PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample

By Silvia G. Acinas, R. Sarma-Rupavtarm, V. Klepac‐Ceraj, M. Polz. Applied and Environmental Microbiology, 2005

615 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/3ebc7ba351c1566e7d70762f61ca082961910416

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Citations in the corpus

Who is eating what: diet assessment using next generation sequencing (2012, background): “However, results from many different fields of research have shown that obtaining quantitative data in amplicon sequencing studies is fraught with problems (e.g. von Wintzingerode et al. 1997; Polz & Cavanaugh 1998; Acinas et al. 2005; Porazinska et al. 2009; Amend et al. 2010).”
DNA-based methods in paleolimnology: new opportunities for investigating long-term dynamics of lacustrine biodiversity (2017, background): “PCR-generated errors include formation of chimeras (Acinas et al. 2005) that can be detected by specific applications (Uchime; Edgar et al.”
Environmental DNA - An emerging tool in conservation for monitoring past and present biodiversity (2015, background): “PCR-generated errors include point mutations and formation of chimeric molecules (Acinas et al., 2005).”
Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? (2010, neutral): “several PCR products in each metasample (Acinas et al. 2005).”
Estuarine Nitrifiers: New Players, Patterns and Processes (2010, positive): “Biases associated with DNA extractions and PCR 11 amplification have also been well-documented (e. g. Suzuki et al., 1998; Acinas et al., 2005), and 12 are often not fully explored or controlled for in most studies due to time and financial 13 constraints.”
Conducting a Microbiome Study (2014, methodology): “…Cell 158, July 17, 2014 ª2014 Elsevier Inc. practice to perform and pool multiple (i.e., triplicate) PCRs for each sample, to minimize PCR cycle number, and to use a standard but relatively high DNA template concentration across samples (Acinas et al., 2005; Aird et al., 2011; Sipos et al., 2007).”
Resource Exchange in the Rhizosphere: Molecular Tools and the Microbial Perspective (2006, methodology): “…limitations of methods commonly used for analyzing microbial diversitya Strengths Limitations PCR-based methods: DGGE, RFLP, and related techniques (Acinas et al. 2005; Blackwood & Paul 2003; Marschner et al. 2001; Smalla et al. 1998, 2001; Spiegelman et al. 2005) -Amenable to high throughput…”
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (2011, background): “Multiple factors including pairwise sequence identity between 16S rRNA genes, number of PCR cycles, and relative abundance of gene-specific PCR templates have been shown to influence chimera formation (Wang and Wang 1996; Wang and Wang 1997; Thompson et al. 2002; Acinas et al. 2005; Lahr and Katz 20”
Illumina metabarcoding of a soil fungal community (2013, background): “Previous studies suggest that low annealing temperatures should be used to maximize taxon recovery, because low annealing temperatures may help dealing with mismatch problems in the primer sequence (Ishii and Fukui, 2001; Acinas et al., 2005; Sipos et al., 2007).”