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Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting

Esben Bjørn Madsen, Thomas Kvist, Ida Höijer, Adam Ameur, Marie Just Mikkelsen
doi: https://doi.org/10.1101/409086
Esben Bjørn Madsen
1Samplix, Herlev, Denmark
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Thomas Kvist
1Samplix, Herlev, Denmark
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Ida Höijer
2Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
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Adam Ameur
2Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
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Marie Just Mikkelsen
1Samplix, Herlev, Denmark
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Abstract

Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore such technologies are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements. Here we introduce the Xdrop technology: a novel microfluidic-based system that allows for targeted enrichment of long DNA molecules starting from only a few nanograms of genomic DNA. Xdrop is based on isolation of long DNA fragments in millions of double emulsion (DE) droplets, where the DE droplets containing a target sequence of interest are fluorescently labeled and sorted using flow cytometry. The final product from the Xdrop procedure is an enriched population of long DNA molecules that can be investigated by sequencing. To demonstrate the capability of Xdrop, we performed enrichment of the human papilloma virus (HPV) 18 integrated in the genome of human HeLa cells. The enriched DNA was sequenced both on long-read (PacBio and Oxford Nanopore) and short-read (Illumina) platforms. Analysis of the sequencing reads resolved three HPV18-chr8 integrations at base pair resolution, and the captured fragments extended up to 30 kb into the human genome at the integration sites. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex regions of the genome where long-range information is required.

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Posted September 06, 2018.
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Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting
Esben Bjørn Madsen, Thomas Kvist, Ida Höijer, Adam Ameur, Marie Just Mikkelsen
bioRxiv 409086; doi: https://doi.org/10.1101/409086
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Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting
Esben Bjørn Madsen, Thomas Kvist, Ida Höijer, Adam Ameur, Marie Just Mikkelsen
bioRxiv 409086; doi: https://doi.org/10.1101/409086

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