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Series GSE59537 Query DataSets for GSE59537
Status Public on Dec 31, 2014
Title Bone marrows from neuroblastoma patients: an excellent source for tumor genome analyses
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Neuroblastoma is the most common extra-cranial solid tumor in childhood. Presence of disseminated tumor cells (DTCs) in the bone marrow (BM) at diagnosis and at relapse is a common event in stage M neuroblastomas. Although the clinical heterogeneity of disseminated neuroblastomas is frequently associated with genomic diversity, so far, only little information exists about the genomic status of DTCs. This lack of knowledge is mainly due to the varying amount of BM infiltrating tumor cells, which is usually below 30% even at diagnosis thereby hampering systematic analyses. Thus, a valuable chance to analyze metastatic and relapse clones is, so far, completely unexploited. In this study, we show that the enrichment of tumor cells in fresh or DMSO frozen BM samples with a minimum of 0.05% or 0.1% infiltration rate, respectively, by applying magnetic beads technique increased the DTC content to a sufficient level to allow SNP array analyses in 49 out of 69 samples. In addition, we successfully used non-enriched BM samples with ≥30% DTCs including non-stained and immunostained cytospin and BM smear slides for SNP array analyses in 44 cases. We analyzed the genomic profile of DTCs by an ultra-high density SNP array technique with highest performance detecting all segmental chromosomal aberrations, amplified regions, acquired loss of heterozygosity events and minor aberrations affecting single genes or parts thereof.
Overall design Affymetrix CytoScan HD arrays were performed according to the manufacturer's directions on DNA extracted from disseminated tumor cells in the bone marrow or tumor samples.
Contributor(s) Abbasi MR, Rifatbegovic F, Brunner C, Ladenstein R, Ambros IM, Ambros PF
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Submission date Jul 17, 2014
Last update date Jul 13, 2018
Contact name Peter. F. Ambros
Organization name Children's Cancer Research Institute
Department Tumor Biology
Lab 4
Street address Zimmermannplatz 10
City Vienna
ZIP/Postal code 1090
Country Austria
Platforms (1)
GPL16131 [CytoScanHD_Array] Affymetrix CytoScan HD Array
Samples (9)
GSM1438977 PT1
GSM1438978 PT2
GSM1438979 PT3
BioProject PRJNA255640

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

Supplementary file Size Download File type/resource
GSE59537_RAW.tar 998.7 Mb (http)(custom) TAR (of CEL, CYCHP)
Processed data included within Sample table
Processed data provided as supplementary file

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