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The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure

Eduardo A. González-Solares, Ali Dariush, Carlos González-Fernández, Aybüke Küpcü Yoldaş, Mohammad Al Sa’d, Neil Millar, Tristan Whitmarsh, Nicholas Chornay, Ilaria Falciatori, Atefeh Fatemi, Daniel Goodwin, Laura Kuett, Claire M. Mulvey, Marta Páez Ribes, Fatime Qosaj, Andrew Roth, Ignacio Vázquez-García, Spencer S. Watson, Jonas Windhager, Samuel Aparicio, Bernd Bodenmiller, Ed Boyden, Carlos Caldas, Owen Harris, Sohrab P. Shah, Simon Tavaré, CRUK IMAXT Grand Challenge Team, Dario Bressan, Gregory J. Hannon, View ORCID ProfileNicholas A. Walton
doi: https://doi.org/10.1101/2021.06.22.448403
Eduardo A. González-Solares
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Ali Dariush
1Institute of Astronomy, University of Cambridge, Cambridge, UK
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Carlos González-Fernández
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Aybüke Küpcü Yoldaş
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Mohammad Al Sa’d
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Neil Millar
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Tristan Whitmarsh
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Nicholas Chornay
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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Ilaria Falciatori
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Atefeh Fatemi
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Daniel Goodwin
6McGovern Institute, Departments of Biological Engineering and of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Laura Kuett
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
5Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Claire M. Mulvey
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Marta Páez Ribes
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Fatime Qosaj
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Andrew Roth
14Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
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Ignacio Vázquez-García
9Herbert and Florence Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
11Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Spencer S. Watson
10Department of Oncology and Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
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Jonas Windhager
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
5Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Samuel Aparicio
7Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Bernd Bodenmiller
3Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
5Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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Ed Boyden
6McGovern Institute, Departments of Biological Engineering and of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
13Howard Hughes Medical Institute, Department of Physics and of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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Carlos Caldas
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
4Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
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Owen Harris
8Súil Interactive, Dublin, UK
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Sohrab P. Shah
11Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Simon Tavaré
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
9Herbert and Florence Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
12New York Genome Center, New York, NY, USA
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Dario Bressan
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Gregory J. Hannon
2CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
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Nicholas A. Walton
1Institute of Astronomy, University of Cambridge, Cambridge, UK
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  • ORCID record for Nicholas A. Walton
  • For correspondence: naw@ast.cam.ac.uk
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Abstract

With the aim of producing a 3D representation of tumours, IMAXT uses a large variety of modalities in order to acquire tumour samples and produce a map of every cell in the tumour and its host environment. With the large volume and variety of data produced in the project we develop automatic data workflows and analysis pipelines and introduce a research methodology where scientists connect to a cloud environment to perform analysis close to where data are located instead of bringing data to their local computers. Here we present the data and analysis infrastructure, discuss the unique computational challenges and describe the analysis chains developed and deployed to generate molecularly annotated tumour models. Registration is achieved by use of a novel technique involving spherical fiducial marks that are visible in all imaging modalities used within IMAXT.

Competing Interest Statement

Sohrab P. Shah is a founder and shareholder of Canexia Health Inc.

Footnotes

  • ↵15 The list of CRUK IMAXT Grand Challenge Consortium members appears at the end of the paper.

  • https://imaxt.ast.cam.ac.uk/release

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 23, 2021.
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The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure
Eduardo A. González-Solares, Ali Dariush, Carlos González-Fernández, Aybüke Küpcü Yoldaş, Mohammad Al Sa’d, Neil Millar, Tristan Whitmarsh, Nicholas Chornay, Ilaria Falciatori, Atefeh Fatemi, Daniel Goodwin, Laura Kuett, Claire M. Mulvey, Marta Páez Ribes, Fatime Qosaj, Andrew Roth, Ignacio Vázquez-García, Spencer S. Watson, Jonas Windhager, Samuel Aparicio, Bernd Bodenmiller, Ed Boyden, Carlos Caldas, Owen Harris, Sohrab P. Shah, Simon Tavaré, CRUK IMAXT Grand Challenge Team, Dario Bressan, Gregory J. Hannon, Nicholas A. Walton
bioRxiv 2021.06.22.448403; doi: https://doi.org/10.1101/2021.06.22.448403
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The Imaging and Molecular Annotation of Xenografts and Tumours (IMAXT) High Throughput Data and Analysis Infrastructure
Eduardo A. González-Solares, Ali Dariush, Carlos González-Fernández, Aybüke Küpcü Yoldaş, Mohammad Al Sa’d, Neil Millar, Tristan Whitmarsh, Nicholas Chornay, Ilaria Falciatori, Atefeh Fatemi, Daniel Goodwin, Laura Kuett, Claire M. Mulvey, Marta Páez Ribes, Fatime Qosaj, Andrew Roth, Ignacio Vázquez-García, Spencer S. Watson, Jonas Windhager, Samuel Aparicio, Bernd Bodenmiller, Ed Boyden, Carlos Caldas, Owen Harris, Sohrab P. Shah, Simon Tavaré, CRUK IMAXT Grand Challenge Team, Dario Bressan, Gregory J. Hannon, Nicholas A. Walton
bioRxiv 2021.06.22.448403; doi: https://doi.org/10.1101/2021.06.22.448403

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