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Sequencing Metrics of Human Genomes Extracted from Single Cancer Cells Individually Isolated in a Valveless Microfluidic Device

View ORCID ProfileRodolphe Marie, Marie Pødenphant, Kamila Koprowska, Loic Bærlocher, Roland C.M. Vulders, Jennifer Wilding, View ORCID ProfileNeil Ashley, View ORCID ProfileSimon J. McGowan, Dianne van Strijp, Freek van Hemert, Tom Olesen, Niels Agersnap, Brian Bilenberg, Celine Sabatel, Julien Schira, View ORCID ProfileAnders Kristensen, View ORCID ProfileWalter Bodmer, Pieter J. van der Zaag, View ORCID ProfileKalim U. Mir
doi: https://doi.org/10.1101/258780
Rodolphe Marie
1Technical University of Denmark, Department for Micro and Nanotechnology, Ørsteds Plads Building 345C, 2800 Kgs. Lyngby, Denmark.
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  • ORCID record for Rodolphe Marie
  • For correspondence: rodolphe.marie@nanotech.dtu.dk kalim.u.mir@gmail.com walter.bodmer@hertford.ox.ac.uk p.j.van.der.zaag@philips.com
Marie Pødenphant
1Technical University of Denmark, Department for Micro and Nanotechnology, Ørsteds Plads Building 345C, 2800 Kgs. Lyngby, Denmark.
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Kamila Koprowska
2Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Loic Bærlocher
3Fasteris SA, Chemin du Pont-du-Centenaire 109 CH-1228 Plan-les-Ouates, Switzerland.
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Roland C.M. Vulders
4Philips Research Laboratories, High Tech Campus 11 5656 AE Eindhoven, The Netherlands.
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Jennifer Wilding
2Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Neil Ashley
2Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Simon J. McGowan
2Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Dianne van Strijp
4Philips Research Laboratories, High Tech Campus 11 5656 AE Eindhoven, The Netherlands.
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Freek van Hemert
4Philips Research Laboratories, High Tech Campus 11 5656 AE Eindhoven, The Netherlands.
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Tom Olesen
5Philips Biocell, Gydevang 42, 3450 Lillerød, Denmark
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Niels Agersnap
5Philips Biocell, Gydevang 42, 3450 Lillerød, Denmark
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Brian Bilenberg
6NIL Technology ApS, Diplomvej 381, 2800 Kgs. Lyngby, Denmark.
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Celine Sabatel
7Diagenode SA, Liege Science Park, Rue Bois Saint-Jean, 3, 4102 Seraing, Belgium
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Julien Schira
3Fasteris SA, Chemin du Pont-du-Centenaire 109 CH-1228 Plan-les-Ouates, Switzerland.
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Anders Kristensen
1Technical University of Denmark, Department for Micro and Nanotechnology, Ørsteds Plads Building 345C, 2800 Kgs. Lyngby, Denmark.
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Walter Bodmer
2Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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  • ORCID record for Walter Bodmer
  • For correspondence: rodolphe.marie@nanotech.dtu.dk kalim.u.mir@gmail.com walter.bodmer@hertford.ox.ac.uk p.j.van.der.zaag@philips.com
Pieter J. van der Zaag
4Philips Research Laboratories, High Tech Campus 11 5656 AE Eindhoven, The Netherlands.
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  • For correspondence: rodolphe.marie@nanotech.dtu.dk kalim.u.mir@gmail.com walter.bodmer@hertford.ox.ac.uk p.j.van.der.zaag@philips.com
Kalim U. Mir
8XGenomes, Pagliuca Harvard Life Lab, 127 Western Ave, Boston, MA 02134 USA.
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  • ORCID record for Kalim U. Mir
  • For correspondence: rodolphe.marie@nanotech.dtu.dk kalim.u.mir@gmail.com walter.bodmer@hertford.ox.ac.uk p.j.van.der.zaag@philips.com
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Abstract

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 cell (LS174T, LS180 and RKO) lines and fresh colorectal cancers are 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 extraction is in sub-nanoliter volumes. Our data also demonstrates that high quality single cell sequencing can be achieved using a relatively simple, inexpensive and scalable device.

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Posted February 01, 2018.
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Sequencing Metrics of Human Genomes Extracted from Single Cancer Cells Individually Isolated in a Valveless Microfluidic Device
Rodolphe Marie, Marie Pødenphant, Kamila Koprowska, Loic Bærlocher, Roland C.M. Vulders, Jennifer Wilding, Neil Ashley, Simon J. McGowan, Dianne van Strijp, Freek van Hemert, Tom Olesen, Niels Agersnap, Brian Bilenberg, Celine Sabatel, Julien Schira, Anders Kristensen, Walter Bodmer, Pieter J. van der Zaag, Kalim U. Mir
bioRxiv 258780; doi: https://doi.org/10.1101/258780
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Sequencing Metrics of Human Genomes Extracted from Single Cancer Cells Individually Isolated in a Valveless Microfluidic Device
Rodolphe Marie, Marie Pødenphant, Kamila Koprowska, Loic Bærlocher, Roland C.M. Vulders, Jennifer Wilding, Neil Ashley, Simon J. McGowan, Dianne van Strijp, Freek van Hemert, Tom Olesen, Niels Agersnap, Brian Bilenberg, Celine Sabatel, Julien Schira, Anders Kristensen, Walter Bodmer, Pieter J. van der Zaag, Kalim U. Mir
bioRxiv 258780; doi: https://doi.org/10.1101/258780

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