title: viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.
abstract: New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data. viSNE plots individual cells in a visual similar to a scatter plot, while using all pairwise distances in high dimension to determine each cell's location in the plot. We integrated mass cytometry with viSNE to map healthy and cancerous bone marrow samples. Healthy bone marrow automatically maps into a consistent shape, whereas leukemia samples map into malformed shapes that are distinct from healthy bone marrow and from each other. We also use viSNE and mass cytometry to compare leukemia diagnosis and relapse samples, and to identify a rare leukemia population reminiscent of minimal residual disease. viSNE can be applied to any multi-dimensional single-cell technology.
authors.affiliation: Department of Biological Sciences, Columbia Initiative for Systems Biology, Columbia University, New York, New York, USA.
authors.forename: El-ad David
authors.initials: el-AD
authors.lastname: Amir
authors.forename: Kara L
authors.initials: KL
authors.lastname: Davis
authors.forename: Michelle D
authors.initials: MD
authors.lastname: Tadmor
authors.forename: Erin F
authors.initials: EF
authors.lastname: Simonds
authors.forename: Jacob H
authors.initials: JH
authors.lastname: Levine
authors.forename: Sean C
authors.initials: SC
authors.lastname: Bendall
authors.forename: Daniel K
authors.initials: DK
authors.lastname: Shenfeld
authors.forename: Smita
authors.initials: S
authors.lastname: Krishnaswamy
authors.forename: Garry P
authors.initials: GP
authors.lastname: Nolan
authors.forename: Dana
authors.initials: D
authors.lastname: Pe'er
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism; D019046:Bone Marrow Neoplasms / Q000175:diagnosis / Q000473:pathology*; D019070:Cell Lineage; D006801:Humans; D019044:Image Cytometry; D016130:Immunophenotyping; D007938:Leukemia / Q000175:diagnosis / Q000473:pathology*; D009364:Neoplasm Recurrence, Local / Q000175:diagnosis / Q000473:pathology; D012008:Recurrence; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D014408:Biomarkers, Tumor