ArticlePloS one2014
Extensive recombination due to heteroduplexes generates large amounts of artificial gene fragments during PCR.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Improved high-throughput MHC typing for non-model species using long-read sequencing.Molecular ecology resources · 2022Pooled it
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- AmpliFuse: an amplicon simulation tool with enhanced chimera generation for Illumina platforms.Microbiology resource announcements · 2026Article
- A versatile platform for combinatorial antibody library cloning and NGS-based quality control with high accuracy.Nucleic acids research · 2025Article
- CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.Molecular ecology resources · 2025Article
- Near extinction of the HBV quasispecies driven by the hard selective sweep in chronic hepatitis B.mBio · 2025Article
- Portable Nanopore sequencing solution for next-generation HIV drug resistance testing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2024Article
- Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2023Article
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- Nanopore sequencing of PCR products enables multicopy gene family reconstruction.Computational and structural biotechnology journal · 2023Article
- A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike.bioRxiv : the preprint server for biology · 2022Article
- Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections.Virus evolution · 2021Article
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- Determining the Suitability of MinION's Direct RNA and DNA Amplicon Sequencing for Viral Subtype Identification.Viruses · 2020Article
- Amplicon-Based, Next-Generation Sequencing Approaches to Characterize Single Nucleotide Polymorphisms ofFrontiers in cellular and infection microbiology · 2020Article
- Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries.BMC genomics · 2019Article
- Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- High-Resolution Maps of Mouse Reference Populations.G3 (Bethesda, Md.) · 2017Article
- Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing.Plant biotechnology journal · 2017Article
Corrections and comments
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7 authors.
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Abstract
Artificial recombinants can be generated during PCR when more than two genetically distinct templates coexist in a single PCR reaction. These recombinant amplicons can lead to the false interpretation of genetic diversity and incorrect identification of biological phenotypes that do not exist in vivo. We investigated how recombination between 2 or 35 genetically distinct HIV-1 genomes was affected by different PCR conditions using the parallel allele-specific sequencing (PASS) assay and the next generation sequencing method. In a standard PCR condition, about 40% of amplicons in a PCR reaction were recombinants. The high recombination frequency could be significantly reduced if the number of amplicons in a PCR reaction was below a threshold of 10(13)-10(14) using low thermal cycles, fewer input templates, and longer extension time. Heteroduplexes (each DNA strand from a distinct template) were present at a large proportion in the PCR products when more thermal cycles, more templates, and shorter extension time were used. Importantly, the majority of recombinants were identified in heteroduplexes, indicating that the recombinants were mainly generated through heteroduplexes. Since prematurely terminated extension fragments can form heteroduplexes by annealing to different templates during PCR amplification, recombination has a better chance to occur with samples containing different genomes when the number of amplicons accumulate over the threshold. New technologies are warranted to accurately characterize complex quasispecies gene populations.
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