The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
Open accessAbstract
As researchers begin probing deep coverage sequencing data for increasingly rare mutations and subclonal events, the fidelity of next generation sequencing (NGS) laboratory methods will become increasingly critical. Although error rates for sequencing and polymerase chain reaction (PCR) are well documented, the effects that DNA extraction and other library preparation steps could have on downstream sequence integrity have not been thoroughly evaluated. Here, we describe the discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data. Characteristics such as sequencer read orientation and presence in both tumor and normal samples strongly indicated a non-biological mechanism. We identified the source as oxidation of DNA during acoustic shearing in samples containing reactive contaminants from the extraction process. We show generation of 8-oxoguanine (8-oxoG) lesions during DNA shearing, present analysis tools to detect oxidation in sequencing data and suggest methods to reduce DNA oxidation through the introduction of antioxidants. Further, informatics methods are presented to confidently filter these artifacts from sequencing data sets. Though only seen in a low percentage of reads in affected samples, such artifacts could have profoundly deleterious effects on the ability to confidently call rare mutations, and eliminating other possible sources of artifacts should become a priority for the research community.
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
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Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774
Instability and decay of the primary structure of DNA
Lindahl, T. (1993) · Nature · doi:10.1038/362709a0 · Cited by 5,679
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
Puente, X. S., Pinyol, M., Quesada, V., Conde, L., Ordóñez, G. R., Villamor, N., Escaramis, G., Jares, P., Beà, S., González-Díaz, M., et al. (2011) · Nature · doi:10.1038/nature10113 · Cited by 1,514
Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433
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Chapman, M. A., Lawrence, M. S., Keats, J. J., Cibulskis, K., Sougnez, C., Schinzel, A. C., Harview, C. L., Brunet, J.-P., Ahmann, G. J., Adli, M., et al. (2011) · Nature · doi:10.1038/nature09837 · Cited by 1,433
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Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayir, A., Bakkaloğlu, A., Özen, S., Sanjad, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,329
Forshew, T., Murtaza, M., Parkinson, C., Gale, D., Tsui, D. W. Y., Kaper, F., Dawson, S.-J., Piskorz, A. M., Jimenez-Linan, M., Bentley, D., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003726 · Cited by 1,297
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Wang, L., Lawrence, M. S., Wan, Y., Stojanov, P., Sougnez, C., Stevenson, K., Werner, L., Sivachenko, A., DeLuca, D. S., Zhang, L., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1109016 · Cited by 1,080
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Metadata
- Authors
- Costello, M., Pugh, T. J., Fennell, T. J., Stewart, C., Lichtenstein, L., Meldrim, J. C., Fostel, J. L., Friedrich, D. C., Perrin, D., Dionne, D., Kim, S., Gabriel, S. B., Lander, E. S., Fisher, S., & Getz, G.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-01-07
- Volume
- 41
- Issue
- 6
- Pages
- e67-e67
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2107356675
- Cited by
- 522
- References
- 44
- FWCI
- 8.61
- Type
- journal article
- Language
- en
- Open access
- gold
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- Costello, M., Pugh, T. J., Fennell, T. J., Stewart, C., Lichtenstein, L., Meldrim, J. C., Fostel, J. L., Friedrich, D. C., Perrin, D., Dionne, D., Kim, S., Gabriel, S. B., Lander, E. S., Fisher, S., & Getz, G. (2013). Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Research. https://doi.org/10.1093/nar/gks1443
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