title: ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.
abstract: BACKGROUND
  Tumour samples containing distinct sub-populations of cancer and normal cells present challenges in the development of reproducible biomarkers, as these biomarkers are based on bulk signals from mixed tumour profiles. ISOpure is the only mRNA computational purification method to date that does not require a paired tumour-normal sample, provides a personalized cancer profile for each patient, and has been tested on clinical data. Replacing mixed tumour profiles with ISOpure-preprocessed cancer profiles led to better prognostic gene signatures for lung and prostate cancer.
  
  
  RESULTS
  To simplify the integration of ISOpure into standard R-based bioinformatics analysis pipelines, the algorithm has been implemented as an R package. The ISOpureR package performs analogously to the original code in estimating the fraction of cancer cells and the patient cancer mRNA abundance profile from tumour samples in four cancer datasets.
  
  
  CONCLUSIONS
  The ISOpureR package estimates the fraction of cancer cells and personalized patient cancer mRNA abundance profile from a mixed tumour profile. This open-source R implementation enables integration into existing computational pipelines, as well as easy testing, modification and extension of the model.
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Suite 510, M5G 0A3, ON, Canada. Catalina.Anghel@oicr.on.ca.
authors.forename: Catalina V
authors.initials: CV
authors.lastname: Anghel
authors.affiliation: Department of Computer Science, University of Toronto, 10 King's College Road, Room 3303, M5S 3G4, Toronto, ON, Canada. gquon@mit.edu.
authors.forename: Gerald
authors.initials: G
authors.lastname: Quon
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Suite 510, M5G 0A3, ON, Canada. Syed.Haider@oicr.on.ca.|Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom. Syed.Haider@oicr.on.ca.
authors.forename: Syed
authors.initials: S
authors.lastname: Haider
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Suite 510, M5G 0A3, ON, Canada. F-Nguyen@hotmail.com.
authors.forename: Francis
authors.initials: F
authors.lastname: Nguyen
authors.affiliation: Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College, Room SFB540, Toronto, M5S 3G4, ON, Canada. Amit.Deshwar@utoronto.ca.
authors.forename: Amit G
authors.initials: AG
authors.lastname: Deshwar
authors.affiliation: Department of Computer Science, University of Toronto, 10 King's College Road, Room 3303, M5S 3G4, Toronto, ON, Canada. Quaid.Morris@utoronto.ca.|Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College, Room SFB540, Toronto, M5S 3G4, ON, Canada. Quaid.Morris@utoronto.ca.|Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Room 4396, Toronto, M4S 1A8, ON, Canada. Quaid.Morris@utoronto.ca.|The Donnelly Centre, 160 College Street, Room 230, Toronto, M5S 3E1, ON, Canada. Quaid.Morris@utoronto.ca.
authors.forename: Quaid D
authors.initials: QD
authors.lastname: Morris
authors.affiliation: Informatics and Biocomputing Program, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Suite 510, M5G 0A3, ON, Canada. Paul.Boutros@oicr.on.ca.|Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, M5G 1L7, ON, Canada. Paul.Boutros@oicr.on.ca.|Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8, ON, Canada. Paul.Boutros@oicr.on.ca.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008962:Models, Theoretical; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000235:genetics*; D012984:Software