Tumour heterogeneity and metastasis at single-cell resolution

Signatures of mutational processes in human cancer

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Microenvironmental regulation of tumor progression and metastasis

Quail, D. F., & Joyce, J. A. (2013) · Nature Medicine · doi:10.1038/nm.3394 · Cited by 7,994

Cancer Genome Landscapes

Vogelstein, B., Papadopoulos, N., Velculescu, V. E., Zhou, S., Diaz, L. A., & Kinzler, K. W. (2013) · Science · doi:10.1126/science.1235122 · Cited by 7,863

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2009.12.020 · Cited by 7,575

Massively parallel digital transcriptional profiling of single cells

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Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.002 · Cited by 7,110

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., Cahill, D. P., Nahed, B. V., Curry, W. T., Martuza, R. L., et al. (2014) · Science · doi:10.1126/science.1254257 · Cited by 5,063

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944

Full-length RNA-seq from single cells using Smart-seq2

Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137

Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells

Klein, A. M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D. A., & Kirschner, M. W. (2015) · Cell · doi:10.1016/j.cell.2015.04.044 · Cited by 3,356

Simultaneous epitope and transcriptome measurement in single cells

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Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

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Spatially resolved, highly multiplexed RNA profiling in single cells

Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015) · Science · doi:10.1126/science.aaa6090 · Cited by 2,969

Cancer stem cells revisited

Batlle, E., & Clevers, H. (2017) · Nature Medicine · doi:10.1038/nm.4409 · Cited by 2,769

Metastasis: from dissemination to organ-specific colonization

Nguyen, D. X., Bos, P. D., & Massagué, J. (2009) · Nature reviews. Cancer · doi:10.1038/nrc2622 · Cited by 2,716

Tumour evolution inferred by single-cell sequencing

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Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer

Puram, S. V., Tirosh, I., Parikh, A. S., Patel, A. P., Yizhak, K., Gillespie, S., Rodman, C., Luo, C. L., Mroz, E. A., Emerick, K. S., et al. (2017) · Cell · doi:10.1016/j.cell.2017.10.044 · Cited by 2,557

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

Aceto, N., Bardia, A., Miyamoto, D. T., Collier, M. D., Wittner, B. S., Spencer, J. A., Yu, M., Pely, A., Engstrom, A., Zhu, H., et al. (2014) · Cell · doi:10.1016/j.cell.2014.07.013 · Cited by 2,516

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

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Massive genomic rearrangement acquired in a single catastrophic event during cancer development

Stephens, P. J., Greenman, C. D., Fu, B., Yang, F., Bignell, G. R., Mudie, L. J., Pleasance, E. D., Lau, K. W., Beare, D., Stebbings, L. A., et al. (2011) · Cell · doi:10.1016/j.cell.2010.11.055 · Cited by 2,414

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358

Single-cell chromatin accessibility reveals principles of regulatory variation

Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308

Evolution of the Cancer Stem Cell Model

Kreso, A., & Dick, J. E. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.02.006 · Cited by 2,304

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

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Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

Bendall, S. C., Simonds, E. F., Qiu, P., Amir, E.-A. D., Krutzik, P. O., Finck, R., Bruggner, R. V., Melamed, R., Trejo, A., Ornatsky, O. I., et al. (2011) · Science · doi:10.1126/science.1198704 · Cited by 2,279

The immune contexture in cancer prognosis and treatment

Fridman, W. H., Zitvogel, L., Sautès–Fridman, C., & Kroemer, G. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2017.101 · Cited by 2,263

Metastatic colonization by circulating tumour cells

Massagué, J., & Obenauf, A. C. (2016) · Nature · doi:10.1038/nature17038 · Cited by 2,062

Intra-tumour heterogeneity: a looking glass for cancer?

Marusyk, A., Almendro, V., & Polyák, K. (2012) · Nature reviews. Cancer · doi:10.1038/nrc3261 · Cited by 2,058

Pan-cancer patterns of somatic copy number alteration

Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C., Wala, J. A., Mermel, C. H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2760 · Cited by 1,893

Efficient tumour formation by single human melanoma cells

Quintana, E., Shackleton, M. J., Sabel, M. S., Fullen, D. R., Johnson, T. M., & Morrison, S. J. (2008) · Nature · doi:10.1038/nature07567 · Cited by 1,836

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795

Deep profiling of mouse splenic architecture with CODEX multiplexed imaging

Goltsev, Y., Samusik, N., Kennedy-Darling, J., Bhate, S., Hale, M., Vazquez, G., Black, S., & Nolan, G. P. (2018) · Cell · doi:10.1016/j.cell.2018.07.010 · Cited by 1,501

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

Rosenberg, A. B., Roco, C. M., Muscat, R. A., Kuchina, A., Sample, P., Yao, Z., Graybuck, L. T., Peeler, D. J., Mukherjee, S., Chen, W., et al. (2018) · Science · doi:10.1126/science.aam8999 · Cited by 1,422

Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing

Cao, J., Packer, J. S., Ramani, V., Cusanovich, D. A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S. N., Steemers, F. J., et al. (2017) · doi:10.1101/104844 · Cited by 1,402

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma

Johnson, B. E., Mazor, T., Hong, C., Barnes, M., Aihara, K., McLean, C. Y., Fouse, S. D., Yamamoto, S., Ueda, H., Tatsuno, K., et al. (2014) · Science · doi:10.1126/science.1239947 · Cited by 1,362

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., Desai, T. J., Krasnow, M. A., & Quake, S. R. (2014) · Nature · doi:10.1038/nature13173 · Cited by 1,342

Interactions between cancer stem cells and their niche govern metastatic colonization

Malanchi, I., Santamaria-Martínez, A., Susanto, E., Peng, H., Lehr, H.-A., Delaloye, J.-F., & Huelsken, J. (2012) · Nature · doi:10.1038/nature10694 · Cited by 1,339

Single-cell genome sequencing: current state of the science

Gawad, C., Koh, W., & Quake, S. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.16 · Cited by 1,334

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

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Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

Tirosh, I., Venteicher, A. S., Hebert, C. M., Escalante, L. E., Patel, A. P., Yizhak, K., Fisher, J. M., Rodman, C., Mount, C., Filbin, M. G., et al. (2016) · Nature · doi:10.1038/nature20123 · Cited by 1,245

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

Gerlinger, M., Horswell, S. D., Larkin, J., Rowan, A., Salm, M., Varela, I., Fisher, R. A., McGranahan, N., Matthews, N., Santos, C. R., et al. (2014) · Nature Genetics · doi:10.1038/ng.2891 · Cited by 1,236

Systemic Spread Is an Early Step in Breast Cancer

Hüsemann, Y., Geigl, J. B., Schubert, F., Musiani, P., Meyer, M., Burghart, E., Forni, G., Eils, R., Fehm, T. N., Riethmüller, G., et al. (2008) · Cancer Cell · doi:10.1016/j.ccr.2007.12.003 · Cited by 1,220

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

Roberts, S. A., Lawrence, M. S., Klimczak, L. J., Grimm, S. A., Fargo, D. C., Stojanov, P., Kieżun, A., Kryukov, G. V., Carter, S. L., Saksena, G., et al. (2013) · Nature Genetics · doi:10.1038/ng.2702 · Cited by 1,162

Genome remodelling in a basal-like breast cancer metastasis and xenograft

Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., Wallis, J. W., Harris, C. C., McLellan, M. D., Fulton, R. S., Fulton, L., et al. (2010) · Nature · doi:10.1038/nature08989 · Cited by 1,144

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

Smallwood, S. A., Lee, H. J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S. R., Stegle, O., Reik, W., & Kelsey, G. (2014) · Nature Methods · doi:10.1038/nmeth.3035 · Cited by 1,125

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

Kim, C. R., Gao, R., Sei, E., Brandt, R., Hartman, J., Hatschek, T., Crosetto, N., Foukakis, T., & Navin, N. E. (2018) · Cell · doi:10.1016/j.cell.2018.03.041 · Cited by 1,114

Biological and therapeutic impact of intratumor heterogeneity in cancer evolution

McGranahan, N., & Swanton, C. (2015) · Cancer Cell · doi:10.1016/j.ccell.2014.12.001 · Cited by 1,077

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

van den Brink, S. C., Sage, F., Vértesy, Á., Spanjaard, B., Peterson-Maduro, J., Baron, C. S., Robin, C., & van Oudenaarden, A. (2017) · Nature Methods · doi:10.1038/nmeth.4437 · Cited by 1,072

Massively parallel single-nucleus RNA-seq with DroNc-seq

Habib, N., Avraham-Davidi, I., Basu, A., Burks, T., Shekhar, K., Hofree, M., Choudhury, S. R., Aguet, F., Gelfand, E., Ardlie, K., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4407 · Cited by 1,069

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

Wang, Y., Waters, J., Leung, M. L., Unruh, A., Roh, W., Shi, X., Chen, K., Scheet, P., Vattathil, S., Liang, H., et al. (2014) · Nature · doi:10.1038/nature13600 · Cited by 1,029

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

Venteicher, A. S., Tirosh, I., Hebert, C. M., Yizhak, K., Neftel, C., Filbin, M. G., Hovestadt, V., Escalante, L. E., Shaw, M. L., Rodman, C., et al. (2017) · Science · doi:10.1126/science.aai8478 · Cited by 994

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

Chung, W., Eum, H. H., Lee, H.-O., Lee, K.-M., Lee, H.-B., Kim, K.-T., Ryu, H. S., Kim, S., Lee, J. E., Park, Y. H., et al. (2017) · Nature Communications · doi:10.1038/ncomms15081 · Cited by 992

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

Darmanis, S., Sloan, S. A., Croote, D., Mignardi, M., Chernikova, S. B., Samghababi, P., Zhang, Y., Neff, N. F., Kowarsky, M., Caneda, C., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.10.030 · Cited by 991

Highly Multiplexed Subcellular RNA Sequencing in Situ

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., et al. (2014) · Science · doi:10.1126/science.1250212 · Cited by 973

Systemic Immunity Is Required for Effective Cancer Immunotherapy

Spitzer, M. H., Carmi, Y., Reticker-Flynn, N. E., Kwek, S. S., Madhireddy, D., Martins, M. M., Gherardini, P. F., Prestwood, T. R., Chabon, J., Bendall, S. C., et al. (2017) · Cell · doi:10.1016/j.cell.2016.12.022 · Cited by 963

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

Lake, B. B., Ai, R., Kaeser, G. E., Salathia, N. S., Yung, Y. C., Liu, R., Wildberg, A., Gao, D., Fung, H.-L., Chen, S., et al. (2016) · Science · doi:10.1126/science.aaf1204 · Cited by 957

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

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Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

Lawson, D. A., Bhakta, N. R., Kessenbrock, K., Prummel, K. D., Yu, Y., Takai, K., Zhou, A. Y., Eyob, H., Balakrishnan, S., Wang, C., et al. (2015) · Nature · doi:10.1038/nature15260 · Cited by 908

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn, T. M., Wadsworth, M. H., Hughes, T. K., Bryson, B. D., Butler, A., Satija, R., Fortune, S. M., Love, J. C., & Shalek, A. K. (2017) · Nature Methods · doi:10.1038/nmeth.4179 · Cited by 882

Collective Invasion in Breast Cancer Requires a Conserved Basal Epithelial Program

Cheung, K. J., Gabrielson, E. W., Werb, Z., & Ewald, A. J. (2013) · Cell · doi:10.1016/j.cell.2013.11.029 · Cited by 859

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

Rotem, A., Ram, O., Shoresh, N., Sperling, R. A., Goren, A., Weitz, D. A., & Bernstein, B. E. (2015) · Nature Biotechnology · doi:10.1038/nbt.3383 · Cited by 854

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

Yates, L. R., Gerstung, M., Knappskog, S., Desmedt, C., Gundem, G., Loo, P. V., Aas, T., Alexandrov, L. B., Larsimont, D., Davies, H., et al. (2015) · Nature Medicine · doi:10.1038/nm.3886 · Cited by 833

Multiplexed quantification of proteins and transcripts in single cells

Peterson, V. M., Zhang, K. X., Kumar, N., Wong, J., Li, L., Wilson, D. C., Moore, R., McClanahan, T. K., Sadekova, S., & Klappenbach, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3973 · Cited by 832

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

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Defining cell types and states with single-cell genomics

Trapnell, C. (2015) · Genome Research · doi:10.1101/gr.190595.115 · Cited by 813

Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT

Malladi, S., Macalinao, D. G., Jin, X., He, L., Basnet, H., Zou, Y., de Stanchina, E., & Massagué, J. (2016) · Cell · doi:10.1016/j.cell.2016.02.025 · Cited by 791

Early dissemination seeds metastasis in breast cancer

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Evidence for APOBEC3B mutagenesis in multiple human cancers

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G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

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Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

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RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance

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Single-cell dissection of transcriptional heterogeneity in human colon tumors

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Ploidy and Large-Scale Genomic Instability Consistently Identify Basal-like Breast Carcinomas with BRCA1/2 Inactivation

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Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment

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Tumor heterogeneity.

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Flow cytometric immunophenotyping for hematologic neoplasms

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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

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Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas

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From latent disseminated cells to overt metastasis: Genetic analysis of systemic breast cancer progression

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Revealing the vectors of cellular identity with single-cell genomics

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Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

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