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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank). / Tsangaras, Kyriakos; Wales, Nathan; Sicheritz-Pontén, Thomas; Rasmussen, Simon; Michaux, Johan; Ishida, Yasuko; Morand, Serge; Kampmann, Marie-Louise; Gilbert, M. Thomas P.; Greenwood, Alex D.

In: PLoS ONE, Vol. 9, No. 10, e109101, 2014.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Tsangaras, K, Wales, N, Sicheritz-Pontén, T, Rasmussen, S, Michaux, J, Ishida, Y, Morand, S, Kampmann, M-L, Gilbert, MTP & Greenwood, AD 2014, 'Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)', PLoS ONE, vol. 9, no. 10, e109101. https://doi.org/10.1371/journal.pone.0109101

APA

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

Vancouver

Tsangaras K, Wales N, Sicheritz-Pontén T, Rasmussen S, Michaux J, Ishida Y et al. Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank). PLoS ONE. 2014;9(10). e109101. https://doi.org/10.1371/journal.pone.0109101

Author

Tsangaras, Kyriakos ; Wales, Nathan ; Sicheritz-Pontén, Thomas ; Rasmussen, Simon ; Michaux, Johan ; Ishida, Yasuko ; Morand, Serge ; Kampmann, Marie-Louise ; Gilbert, M. Thomas P. ; Greenwood, Alex D. / Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank). In: PLoS ONE. 2014 ; Vol. 9, No. 10.

Bibtex

@article{83b8bcd653914a5585b3e3de823ea7e9,
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.",
author = "Kyriakos Tsangaras and Nathan Wales and Thomas Sicheritz-Pont{\'e}n and Simon Rasmussen and Johan Michaux and Yasuko Ishida and Serge Morand and Marie-Louise Kampmann and Gilbert, {M. Thomas P.} and Greenwood, {Alex D.}",
year = "2014",
doi = "10.1371/journal.pone.0109101",
language = "English",
volume = "9",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

RIS

TY - JOUR

T1 - Hybridization capture using short PCR products enriches small genomes by Capturing Flanking Sequences (CapFlank)

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

Y1 - 2014

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.

U2 - 10.1371/journal.pone.0109101

DO - 10.1371/journal.pone.0109101

M3 - Journal article

C2 - 25275614

VL - 9

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 10

M1 - e109101

ER -

ID: 129542559