GEO series

Affymetrix SNP array data for soft tissue sarcoma samples

GSE21123 Homo sapiens (human) Genome variation profiling by SNP array 415 samples Submitted 2010/07/06 Platform GPL3720

At a glance

human · 415 samples

Organism: Homo sapiens (human)
Topic: Gastrointestinal stromal tumourThis series is part of our curated briefing on it.
Samples: 415 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

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.

Read the full summary ↓

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.

This dataset

Open GSE21123 in finder → Find more human datasets → Gastrointestinal stromal tumour landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE21123_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA129709. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20601955) ↗

Samples in this study

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+ 415 more — browse all 415 samples with per-sample file links →

More Gastrointestinal stromal tumour datasets

GSE241924 Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (ChIP-Seq) 45 samples same disease briefing
GSE240411 Identification of potential targets of FTO in GIST via transcriptome-wide RNA-seq 24 samples same disease briefing
GSE282434 Effect of SHP2 Inhibition on mRNA Expression Profiles of GIST Cells 18 samples same disease briefing
GSE289088 Dual Role of IL-6 in Maintaining the resistance of Gastrointestinal stromal tumor and tumor angiogenesis 12 samples same disease briefing
GSE241926 Dissection of a CTCF insulator and its impact on chromosome topology and oncogene expression in gastrointestinal stromal tumor (RNA-Seq) 10 samples same disease briefing
GSE254762 Deciphering the Tumor Immune Microenvironment of Imatinib-Resistance in Advanced Gastrointestinal Stromal Tumors at Single-Cell Resolution 9 samples same disease briefing
GSE296175 Claudin-1 contributes to gastrointestinal stromal tumors (GIST) resistance to imatinib mesylate (IM) via regulation of FGFR2-mediated signaling. 9 samples same disease briefing
GSE330412 Bulk RNA-sequencing after estrogen-related receptorr knockdown (ESRRA) knockdown in human GIST-T1 cell line 9 samples same disease briefing

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