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E-GEOD-46745 - Genome-wide Genotyping of Acute Myeloid Leukemia with Translocation t(9;11)(p22;q23) Reveals Novel Recurrent Genomic Alterations

Status
Released on 22 May 2014, last updated on 3 June 2014
Organism
Homo sapiens
Samples (55)
Array (1)
Protocols (8)
Description
To identify cooperating lesions in de novo and therapy-related acute myeloid leukemia (t-AML) with translocation t(9;11)(p22;q23) we performed high-resolution SNP-array profiling on 40 leukemia samples [de novo: n=22; t-AML: n=16; unknown: n=2]. A mean of 1.73 copy number alterations (CNAs)/case were identified with no differences between de novo and t-AML cases. We identified a novel minimally deleted region (MDR) at 7q36.1-q36.2 partly overlapping with a MDR previously identified in core-binding factor AML; MLL3 was the only gene affected in both regions. In addition, a recurrent gain was found at 13q21.33-q22.1 harboring the potential oncogene KLF5. Sequence/expression analysis of selected candidate genes revealed deregulated EVI1 at high frequency (50%). Copy-neutral loss-of-heterozygosity (CN-LOH) was absent in the paired cohort Further analysis of the candidate genes might provide novel insights into the pathogenesis of t(9;11) AML SNP genotyping was performed on 40 de novo and therapy-related MLL-MLLT3-rearranged acute myeloid leukemia samples; Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 15 patients. Data were processed using reference alignment, dChipSNP and circular binary segmentation.
Experiment type
genotyping by array 
Contacts
Michael Kuehn <michael.kuehn@uniklinik-ulm.de>, Frank G Rücker, Hartmut Döhner, Jan Krönke, Jennifer Edelmann, Karina Eiwen, Karlheinz Holzmann, Konstanze Döhner, Lars Bullinger, Michael W Kühn, Peter Paschka, Richard F Schlenk, Stefan Gröschel, Verena I Gaidzik
MIAME
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