Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

By Micah Hamady, Jeffrey J. Walker, J. K. Harris, Nicholas J Gold, Rob Knight. Nature Methods, 2008

1,306 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/81214f239ea1bb4cd46f323f5f3e057527123da5

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Citations in the corpus

Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution (2010, background): “Pyrosequencing 1 has revolutionized microbial community analysis by allowing the simultaneous assessment of hundreds of microbial communities in multiplex with sufficient depth to resolve meaningful biological patterns 2 .”
Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer (2012, background): “Sequences that were less than 150 nt, contained ambiguous characters, contained over two mismatches to the primers, or contained mononucleotide repeats of over six nt were removed [16].”
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses (2009, methodology): “Sequences were processed and analyzed following previously described procedures (Hamady et al., 2008).”
Conducting a Microbiome Study (2014, background): “Error-correcting barcodes have the added advantage of reducing the possibility that a sequence will be assigned to the wrong sample (Hamady et al., 2008).”
Target-enrichment strategies for next-generation sequencing (2010, positive): “Finally, the use of error-correcting barcodes would allow a greater proportion of pooled sequences to be deconvoluted 17 .”
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing (2008, methodology): “followed a similar strategy using the V9 region to analyze North American soil samples [40,44], and a group led by Knight have focused on a longer tag that includes the V2 region in macaque gut samples and in a mixture of five diverse microbial habitats [45,46].”
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys (2011, background): “Barcodes unique for each sample, and added to sequences in the PCR step, allow the multiplexing of hundreds or more samples per instrument run, enabling robust study designs to be used economically in place of anecdotal descriptions of microbiota (Binladen et al., 2007; Hoffmann et al., 2007; Huber ”
Mechanisms of soil acidification reducing bacterial diversity (2015, methodology): “In order to measure bacterial composition of all 42 samples in one run, a unique 10-mer tag for each soil DNA sample was added to the 50-end of the primer 338R (Hamady et al., 2008).”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, methodology): “…some widely used primers such as 8F (Meyer et al. 2004; Edwards et al. 2006; Frank et al. 2008), 337F (Huse et al. 2007), 338R (Harris et al. 2004; Hamady et al. 2008), 515F (Marcille et al. 2002; Meyer et al. 2004), 915F (Marcille et al. 2002), 930R (Marcille et al. 2002), 1046R (Sogin et al.…”
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns (2010, methodology): “For each sample, variable region 2 (V2) of the bacterial 16S rRNA gene was PCR-amplified using a primer-set with a unique error-correcting barcode (23, 24).”
The Potential of Metagenomic Approaches for Understanding Soil Microbial Processes (2014, background): “This has become known as pyrotagged sequencing and, with the incorporation of barcoded primers or tags (Hamady et al., 2008), has rapidly became the standard approach for describing the taxonomic composition of soil microbial communities—the soil “microbiome”.”
Human oral, gut, and plaque microbiota in patients with atherosclerosis (2010, methodology): “16S rRNA genes were amplified by PCR with a forward primer containing the 454 Life Sciences primer B sequence and the broadly conserved bacterial primer 27F, and a reverse primer containing the 454 Life Sciences primer A sequence, a unique 12-nucleotide error-correcting barcode used to tag each PCR ”