Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

Kyriakos Tsangaras, Nathan Wales, Thomas Sicheritz-Pontén, Simon Rasmussen, Johan Michaux, Yasuko Ishida, Serge Morand, Marie-Louise Kampmann, M. Thomas P. Gilbert, Alex D. Greenwood

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    Abstract

    Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information.
    Original languageEnglish
    Article numbere109101
    JournalPLOS ONE
    Volume9
    Issue number10
    Number of pages10
    ISSN1932-6203
    DOIs
    Publication statusPublished - 2014

    Cite this

    Tsangaras, K., Wales, N., Sicheritz-Pontén, T., Rasmussen, S., Michaux, J., Ishida, Y., Morand, S., Kampmann, M-L., Gilbert, M. T. P., & Greenwood, A. D. (2014). Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank). PLOS ONE, 9(10), [e109101]. https://doi.org/10.1371/journal.pone.0109101