GEO series

Affymetrix SNP array data for myelodysplastic syndromes (MDS) and related neoplasms

GSE31174 Homo sapiens (human) SNP genotyping by SNP array 58 samples Submitted 2011/09/12 Platform GPL3718

At a glance

human · 58 samples

Organism: Homo sapiens (human)
Topic: Myelodysplastic syndromesThis series is part of our curated briefing on it.
Samples: 58 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

In this study, to obtain a complete registry of genetic lesions in MDS and to identify novel therapeutic targets, we performed SNP array analysis and whole exome analysis for novel mutations using high-throughput sequencing technologies. In whole exome analysis, paired CD3-positive T cells were used as a normal control. By comparing sequences in tumors and paired T cells, 268 non-synonymous somatic mutations were confirmed with an overall true positive rate of 53.9 %, including 206 missense, 25 nonsense, and 10 splice site mutations, and 27 frameshift-causing insertions/deletions (indels).

Read the full summary ↓

The mutations of the known gene targets, however, accounted for only 12.3 % of all detected mutations (N = 33), and the remaining 235 mutations involved previously unreported genes. Combined with the genomic copy number profile obtained by SNP array karyotyping, this array of somatic mutations provided a landscape of myelodysplasia genomes.

This dataset

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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 (GSE31174_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 PRJNA144789. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21909114) ↗

Samples in this study

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+ 58 more — browse all 58 samples with per-sample file links →

More Myelodysplastic syndromes datasets

GSE211032 Expression Analysis (RNA-Seq) of adult Myelodysplastic Syndromes (MDS)/Acute Myeloid Leukemia (AML) with isolated monosomy 7 compared to controls 45 samples same disease briefing · shares mds, myelodysplastic, syndromes
GSE19523 Affymetrix SNP array data for Genomic Instability and Myelodysplasia with Monosomy 7 12 samples same disease briefing · shares snp, affymetrix, array
GSE284647 The genotype-integrated gene expression profile at the single-cell level of bone marrow CD34-positive hematopoietic stem and progenitor cells (HSPCs) from a patient with myelodysplastic neoplasms (MDS) harboring germline and somatic DDX41 variants. 1 samples same disease briefing · shares mds, myelodysplastic, neoplasms
GSE256396 Somatic mutations and DNA methylation identify a subgroup of poor prognosis within lower risk myelodysplastic syndromes 374 samples same disease briefing · shares myelodysplastic, syndromes
GSE21991 Myelodysplastic/myeloproliferative neoplasms 156 samples same disease briefing · shares myelodysplastic, neoplasms
GSE129828 DNA Methylation Identifies Genetically and Prognostically Distinct Subtypes of Myelodysplastic Syndromes 141 samples same disease briefing · shares myelodysplastic, syndromes
GSE15688 Acquired mutations in TET2 are common in myelodysplastic syndromes 122 samples same disease briefing · shares myelodysplastic, syndromes
GSE292039 Splicing of erythroid transcription factor is associated with therapeutic response in myelodysplastic syndromes 27 samples same disease briefing · shares myelodysplastic, syndromes

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