title: Clonality inference in multiple tumor samples using phylogeny.
abstract: BACKGROUND
  Intra-tumor heterogeneity presents itself through the evolution of subclones during cancer progression. Although recent research suggests that this heterogeneity has clinical implications, in silico determination of the clonal subpopulations remains a challenge.
  
  
  RESULTS
  We address this problem through a novel combinatorial method, named clonality inference in tumors using phylogeny (CITUP), that infers clonal populations and their frequencies while satisfying phylogenetic constraints and is able to exploit data from multiple samples. Using simulated datasets and deep sequencing data from two cancer studies, we show that CITUP predicts clonal frequencies and the underlying phylogeny with high accuracy.
  
  
  METHODS
  CITUP is freely available at: http://sourceforge.net/projects/citup/.
  
  
  BACKGROUND
  cenk@sfu.ca
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Salem
authors.initials: S
authors.lastname: Malikic
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Andrew W
authors.initials: AW
authors.lastname: McPherson
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Nilgun
authors.initials: N
authors.lastname: Donmez
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, BC Cancer Agency, Vancouver, BC, Canada, Vancouver Prostate Center, Vancouver, BC, Canada and School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
authors.forename: Cenk S
authors.initials: CS
authors.lastname: Sahinalp
mesh_terms: D000465:Algorithms; D060965:Clonal Evolution; D004252:DNA Mutational Analysis; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000235:genetics; D015470:Leukemia, Myeloid, Acute / Q000235:genetics; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D010802:Phylogeny