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

Zanini, Fabio; Brodin, Johanna; Albert, Jan; Neher, Richard A.

doi:10.1016/j.virusres.2016.12.009

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

MPS-Authors

Zanini, Fabio
Max Planck Institute for Developmental Biology, Max Planck Society;

Neher, Richard A.
Max Planck Institute for Developmental Biology, Max Planck Society;

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https://www.sciencedirect.com/science/article/pii/S0168170216304221?via%3Dihub
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Citation

Zanini, F., Brodin, J., Albert, J., & Neher, R. A. (2017). Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing. Virus Research, 239, 106-114. doi:10.1016/j.virusres.2016.12.009.

Cite as: https://hdl.handle.net/21.11116/0000-0002-1A97-7

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. (C) 2016 Elsevier B.V. All rights reserved.