Genomics

Dataset Information

32

Bioinformatic evaluation and comparison of parallel aSNP and aCGH analyses of myelodysplastic syndromes patients with normal karyotype


ABSTRACT: Parallel aSNP and aCGH analyses were performed on 22 samples from MDS patients with a normal karyotype. 55 overlapping alterations, most of these corresponding to CNVs were identified with both methods. Putative tumour specific imbalances were found with both methods in three cases, a deletion of TET2, a larger deletion containing DNMT3A and one complex molecular karyotype. In two cases putative tumour specific imbalances were only seen with aCGH: a 16p deletion in a low number of cells and a small homozygous deletion in WWOX. Telomeric UPDs were only detected with aSNP in two cases: one affecting chromosome 3q and in the other, two UPD regions were present on 4q and 5p. In total, putative relevant tumour specific genomic alterations were found in seven cases (32%). Three small aberrations only detected by aCGH were present in T-cells, suggestive of germ line alterations which may confer a risk for MDS development. This part contains the aCGH analyses, for aSNP see GSE49004. Overall design: Array CGH experiment, 22 MDS tumor cells and 5 blood cells vs. control DNA.

INSTRUMENT(S): Agilent-022060 SurePrint G3 Human CGH Microarray 4x180K (Feature Number version)

SUBMITTER: Brigitte Royer-Pokora  

PROVIDER: GSE50897 | GEO | 2017-01-01

SECONDARY ACCESSION(S): PRJNA219313

REPOSITORIES: GEO

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