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Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
Open accessAbstract
Background: Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. Results: All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni , also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Conclusion: Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
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A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis
Andries, K., Verhasselt, P., Guillemont, J., Göhlmann, H. W. H., Neefs, J.-M., Winkler, H., Van Gestel, J., Timmerman, P., Zhu, M., Lee, E., et al. (2005) · Science · doi:10.1126/science.1106753 · Cited by 2,191 · cited 1×
“Background Continued improvement in sequencing quality, combined with increasingly sophisticated bioinformatic analysis of sequence data, has increased the relevance of whole genome sequencing to many fields of biological science including the pharmaceutical industry, agriculture, national defence and medicine [1].”
Genetic analyses from ancient DNA
Pääbo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., & Hofreiter, M. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.143214 · Cited by 1,333
Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M., & Pääbo, S. (2001) · Nature Reviews Genetics · doi:10.1038/35072071 · Cited by 781
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Advances in understanding cancer genomes through second-generation sequencing
Meyerson, M., Gabriel, S., & Getz, G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,116
Laboratory procedures to generate viral metagenomes
Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L., & Rohwer, F. (2009) · Nature Protocols · doi:10.1038/nprot.2009.10 · Cited by 599
A Bioinformatician's Guide to Metagenomics
Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K., & Hugenholtz, P. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00009-08 · Cited by 490
Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
Schlebusch, C. M., Skoglund, P., Sjödin, P., Gattepaille, L. M., Hernandez, D., Jay, F., Li, S., De Jongh, M., Singleton, A., Blum, M. G. B., et al. (2012) · Science · doi:10.1126/science.1227721 · Cited by 468
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
Pinto, A. J., & Raskin, L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043093 · Cited by 443
Metadata
- Authors
- Pinard, R., de Winter, A., Sarkis, G. J., Gerstein, M. B., Tartaro, K. R., Plant, R. N., Egholm, M., Rothberg, J. M., & Leamon, J. H.
- Venue
- BMC Genomics
- Published
- 2006-08-23
- Volume
- 7
- Issue
- 1
- Pages
- 216-216
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W2157450307
- Cited by
- 318
- References
- 3
- FWCI
- 6.75
- Type
- journal article
- Language
- en
- Open access
- gold
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- Pinard, R., de Winter, A., Sarkis, G. J., Gerstein, M. B., Tartaro, K. R., Plant, R. N., Egholm, M., Rothberg, J. M., & Leamon, J. H. (2006). Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics. https://doi.org/10.1186/1471-2164-7-216
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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