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

doi:10.1371/journal.pone.0109101

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

16 Citations (Scopus)

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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 language	English
Article number	e109101
Journal	PLoS ONE
Volume	9
Issue number	10
Number of pages	10
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0109101
Publication status	Published - 2 Oct 2014

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10.1371/journal.pone.0109101Licence: CC BY

Tsangaras_2014_Hybridization_captureFinal published version, 876 KBLicence: CC BY

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title = "Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)",

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.",

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AU - Tsangaras, Kyriakos

AU - Wales, Nathan

AU - Sicheritz-Pontén, Thomas

AU - Rasmussen, Simon

AU - Michaux, Johan

AU - Ishida, Yasuko

AU - Morand, Serge

AU - Kampmann, Marie-Louise

AU - Gilbert, M. Thomas P.

AU - Greenwood, Alex D.

PY - 2014/10/2

Y1 - 2014/10/2

N2 - 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.

AB - 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.

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DO - 10.1371/journal.pone.0109101

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Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)

Abstract

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