RT Journal Article
SR Electronic
T1 Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 409086
DO 10.1101/409086
A1 Esben Bjørn Madsen
A1 Thomas Kvist
A1 Ida Höijer
A1 Adam Ameur
A1 Marie Just Mikkelsen
YR 2018
UL http://biorxiv.org/content/early/2018/09/06/409086.abstract
AB 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.