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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: Genomics; DNA methylation analysis.
Omics: Genomics; Whole exome sequencing.
Omics: Phenotyping; Drug screening.
Omics: Proteomics; Quantitative.
Omics: Transcriptomics; Microarray.
Omics: Transcriptomics; RNAseq.
Omics: Variations; SNP array analysis.
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; HGNC:18318; ASXL1; Simple; p.Tyr591Ter (c.1773C>A); ClinVar=VCV000451016; Zygosity=Homozygous (PubMed=27750403).
  • Mutation; HGNC; 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; HGNC:3527; EZH2; Simple; p.Tyr646Cys (c.1937A>G); Zygosity=Heterozygous (Cosmic-CLP=909722; DepMap=ACH-000373).
  • Mutation; HGNC; HGNC:6407; KRAS; Simple; p.Lys117Asn (c.351A>C); ClinVar=VCV000375965; Zygosity=Homozygous (Cosmic-CLP=909722; DepMap=ACH-000373).
  • Mutation; HGNC; 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
Toshitaro Nakagawa, Sachiko Matozaki, Tohru Murayama, Ryuichiro Nishimura, Masayoshi Tsutsumi, Ryuji Kawaguchi, Yasunobu Yokoyama, Kazumasa Hikiji, Takashi Isobe, Kazuo Chihara;
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
Toshitaro Nakagawa, Sachiko Matozaki;
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
Hans Gunther Drexler;
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
Hilmar Quentmeier, Roderick A.F. MacLeod, Margarete Zaborski, Hans Gunther Drexler;
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
Graham Robert Bignell, Christopher D. Greenman, Helen R. Davies, Adam P. Butler, Sarah Edkins, Jenny M. Andrews, Gemma Buck, Lina Chen, David Beare, Calli Latimer, Sara Widaa, Jonathan Hinton, Ciara Fahey ...Show all 22 authors... , Bei-Yuan Fu, Sajani Swamy, Gillian L. Dalgliesh, Bin Tean Teh, Panos Deloukas, Feng-Tang Yang, Peter J. Campbell, P. Andrew Futreal, Michael Rudolf Stratton; Show fewer authors
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
Meng Li, Roxane Collins, Yu-Chen Jiao, Peter Ouillette, Dale Bixby, Harry Erba, Bert Vogelstein, Kenneth Wayne Kinzler, Nickolas Papadopoulos, Sami N. Malek;
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
Jordi Ginesta Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A. Margolin, Sungjoon Kim, Christopher J. Wilson, Joseph Lehar, Gregory V. Kryukov, Dmitriy Sonkin, Anupama Reddy, Manway Liu, Lauren Murray ...Show all 61 authors... , Michael F. Berger, John E. Monahan, Paula Morais, Jodi Meltzer, Adam Korejwa, Judit Jane-Valbuena, Felipa A. Mapa, Joseph Thibault, Eva Bric-Furlong, Pichai Raman, Aaron Shipway, Ingo H. Engels, Jill Cheng, Guo-Ying K. Yu, Jian-Jun Yu, Peter Aspesi Jr., Melanie de Silva, Kalpana Jagtap, Michael D. Jones, Li Wang, Charles Hatton, Emanuele Palescandolo, Supriya Gupta, Scott Mahan, Carrie Sougnez, Robert C. Onofrio, Ted Liefeld, Laura E. MacConaill, Wendy Winckler, Michael Reich, Nan-Xin Li, Jill P. Mesirov, Stacey B. Gabriel, Gad Getz, Kristin Ardlie, Vivien Chan, Vic E. Myer, Barbara L. Weber, Jeff Porter, Markus Warmuth, Peter Finan, Jennifer L. Harris, Matthew Langer Meyerson, Todd Robert Golub, Michael P. Morrissey, William Raj Sellers, Robert Schlegel, Levi Alexander Garraway; Show fewer authors
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Nature 483:603-607(2012)

PubMed=25485619; DOI=10.1038/nbt.3080
Christiaan Klijn, Steffen Durinck, Eric W. Stawiski, Peter M. Haverty, Zhao-Shi Jiang, Han-Bin Liu, Jeremiah Degenhardt, Oleg Mayba, Florian Gnad, Jin-Feng Liu, Gregoire Pau, Jens Reeder, Yi Cao ...Show all 30 authors... , Kiran Mukhyala, Suresh K. Selvaraj, Ma-Mie Yu, Gregory J. Zynda, Matthew J. Brauer, Thomas D. Wu, Robert Clifford Gentleman, Gerard Manning, Robert L. Yauch, Richard Bourgon, David Stokoe, Zora Modrusan, Richard M. Neve, Frederic J. de Sauvage, Jeffrey Settleman, Somasekar Seshagiri, Ze-Min Zhang; Show fewer authors
A comprehensive transcriptional portrait of human cancer cell lines.
Nat. Biotechnol. 33:306-312(2015)

PubMed=25877200; DOI=10.1038/nature14397
Ma-Mie Yu, Suresh K. Selvaraj, May M.Y. Liang-Chu, Sahar Aghajani, Matthew Busse, Jean Yuan, Genee Lee, Franklin V. Peale, Christiaan Klijn, Richard Bourgon, Joshua S. Kaminker, Richard M. Neve;
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
Jelle Scholtalbers, Sebastian Boegel, Thomas Bukur, Marius Byl, Sebastian Goerges, Patrick Sorn, Martin Loewer, Ugur Sahin, John C. Castle;
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
Francesco Iorio, Theo A. Knijnenburg, Daniel J. Vis, Graham Robert Bignell, Michael Patrick Menden, Michael Schubert, Nanne Aben, Emanuel Goncalves, Syd Barthorpe, Howard Lightfoot, Thomas Cokelaer, Patricia Greninger, Ewald van Dyk ...Show all 39 authors... , Han Chang, Heshani de Silva, Holger Heyn, Xian-Ming Deng, Regina K. Egan, Qing-Song Liu, Tatiana Mironenko, Xeni Mitropoulos, Laura Richardson, Jin-Hua Wang, Ting-Hu Zhang, Sebastian Moran, Sergi Sayols, Maryam Soleimani, David Tamborero, Nuria Lopez-Bigas, Petra Ross-Macdonald, Manel Esteller, Nathanael S. Gray, Daniel Arie Haber, Michael Rudolf Stratton, Cyril Henri Benes, Lodewyk F.A. Wessels, Julio Saez-Rodriguez, Ultan McDermott, Mathew J. Garnett; Show fewer authors
A landscape of pharmacogenomic interactions in cancer.
Cell 166:740-754(2016)

PubMed=27750403; DOI=10.1002/gcc.22430
Anna Palau, Mar Mallo, Laura Palomo, Ines Rodriguez-Hernandez, Jeannine Diesch, Diana Campos, Isabel Granada, Jordi Junca, Hans Gunther Drexler, Francesc Sole, Marcus Buschbeck;
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
Kar-Tong Tan, Ling-Wen Ding, Qiao-Yang Sun, Zhen-Tang Lao, Wenwen Chien, Xi Ren, Jin-Fen Xiao, Xin-Yi Loh, Liang Xu, Michael Lill, Anand Mayakonda, De-Chen Lin, Henry He Yang ...Show all 14 authors... , Harold Phillip Koeffler; Show fewer authors
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
Cord C. Uphoff, Claudia Pommerenke, Sabine A. Denkmann, Hans Gunther Drexler;
Screening human cell lines for viral infections applying RNA-Seq data analysis.
PLoS ONE 14:e0210404.1-e0210404.22(2019)

PubMed=30894373; DOI=10.1158/0008-5472.CAN-18-2747; PMCID=PMC6445675
Julie Dutil, Zhi-Hua Chen, Alvaro N.A. Monteiro, Jamie K. Teer, Steven A. Eschrich;
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
Mahmoud Ghandi, Franklin W. Huang, Judit Jane-Valbuena, Gregory V. Kryukov, Christopher C. Lo, E. Robert McDonald 3rd, Jordi Ginesta Barretina, Ellen T. Gelfand, Craig M. Bielski, Hao-Xin Li, Kevin Hu, Alexander Y. Andreev-Drakhlin, Jaegil Kim ...Show all 68 authors... , Julian M. Hess, Brian J. Haas, Francois Aguet, Barbara A. Weir, Michael V. Rothberg, Brenton R. Paolella, Michael Scott Lawrence, Rehan Akbani, Yi-Ling Lu, Hong L. Tiv, Prafulla C. Gokhale, Antoine de Weck, Ali Amin Mansour, Coyin Oh, Juliann Shih, Kevin Hadi, Yanay Rosen, Jonathan Bistline, Kavitha Venkatesan, Anupama Reddy, Dmitriy Sonkin, Manway Liu, Joseph Lehar, Joshua M. Korn, Dale A. Porter, Michael D. Jones, Javad Golji, Giordano Caponigro, Jordan E. Taylor, Caitlin M. Dunning, Amanda L. Creech, Allison C. Warren, James M. McFarland, Mahdi Zamanighomi, Audrey Kauffmann, Nicolas Stransky, Marcin Imielinski, Yosef E. Maruvka, Andrew D. Cherniack, Aviad Tsherniak, Francisca Vazquez, Jacob D. Jaffe, Andrew Alan Lane, David M. Weinstock, Cory M. Johannessen, Michael P. Morrissey, Frank Stegmeier, Robert Schlegel, William Chun Hahn, Gad Getz, Gordon B. Mills, Jesse S. Boehm, Todd Robert Golub, Levi Alexander Garraway, William Raj Sellers; Show fewer authors
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
Emanuel Goncalves, Rebecca C. Poulos, Zhao-Xiang Cai, Syd Barthorpe, Srikanth S. Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh, Howard Lightfoot ...Show all 32 authors... , Sadia Mahboob, Iman Mali, James Morris, Laura Richardson, Akila J. Seneviratne, Rebecca Shepherd, Erin Sykes, Frances Thomas, Sara Valentini, Steven G. Williams, Yang-Xiu Wu, Dylan Xavier, Karen L. MacKenzie, Peter G. Hains, Brett Tully, Phillip James Robinson, Qing Zhong, Mathew J. Garnett, Roger Robert Reddel; Show fewer authors
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-2706
ArrayExpress; E-MTAB-2770
ArrayExpress; E-MTAB-3610
FANTOM5_SSTAR; 10772-110F7
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 update10-Apr-2025
Version number43