from a patient with progression to myelomonocytic leukemia in myelodysplastic syndrome (MDS)-contribution to better understanding of MDS.
Leuk. Lymphoma 17:335-339(1995)

DOI=10.1016/B978-0-12-221970-2.50457-5
Drexler H.G.
The leukemia-lymphoma cell line factsbook.
(In book) ISBN 9780122219702; pp.1-733; Academic Press; London; United Kingdom (2001)

PubMed=16408098; DOI=10.1038/sj.leu.2404081
Quentmeier H., MacLeod R.A.F., Zaborski M., Drexler H.G.
JAK2 V617F tyrosine kinase mutation in cell lines derived from myeloproliferative disorders.
Leukemia 20:471-476(2006)

PubMed=20164919; DOI=10.1038/nature08768; PMCID=PMC3145113
Bignell G.R., Greenman C.D., Davies H.R., 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=21989985; DOI=10.1182/blood-2011-05-356204; PMCID=PMC3228503
Li M., Collins R., Jiao Y.-C., Ouillette P., Bixby D., Erba H., Vogelstein B., Kinzler K.W., Papadopoulos N., Malek S.N.
Somatic mutations in the transcriptional corepressor gene BCORL1 in adult acute myelogenous leukemia.
Blood 118:5914-5917(2011)

PubMed=22460905; DOI=10.1038/nature11003; PMCID=PMC3320027
Barretina J.G., Caponigro G., Stransky N., Venkatesan K., Margolin A.A., Kim S., Wilson C.J., Lehar J., Kryukov G.V., Sonkin D., Reddy A., Liu M., Murray L., Berger M.F., Monahan J.E., Morais P., Meltzer J., Korejwa A., Jane-Valbuena J., Mapa F.A., Thibault J., Bric-Furlong E., Raman P., Shipway A., Engels I.H., Cheng J., Yu G.-Y.K., Yu J.-J., Aspesi P. Jr., de Silva M., Jagtap K., Jones M.D., Wang L., Hatton C., Palescandolo E., Gupta S., Mahan S., Sougnez C., Onofrio R.C., Liefeld T., MacConaill L.E., Winckler W., Reich M., Li N.-X., Mesirov J.P., Gabriel S.B., Getz G., Ardlie K., Chan V., Myer V.E., Weber B.L., Porter J., Warmuth M., Finan P., Harris J.L., Meyerson M.L., Golub T.R., Morrissey M.P., Sellers W.R., Schlegel R., Garraway L.A.
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Nature 483:603-607(2012)

PubMed=25485619; DOI=10.1038/nbt.3080
Klijn C., Durinck S., Stawiski E.W., Haverty P.M., Jiang Z.-S., Liu H.-B., Degenhardt J., Mayba O., Gnad F., Liu J.-F., Pau G., Reeder J., Cao Y., Mukhyala K., Selvaraj S.K., Yu M.-M., Zynda G.J., Brauer M.J., Wu T.D., Gentleman R.C., Manning G., Yauch R.L., Bourgon R., Stokoe D., Modrusan Z., Neve R.M., de Sauvage F.J., Settleman J., Seshagiri S., Zhang Z.-M.
A comprehensive transcriptional portrait of human cancer cell lines.
Nat. Biotechnol. 33:306-312(2015)

PubMed=25877200; DOI=10.1038/nature14397
Yu M., Selvaraj S.K., Liang-Chu M.M.Y., Aghajani S., Busse M., Yuan J., Lee G., Peale F.V., Klijn C., Bourgon R., Kaminker J.S., Neve R.M.
A resource for cell line authentication, annotation and quality control.
Nature 520:307-311(2015)

PubMed=26589293; DOI=10.1186/s13073-015-0240-5; PMCID=PMC4653878
Scholtalbers J., Boegel S., Bukur T., Byl M., Goerges S., Sorn P., Loewer M., Sahin U., Castle J.C.
TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression.
Genome Med. 7:118.1-118.7(2015)

PubMed=27397505; DOI=10.1016/j.cell.2016.06.017; PMCID=PMC4967469
Iorio F., Knijnenburg T.A., Vis D.J., Bignell G.R., Menden M.P., Schubert M., Aben N., Goncalves E., Barthorpe S., Lightfoot H., Cokelaer T., Greninger P., van Dyk E., Chang H., de Silva H., Heyn H., Deng X.-M., Egan R.K., Liu Q.-S., Mironenko T., Mitropoulos X., Richardson L., Wang J.-H., Zhang T.-H., Moran S., Sayols S., Soleimani M., Tamborero D., Lopez-Bigas N., Ross-Macdonald P., Esteller M., Gray N.S., Haber D.A., Stratton M.R., Benes C.H., Wessels L.F.A., Saez-Rodriguez J., McDermott U., Garnett M.J.
A landscape of pharmacogenomic interactions in cancer.
Cell 166:740-754(2016)

PubMed=27750403; DOI=10.1002/gcc.22430
Palau A., Mallo M., Palomo L., Rodriguez-Hernandez I., Diesch J., Campos D., Granada I., Junca J., Drexler H.G., Sole F., Buschbeck M.
Immunophenotypic, cytogenetic, and mutational characterization of cell lines derived from myelodysplastic syndrome patients after progression to acute myeloid leukemia.
Genes Chromosomes Cancer 56:243-252(2017)

PubMed=30285677; DOI=10.1186/s12885-018-4840-5; PMCID=PMC6167786
Tan K.-T., Ding L.-W., Sun Q.-Y., Lao Z.-T., Chien W., Ren X., Xiao J.-F., Loh X.-Y., Xu L., Lill M., Mayakonda A., Lin D.-C., Yang H.H., Koeffler H.P.
Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines.
BMC Cancer 18:940.1-940.13(2018)

PubMed=30629668; DOI=10.1371/journal.pone.0210404; PMCID=PMC6328144
Uphoff C.C., Pommerenke C., Denkmann S.A., Drexler H.G.
Screening human cell lines for viral infections applying RNA-Seq data analysis.
PLoS ONE 14:E0210404-E0210404(2019)

PubMed=30894373; DOI=10.1158/0008-5472.CAN-18-2747; PMCID=PMC6445675
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=31068700; DOI=10.1038/s41586-019-1186-3; PMCID=PMC6697103
Ghandi M., Huang F.W., Jane-Valbuena J., Kryukov G.V., Lo C.C., McDonald E.R. 3rd, 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)

PubMed=35839778; DOI=10.1016/j.ccell.2022.06.010; PMCID=PMC9387775
Goncalves E., Poulos R.C., Cai Z.-X., Barthorpe S., Manda S.S., Lucas N., Beck A., Bucio-Noble D., Dausmann M., Hall C., Hecker M., Koh J., Lightfoot H., Mahboob S., Mali I., Morris J., Richardson L., Seneviratne A.J., Shepherd R., Sykes E., Thomas F., Valentini S., Williams S.G., Wu Y.-X., Xavier D., MacKenzie K.L., Hains P.G., Tully B., Robinson P.J., Zhong Q., Garnett M.J., Reddel R.R.
Pan-cancer proteomic map of 949 human cell lines.
Cancer Cell 40:835-849.e8(2022)

Cross-references
Cell line collections (Providers) DSMZ; ACC-547
JCRB; JCRB0118
JCRB; NIHS0147 - Discontinued
Cell line databases/resources CLO; CLO_0037289
cancercelllines; CVCL_0098
Cell_Model_Passport; SIDM00380
Cosmic-CLP; 909722
DepMap; ACH-000373
DSMZCellDive; ACC-547
Anatomy/cell type resources BTO; BTO:0006520
Biological sample resources BioSample; SAMN03470798
BioSample; SAMN03473113
BioSample; SAMN10988125
CRISP screens repositories BioGRID_ORCS_Cell_line; 218
Chemistry resources ChEMBL-Cells; CHEMBL3308216
ChEMBL-Targets; CHEMBL2366085
GDSC; 909722
PharmacoDB; SKM1_1418_2019
PubChem_Cell_line; CVCL_0098
Encyclopedic resources Wikidata; Q54954746
Experimental variables resources EFO; EFO_0006753
Gene expression databases ArrayExpress; E-MTAB-783
ArrayExpress; E-MTAB-2770
ArrayExpress; E-MTAB-2706
ArrayExpress; E-MTAB-3610
GEO; GSM482513
GEO; GSM887581
GEO; GSM888664
GEO; GSM1374880
GEO; GSM1446741
GEO; GSM1670435
GEO; GSM2124121
Polymorphism and mutation databases Cosmic; 787477
Cosmic; 909722
Cosmic; 975300
Cosmic; 1012119
Cosmic; 1078731
Cosmic; 1465964
Cosmic; 1551462
Cosmic; 2131566
Cosmic; 2750855
IARC_TP53; 27238
LiGeA; CCLE_537
Progenetix; CVCL_0098
Proteomic databases PRIDE; PXD030304
Sequence databases EGA; EGAS00001000610
EGA; EGAS00001000978
EGA; EGAS00001002554
Entry history
Entry creation04-Apr-2012
Last entry update02-May-2024
Version number41