title: HitWalker: variant prioritization for personalized functional cancer genomics.
abstract: CONCLUSIONS
  Determining the functional relevance of identified sequence variants in cancer is a prerequisite to ultimately matching specific therapies with individual patients. This level of mechanistic understanding requires integration of genomic information with complementary functional analyses to identify oncogenic targets and relies on the development of computational frameworks to aid in the prioritization and visualization of these diverse data types. In response to this, we have developed HitWalker, which prioritizes patient variants relative to their weighted proximity to functional assay results in a protein-protein interaction network. It is highly extensible, allowing incorporation of diverse data types to refine prioritization. In addition to a ranked list of variants, we have also devised a simple shortest path-based approach of visualizing the results in an intuitive manner to provide biological interpretation.
  
  
  METHODS
  The program, documentation and example data are available as an R package from www.biodevlab.org/HitWalker.html.
authors.affiliation: Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA. bottomly@ohsu.edu
authors.forename: Daniel
authors.initials: D
authors.lastname: Bottomly
authors.forename: Beth
authors.initials: B
authors.lastname: Wilmot
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Tyner
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Eide
authors.forename: Marc M
authors.initials: MM
authors.lastname: Loriaux
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Druker
authors.forename: Shannon K
authors.initials: SK
authors.lastname: McWeeney
mesh_terms: D000465:Algorithms; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics*; D025941:Protein Interaction Mapping; D012984:Software