title: Genome Fusion Detection: a novel method to detect fusion genes from SNP-array data.
abstract: BACKGROUND
  Fusion genes result from genomic rearrangements, such as deletions, amplifications and translocations. Such rearrangements can also frequently be observed in cancer and have been postulated as driving event in cancer development. to detect them, one needs to analyze the transition region of two segments with different copy number, the location where fusions are known to occur. Finding fusion genes is essential to understanding cancer development and may lead to new therapeutic approaches.
  
  
  RESULTS
  Here we present a novel method, the Genomic Fusion Detection algorithm, to predict fusion genes on a genomic level based on SNP-array data. This algorithm detects genes at the transition region of segments with copy number variation. With the application of defined constraints, certain properties of the detected genes are evaluated to predict whether they may be fused. We evaluated our prediction by calculating the observed frequency of known fusions in both primary cancers and cell lines. We tested a set of cell lines positive for the BCR-ABL1 fusion and prostate cancers positive for the TMPRSS2-ERG fusion. We could detect the fusions in all positive cell lines, but not in the negative controls.
authors: Department of Theoretical Biophysics, Humboldt-University of Berlin, 10115 Berlin, Germany and Therapeutic Research Group Oncology, Bayer Pharma AG, 13353 Berlin, Germany.
authors: Sebastian
authors: S
authors: Thieme
authors: Philip
authors: P
authors: Groth
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D056905:Chromosome Breakpoints; D056915:DNA Copy Number Variations; D016044:Fusion Proteins, bcr-abl / Q000235:genetics; D050939:Gene Fusion; D016678:Genome; D006801:Humans; D008297:Male; D009369:Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000235:genetics
chemical_list: C581634:BCR-ABL1 fusion protein, human; D016044:Fusion Proteins, bcr-abl