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Tumour evolution inferred by single-cell sequencing

Author

Listed:
  • Nicholas Navin

    (Cold Spring Harbor Laboratory, Cold Spring Harbor
    University of Texas MD Anderson Cancer Center)

  • Jude Kendall

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Jennifer Troge

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Peter Andrews

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Linda Rodgers

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Jeanne McIndoo

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Kerry Cook

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Asya Stepansky

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Dan Levy

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Diane Esposito

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Lakshmi Muthuswamy

    (Ontario Institute for Cancer Research)

  • Alex Krasnitz

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • W. Richard McCombie

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • James Hicks

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

  • Michael Wigler

    (Cold Spring Harbor Laboratory, Cold Spring Harbor)

Abstract

Single tumour cells observed Tumours are known to be genetically heterogeneous, but it is proving difficult to dissect this heterogeneity at the single-cell level. A combination of whole-genome amplification and sequencing of single nuclei separated by fluorescence activated cell sorting now reveals the population structure of breast tumours from two patients. In both, tumour growth is by punctuated clonal expansions with few persistent intermediates, in contrast to the many gradual models of tumour progression. Single-cell sequencing of this type — once it becomes cheaper — is likely to have clinical implications for cancer prognosis and staging.

Suggested Citation

  • Nicholas Navin & Jude Kendall & Jennifer Troge & Peter Andrews & Linda Rodgers & Jeanne McIndoo & Kerry Cook & Asya Stepansky & Dan Levy & Diane Esposito & Lakshmi Muthuswamy & Alex Krasnitz & W. Rich, 2011. "Tumour evolution inferred by single-cell sequencing," Nature, Nature, vol. 472(7341), pages 90-94, April.
    • Handle: RePEc:nat:nature:v:472:y:2011:i:7341:d:10.1038_nature09807
    DOI: 10.1038/nature09807
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    Cited by:

    1. Brandon Monier & Adam McDermaid & Cankun Wang & Jing Zhao & Allison Miller & Anne Fennell & Qin Ma, 2019. "IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis," PLOS Computational Biology, Public Library of Science, vol. 15(2), pages 1-15, February.
    2. Xian F Mallory & Mohammadamin Edrisi & Nicholas Navin & Luay Nakhleh, 2020. "Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data," PLOS Computational Biology, Public Library of Science, vol. 16(7), pages 1-24, July.
    3. Jinhyun Kim & Sungsik Kim & Huiran Yeom & Seo Woo Song & Kyoungseob Shin & Sangwook Bae & Han Suk Ryu & Ji Young Kim & Ahyoun Choi & Sumin Lee & Taehoon Ryu & Yeongjae Choi & Hamin Kim & Okju Kim & Yu, 2023. "Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    4. Joanna Hård & Jeff E. Mold & Jesper Eisfeldt & Christian Tellgren-Roth & Susana Häggqvist & Ignas Bunikis & Orlando Contreras-Lopez & Chen-Shan Chin & Jessica Nordlund & Carl-Johan Rubin & Lars Feuk &, 2023. "Long-read whole-genome analysis of human single cells," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Chunyang Bao & Richard W. Tourdot & Gregory J. Brunette & Chip Stewart & Lili Sun & Hideo Baba & Masayuki Watanabe & Agoston T. Agoston & Kunal Jajoo & Jon M. Davison & Katie S. Nason & Gad Getz & Ken, 2023. "Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    6. Salim Akhter Chowdhury & Stanley E Shackney & Kerstin Heselmeyer-Haddad & Thomas Ried & Alejandro A Schäffer & Russell Schwartz, 2014. "Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-19, July.
    7. Adam C. Weiner & Marc J. Williams & Hongyu Shi & Ignacio Vázquez-García & Sohrab Salehi & Nicole Rusk & Samuel Aparicio & Sohrab P. Shah & Andrew McPherson, 2024. "Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    8. Claudia Bühnemann & Simon Li & Haiyue Yu & Harriet Branford White & Karl L Schäfer & Antonio Llombart-Bosch & Isidro Machado & Piero Picci & Pancras C W Hogendoorn & Nicholas A Athanasou & J Alison No, 2014. "Quantification of the Heterogeneity of Prognostic Cellular Biomarkers in Ewing Sarcoma Using Automated Image and Random Survival Forest Analysis," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-14, September.
    9. Noushin Niknafs & Violeta Beleva-Guthrie & Daniel Q Naiman & Rachel Karchin, 2015. "SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-26, October.
    10. Camila P. E. de Souza & Mirela Andronescu & Tehmina Masud & Farhia Kabeer & Justina Biele & Emma Laks & Daniel Lai & Patricia Ye & Jazmine Brimhall & Beixi Wang & Edmund Su & Tony Hui & Qi Cao & Marcu, 2020. "Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data," PLOS Computational Biology, Public Library of Science, vol. 16(9), pages 1-24, September.
    11. Udit Singhal & Srinivas Nallandhighal & Jeffrey J. Tosoian & Kevin Hu & Trinh M. Pham & Judith Stangl-Kremser & Chia-Jen Liu & Razeen Karim & Komal R. Plouffe & Todd M. Morgan & Marcin Cieslik & Rober, 2024. "Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    12. Noa Chapal-Ilani & Yosef E Maruvka & Adam Spiro & Yitzhak Reizel & Rivka Adar & Liran I Shlush & Ehud Shapiro, 2013. "Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-17, November.
    13. Yidong Zhou & Changjun Wang & Hanjiang Zhu & Yan Lin & Bo Pan & Xiaohui Zhang & Xin Huang & Qianqian Xu & Yali Xu & Qiang Sun, 2016. "Diagnostic Accuracy of PIK3CA Mutation Detection by Circulating Free DNA in Breast Cancer: A Meta-Analysis of Diagnostic Test Accuracy," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-15, June.

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