viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

Nature Biotechnology
El-ad David AmirDana Pe'er

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.

References

Mar 5, 2003·Annual Review of Immunology·Motonari KondoIrving L Weissman
Jun 21, 2006·Nature Immunology·Leonore A HerzenbergDavid R Parks
Sep 29, 2007·Nature Methods·Dale S CornettRichard M Caprioli
Mar 29, 2008·Cell Stem Cell·Ravindra MajetiIrving L Weissman
Jun 24, 2008·Nature Reviews. Neuroscience·UNKNOWN Petilla Interneuron Nomenclature GroupRafael Yuste
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Mar 3, 2009·Seminars in Radiation Oncology·Catherine Adell O'BrienJohn E Dick
May 16, 2009·Proceedings of the National Academy of Sciences of the United States of America·Saumyadipta PyneJill P Mesirov
Dec 22, 2009·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Attila TárnokJozsef Bocsi
Dec 31, 2010·Nature Reviews. Genetics·Fatih Ozsolak, Patrice M Milos
Mar 10, 2011·British Journal of Haematology·Gert J OssenkoppeleGerrit Jan Schuurhuis
May 10, 2011·Science·Christophe Benoist, Nir Hacohen
Oct 4, 2011·Nature Biotechnology·Peng QiuSylvia K Plevritis
Nov 15, 2011·Nature Biotechnology·Piero DalerbaStephen R Quake
Apr 6, 2012·Trends in Immunology·Sean C BendallPratip K Chattopadhyay
Jul 12, 2012·Nature Biotechnology·Sean C Bendall, Garry P Nolan
Aug 21, 2012·Nature Biotechnology·Bernd BodenmillerGarry P Nolan

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Citations

Dec 18, 2013·Proceedings of the National Academy of Sciences of the United States of America·Karthik ShekharArup K Chakraborty
Jan 21, 2014·Nature Biotechnology·Vladimir BrusicUNKNOWN HIPC steering committee
Jan 21, 2014·Nature Biotechnology·Evan W Newell, Mark M Davis
Jan 16, 2014·Annual Review of Immunology·Marcela V MausCarl H June
Jan 23, 2014·Nature Immunology·Pratip K ChattopadhyayJ Christopher Love
Jan 23, 2014·Nature Immunology·Brian A KiddJoel T Dudley
Feb 4, 2014·Cancer Immunology, Immunotherapy : CII·Serena ChangHolden T Maecker
Apr 22, 2014·Trends in Immunology·Rahul Satija, Alex K Shalek
Jul 6, 2014·Clinical Proteomics·Emily S Boja, Henry Rodriguez
Aug 8, 2014·Nature Biotechnology·Berend SnijderGiulio Superti-Furga
Oct 13, 2014·Nature Immunology·Burkhard BecherEvan W Newell
Sep 25, 2014·Immunology Letters·José-Enrique O'ConnorRobert C Callaghan
Sep 25, 2014·Immunology Letters·José-Enrique O'ConnorRobert C Callaghan
Jul 2, 2014·Analytical and Bioanalytical Chemistry·Alexandra J DickinsonNancy L Allbritton
Nov 15, 2014·Nature Immunology·Jonathan Michael Irish
Jan 26, 2016·Nature Methods·Andreas P FreiPier Federico Gherardini
Dec 17, 2015·Nature Reviews. Drug Discovery·James R HeathPaul S Mischel
Jan 26, 2016·Critical Reviews in Biochemistry and Molecular Biology·Oren Z Kraus, Brendan J Frey
Dec 25, 2015·Proceedings of the National Academy of Sciences of the United States of America·Prabhat K SinghalBrian Seed
Oct 9, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Nima AghaeepourRyan R Brinkman
Nov 10, 2015·European Journal of Immunology·Florian MairBurkhard Becher
Dec 24, 2015·Neoplasia : an International Journal for Oncology Research·Amy T ShahMelissa C Skala
Dec 17, 2015·Trends in Immunology·Julie G BurelDenise L Doolan
Dec 18, 2014·Genome Biology·Assieh SaadatpourGuo-Cheng Yuan
Aug 16, 2014·Current Opinion in Biotechnology·Serena Di Palma, Bernd Bodenmiller
Nov 19, 2015·Immunology and Cell Biology·Steven WoodhouseJasmin Fisher
Dec 8, 2015·Journal of Neuro-oncology·Jonathan B LamanoOrin Bloch
Mar 1, 2016·Stem Cell Reports·Christian M NefzgerJose M Polo
Nov 26, 2015·Frontiers in Immunology·Anne-Sophie ChretienDaniel Olive
Apr 25, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Lin LinRaphael Gottardo
Mar 11, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Peng Qiu
Jan 13, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Sofie Van GassenYvan Saeys
Nov 25, 2014·Cell·Jan Philipp JunkerAlexander van Oudenaarden
Jul 22, 2014·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Juliet FrederiksenOle Lund
Feb 20, 2016·Expert Review of Molecular Diagnostics·Bjørn T GjertsenJörn Skavland
Jan 29, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Victoria Moignard, Berthold Göttgens
Jun 21, 2015·Drug Discovery Today·Ala F NassarAdam V Wisnewski
Nov 26, 2015·Nature Reviews. Immunology·Yonit LavinMiriam Merad
Nov 26, 2015·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Katherine J NicholasSpyros A Kalams
Oct 10, 2015·Trends in Genetics : TIG·Assieh SaadatpourGuo-Cheng Yuan
Oct 7, 2015·Frontiers in Genetics·Jennifer EncisoRosana Pelayo

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