Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

The CRUK IMAXT Grand Challenge Team

doi:10.1016/j.cell.2019.10.026

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

The CRUK IMAXT Grand Challenge Team

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

Research output: Contribution to journal › Article › peer-review

143 Scopus citations

Abstract

A high-throughput method for amplication-free single-cell whole-genome sequencing can be scaled up to analyze tens of thousands of cells from different tissues and clinical sample types and identifies replication states, aneuploidies, and subclonal mutations.

Original language	English
Pages (from-to)	1207-1221.e22
Journal	Cell
Volume	179
Issue number	5
DOIs	https://doi.org/10.1016/j.cell.2019.10.026
State	Published - 14 Nov 2019

Bibliographical note

Publisher Copyright:
© 2019 The Authors

Funding

The work described and the laboratories of S.A. and S.S. are supported by BC Cancer Foundation, Canadian Institutes of Health Research (CIHR), Canadian Cancer Society Research Institute (CCSRI), Terry Fox Research Institute (TFRI), Canada Foundation for Innovation (CFI), Canada Research Chairs program, Michael Smith Foundation for Health Research (MSFHR), Genome British Columbia, Genome Canada, CANARIE, Cancer Research UK Grand challenge IMAXT award (CRUK), Susan G. Komen, and Cycle for Survival benefiting Memorial Sloan-Kettering Cancer Center. We would like to thank Microsoft Azure for providing cloud computing credits that made this study possible. S.A. S.P.S. and C.H. conceived and organized the research and wrote and reviewed the manuscript. E.L. H.Z. A.S. A.M.P. and D.L. developed and tested methods, performed analysis, and wrote the manuscript. J. Brimhall, J. Biele, and B.W. carried out tissue preparation, DLP+ library construction, and sequencing. T.M. and J.T. developed the 184-hTERT TP53 null line 95.22 and 99.5. C.N. S.L. V.B. M.S. and O.G. developed and deployed Montage and https://www.cellmine.org. P.E. F.K. T.R.d.A. and S.R.L. performed PDX transplants and passaging. S. Poon developed the microscope image analysis SmartChipApp. M.J.T. J.N. S.V.-W. N.A. and M.W. developed Colossus. C.H. T.C. P.W. and S.C. developed Sisyphus. A.M.P. J.N. S.V.-W. N.A. and M.W. developed Tantalus. D.G. C.H. T.C. P.W. and S.C. developed and ran the single-cell analysis pipeline. L.M. R.W.S. and T.M.U. developed the mouse synovial sarcoma model and isolated and supplied the cells. E.C. and C.S. provided follicular lymphoma samples. R.J.N.C. and H.Z. developed custom parts for DLP+. D.D.C. provided LabView assistance. S. Pleasance, Y.M. R.C. R.M. A.J.M. and M.A.M. assisted with sequence generations and single-cell experiments. S.P.S. and S.A. are founders and shareholders of Contextual Genomics Inc. The work described and the laboratories of S.A. and S.S. are supported by BC Cancer Foundation , Canadian Institutes of Health Research (CIHR), Canadian Cancer Society Research Institute (CCSRI), Terry Fox Research Institute (TFRI), Canada Foundation for Innovation (CFI), Canada Research Chairs program, Michael Smith Foundation for Health Research (MSFHR), Genome British Columbia , Genome Canada , CANARIE , Cancer Research UK Grand challenge IMAXT award (CRUK), Susan G. Komen, and Cycle for Survival benefiting Memorial Sloan-Kettering Cancer Center . We would like to thank Microsoft Azure for providing cloud computing credits that made this study possible.

Funders	Funder number
A.M.P.
BC Cancer Foundation
Cancer Research UK Grand
Contextual Genomics Inc
E.C.
L.M.
S.C.
T.M.U.
Microsoft
Memorial Sloan-Kettering Cancer Center
E.L. Wiegand Foundation
Canarie
Genome Canada
M.S.I. Foundation
Canadian Cancer Society Research Institute
Canadian Institutes of Health Research
Canada Foundation for Innovation
Genome British Columbia
Michael Smith Foundation for Health Research
Cancer Research UK
Canada Research Chairs
Terry Fox Research Institute

Keywords

DNA sequencing
aneuploidy
cancer genomics
cell cycle
copy number
genomic instability
single cell
tumor evolution
tumor heterogeneity

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.cell.2019.10.026

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title = "Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing",

abstract = "A high-throughput method for amplication-free single-cell whole-genome sequencing can be scaled up to analyze tens of thousands of cells from different tissues and clinical sample types and identifies replication states, aneuploidies, and subclonal mutations.",

keywords = "DNA sequencing, aneuploidy, cancer genomics, cell cycle, copy number, genomic instability, single cell, tumor evolution, tumor heterogeneity",

author = "{The CRUK IMAXT Grand Challenge Team} and Emma Laks and Andrew McPherson and Hans Zahn and Daniel Lai and Adi Steif and Jazmine Brimhall and Justina Biele and Beixi Wang and Tehmina Masud and Jerome Ting and Diljot Grewal and Cydney Nielsen and Samantha Leung and Viktoria Bojilova and Maia Smith and Oleg Golovko and Steven Poon and Peter Eirew and Farhia Kabeer and {Ruiz de Algara}, Teresa and Lee, {So Ra} and Taghiyar, {M. Jafar} and Curtis Huebner and Jessica Ngo and Tim Chan and Spencer Vatrt-Watts and Pascale Walters and Nafis Abrar and Sophia Chan and Matt Wiens and Lauren Martin and Scott, {R. Wilder} and Underhill, {T. Michael} and Elizabeth Chavez and Christian Steidl and {Da Costa}, Daniel and Yussanne Ma and Coope, {Robin J.N.} and Richard Corbett and Stephen Pleasance and Richard Moore and Mungall, {Andrew J.} and Colin Mar and Fergus Cafferty and Karen Gelmon and Stephen Chia and Hannon, {Gregory J.} and Giorgia Battistoni and Dario Bressan and Shahar Alon",

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AU - Steif, Adi

AU - Brimhall, Jazmine

AU - Biele, Justina

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AU - Bojilova, Viktoria

AU - Smith, Maia

AU - Golovko, Oleg

AU - Poon, Steven

AU - Eirew, Peter

AU - Kabeer, Farhia

AU - Ruiz de Algara, Teresa

AU - Lee, So Ra

AU - Taghiyar, M. Jafar

AU - Huebner, Curtis

AU - Ngo, Jessica

AU - Chan, Tim

AU - Vatrt-Watts, Spencer

AU - Walters, Pascale

AU - Abrar, Nafis

AU - Chan, Sophia

AU - Wiens, Matt

AU - Martin, Lauren

AU - Scott, R. Wilder

AU - Underhill, T. Michael

AU - Chavez, Elizabeth

AU - Steidl, Christian

AU - Da Costa, Daniel

AU - Ma, Yussanne

AU - Coope, Robin J.N.

AU - Corbett, Richard

AU - Pleasance, Stephen

AU - Moore, Richard

AU - Mungall, Andrew J.

AU - Mar, Colin

AU - Cafferty, Fergus

AU - Gelmon, Karen

AU - Chia, Stephen

AU - Hannon, Gregory J.

AU - Battistoni, Giorgia

AU - Bressan, Dario

AU - Alon, Shahar

PY - 2019/11/14

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KW - aneuploidy

KW - cancer genomics

KW - cell cycle

KW - copy number

KW - genomic instability

KW - single cell

KW - tumor evolution

KW - tumor heterogeneity

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Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Abstract

Bibliographical note

Funding

Keywords

UN SDGs

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