Hybrid selection for sequencing pathogen genomes from clinical samples

Alexandre Melnikov; Kevin Galinsky; Peter Rogov; Timothy Fennell; Daria V. Tyne; Carsten Russ; Rachel Daniels; Kayla Barnes; James Bochicchio; Daouda Ndiaye; Papa D. Sene; Dyann F. Wirth; Chad Nusbaum; Sarah K. Volkman; Bruce W. Birren; Andreas Gnirke; Daniel E. Neafsey

doi:10.1186/gb-2011-12-8-r73

Hybrid selection for sequencing pathogen genomes from clinical samples

Alexandre Melnikov
, Kevin Galinsky
, Peter Rogov
, Timothy Fennell
, Daria V. Tyne
, Carsten Russ
, Rachel Daniels
, Kayla Barnes
, James Bochicchio
, Daouda Ndiaye
, Papa D. Sene
, Dyann F. Wirth
, Chad Nusbaum
, Sarah K. Volkman
, Bruce W. Birren
, Andreas Gnirke
, Daniel E. Neafsey

Broad Institute
Harvard University
Université Cheikh Anta Diop de Dakar

Research output: Contribution to journal › Article › peer-review

91 Citations (Scopus)

Abstract

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.

Original language	English
Article number	r73
Journal	Genome Biology
Volume	12
Issue number	8
DOIs	https://doi.org/10.1186/gb-2011-12-8-r73
Publication status	Published - 11 Aug 2011
Externally published	Yes

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SDG 3 Good Health and Well-being

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10.1186/gb-2011-12-8-r73Licence: CC BY

Cite this

Melnikov, A., Galinsky, K., Rogov, P., Fennell, T., Tyne, D. V., Russ, C., Daniels, R., Barnes, K., Bochicchio, J., Ndiaye, D., Sene, P. D., Wirth, D. F., Nusbaum, C., Volkman, S. K., Birren, B. W., Gnirke, A., & Neafsey, D. E. (2011). Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biology, 12(8), Article r73. https://doi.org/10.1186/gb-2011-12-8-r73

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title = "Hybrid selection for sequencing pathogen genomes from clinical samples",

abstract = "We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.",

author = "Alexandre Melnikov and Kevin Galinsky and Peter Rogov and Timothy Fennell and Tyne, \{Daria V.\} and Carsten Russ and Rachel Daniels and Kayla Barnes and James Bochicchio and Daouda Ndiaye and Sene, \{Papa D.\} and Wirth, \{Dyann F.\} and Chad Nusbaum and Volkman, \{Sarah K.\} and Birren, \{Bruce W.\} and Andreas Gnirke and Neafsey, \{Daniel E.\}",

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month = aug,

day = "11",

doi = "10.1186/gb-2011-12-8-r73",

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AU - Melnikov, Alexandre

AU - Galinsky, Kevin

AU - Rogov, Peter

AU - Fennell, Timothy

AU - Tyne, Daria V.

AU - Russ, Carsten

AU - Daniels, Rachel

AU - Barnes, Kayla

AU - Bochicchio, James

AU - Ndiaye, Daouda

AU - Sene, Papa D.

AU - Wirth, Dyann F.

AU - Nusbaum, Chad

AU - Volkman, Sarah K.

AU - Birren, Bruce W.

AU - Gnirke, Andreas

AU - Neafsey, Daniel E.

PY - 2011/8/11

Y1 - 2011/8/11

N2 - We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.

AB - We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.

U2 - 10.1186/gb-2011-12-8-r73

DO - 10.1186/gb-2011-12-8-r73

M3 - Article

SN - 1474-7596

VL - 12

JO - Genome Biology

JF - Genome Biology

IS - 8

M1 - r73

ER -

Hybrid selection for sequencing pathogen genomes from clinical samples

Abstract

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