GEO series

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

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

Summary

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). 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.

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Direct links to NCBI, no account and no request form: the whole study as GSE31174_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 58 samples.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗

Also filed as BioProject PRJNA144789. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21909114) ↗

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