Long‐read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore 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 DNA. Xdrop is based on the isolation of long DNA fragments in millions of droplets, where the 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 18 integrated into the genome of human HeLa cells. 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. Further, we enriched the complete TP53 locus in a leukemia cell line and could successfully phase coexisting mutations using PacBio sequencing. In summary, our results show that Xdrop is an efficient enrichment technology for studying complex genomic regions.

中文翻译：

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Xdrop：使用液滴分选技术对低输入样品中的长 DNA 分子进行靶向测序。

长读长测序可以解析短读长无法访问的基因组区域，因此非常适合基因组缺口闭合、解决结构重排和通过重复元件进行测序。在这里，我们介绍 Xdrop 技术：一种基于微流体的新型系统，可以从几纳克的 DNA 开始有针对性地富集长 DNA 分子。Xdrop 基于数百万个液滴中的长 DNA 片段的分离，其中包含感兴趣的目标序列的液滴使用流式细胞术进行荧光标记和分选。Xdrop 程序的最终产品是富集的长 DNA 分子群，可以通过测序进行研究。为了证明 Xdrop 的功能，我们对整合到人类 HeLa 细胞基因组中的人类乳头状瘤病毒 18 进行了富集。测序读数分析以碱基对分辨率解析了三个 HPV18-chr8 整合，捕获的片段在整合位点延伸至人类基因组中长达 30 kb。此外，我们富集了白血病细胞系中的完整TP53基因座，并且可以使用 PacBio 测序成功地对共存突变进行定相。总之，我们的结果表明 Xdrop 是一种用于研究复杂基因组区域的有效富集技术。