Affymetrix SNP array data for soft tissue sarcoma samples

·Released July 5, 2010 ·Updated May 2, 2014

415

Samples

415

Assays

Array Platforms

References

Description

Soft tissue sarcomas are aggressive mesenchymal cancers that affect more than 10,600 new patients per year in the US, about 40% of whom will die of their disease. Soft tissue sarcomas exhibit remarkable histologic diversity, with more than 50 recognized subtypes, but our knowledge of their genomic alterations is limited. Here we describe the results of an integrative analysis of DNA sequence, copy number, and mRNA expression in 207 samples encompassing seven major subtypes. Genes mutated in more than 5% of samples within a subtype were KIT (in gastrointestinal stromal cell tumors, or GISTs), TP53 (pleomorphic liposarcomas), PIK3CA (myxoid/round-cell liposarcoma), and NF1 (both myxofibrosarcoma and pleomorphic liposarcoma). We show evidence that PIK3CA mutations, found in 18% of myxoid/round-cell liposarcomas, activate AKT in vivo and are associated with poor outcomes. Point mutations in the tumor suppressor gene NF1 were discovered in both myxofibrosarcomas and pleomorphic liposarcomas, while genomic deletions were observed in all subtypes at varying frequencies. Finally, we found that short hairpin RNA-based knockdown of a subset of genes that are amplified in dedifferentiated liposarcoma, including CDK4 and YEATS4, decreased cell proliferation. Our study yields the most detailed map of molecular alterations across diverse sarcoma subtypes to date and provides potential subtype-specific targets for therapy. Human soft tissue sarcoma samples and their matched normal DNA were profiled on Affymetrix 250K SNP (Sty) arrays per manufacturer's instructions

References

Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy.

Barretina J, Taylor BS, Banerji S, Ramos AH, Lagos-Quintana M, Decarolis PL, Shah K, Socci ND, Weir BA, Ho A, Chiang DY, Reva B, Mermel CH, Getz G, Antipin Y, Beroukhim R, Major JE, Hatton C, Nicoletti R, Hanna M, Sharpe T, Fennell TJ, Cibulskis K, Onofrio RC, Saito T, Shukla N, Lau C, Nelander S, Silver SJ, Sougnez C, Viale A, Winckler W, Maki RG, Garraway LA, Lash A, Greulich H, Root DE, Sellers WR, Schwartz GK, Antonescu CR, Lander ES, Varmus HE, Ladanyi M, Sander C, Meyerson M, Singer S

PMID: 20601955

Array Platforms

A-AFFY-72

Affymetrix GeneChip Human Mapping 250K Array Sty [Mapping250K_Sty]（415 items）

Sample Attributes

cell line

DDLS8817, FU-DD-LS1, LPS141

disease status

GIST:Epitheloid, GIST:Mixed, GIST:N/A, GIST:Spindle, Leiomyosarcoma:N/A, Liposarcoma:Dedifferentiated, Liposarcoma:Myxoid/RC, Liposarcoma:Pleomorphic, MFH:Myxofibrosarcoma, MFH:Pleomorphic, normal, Synovial:Biphasic, Synovial:Monophasic, Synovial:N/A

Organism

Homo sapiens

organism part

Matched normal tissue, Soft-tissue sarcoma

sample id

DDLS8817, FUDDLS1, LPS141, PT100MF, PT101MF, PT102MF, PT103MF, PT104MF, PT105MF, PT106MF, PT107MF, PT108MF, PT109MF, PT10DD, PT110MF, PT111MF, PT112MF, PT113MF, PT114MF, PT115MF, PT116MF, PT117MF, PT118MF, PT119MF, PT11DD, PT120MF, PT121MF, PT122MF, PT123MF, PT124MF, PT125MF, PT126MF, PT127MF, PT128MF, PT129MF, PT12DD, PT130MF, PT131MF, PT132MF, PT133MF, PT134MF, PT135MF, PT136MF, PT137MF, PT138MRC, PT139MRC, PT13DD, PT140MRC, PT141MRC, PT142MRC, PT143MRC, PT144MRC, PT145MRC, PT146MRC, PT147MRC, PT148MRC, PT149MRC, PT14DD, PT150MRC, PT151MRC, PT152MRC, PT153MRC, PT154MRC, PT155MRC, PT156MRC, PT157MRC, PT158MRC, PT159PL, PT15DD, PT160PL, PT161PL, PT162PL, PT163PL, PT164PL, PT165PL, PT166PL, PT167PL, PT168PL, PT169PL, PT16DD, PT170PL, PT171PL, PT172PL, PT173PL, PT174PL, PT175PL, PT176PL, PT177PL, PT178PL, PT179PL, PT17DD, PT180PL, PT181PL, PT182PL, PT183SYN, PT184SYN, PT185SYN, PT186SYN, PT187SYN, PT188SYN, PT189SYN, PT18DD, PT190SYN, PT191SYN, PT192SYN, PT193SYN, PT194SYN, PT195SYN, PT196SYN, PT197SYN, PT198SYN, PT199SYN, PT19DD, PT1DD, PT200SYN, PT201SYN, PT202SYN, PT203SYN, PT204SYN, PT205SYN, PT206SYN, PT207SYN, PT20DD, PT21DD, PT22DD, PT23DD, PT24DD, PT25DD, PT26DD, PT27DD, PT28DD, PT29DD, PT2DD, PT30DD, PT31DD, PT32DD, PT33DD, PT34DD, PT35DD, PT36DD, PT37DD, PT38DD, PT39DD, PT3DD, PT40DD, PT41DD, PT42DD, PT43DD, PT44DD, PT45DD, PT46DD, PT47DD, PT48DD, PT49DD, PT4DD, PT50DD, PT51GT, PT52GT, PT53GT, PT54GT, PT55GT, PT56GT, PT57GT, PT58GT, PT59GT, PT5DD, PT60GT, PT61GT, PT62GT, PT63GT, PT64GT, PT65GT, PT66GT, PT67GT, PT68GT, PT69GT, PT6DD, PT70GT, PT71GT, PT72GT, PT73LMS, PT74LMS, PT75LMS, PT76LMS, PT77LMS, PT78LMS, PT79LMS, PT7DD, PT80LMS, PT81LMS, PT82LMS, PT83LMS, PT84LMS, PT85LMS, PT86LMS, PT87LMS, PT88LMS, PT89LMS, PT8DD, PT90LMS, PT91LMS, PT92LMS, PT93LMS, PT94LMS, PT95LMS, PT96LMS, PT97LMS, PT98LMS, PT99LMS, PT9DD

Experiment Info

Accession

E-GEOD-21123

GEO ID

GSE21123

Type

comparative genomic hybridization by array

Organism

Homo sapiens

Released

July 5, 2010

Updated

May 2, 2014

Submitter

Barry Stephen Taylor、 Jordi Barretina、 Barry S Taylor、 Samuel Singer、 Matthew Meyerson

External Links

ArrayExpress source NCBI GEO：GSE21123

Analysis Services

Affymetrix SNP array data for soft tissue sarcoma samples

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