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Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing

Zanini, Fabio and Brodin, Johanna and Albert, Jan and Neher, Richard A.. (2016) Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Research , 239. pp. 106-114.

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Official URL: http://edoc.unibas.ch/53976/

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Abstract

Deep sequencing is a powerful and cost-effective tool to characterize the genetic diversity and evolution of virus populations. While modern sequencing instruments readily cover viral genomes many thousand fold and very rare variants can in principle be detected, sequencing errors, amplification biases, and other artifacts can limit sensitivity and complicate data interpretation. For this reason, the number of studies using whole genome deep sequencing to characterize viral quasi-species in clinical samples is still limited. We have previously undertaken a large scale whole genome deep sequencing study of HIV-1 populations. Here we discuss the challenges, error profiles, control experiments, and computational test we developed to quantify the accuracy of variant frequency estimation.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard
Item Type:Article, refereed
Article Subtype:Further Journal Contribution
Publisher:Elsevier
ISSN:0168-1702
e-ISSN:1872-7492
Note:Publication type according to Uni Basel Research Database: Journal item
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Last Modified:18 Sep 2019 05:55
Deposited On:26 Oct 2017 15:21

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