title: Tumor Touch Imprints as Source for Whole Genome Analysis of Neuroblastoma Tumors.
abstract: BACKGROUND
  Tumor touch imprints (TTIs) are routinely used for the molecular diagnosis of neuroblastomas by interphase fluorescence in-situ hybridization (I-FISH). However, in order to facilitate a comprehensive, up-to-date molecular diagnosis of neuroblastomas and to identify new markers to refine risk and therapy stratification methods, whole genome approaches are needed. We examined the applicability of an ultra-high density SNP array platform that identifies copy number changes of varying sizes down to a few exons for the detection of genomic changes in tumor DNA extracted from TTIs.
  
  
  METHODS
  DNAs were extracted from TTIs of 46 neuroblastoma and 4 other pediatric tumors. The DNAs were analyzed on the Cytoscan HD SNP array platform to evaluate numerical and structural genomic aberrations. The quality of the data obtained from TTIs was compared to that from randomly chosen fresh or fresh frozen solid tumors (n = 212) and I-FISH validation was performed.
  
  
  RESULTS
  SNP array profiles were obtained from 48 (out of 50) TTI DNAs of which 47 showed genomic aberrations. The high marker density allowed for single gene analysis, e.g. loss of nine exons in the ATRX gene and the visualization of chromothripsis. Data quality was comparable to fresh or fresh frozen tumor SNP profiles. SNP array results were confirmed by I-FISH.
  
  
  CONCLUSIONS
  TTIs are an excellent source for SNP array processing with the advantage of simple handling, distribution and storage of tumor tissue on glass slides. The minimal amount of tumor tissue needed to analyze whole genomes makes TTIs an economic surrogate source in the molecular diagnostic work up of tumor samples.
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors: Clemens
authors: C
authors: Brunner
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors: Bettina
authors: B
authors: Brunner-Herglotz
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors: Andrea
authors: A
authors: Ziegler
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors: Christian
authors: C
authors: Frech
authors: Institute of Clinical Pathology, Medical University Vienna, Vienna, Austria.
authors: Gabriele
authors: G
authors: Amann
authors: S2IRP, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.|Department of Pediatrics, Medical University Vienna, Vienna, Austria.
authors: Ruth
authors: R
authors: Ladenstein
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.
authors: Inge M
authors: IM
authors: Ambros
authors: Department of Tumor Biology, CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria.|Department of Pediatrics, Medical University Vienna, Vienna, Austria.
authors: Peter F
authors: PF
authors: Ambros
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics; D002869:Chromosome Aberrations; D019295:Computational Biology; D004273:DNA, Neoplasm / Q000235:genetics; D005240:Feasibility Studies; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D019656:Loss of Heterozygosity; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D009447:Neuroblastoma / Q000175:diagnosis* / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012815:Signal Processing, Computer-Assisted
chemical_list: D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm