Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity

• Thomas B. K. Watkins ,

  Contributed equally to this work with: Thomas B. K. Watkins, Emma C. Colliver, Matthew R. Huska

  Roles Conceptualization, Data curation, Formal analysis, Methodology, Software, Writing – original draft, Writing – review & editing

  Affiliations Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom, The Francis Crick Institute, London, United Kingdom

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• Emma C. Colliver ,

  Contributed equally to this work with: Thomas B. K. Watkins, Emma C. Colliver, Matthew R. Huska

  Roles Data curation, Methodology, Software, Writing – original draft, Writing – review & editing

  Affiliation The Francis Crick Institute, London, United Kingdom

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• Matthew R. Huska ,

  Contributed equally to this work with: Thomas B. K. Watkins, Emma C. Colliver, Matthew R. Huska

  Roles Methodology, Software

  Current address: Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany

  Affiliation Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany

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• Tom L. Kaufmann,

  Roles Data curation, Formal analysis, Methodology, Software, Writing – original draft, Writing – review & editing

  Affiliations BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany, Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany

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• Emilia L. Lim,

  Roles Data curation, Formal analysis

  Affiliations The Francis Crick Institute, London, United Kingdom, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom

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• Cody B. Duncan,

  Roles Data curation, Formal analysis, Methodology, Software, Writing – original draft, Writing – review & editing

  Affiliation Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany

  https://orcid.org/0000-0003-3127-228X

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• Kerstin Haase,

  Roles Methodology, Writing – original draft, Writing – review & editing

  Affiliations German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany, Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany, Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany

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• Peter Van Loo,

  Roles Conceptualization, Methodology, Writing – original draft, Writing – review & editing

  Affiliations The Francis Crick Institute, London, United Kingdom, Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America

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• Charles Swanton ,

  Roles Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

  ¶‡ These authors are joint senior authors on this work.

  Affiliations The Francis Crick Institute, London, United Kingdom, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom, Department of Medical Oncology, University College London Hospitals, London, United Kingdom

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• Nicholas McGranahan ,

  Roles Conceptualization, Funding acquisition, Methodology, Software, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: nicholas.mcgranahan.10@ucl.ac.uk (NMG); roland.schwarz@uni-koeln.de (RFS)

  ¶‡ These authors are joint senior authors on this work.

  Affiliations Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom, Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom

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• Roland F. Schwarz

  Roles Conceptualization, Funding acquisition, Methodology, Software, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: nicholas.mcgranahan.10@ucl.ac.uk (NMG); roland.schwarz@uni-koeln.de (RFS)

  ¶‡ These authors are joint senior authors on this work.

  Affiliations Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany, BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany

  https://orcid.org/0000-0001-9155-4268

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