title: Deep profiling of multitube flow cytometry data.
abstract: BACKGROUND
  Deep profiling the phenotypic landscape of tissues using high-throughput flow cytometry (FCM) can provide important new insights into the interplay of cells in both healthy and diseased tissue. But often, especially in clinical settings, the cytometer cannot measure all the desired markers in a single aliquot. In these cases, tissue is separated into independently analysed samples, leaving a need to electronically recombine these to increase dimensionality. Nearest-neighbour (NN) based imputation fulfils this need but can produce artificial subpopulations. Clustering-based NNs can reduce these, but requires prior domain knowledge to be able to parameterize the clustering, so is unsuited to discovery settings.
  
  
  RESULTS
  We present flowBin, a parameterization-free method for combining multitube FCM data into a higher-dimensional form suitable for deep profiling and discovery. FlowBin allocates cells to bins defined by the common markers across tubes in a multitube experiment, then computes aggregate expression for each bin within each tube, to create a matrix of expression of all markers assayed in each tube. We show, using simulated multitube data, that flowType analysis of flowBin output reproduces the results of that same analysis on the original data for cell types of >10% abundance. We used flowBin in conjunction with classifiers to distinguish normal from cancerous cells. We used flowBin together with flowType and RchyOptimyx to profile the immunophenotypic landscape of NPM1-mutated acute myeloid leukemia, and present a series of novel cell types associated with that mutation.
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Kieran
authors.initials: K
authors.lastname: O'Neill
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Nima
authors.initials: N
authors.lastname: Aghaeepour
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Parker
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Donna
authors.initials: D
authors.lastname: Hogge
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Aly
authors.initials: A
authors.lastname: Karsan
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Bakul
authors.initials: B
authors.lastname: Dalal
authors.affiliation: Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada Terry Fox Laboratory, BC Cancer Agency, Bioinformatics Graduate Program, University of British Columbia, Department of Hematopathology, Vancouver General Hospital and Faculty of Medical Genetics, University of British Columbia, Vancouver, Canada.
authors.forename: Ryan R
authors.initials: RR
authors.lastname: Brinkman
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics*; D016022:Case-Control Studies; D019070:Cell Lineage; D002469:Cell Separation; D005434:Flow Cytometry / Q000379:methods*; D006801:Humans; D016130:Immunophenotyping; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000473:pathology; D007963:Leukocytes, Mononuclear / Q000166:cytology / Q000378:metabolism*; D009154:Mutation / Q000235:genetics*; D009687:Nuclear Proteins / Q000235:genetics; D000090243:Nucleophosmin; D012984:Software
chemical_list: D014408:Biomarkers, Tumor; C000716967:NPM1 protein, human; D009687:Nuclear Proteins; D000090243:Nucleophosmin