REFERENCES
1. Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SWG, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012;486:395.
2. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New Engl J Med 2012;366:883-92.
3. Davis A, Gao R, Navin N. Tumor evolution: Linear, branching, neutral or punctuated? Biochim Biophys Acta, Rev Cancer 2017;1867:151-61.
4. McGranahan N, Swanton C. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell 2015;27:15-26.
5. Fidler IJ, Hart IR. Biological diversity in metastatic neoplasms: origins and implications. Science 1982;217:998-1003.
6. Friedl P, Alexander S. Cancer invasion and the microenvironment: plasticity and reciprocity. Cell 2011;147:992-1009.
7. McGranahan N, Swanton C. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell 2017;168:613-28.
8. Swanton C. Intratumor heterogeneity: evolution through space and time. Cancer Res 2012;72:4875-82.
9. Jamal-Hanjani M, Thanopoulou E, Peggs KS, Quezada SA, Swanton C. Tumour heterogeneity and immune-modulation. Curr Opin Pharm 2013;13:497-503.
10. Nassar A, Radhakrishnan A, Cabrero IA, Cotsonis GA, Cohen C. Intratumoral heterogeneity of immunohistochemical marker expression in breast carcinoma: a tissue microarray-based study. Appl Immunohistochem Mol Morphol 2010;18:433-41.
11. Negrini S, Gorgoulis VG, Halazonetis TD. Genomic instability—an evolving hallmark of cancer. Nat Rev Mol Cell Biol 2010;11:220.
13. Caswell DR, Swanton C. The role of tumour heterogeneity and clonal cooperativity in metastasis, immune evasion and clinical outcome. BMC Med 2017;15:133.
15. Venkatesan S, Swanton C, Taylor BS, Costello JF. Treatment-induced mutagenesis and selective pressures sculpt cancer evolution. Cold Spring Harb Perspect Med 2017;7:a026617.
16. Dagogo-Jack I, Shaw AT. Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol 2017;15:81.
17. Turajlic S, Xu H, Litchfield K, Rowan A, Chambers T, Lopez JI, Nicol D, O'Brien T, Larkin J, Horswell S, Stares M, Au L, Jamal-Hanjani M, Challacombe B, Chandra A, Hazell S, Eichler-Jonsson C, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Jabbar F, Spain L, Lall S, Guarch R, Falzon M, Proctor I, Pickering L, Gore M, Watkins TBK, Ward S, Stewart A, DiNatale R, Becerra MF, Reznik E, Hsieh JJ, Richmond TA, Mayhew GF, Hill SM, McNally CD, Jones C, Rosenbaum H, Stanislaw S, Burgess DL, Alexander NR, Swanton C. Tracking cancer evolution reveals constrained routes to metastases: TRACERx Renal. Cell 2018;173:581-94.e12.
18. Wilting RH, Dannenberg JH. Epigenetic mechanisms in tumorigenesis, tumor cell heterogeneity and drug resistance. Drug Resist Updat 2012;15:21-38.
19. Brakensiek K, Wingen LU, Länger F, Kreipe H, Lehmann U. Quantitative high-resolution CpG island mapping with pyrosequencing TM reveals disease-specific methylation patterns of the CDKN2B gene in myelodysplastic syndrome and myeloid leukemia. Clin Chem 2006; doi: 10.1373/clinchem.2007.072629.
20. Candiloro ILM, Mikeska T, Hokland P, Dobrovic A. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene. Epigenetics & Chromatin 2008;1:7.
21. Petrovic N, Ergün S, Isenovic ER. Levels of microRNA heterogeneity in cancer biology. Mol Diagn Ther 2017;21:511-23.
22. Zedan AH, Blavnsfeldt SG, Hansen TF, Nielsen BS, Marcussen N, Pleckaitis M, Osther PJS, Sørensen FB. Heterogeneity of miRNA expression in localized prostate cancer with clinicopathological correlations. PLoS One 2017;12:e0179113.
23. Li H, Fan X, Houghton J. Tumor microenvironment: the role of the tumor stroma in cancer. J Cell Biochem 2007;101:805-15.
24. Kumar V, Patel S, Tcyganov E, Gabrilovich DI. The nature of myeloid-derived suppressor cells in the tumor microenvironment. Trends Immunol 2016;37:208-20.
25. Joyce JA, Fearon DT. T cell exclusion, immune privilege, and the tumor microenvironment. Science 2015;348:74-80.
26. Tlsty TD, Coussens LM. Tumor stroma and regulation of cancer development. Annu Rev Pathol Mech Dis 2006;1:119-50.
27. Hanahan D, Coussens LM. Accessories to the crime: functions of cells recruited to the tumor microenvironment. Cancer Cell 2012;21:309-22.
28. Gainor JF, Dardaei L, Yoda S, Friboulet L, Leshchiner I, Katayama R, Dagogo-Jack I, Gadgeel S, Schultz K, Singh M, Chin E, Parks M, Lee D, DiCecca RH, Lockerman E, Huynh T, Logan J, Ritterhouse LL, Le LP, Muniappan A, Digumarthy S, Channick C, Keyes C, Getz G, Dias-Santagata D, Heist RS, Lennerz J, Sequist LV, Benes CH, Iafrate AJ, Mino-Kenudson M, Engelman JA, Shaw AT. Molecular mechanisms of resistance to first- and second-generation ALK inhibitors in ALK-rearranged lung cancer. Cancer Discovery 2016;6:1118-33.
29. Pao W, Miller VA, Politi KA, Riely GJ, Somwar R, Zakowski MF, Kris MG, Varmus H. Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med 2005;2:e73.
30. Engelman JA, Zejnullahu K, Mitsudomi T, Song Y, Hyland C, Park JO, Lindeman N, Gale CM, Zhao X, Christensen J, Kosaka T, Holmes AJ, Rogers AM, Cappuzzo F, Mok T, Lee C, Johnson BE, Cantley LC, Jänne PA. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 2007;316:1039-43.
31. Eng J, Woo KM, Sima CS, Plodkowski A, Hellmann MD, Chaft JE, Kris MG, Arcila ME, Ladanyi M, Drilon A. Impact of concurrent PIK3CA mutations on response to EGFR tyrosine kinase inhibition in EGFR-mutant lung cancers and on prognosis in oncogene-driven lung adenocarcinomas. J Thorac Oncol 2015;10:1713-9.
32. Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, Crosetto N, Foukakis T, Navin NE. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing. Cell 2018;173:879-93.e13.
33. Turner NC, Reis-Filho JS. Genetic heterogeneity and cancer drug resistance. Lancet Oncol 2012;13:e178-85.
34. Danielsen HE, Pradhan M, Novelli M. Revisiting tumour aneuploidy—the place of ploidy assessment in the molecular era. Nat Rev Clin Oncol 2016;13:291.
35. Cyll K, Ersvær E, Vlatkovic L, Pradhan M, Kildal W, Avranden Kjær M, Kleppe A, Hveem TS, Carlsen B, Gill S, Löffeler S, Haug ES, Wæhre H, Sooriakumaran P, Danielsen HE. Tumour heterogeneity poses a significant challenge to cancer biomarker research. Br J Cancer 2017;117:367.
36. Wei SH, Chen CM, Strathdee G, Harnsomburana J, Shyu CR, Rahmatpanah F, Shi H, Ng SW, Yan PS, Nephew KP, Brown R, Huang THM. Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin Cancer Res 2002;8:2246-52.
37. Wei SH, Balch C, Paik HH, Kim YS, Baldwin RL, Liyanarachchi S, Li L, Wang Z, Wan JC, Davuluri RV, Karlan BY, Gifford G, Brown R, Kim S, Huang THM, Nephew KP. Prognostic DNA methylation biomarkers in ovarian cancer. Clin Cancer Res 2006;12:2788-94.
38. Rajaram S, Heinrich LE, Gordan JD, Avva J, Bonness KM, Witkiewicz AK, Malter JS, Atreya CE, Warren RS, Wu LF, Altschuler SJ. Sampling strategies to capture single-cell heterogeneity. Nat Methods 2017;14:967.
39. Foley JW, Zhu C, Jolivet P, Zhu SX, Lu P, Meaney MJ, West RB. Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. bioRxiv 2018; doi: 10.1101/207340.
40. Hayashida Y, Partida GJ, Ishida AT. Dissociation of retinal ganglion cells without enzymes. J Neurosci Methods 2004;137:25-35.
41. Gomez GG, Kruse CA. Isolation and culture of human brain tumor cells. Cancer Cell Culture. Methods Mol Med: Springer; 2004. pp. 101-9.
42. Louis SA, Mak CK, Reynolds BA. Methods to culture, differentiate, and characterize neural stem cells from the adult and embryonic mouse central nervous system. Methods Mol Med: Springer; 2013. pp. 479-506.
43. Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 2014;344:1396-401.
44. Yan Y, Xu Y, Gao YY, Zong ZH, Zhang Q, Li C, Wang HQ. Implication of 14-3-3ε and 14-3-3θ/τ in proteasome inhibition-induced apoptosis of glioma cells. Cancer Sci 2013;104:55-61.
45. Panchision DM, Chen HL, Pistollato F, Papini D, Ni HT, Hawley TS. Optimized flow cytometric analysis of central nervous system tissue reveals novel functional relationships among cells expressing CD133, CD15, and CD24. Stem Cells 2007;25:1560-70.
46. Galli R, Binda E, Orfanelli U, Cipelletti B, Gritti A, De Vitis S, Fiocco R, Foroni C, Dimeco F, Vescovi A. Isolation and characterization of tumorigenic, stem-like neural precursors from human glioblastoma. Cancer Res 2004;64:7011-21.
47. Singh SK, Hawkins C, Clarke ID, Squire JA, Bayani J, Hide T, Henkelman RM, Cusimano MD, Dirks PB. Identification of human brain tumour initiating cells. Nature 2004;432:396.
48. Wolters GH, Vos-Scheperkeuter GH, Lin HC, van Schilfgaarde R. Different roles of class I and class II Clostridium histolyticum collagenase in rat pancreatic islet isolation. Diabetes 1995;44:227-33.
50. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou W, Coukos G, Geho DH, Petricoin III EF, Liotta LA. Laser-capture microdissection. Nat Protoc 2006;1:586.
51. Obiakor H, Sehgal D, Dasso JF, Bonner RF, Malekafzali A, Mage RG. A comparison of hydraulic and laser capture microdissection methods for collection of single B cells, PCR, and sequencing of antibody VDJ. Anal Biochem 2002;306:55-62.
52. Suarez-Quian C, Goldstein S, Pohida T, Smith P, Peterson J, Wellner E, Ghany M, Bonner R. Laser capture microdissection of single cells from complex tissues. BioTechniques 1999;26:328-35.
53. Keays KM, Owens GP, Ritchie AM, Gilden DH, Burgoon MP. Laser capture microdissection and single-cell RT-PCR without RNA purification. J Immunol Methods 2005;302:90-8.
54. Dasgupta A, Lim AR, Ghajar CM. Circulating and disseminated tumor cells: harbingers or initiators of metastasis? Mol Oncol 2017;11:40-61.
55. Heitzer E, Auer M, Gasch C, Pichler M, Ulz P, Hoffmann EM, Lax S, Waldispuehl-Geigl J, Mauermann O, Lackner C, Höfler G, Eisner F, Sill H, Samonigg H, Pantel K, Riethdorf S, Bauernhofer T, Geigl JB, Speicher MR. Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing. Cancer Res 2013;73:2965-75.
56. Ni X, Zhuo M, Su Z, Duan J, Gao Y, Wang Z, Zong C, Bai H, Chapman AR, Zhao J, Xu L, An T, Ma Q, Wang Y, Wu M, Sun Y, Wang S, Li Z, Yang X, Yong J, Su XD, Lu Y, Bai F, Xie XS, Wang J. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc Natl Acad Sci U S A 2013;110:21083-8.
57. Rantalainen M. Application of single-cell sequencing in human cancer. Brief Funct Genomics 2018;17:273-82.
58. Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GSM, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol 2014;32:479.
60. Gabriel MT, Calleja LR, Chalopin A, Ory B, Heymann D. Circulating tumor cells: a review of non-EpCAM-based approaches for cell enrichment and isolation. Clin Chem 2016;62:571-81.
61. Nagrath S, Sequist LV, Maheswaran S, Bell DW, Irimia D, Ulkus L, Smith MR, Kwak EL, Digumarthy S, Muzikansky A, Ryan P, Balis UJ, Tompkins RG, Haber DA, Toner M. Isolation of rare circulating tumour cells in cancer patients by microchip technology. Nature 2007;450:1235.
62. Stott SL, Lee RJ, Nagrath S, Yu M, Miyamoto DT, Ulkus L, Inserra EJ, Ulman M, Springer S, Nakamura Z, Moore AL, Tsukrov DI, Kempner ME, Dahl DM, Wu CL, Iafrate AJ, Smith MR, Tompkins RG, Sequist LV, Toner M, Haber DA, Maheswaran S. Isolation and characterization of circulating tumor cells from patients with localized and metastatic prostate cancer. Sci Trans Med 2010;2:25ra3-ra3.
63. Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, Inserra E, Diederichs S, Iafrate AJ, Bell DW, Digumarthy S, Muzikansky A, Irimia D, Settleman J, Tompkins RG, Lynch TJ, Toner M, Haber DA. Detection of mutations in EGFR in circulating lung-cancer cells. New Engl J Med 2008;359:366-77.
64. Stott SL, Hsu CH, Tsukrov DI, Yu M, Miyamoto DT, Waltman BA, Rothenberg SM, Shah AM, Smas ME, Korir GK, Floyd FP, Gilman AJ, Lord JB, Winokur D, Springer S, Irimia D, Nagrath S, Sequist LV, Lee RJ, Isselbacher KJ, Maheswaran S, Haber DA, Toner M. Isolation of circulating tumor cells using a microvortex-generating herringbone-chip. Proc Natl Acad Sci U S A 2010;107:18392-7.
65. Morimoto A, Mogami T, Watanabe M, Iijima K, Akiyama Y, Katayama K, Futami T, Yamamoto N, Sawada T, Koizumi F, Koh Y. High-density dielectrophoretic microwell array for detection, capture, and single-cell analysis of rare tumor cells in peripheral blood. PLoS One 2015;10:e0130418.
66. Lin CH, Chang HC, Hsu CH. A microfluidic platform for high-throughput single-cell Isolation and culture. J Vis Exp 2016.
67. Zhang Q, Wang T, Zhou Q, Zhang P, Gong Y, Gou H, Xu J, Ma B. Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms. Sci Rep 2017;7:41192.
68. Bolognesi C, Forcato C, Buson G, Fontana F, Mangano C, Doffini A, Sero V, Lanzellotto R, Signorini G, Calanca A, Sergio M, Romano R, Gianni S, Medoro G, Giorgini G, Morreau H, Barberis M, Corver WE, Manaresi N. Digital sorting of pure cell populations enables unambiguous genetic analysis of heterogeneous formalin-fixed paraffin-embedded tumors by next generation sequencing. Sci Rep 2016;6:20944.
69. Fernandez SV, Bingham C, Fittipaldi P, Austin L, Palazzo J, Palmer G, Alpaugh K, Cristofanilli M. TP53 mutations detected in circulating tumor cells present in the blood of metastatic triple negative breast cancer patients. Breast Cancer Res 2014;16:445.
70. Pestrin M, Salvianti F, Galardi F, De Luca F, Turner N, Malorni L, Pazzagli M, Di Leo A, Pinzani P. Heterogeneity of PIK3CA mutational status at the single cell level in circulating tumor cells from metastatic breast cancer patients. Mol Oncol 2015;9:749-57.
71. Talasaz AH, Powell AA, Huber DE, Berbee JG, Roh KH, Yu W, Xiao W, Davis MM, Pease RF, Mindrinos MN, Jeffrey SS, Davis RW. Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device. Proc Natl Acad Sci U S A 2009;106:3970-5.
72. Powell AA, Talasaz AH, Zhang H, Coram MA, Reddy A, Deng G, Telli ML, Advani RH, Carlson RW, Mollick JA, Sheth S, Kurian AW, Ford JM, Stockdale FE, Quake SR, Pease RF, Mindrinos MN, Bhanot G, Dairkee SH, Davis RW, Jeffrey SS. Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PLoS One 2012;7:e33788.
73. Hulett HR, Bonner WA, Barrett J, Herzenberg LA. Cell sorting: automated separation of mammalian cells as a function of intracellular fluorescence. Science 1969;166:747-9.
74. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D. Tumour evolution inferred by single-cell sequencing. Nature 2011;472:90.
75. Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, Riggs M, D'Italia S, Sun G, Yong M, Miskimen K, Gilmore H, Saborowski M, Dimitrova N, Krasnitz A, Harris L, Wigler M, Hicks J. Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Res 2015;25:714-24.
76. Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell 2012;148:886-95.
77. Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 2014;512:155.
78. Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, Wu H, Ye X, Ye C, Wu R, Jian M, Chen Y, Xie W, Zhang R, Chen L, Liu X, Yao X, Zheng H, Yu C, Li Q, Gong Z, Mao M, Yang X, Yang L, Li J, Wang W, Lu Z, Gu N, Laurie G, Bolund L, Kristiansen K, Wang J, Yang H, Li Y, Zhang X, Wang J. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 2012;148:873-85.
79. Leung ML, Wang Y, Waters J, Navin NE. SNES: single nucleus exome sequencing. Genome Biol 2015;16:55.
80. Zong C, Lu S, Chapman AR, Xie XS. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science 2012;338:1622-6.
81. Zhang CZ, Adalsteinsson VA, Francis J, Cornils H, Jung J, Maire C, Ligon KL, Meyerson M, Love JC. Calibrating genomic and allelic coverage bias in single-cell sequencing. Nat Commun 2015;6:6822.
82. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA. mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 2009;6:377.
83. Ramsköld D, Luo S, Wang YC, Li R, Deng Q, Faridani OR, Daniels GA, Khrebtukova I, Loring JF, Laurent LC, Schroth GP, Sandberg R. Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells. Nat Biotechnol 2012;30:777-82.
84. Picelli S, Faridani OR, Björklund ÅK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 2014;9:171.
85. Zhu Y, Machleder E, Chenchik A, Li R, Siebert P. Reverse transcriptase template switching: A SMART? approach for full-length cDNA library construction. BioTechniques 2001;30:892-7.
86. Morris J, Singh JM, Eberwine JH. Transcriptome analysis of single cells. J Vis Exp 2011;(50):2634.
87. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, Mildner A, Cohen N, Jung S, Tanay A, Amit I. Massively parallel single cell RNA-Seq for marker-free decomposition of tissues into cell types. Science (New York, NY) 2014;343:776-9.
88. Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep 2012;2:666-73.
89. Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, Donachie SP, Hoang TT. Transcript amplification from single bacterium for transcriptome analysis. Genome Res 2011;21:925-35.
90. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, LaMotte RH, Park IH, Snyder MP, Mason CE, Weissman SM. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A 2013;110:594-9.
91. Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat Protoc 2012;7:829.
92. Streets AM, Zhang X, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L, Tang F. Microfluidic single-cell whole-transcriptome sequencing. Proc Natl Acad Sci U S A 2014;111:7048-53.
93. Toriello NM, Douglas ES, Thaitrong N, Hsiao SC, Francis MB, Bertozzi CR, Mathies RA. Integrated microfluidic bioprocessor for single-cell gene expression analysis. Proc Natl Acad Sci U S A 2008;105:20173-8.
94. White AK, VanInsberghe M, Petriv I, Hamidi M, Sikorski D, Marra MA, Piret J, Aparicio S, Hansen CL. High-throughput microfluidic single-cell RT-qPCR. Proc Natl Acad Sci U S A 2011;108:13999-4004.
95. White A, Heyries K, Doolin C, Vaninsberghe M, Hansen C. High-throughput microfluidic single-cell digital polymerase chain reaction. Anal Chem 2013;85:7182-90.
96. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J, Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 2011;29:1120.
97. Potter NE, Ermini L, Papaemmanuil E, Cazzaniga G, Vijayaraghavan G, Titley I, Ford A, Campbell P, Kearney L, Greaves M. Single-cell mutational profiling and clonal phylogeny in cancer. Genome Res 2013;23:2115-25.
98. Lawson DA, Bhakta NR, Kessenbrock K, Prummel KD, Yu Y, Takai K, Zhou A, Eyob H, Balakrishnan S, Wang CY, Yaswen P, Goga A, Werb Z. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature 2015;526:131.
99. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods 2014;11:163.
100. Macosko Evan Z, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas Allison R, Kamitaki N, Martersteck Emily M, Trombetta John J, Weitz David A, Sanes Joshua R, Shalek Alex K, Regev A, McCarroll Steven A. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 2015;161:1202-14.
101. Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 2016;166:1308-23.e30.
102. McGranahan N, Burrell RA, Endesfelder D, Novelli MR, Swanton C. Cancer chromosomal instability: therapeutic and diagnostic challenges:'Exploring aneuploidy: the significance of chromosomal imbalance'review series. EMBO reports 2012;13:528-38.
103. Bakker B, van den Bos H, Lansdorp PM, Foijer F. How to count chromosomes in a cell: an overview of current and novel technologies. Bioessays 2015;37:570-7.
104. Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, Martinez P, Phillimore B, Begum S, Rabinowitz A, Spencer-Dene B, Gulati S, Bates PA, Stamp G, Pickering L, Gore M, Nicol DL, Hazell S, Futreal PA, Stewart A, Swanton C. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014;46:225.
105. Hughes AEO, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, Eades WC, Elliott K, Heath S, Westervelt P, Ding L, Conrad DF, White BS, Shao J, Link DC, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Walter MJ, Graubert TA. Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLoS Genet 2014;10:e1004462.
106. Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA. Single-cell sequencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol 2016;12:889.
107. Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat Genet 2003;33:49.
108. Scheel C, Onder T, Karnoub A, Weinberg RA. Adaptation versus selection: the origins of metastatic behavior. Cancer Res 2007;67:11476-80.
109. Gawad C, Koh W, Quake SR. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proc Natl Acad Sci U S A 2014;111:17947-52.
110. Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S, Li F, Im KM, Wu K, Wu H, Ye X, Li G, Wang L, Zhang B, Liang J, Xie W, Wu R, Jiang H, Liu X, Yu C, Zheng H, Jian M, Nie L, Wan L, Shi M, Sun X, Tang A, Guo G, Gui Y, Cai Z, Li J, Wang W, Lu Z, Zhang X, Bolund L, Kristiansen K, Wang J, Yang H, Dean M, Wang J. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. GigaScience 2012;1:12.
111. Yu C, Yu J, Yao X, Wu WKK, Lu Y, Tang S, Li X, Bao L, Li X, Hou Y, Wu R, Jian M, Chen R, Zhang F, Xu L, Fan F, He J, Liang Q, Wang H, Hu X, He M, Zhang X, Zheng H, Li Q, Wu H, Chen Y, Yang X, Zhu S, Xu X, Yang H, Wang J, Zhang X, Sung JJY, Li Y, Wang J. Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res 2014;24:701.
112. Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, Majeti R. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Trans Med 2012;4:149ra18.
113. Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang CZ, Kharchenko PV, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 2017;27:1300-11.
114. Rhim AD, Thege FI, Santana SM, Lannin TB, Saha TN, Tsai S, Maggs LR, Kochman ML, Ginsberg GG, Lieb JG, Chandrasekhara V, Drebin JA, Ahmad N, Yang YX, Kirby BJ, Stanger BZ. Detection of circulating pancreas epithelial cells in patients with pancreatic cystic lesions. Gastroenterology 2014;146:647-51.
115. Clawson GA, Matters GL, Xin P, McGovern C, Wafula E, dePamphilis C, Meckley M, Wong J, Stewart L, D'Jamoos C, Altman N, Imamura Kawasawa Y, Du Z, Honaas L, Abraham T. "Stealth dissemination" of macrophage-tumor cell fusions cultured from blood of patients with pancreatic ductal adenocarcinoma. PLoS One 2017;12:e0184451.
116. Francis JM, Zhang CZ, Maire CL, Jung J, Manzo VE, Adalsteinsson VA, Homer H, Haidar S, Blumenstiel B, Pedamallu CS, Ligon AH, Love JC, Meyerson M, Ligon KL. EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing. Cancer discovery 2014;4:956-71.
117. Bakker B, Taudt A, Belderbos ME, Porubsky D, Spierings DCJ, de Jong TV, Halsema N, Kazemier HG, Hoekstra-Wakker K, Bradley A, de Bont ESJM, van den Berg A, Guryev V, Lansdorp PM, Colomé-Tatché M, Foijer F. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol 2016;17:115.
118. Ruiz C, Li J, Luttgen MS, Kolatkar A, Kendall JT, Flores E, Topp Z, Samlowski WE, McClay E, Bethel K, Ferrone S, Hicks J, Kuhn P. Limited genomic heterogeneity of circulating melanoma cells in advanced stage patients. Phys Biol 2015;12:016008.
119. Amatu A, Sartore-Bianchi A, Siena S. NTRK gene fusions as novel targets of cancer therapy across multiple tumour types. ESMO open 2016;1:e000023.
120. Aceto N, Bardia A, Miyamoto David T, Donaldson Maria C, Wittner Ben S, Spencer Joel A, Yu M, Pely A, Engstrom A, Zhu H, Brannigan Brian W, Kapur R, Stott Shannon L, Shioda T, Ramaswamy S, Ting David T, Lin Charles P, Toner M, Haber Daniel A, Maheswaran S. Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell 2014;158:1110-22.
121. Medler TR, Cotechini T, Coussens LM. Immune response to cancer therapy: mounting an effective antitumor response and mechanisms of resistance. Trends Cancer 2015;1:66-75.
122. Tran E, Ahmadzadeh M, Lu YC, Gros A, Turcotte S, Robbins PF, Gartner JJ, Zheng Z, Li YF, Ray S, Wunderlich JR, Somerville RP, Rosenberg SA. Immunogenicity of somatic mutations in human gastrointestinal cancers. Science 2015;350:1387-90.
123. Rosenberg SA, Yang JC, Sherry RM, Kammula US, Hughes MS, Phan GQ, Citrin DE, Restifo NP, Robbins PF, Wunderlich JR, Morton KE, Laurencot CM, Steinberg SM, White DE, Dudley ME. Durable complete responses in heavily pretreated patients with metastatic melanoma using T-cell transfer immunotherapy. Clin Cancer Res 2011;17:4550-7.
124. Lu YC, Zheng Z, Robbins PF, Tran E, Prickett TD, Gartner JJ, Li YF, Ray S, Franco Z, Bliskovsky V, Fitzgerald PC, Rosenberg SA. An efficient single-cell RNA-seq approach to identify neoantigen-specific T cell receptors. Mol Ther 2018;26:379-89.
125. Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017;17:61.
126. Shitaoka K, Hamana H, Kishi H, Hayakawa Y, Kobayashi E, Sukegawa K, Piao X, Lyu F, Nagata T, Sugiyama D, Nishikawa H, Tanemura A, Katayama I, Murahashi M, Takamatsu Y, Tani K, Ozawa T, Muraguchi A. Identification of tumoricidal TCRs from tumor-infiltrating lymphocytes by single-cell analysis. Cancer Immunology Research 2018;6:378-88.
127. Baitsch L, Fuertes-Marraco SA, Legat A, Meyer C, Speiser DE. The three main stumbling blocks for anticancer T cells. Trends Immunol 2012;33:364-72.
128. Anderson AC, Joller N, Kuchroo VK. Lag-3, Tim-3, and TIGIT: co-inhibitory receptors with specialized functions in immune regulation. Immunity 2016;44:989-1004.
129. Restifo NP, Smyth MJ, Snyder A. Acquired resistance to immunotherapy and future challenges. Nat Rev Cancer 2016;16:121.
130. Zheng C, Zheng L, Yoo JK, Guo H, Zhang Y, Guo X, Kang B, Hu R, Huang JY, Zhang Q, Liu Z, Dong M, Hu X, Ouyang W, Peng J, Zhang Z. Landscape of infiltrating T xells in liver cancer revealed by single-cell sequencing. Cell 2017;169:1342-56.e16.
131. Singer M, Wang C, Cong L, Marjanovic ND, Kowalczyk MS, Zhang H, Nyman J, Sakuishi K, Kurtulus S, Gennert D, Xia J, Kwon JYH, Nevin J, Herbst RH, Yanai I, Rozenblatt-Rosen O, Kuchroo VK, Regev A, Anderson AC. A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells. Cell 2016;166:1500-11.e9.
132. Chung W, Eum HH, Lee HO, Lee KM, Lee HB, Kim KT, Ryu HS, Kim S, Lee JE, Park YH. Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nat Commun 2017;8:15081.
133. Najjar YG, Finke JH. Clinical perspectives on targeting of myeloid derived suppressor cells in the treatment of cancer. Front Oncol 2013;3:49.
134. Damuzzo V, Pinton L, Desantis G, Solito S, Marigo I, Bronte V, Mandruzzato S. Complexity and challenges in defining myeloid-derived suppressor cells. Cytometry Part B: Clinical Cytometry 2015;88:77-91.
135. Grant CR, Liberal R, Mieli-Vergani G, Vergani D, Longhi MS. Regulatory T-cells in autoimmune diseases: challenges, controversies and—yet—unanswered questions. Autoimmun Rev 2015;14:105-16.
136. Miyamoto DT, Zheng Y, Wittner BS, Lee RJ, Zhu H, Broderick KT, Desai R, Fox DB, Brannigan BW, Trautwein J, Arora KS, Desai N, Dahl DM, Sequist LV, Smith MR, Kapur R, Wu CL, Shioda T, Ramaswamy S, Ting DT, Toner M, Maheswaran S, Haber DA. RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance. Science 2015;349:1351-6.
137. Dago AE, Stepansky A, Carlsson A, Luttgen M, Kendall J, Baslan T, Kolatkar A, Wigler M, Bethel K, Gross ME, Hicks J, Kuhn P. Rapid phenotypic and genomic change in response to therapeutic pressure in prostate cancer inferred by high content snalysis of single circulating tumor cells. PLoS One 2014;9:e101777.
