Viral quasispecies assembly via maximal clique enumeration.

Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the s...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Armin Töpfer, Tobias Marschall, Rowena A Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/2064e6e3f9d348efb334daaae6663cd3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2064e6e3f9d348efb334daaae6663cd3
record_format	dspace
spelling	oai:doaj.org-article:2064e6e3f9d348efb334daaae6663cd32021-11-18T05:53:02ZViral quasispecies assembly via maximal clique enumeration.1553-734X1553-735810.1371/journal.pcbi.1003515https://doaj.org/article/2064e6e3f9d348efb334daaae6663cd32014-03-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24675810/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples. We develop a statistical model for paired-end reads accounting for mutations, insertions, and deletions. Using an iterative maximal clique enumeration approach, read pairs are assembled into haplotypes of increasing length, eventually enabling global haplotype assembly. The performance of our quasispecies assembly method is assessed on simulated data for varying population characteristics and sequencing technology parameters. Owing to its paired-end handling, HaploClique compares favorably to state-of-the-art haplotype inference methods. It can reconstruct error-free full-length haplotypes from low coverage samples and detect large insertions and deletions at low frequencies. We applied HaploClique to sequencing data derived from a clinical hepatitis C virus population of an infected patient and discovered a novel deletion of length 357±167 bp that was validated by two independent long-read sequencing experiments. HaploClique is available at https://github.com/armintoepfer/haploclique. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.Armin TöpferTobias MarschallRowena A BullFabio LucianiAlexander SchönhuthNiko BeerenwinkelPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 3, p e1003515 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Armin Töpfer Tobias Marschall Rowena A Bull Fabio Luciani Alexander Schönhuth Niko Beerenwinkel Viral quasispecies assembly via maximal clique enumeration.
description	Virus populations can display high genetic diversity within individual hosts. The intra-host collection of viral haplotypes, called viral quasispecies, is an important determinant of virulence, pathogenesis, and treatment outcome. We present HaploClique, a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples. We develop a statistical model for paired-end reads accounting for mutations, insertions, and deletions. Using an iterative maximal clique enumeration approach, read pairs are assembled into haplotypes of increasing length, eventually enabling global haplotype assembly. The performance of our quasispecies assembly method is assessed on simulated data for varying population characteristics and sequencing technology parameters. Owing to its paired-end handling, HaploClique compares favorably to state-of-the-art haplotype inference methods. It can reconstruct error-free full-length haplotypes from low coverage samples and detect large insertions and deletions at low frequencies. We applied HaploClique to sequencing data derived from a clinical hepatitis C virus population of an infected patient and discovered a novel deletion of length 357±167 bp that was validated by two independent long-read sequencing experiments. HaploClique is available at https://github.com/armintoepfer/haploclique. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.
format	article
author	Armin Töpfer Tobias Marschall Rowena A Bull Fabio Luciani Alexander Schönhuth Niko Beerenwinkel
author_facet	Armin Töpfer Tobias Marschall Rowena A Bull Fabio Luciani Alexander Schönhuth Niko Beerenwinkel
author_sort	Armin Töpfer
title	Viral quasispecies assembly via maximal clique enumeration.
title_short	Viral quasispecies assembly via maximal clique enumeration.
title_full	Viral quasispecies assembly via maximal clique enumeration.
title_fullStr	Viral quasispecies assembly via maximal clique enumeration.
title_full_unstemmed	Viral quasispecies assembly via maximal clique enumeration.
title_sort	viral quasispecies assembly via maximal clique enumeration.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/2064e6e3f9d348efb334daaae6663cd3
work_keys_str_mv	AT armintopfer viralquasispeciesassemblyviamaximalcliqueenumeration AT tobiasmarschall viralquasispeciesassemblyviamaximalcliqueenumeration AT rowenaabull viralquasispeciesassemblyviamaximalcliqueenumeration AT fabioluciani viralquasispeciesassemblyviamaximalcliqueenumeration AT alexanderschonhuth viralquasispeciesassemblyviamaximalcliqueenumeration AT nikobeerenwinkel viralquasispeciesassemblyviamaximalcliqueenumeration
_version_	1718424653411647488

Viral quasispecies assembly via maximal clique enumeration.

Ejemplares similares