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

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 fre...

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Bibliographic Details
Published in:Lab on a chip 2018-01, Vol.18 (13), p.1891-1902
Main Authors: Marie, Rodolphe, Pødenphant, Marie, Koprowska, Kamila, Bærlocher, Loic, Vulders, Roland C M, Wilding, Jennifer, Ashley, Neil, McGowan, Simon J, van Strijp, Dianne, van Hemert, Freek, Olesen, Tom, Agersnap, Niels, Bilenberg, Brian, Sabatel, Celine, Schira, Julien, Kristensen, Anders, Bodmer, Walter, van der Zaag, Pieter J, Mir, Kalim U
Format: Article
Language:English
Subjects:
Amplification
Cancer
Cell Line, Tumor
Deoxyribonucleic acid
DNA
DNA, Neoplasm - genetics
Gene sequencing
Genome, Human - genetics
Genomes
Heterogeneity
Humans
Injection molding
Lab-On-A-Chip Devices
Microfluidic Analytical Techniques - instrumentation
Sequence Analysis, DNA - instrumentation
Single-Cell Analysis - instrumentation
Single-Cell Analysis - methods
Tumors
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Summary: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.
ISSN:1473-0197
1473-0189
DOI:10.1039/c8lc00169c