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 Citationer (Scopus)

137 Downloads (Pure)

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.

Originalsprog	Engelsk
Artikelnummer	e109101
Tidsskrift	PLoS ONE
Vol/bind	9
Udgave nummer	10
Antal sider	10
ISSN	1932-6203
DOI	https://doi.org/10.1371/journal.pone.0109101
Status	Udgivet - 2 okt. 2014

Adgang til dokumentet

10.1371/journal.pone.0109101Licens: CC BY

Tsangaras_2014_Hybridization_captureForlagets udgivne version, 876 KBLicens: CC BY

Citationsformater

@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",

month = oct,

day = "2",

doi = "10.1371/journal.pone.0109101",

language = "English",

volume = "9",

journal = "PLoS Computational Biology",

issn = "1932-6203",

publisher = "Public Library of Science",

number = "10",

}

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 - 2014/10/2

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.

U2 - 10.1371/journal.pone.0109101

DO - 10.1371/journal.pone.0109101

M3 - Journal article

C2 - 25275614

SN - 1932-6203

VL - 9

JO - PLoS Computational Biology

JF - PLoS Computational Biology

IS - 10

M1 - e109101

ER -

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

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater