Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data

Methods

Volumn 82, Issue , 2015, Pages 55-63

  Diggins, Kirsten E ^a   Brent Ferrell, P ^a   Irish, Jonathan M ^a  

^a VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Flow cytometry; Machine learning; Mass cytometry; Single cell biology; Unsupervised analysis

Indexed keywords

ARTICLE; CELL ASSAY; CELL LEVEL; CELL POPULATION; CELLS BY BODY ANATOMY; CYTOMETRY; DATA ANALYSIS; DATA COLLECTION METHOD; FLOW CYTOMETRY; HEATMAP METHOD; HUMAN; MACHINE LEARNING; MASS CYTOMETRY; PRIORITY JOURNAL; PROCESS DEVELOPMENT; SINGLE CELL; SINGLE CELL ANALYSIS; SPADE ALGORITHM; VISNE METHOD; BIOLOGY; PROCEDURES;

COMPUTATIONAL BIOLOGY; FLOW CYTOMETRY; HUMANS; MACHINE LEARNING;

EID: 84983121572     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2015.05.008     Document Type: Article

References (66)

1. Irish J.M., Doxie D.B. Curr. Top. Microbiol. Immunol. 2014, 377:1-21.
2. Bandura D.R., Baranov V.I., Ornatsky O.I., Antonov A., Kinach R., Lou X., Pavlov S., Vorobiev S., Dick J.E., Tanner S.D. Anal. Chem. 2009, 81:6813-6822.
3. Ornatsky O., Bandura D., Baranov V., Nitz M., Winnik M.A., Tanner S. J. Immunol. Methods 2010, 361:1-20.
4. Finak G., Frelinger J., Jiang W., Newell E.W., Ramey J., Davis M.M., Kalams S.A., De Rosa S.C., Gottardo R. PLoS Comput. Biol. 2014, 10:e1003806.
5. Aghaeepour N., Finak G., Flow C.A.P.C., Consortium D., Hoos H., Mosmann T.R., Brinkman R., Gottardo R., Scheuermann R.H. Nat. Methods 2013, 10:228-238.
6. Pyne S., Hu X., Wang K., Rossin E., Lin T.I., Maier L.M., Baecher-Allan C., McLachlan G.J., Tamayo P., Hafler D.A., De Jager P.L., Mesirov J.P. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:8519-8524.
7. Maecker H.T., Rinfret A., D'Souza P., Darden J., Roig E., Landry C., Hayes P., Birungi J., Anzala O., Garcia M., Harari A., Frank I., Baydo R., Baker M., Holbrook J., Ottinger J., Lamoreaux L., Epling C.L., Sinclair E., Suni M.A., Punt K., Calarota S., El-Bahi S., Alter G., Maila H., Kuta E., Cox J., Gray C., Altfeld M., Nougarede N., Boyer J., Tussey L., Tobery T., Bredt B., Roederer M., Koup R., Maino V.C., Weinhold K., Pantaleo G., Gilmour J., Horton H., Sekaly R.P. BMC Immunol. 2005, 6:13.
8. Amir el A.D., Davis K.L., Tadmor M.D., Simonds E.F., Levine J.H., Bendall S.C., Shenfeld D.K., Krishnaswamy S., Nolan G.P., Pe'er D. Nat. Biotechnol. 2013, 31:545-552.
9. Krutzik P.O., Clutter M.R., Nolan G.P. J. Immunol. 2005, 175:2357-2365.
10. Irish J.M. Nat. Immunol. 2014, 15:1095-1097.
11. Bendall S.C., Simonds E.F., Qiu P., Amir el A.D., Krutzik P.O., Finck R., Bruggner R.V., Melamed R., Trejo A., Ornatsky O.I., Balderas R.S., Plevritis S.K., Sachs K., Pe'er D., Tanner S.D., Nolan G.P. Science 2011, 332:687-696.
12. Qiu P., Simonds E.F., Bendall S.C., Gibbs K.D., Bruggner R.V., Linderman M.D., Sachs K., Nolan G.P., Plevritis S.K. Nat. Biotechnol. 2011, 29:886-891.
13. Sugar I.P., Sealfon S.C. BMC Bioinform. 2010, 11:502.
14. Bruggner R.V., Bodenmiller B., Dill D.L., Tibshirani R.J., Nolan G.P. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:E2770-E2777.
15. Newell E.W., Sigal N., Bendall S.C., Nolan G.P., Davis M.M. Immunity 2012, 36:142-152.
16. Mosmann T.R., Naim I., Rebhahn J., Datta S., Cavenaugh J.S., Weaver J.M., Sharma G. Cytometry A 2014.
17. Naim I., Datta S., Rebhahn J., Cavenaugh J.S., Mosmann T.R., Sharma G. Cytometry A 2014.
18. Chen X., Hasan M., Libri V., Urrutia A., Beitz B., Rouilly V., Duffy D., Patin E., Chalmond B., Rogge L., Quintana-Murci L., Albert M.L., Schwikowski B., Milieu Interieur C. Clin. Immunol. 2015.
19. Zare H., Shooshtari P., Gupta A., Brinkman R.R. BMC Bioinform. 2010, 11:403.
20. Tong D.L., Ball G.R., Pockley A.G. Cytometry A 2015.
21. Qian Y., Wei C., Eun-Hyung Lee F., Campbell J., Halliley J., Lee J.A., Cai J., Kong Y.M., Sadat E., Thomson E., Dunn P., Seegmiller A.C., Karandikar N.J., Tipton C.M., Mosmann T., Sanz I., Scheuermann R.H. Cytometry B 2010, 78(Suppl. 1):S69-S82.
22. Roederer M., Moore W., Treister A., Hardy R.R., Herzenberg L.A. Cytometry 2001, 45:47-55.
23. Bagwell C.B., Hudson J.L., Irvin G.L. J. Histochem. Cytochem. 1979, 27:293-296.
24. Overton W.R. Cytometry 1988, 9:619-626.
25. Kotecha N., Krutzik P.O., Irish J.M. Current Protocols in Cytometry/Editorial Board. Chapter 10 2010, Unit10 17.
26. Spidlen J., Breuer K., Brinkman R. Current Protocols in Cytometry/Editorial Board. Chapter 10 2012, Unit 10 18.
27. Tenenbaum J.B., de Silva V., Langford J.C. Science 2000, 290:2319-2323.
28. Becher B., Schlitzer A., Chen J., Mair F., Sumatoh H.R., Teng K.W.W., Low D., Ruedl C., Riccardi-Castagnoli P., Poidinger M., Greter M., Ginhoux F., Newell E.W. Nat. Immunol. 2014, 1181-1189.
29. Roweis S.T., Saul L.K. Science 2000, 290:2323-2326.
30. Pyne S., Lee S.X., Wang K., Irish J., Tamayo P., Nazaire M.D., Duong T., Ng S.K., Hafler D., Levy R., Nolan G.P., Mesirov J., McLachlan G.J. PLoS One 2014, 9:e100334.
31. Bendall S.C., Davis K.L., Amir el A.D., Tadmor M.D., Simonds E.F., Chen T.J., Shenfeld D.K., Nolan G.P., Pe'er D. Cell 2014, 157:714-725.
32. Inokuma M.S., Maino V.C., Bagwell C.B. J. Immunol. Methods 2013, 397:8-17.
33. Becher B., Schlitzer A., Chen J., Mair F., Sumatoh H.R., Teng K.W., Low D., Ruedl C., Riccardi-Castagnoli P., Poidinger M., Greter M., Ginhoux F., Newell E.W. Nat. Immunol. 2014, 15:1181-1189.
34. Ornatsky O., Baranov V.I., Bandura D.R., Tanner S.D., Dick J. J. Immunol. Methods 2006, 308:68-76.
35. Spidlen J., Moore W., Parks D., Goldberg M., Bray C., Bierre P., Gorombey P., Hyun B., Hubbard M., Lange S., Lefebvre R., Leif R., Novo D., Ostruszka L., Treister A., Wood J., Murphy R.F., Roederer M., Sudar D., Zigon R., Brinkman R.R. Cytometry A 2010, 77:97-100.
36. Spidlen J., Barsky A., Breuer K., Carr P., Nazaire M.D., Hill B.A., Qian Y., Liefeld T., Reich M., Mesirov J.P., Wilkinson P., Scheuermann R.H., Sekaly R.P., Brinkman R.R. Source Code Biol. Med. 2013, 8:14.
37. H.P. Ellis B, F. Hahne, N.L. Meur, N. Gopalakrishnan, J. Spidlen, R Package Version 1.34.3, 2015.
38. L. Balkay, MATLAB Central File Exchange, 2014 (retrieved).
39. Finck R., Simonds E.F., Jager A., Krishnaswamy S., Sachs K., Fantl W., Pe'er D., Nolan G.P., Bendall S.C. Cytometry A 2013, 83:483-494.
40. Lee J.A., Spidlen J., Boyce K., Cai J., Crosbie N., Dalphin M., Furlong J., Gasparetto M., Goldberg M., Goralczyk E.M., Hyun B., Jansen K., Kollmann T., Kong M., Leif R., McWeeney S., Moloshok T.D., Moore W., Nolan G., Nolan J., Nikolich-Zugich J., Parrish D., Purcell B., Qian Y., Selvaraj B., Smith C., Tchuvatkina O., Wertheimer A., Wilkinson P., Wilson C., Wood J., Zigon R., F. International Society for Advancement of Cytometry Data Standards Task, Scheuermann R.H., Brinkman R.R. Cytometry A 2008, 73:926-930.
41. Spidlen J., Bray C., I.D.S.T.Force, Brinkman R.R. Cytometry A 2015, 87:86-88.
42. Spidlen J., Leif R.C., Moore W., Roederer M., F.International Society for the Advancement of Cytometry Data Standards Task, Brinkman R.R. Cytometry A 2008, 73A:1151-1157.
43. Kalina T., Flores-Montero J., van der Velden V.H., Martin-Ayuso M., Bottcher S., Ritgen M., Almeida J., Lhermitte L., Asnafi V., Mendonca A., de Tute R., Cullen M., Sedek L., Vidriales M.B., Perez J.J., te Marvelde J.G., Mejstrikova E., Hrusak O., Szczepanski T., van Dongen J.J., Orfao A., EuroFlow C. Leukemia 2012, 26:1986-2010.
44. Mahnke Y., Chattopadhyay P., Roederer M. Cytometry A 2010, 77:814-818.
45. Herzenberg L.A., Tung J., Moore W.A., Herzenberg L.A., Parks D.R. Nat. Immunol. 2006, 7:681-685.
46. Irish J.M., Myklebust J.H., Alizadeh A.A., Houot R., Sharman J.P., Czerwinski D.K., Nolan G.P., Levy R. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:12747-12754.
47. Moore W.A., Parks D.R. Cytometry A 2012, 81A:273-277.
48. Parks D., Roederer M., Moore W.A. Cytometry A 2004, 59A:87.
49. Fienberg H.G., Simonds E.F., Fantl W.J., Nolan G.P., Bodenmiller B. Cytometry A 2012, 81:467-475.
50. van der Maaten L., Hinton G. J. Mach. Learn. Res. 2008, 9:2579-2605.
51. Irish J., Hovland R., Krutzik P., Perez O., Bruserud O., Gjertsen B., Nolan G. Cell 2004, 118:217-228.
52. Q.P. Linderman M, E. Simonds, Z. Bjornson, R Package Version 1.14.0, 2011 .
53. Irish J.M., Hovland R., Krutzik P.O., Perez O.D., Bruserud O., Gjertsen B.T., Nolan G.P. Cell 2004, 118:217-228.
54. Kotecha N., Flores N.J., Irish J.M., Simonds E.F., Sakai D.S., Archambeault S., Diaz-Flores E., Coram M., Shannon K.M., Nolan G.P., Loh M.L. Cancer Cell 2008, 14:335-343.
55. H. Bengtsson, 2015 .
56. B.B. Gregory, R. Warnes, L. Bonebakker, R. Gentleman, W.H.A. Liaw, T. Lumley, M. Maechler, A. Magnusson, S. Moeller, M. Schwartz, B. Venables, R Package Version 2.17.0, 2015 .
57. G.R. Ellis B, F. Hahne, N.L. Meur, D. Sarkar, R Package Version 1.31.1, 2015.
58. Lo K H.F., Brinkman R., Gottardo R. BMC Bioinform. 2009, 10.
59. Abdelrahman A.I., Dai S., Thickett S.C., Ornatsky O., Bandura D., Baranov V., Winnik M.A. J. Am. Chem. Soc. 2009, 131:15276-15283.
60. Abdelrahman A.I., Ornatsky O., Bandura D., Baranov V., Kinach R., Dai S., Thickett S.C., Tanner S., Winnik M.A. J. Anal. At. Spectrom. 2010, 25:260-268.
61. Meehan S., Walther G., Moore W., Orlova D., Meehan C., Parks D., Ghosn E., Philips M., Mitsunaga E., Waters J., Kantor A., Okamura R., Owumi S., Yang Y., Herzenberg L.A., Herzenberg L.A. Immunol. Res. 2014, 58:218-223.
62. Irish J.M., Myklebust J.H., Alizadeh A.A., Houot R., Sharman J.P., Czerwinski D.K., Nolan G.P., Levy R. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:12747-12754.
63. Geoffrey Hinton S.R. Advances in Neural Information Processing Systems 2002.
64. Hahne F., LeMeur N., Brinkman R.R., Ellis B., Haaland P., Sarkar D., Spidlen J., Strain E., Gentleman R. BMC Bioinform. 2009, 10:106.
65. Van Gassen S., Callebaut B., Van Helden M.J., Lambrecht B.N., Demeester P., Dhaene T., Saeys Y. Cytometry A 2015.
66. Shekhar K., Brodin P., Davis M.M., Chakraborty A.K. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:202-207.