Sequencing of human genomes extracted from single cancer cells isolated in a valveless microfluidic device

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review

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  • Author: Marie, Rodolphe

    Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, 2800, Kgs. Lyngby, Denmark

  • Author: Pødenphant, Marie

    Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, 2800, Kgs. Lyngby, Denmark

  • Author: Koprowska, Kamila

    Oxford University Hospitals NHS Foundation Trust, United Kingdom

  • Author: Baerlocher, Loic

    Fasteris SA, Switzerland

  • Author: Vulders, Roland C. M.

    Philips Lighting, Netherlands

  • Author: Wilding, Jennifer

    Oxford University Hospitals NHS Foundation Trust, United Kingdom

  • Author: Ashley, Neil

    Oxford University Hospitals NHS Foundation Trust, United Kingdom

  • Author: McGowan, Simon J.

    Oxford University Hospitals NHS Foundation Trust, United Kingdom

  • Author: van Strijp, Dianne

    Philips Lighting, Netherlands

  • Author: van Hemert, Freek

    Philips Lighting, Netherlands

  • Author: Olesen, Tom

    Philips Biocell A/S, Denmark

  • Author: Agersnap, Niels

    Philips Biocell A/S, Denmark

  • Author: Bilenberg, Brian

    NIL Technology ApS, Denmark

  • Author: Sabatel, Celine

    Diagenode SA, Belgium

  • Author: Schira, Julien

    Fasteris SA, Switzerland

  • Author: Kristensen, Anders

    Optofluidics, Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, 2800, Kgs. Lyngby, Denmark

  • Author: Bodmer, Walter

    Oxford University Hospitals NHS Foundation Trust, United Kingdom

  • Author: van der Zaag, Pieter J.

    Philips Lighting, Netherlands

  • Author: Mir, Kalim U.

    XGenomes, United States

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Sequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cancer derived cell lines (LS174T, LS180 and RKO) and fresh colorectal tumors have been individually trapped, their genomes extracted and prepared for sequencing using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources. In addition, most of the reads are correctly paired, with a low percentage of singletons (0.17 +/- 0.06%) and we obtain genome coverages approaching 90%. To achieve this high quality, our device design and process shows that amplification can be conducted in microliter volumes as long as the lysis is in sub-nanoliter volumes. Our data thus demonstrates that high quality whole genome sequencing of single cells can be achieved using a relatively simple, inexpensive and scalable device. Detection of genetic heterogeneity at the single cell level, as we have demonstrated for freshly obtained single cancer cells, could soon become available as a clinical tool to precisely match treatment with the properties of a patient's own tumor.
Original languageEnglish
JournalLab on a Chip
Volume18
Issue number13
Pages (from-to)1891-1902
Number of pages12
ISSN1473-0197
DOIs
Publication statusPublished - 2018

Bibliographical note

Open Access Article. This article is licensed under a Creative Commons Attribution 3.0 Unported Licence.

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