Error rates, PCR recombination, and sampling depth in HIV-1 Whole Genome Deep Sequencing
| Autor: | Johanna Brodin, Jan Albert, Fabio Zanini, Richard A. Neher |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Cancer Research Genotype HIV Infections Genomics Genome Viral Computational biology Biology Polymerase Chain Reaction Genome Deep sequencing law.invention 03 medical and health sciences INDEL Mutation law Virology Genetic variation Humans Indel Polymerase chain reaction 030304 developmental biology Genetics Recombination Genetic 0303 health sciences Genetic diversity 030306 microbiology Computational Biology Genetic Variation Reproducibility of Results food and beverages Sampling depth Amplicon 3. Good health 030104 developmental biology Infectious Diseases HIV-1 Viral load Recombination |
| Popis: | 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. Here, we describe several control experiments and error correction methods for whole-genome deep sequencing of viral genomes. We developed many of these in the course of a large scale whole genome deep sequencing study of HIV-1 populations. We measured the substitution and indel errors that arose during sequencing and PCR and quantified PCR-mediated recombination. We find that depending on the viral load in the samples, rare mutations down to 0.2% can be reproducibly detected. PCR recombination can be avoided by consistently working at low amplicon concentrations. |
| Databáze: | OpenAIRE |
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