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Series GSE18197 Query DataSets for GSE18197
Status Public on Oct 01, 2009
Title High-resolution SNP-array profiling in myeloproliferative neoplasms
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary SNP arrays allow for genome-wide profiling of copy-number alterations (CNAs) and copy-neutral runs of homozygosity (ROH) at high resolution. To identify novel genetic lesions in myeloproliferative neoplasms (MPN), a large series of 151 clinically well-characterized patients was analyzed in our study. CNAs were rare in essential thrombocythemia and polycythemia vera. In contrast, approximately one third of myelofibrosis patients exhibited small genomic losses (< 5 Mb). In two secondary myelofibrosis cases the tumor suppressor gene NF1 in 17q11.2 was affected. Sequencing analyses revealed a mutation in the remaining NF1 allele of one patient. In terms of ROH, no chromosomes other than 9p were recurrently affected. In conclusion, in our study we identified novel genomic aberrations in MPN, in particular in patients with myelofibrosis. Further analyses on single-gene level are necessary to uncover the mechanisms that are involved in the pathogenesis of MPN.
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic peripheral blood samples.
Copy number analysis of Affymetrix 250K SNP arrays was performed for 151 myeloproliferative neoplasm samples [essential thrombocythemia, n=45; polycythemia vera, n=45; secondary myelofibrosis, n=14; primary myelofibrosis, n=47]. There are also 60 samples from acute myeloid leukemia patients in remission which were used as references for unpaired analysis.
Contributor(s) Stegelmann F, Bullinger L, Griesshammer M, Holzmann K, Habdank M, Kuhn S, Maile C, Schauer S, Döhner H, Döhner K
Citation(s) 20015882
Submission date Sep 21, 2009
Last update date May 17, 2017
Contact name Frank Stegelmann
Organization name University Hospital of Ulm
Department Internal Medicine III
Street address Albert-Einstein-Allee 23
City Ulm
ZIP/Postal code 89081
Country Germany
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (212)
GSM454903 Granulocytes UPN1
GSM454904 Granulocytes UPN2
GSM454905 Granulocytes UPN3
BioProject PRJNA119513

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE18197_RAW.tar 5.3 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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