title: Bone marrows from neuroblastoma patients: an excellent source for tumor genome analyses.
abstract: 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 bead-based 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.
authors.affiliation: Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria. Electronic address: reza.abbasi@ccri.at.
authors.forename: M Reza
authors.initials: MR
authors.lastname: Abbasi
authors.affiliation: Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors.forename: Fikret
authors.initials: F
authors.lastname: Rifatbegovic
authors.affiliation: Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors.forename: Clemens
authors.initials: C
authors.lastname: Brunner
authors.affiliation: SiRP, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
authors.forename: Ruth
authors.initials: R
authors.lastname: Ladenstein
authors.affiliation: Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors.forename: Inge M
authors.initials: IM
authors.lastname: Ambros
authors.affiliation: Tumor Biology, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria. Electronic address: peter.ambros@ccri.at.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Ambros
mesh_terms: D001853:Bone Marrow / Q000473:pathology*; D001932:Brain Neoplasms / Q000235:genetics* / Q000473:pathology*; D004273:DNA, Neoplasm / Q000302:isolation & purification; D005615:Freezing; D015894:Genome, Human; D006801:Humans; D008297:Male; D009360:Neoplastic Cells, Circulating / Q000473:pathology; D009447:Neuroblastoma / Q000235:genetics* / Q000473:pathology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics
chemical_list: D004273:DNA, Neoplasm
keywords: Bone marrow; Disseminated tumor cells; Enrichment; Neuroblastoma; SNP array