The DOI matches its Crossref record.
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
Open accessAbstract
Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available sequencing space. To overcome these limitations, we have devised a novel barcoding approach to allow for pooling and sequencing of DNA from independent samples, and to facilitate subsequent segregation of sequencing capacity. Forty-eight forward-reverse barcode pairs are described: each forward and each reverse barcode unique with respect to at least 4 nt positions. With improved read lengths of pyrosequencers, combinations of forward and reverse barcodes may be used to sequence from as many as n(2) independent libraries for each set of 'n' forward and 'n' reverse barcodes, for each defined set of cloning-linkers. In two pilot series of barcoded sequencing using the GS20 Sequencer (454/Roche), we found that over 99.8% of obtained sequences could be assigned to 25 independent, uniquely barcoded libraries based on the presence of either a perfect forward or a perfect reverse barcode. The false-discovery rate, as measured by the percentage of sequences with unexpected perfect pairings of unmatched forward and reverse barcodes, was estimated to be <0.005%.
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Citations
Cited by
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J., & Knight, R. (2008) · Nature Methods · doi:10.1038/nmeth.1184 · Cited by 1,310
Characterization of the oral fungal microbiome (mycobiome) in healthy individuals
Ghannoum, M. A., Jurevic, R. J., Mukherjee, P. K., Cui, F., Sikaroodi, M., Naqvi, A., & Gillevet, P. M. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000713 · Cited by 1,150
“Several groups have subsequently employed various barcoding strategies to analyze multiple samples and this strategy is now well accepted [18–21].”
BackgroundDetection and quantification of rare mutations with massively parallel sequencing
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105422108 · Cited by 1,144
Zunder, E. R., Finck, R., Behbehani, G. K., Amir, E.-A. D., Krishnaswamy, S., Gonzalez, V. D., Lorang, C. G., Bjornson, Z., Spitzer, M. H., Bodenmiller, B., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2015.020 · Cited by 596
High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome
Novaes, E., Drost, D. R., Farmerie, W. G., Pappas, G. J., Grattapaglia, D., Sederoff, R. R., & Kirst, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-312 · Cited by 493
RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries
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Aanes, H., Winata, C. L., Lin, C. H., Chen, J. P., Srinivasan, K. G., Lee, S. G. P., Lim, A. Y. M., Hajan, H. S., Collas, P., Bourque, G., et al. (2011) · Genome Research · doi:10.1101/gr.116012.110 · Cited by 285
Carew, M. E., Pettigrove, V. J., Metzeling, L., & Hoffmann, A. A. (2013) · Frontiers in Zoology · doi:10.1186/1742-9994-10-45 · Cited by 243
Microbial Communities of the Upper Respiratory Tract and Otitis Media in Children
Laufer, A. S., Metlay, J. P., Gent, J. F., Fennie, K. P., Kong, Y., & Pettigrew, M. M. (2011) · mBio · doi:10.1128/mbio.00245-10 · Cited by 224
Rungrassamee, W., Klanchui, A., Chaiyapechara, S., Maibunkaew, S., Tangphatsornruang, S., Jiravanichpaisal, P., & Karoonuthaisiri, N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0060802 · Cited by 179
“Furthermore, to enable an analysis of multiple samples in parallel within a single run, a barcode tag with a short unique nucleotide sequence was added to distinguish each sample [31].”
BackgroundMethodBastida, F., Torres, I. F., Hernández, T., & García, C. (2017) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2017.06.012 · Cited by 129
Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates
Ling, Z., Liu, X., Luo, Y., Yuan, L., Nelson, K. E., Wang, Y., Xiang, C., & Li, L. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-390 · Cited by 127
Metadata
- Authors
- Parameswaran, P., Jalili, R., Tao, L., Shokralla, S., Gharizadeh, B., Ronaghi, M., & Fire, A. Z.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-10
- Volume
- 35
- Issue
- 19
- Pages
- e130
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2102718644
- Cited by
- 344
- References
- 0
- FWCI
- 9.58
- Type
- journal article
- Language
- en
- Open access
- gold
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