Enhanced detection of circulating tumor DNA by fragment size analysis

Florent Mouliere; Dineika Chandrananda; Anna M. Piskorz; Elizabeth K. Moore; James Morris; Lise Barlebo Ahlborn; Richard Mair; Teodora Goranova; Francesco Marass; Katrin Heider; Jonathan C. M. Wan; Anna Supernat; Irena Hudecova; Ioannis Gounaris; Susana Ros; Mercedes Jimenez-Linan; Javier Garcia-Corbacho; Keval Patel; Olga Østrup; Suzanne Murphy; Matthew D. Eldridge; Davina Gale; Grant D. Stewart; Johanna Burge; Wendy N. Cooper; Michiel S. van der Heijden; Charles E. Massie; Colin Watts; Pippa Corrie; Simon Pacey; Kevin M. Brindle; Richard D. Baird; Morten Mau-Sørensen; Christine A. Parkinson; Christopher G. Smith; James D. Brenton; Nitzan Rosenfeld

doi:10.1126/scitranslmed.aat4921

Research ArticleCancer

Enhanced detection of circulating tumor DNA by fragment size analysis

Florent Mouliere¹,²,*,†,
Dineika Chandrananda¹,²,*,
Anna M. Piskorz¹,²,*,
Elizabeth K. Moore¹,²,³,*,
James Morris¹,²,
Lise Barlebo Ahlborn⁴,⁵,
Richard Mair¹,²,⁶,
Teodora Goranova¹,²,
Francesco Marass¹,²,⁷,⁸,
Katrin Heider¹,²,
Jonathan C. M. Wan¹,²,
Anna Supernat¹,²,⁹,
Irena Hudecova¹,²,
Ioannis Gounaris¹,²,³,
Susana Ros¹,²,
Mercedes Jimenez-Linan²,³,
Javier Garcia-Corbacho¹⁰,
Keval Patel¹,²,
Olga Østrup⁵,
Suzanne Murphy¹,²,
Matthew D. Eldridge¹,²,
Davina Gale¹,²,
Grant D. Stewart²,³,¹¹,
Johanna Burge²,¹¹,
Wendy N. Cooper¹,²,
Michiel S. van der Heijden¹²,¹³,
Charles E. Massie¹,²,¹⁴,
Colin Watts¹⁵,
Pippa Corrie³,
Simon Pacey³,¹⁴,
Kevin M. Brindle¹,²,¹⁶,
Richard D. Baird¹⁷,
Morten Mau-Sørensen⁴,
Christine A. Parkinson¹,²,³,¹⁸,¹⁹,
Christopher G. Smith¹,²,
James D. Brenton¹,²,³,¹⁸,¹⁹,‡,§ and
Nitzan Rosenfeld ¹,²,‡,§

¹Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.
²Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.
³Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.
⁴Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
⁵Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
⁶Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ Cambridge, UK.
⁷Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
⁸Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
⁹Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-211 Gdańsk, Poland.
¹⁰Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, 170 08036 Barcelona, Spain.
¹¹Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK.
¹²Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
¹³Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
¹⁴Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK.
¹⁵Institute of Cancer Genomics Science, University of Birmingham, B15 2TT Birmingham, UK.
¹⁶Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK.
¹⁷Early Phase Clinical Trials and Breast Cancer Research Teams, Cancer Research UK Cambridge Centre, CB2 0QQ Cambridge, UK.
¹⁸Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK.
¹⁹NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK.

↵§Corresponding author. Email: james.brenton{at}cruk.cam.ac.uk (J.D.B.); nitzan.rosenfeld{at}cruk.cam.ac.uk (N.R.)

↵* These authors contributed equally to this work as co-first authors.
↵† Present address: Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, de Boelelaan 1117, 1081 HV Amsterdam, Netherlands.
↵‡ These authors contributed equally to this work as co-senior authors.

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Science Translational Medicine 07 Nov 2018:
Vol. 10, Issue 466, eaat4921
DOI: 10.1126/scitranslmed.aat4921

Florent Mouliere

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Dineika Chandrananda

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Anna M. Piskorz

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Elizabeth K. Moore

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James Morris

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Lise Barlebo Ahlborn

Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.

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Richard Mair

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Teodora Goranova

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Francesco Marass

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.

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Katrin Heider

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Jonathan C. M. Wan

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Anna Supernat

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, 80-211 Gdańsk, Poland.

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Irena Hudecova

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Ioannis Gounaris

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Susana Ros

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Mercedes Jimenez-Linan

Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.

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Javier Garcia-Corbacho

Clinical Trials Unit, Clinic Institute of Haematological and Oncological Diseases, Hospital Clinic de Barcelona, 170 08036 Barcelona, Spain.

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Keval Patel

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Olga Østrup

Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.

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Suzanne Murphy

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Matthew D. Eldridge

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Davina Gale

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Grant D. Stewart

Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK.

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Johanna Burge

Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Academic Urology Group, Department of Surgery, University of Cambridge, CB2 0QQ Cambridge, UK.

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Wendy N. Cooper

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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Michiel S. van der Heijden

Division of Molecular Carcinogenesis, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.Department of Medical Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.

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Charles E. Massie

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Colin Watts

Institute of Cancer Genomics Science, University of Birmingham, B15 2TT Birmingham, UK.

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Pippa Corrie

Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.

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Simon Pacey

Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.Department of Oncology, University of Cambridge, CB2 0XZ Cambridge, UK.

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Kevin M. Brindle

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Richard D. Baird

Early Phase Clinical Trials and Breast Cancer Research Teams, Cancer Research UK Cambridge Centre, CB2 0QQ Cambridge, UK.

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Morten Mau-Sørensen

Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.

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Christine A. Parkinson

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK.NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK.

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Christopher G. Smith

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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James D. Brenton

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK.Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, CB2 0XZ Cambridge, UK.NIHR Cambridge Biomedical Research Centre, CB2 0QQ Cambridge, UK.

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For correspondence: james.brenton@cruk.cam.ac.uk nitzan.rosenfeld@cruk.cam.ac.uk

Nitzan Rosenfeld

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE Cambridge, UK.Cancer Research UK Major Centre–Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE Cambridge, UK.

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For correspondence: james.brenton@cruk.cam.ac.uk nitzan.rosenfeld@cruk.cam.ac.uk

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Sizing up circulating tumor DNA

Unlike solid tumors, which are often hidden deep within a patient’s body, a patient’s blood is easy to access safely. As a result, liquid biopsy, the analysis of tumor DNA in the blood, is an attractive alternative to conventional biopsy. Unfortunately, tumor DNA molecules are usually vastly outnumbered by the fragments of noncancer DNA in the blood, and detecting them can be a challenge, especially in early stages of cancer. Mouliere et al. identified characteristic differences in the size distribution of tumor-derived and noncancer DNA fragments and then used these observations to design a method of tumor DNA detection with greater sensitivity.

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Enhanced detection of circulating tumor DNA by fragment size analysis

Sizing up circulating tumor DNA

Science Translational Medicine

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