Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples

作者: Michael J. Strong , Guorong Xu , Lisa Morici , Sandra Splinter Bon-Durant , Melody Baddoo

DOI: 10.1371/JOURNAL.PPAT.1004437

关键词:

摘要: The high level of accuracy and sensitivity of next generation sequencing for quantifying genetic material across organismal boundaries gives it tremendous potential for pathogen …

参考文章(33)
Martin Laurence, Christos Hatzis, Douglas E. Brash, Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes PLoS ONE. ,vol. 9, pp. e97876- ,(2014) , 10.1371/JOURNAL.PONE.0097876
Michael J. Strong, Guorong Xu, Joseph Coco, Carl Baribault, Dass S. Vinay, Michelle R. Lacey, Amy L. Strong, Teresa A. Lehman, Michael B. Seddon, Zhen Lin, Monica Concha, Melody Baddoo, MaryBeth Ferris, Kenneth F. Swan, Deborah E. Sullivan, Matthew E. Burow, Christopher M. Taylor, Erik K. Flemington, Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy PLoS Pathogens. ,vol. 9, pp. e1003341- ,(2013) , 10.1371/JOURNAL.PPAT.1003341
Tuuli Lappalainen, , Michael Sammeth, Marc R. Friedländer, Peter A. C. ‘t Hoen, Jean Monlong, Manuel A. Rivas, Mar Gonzàlez-Porta, Natalja Kurbatova, Thasso Griebel, Pedro G. Ferreira, Matthias Barann, Thomas Wieland, Liliana Greger, Maarten van Iterson, Jonas Almlöf, Paolo Ribeca, Irina Pulyakhina, Daniela Esser, Thomas Giger, Andrew Tikhonov, Marc Sultan, Gabrielle Bertier, Daniel G. MacArthur, Monkol Lek, Esther Lizano, Henk P. J. Buermans, Ismael Padioleau, Thomas Schwarzmayr, Olof Karlberg, Halit Ongen, Helena Kilpinen, Sergi Beltran, Marta Gut, Katja Kahlem, Vyacheslav Amstislavskiy, Oliver Stegle, Matti Pirinen, Stephen B. Montgomery, Peter Donnelly, Mark I. McCarthy, Paul Flicek, Tim M. Strom, Hans Lehrach, Stefan Schreiber, Ralf Sudbrak, Ángel Carracedo, Stylianos E. Antonarakis, Robert Häsler, Ann-Christine Syvänen, Gert-Jan van Ommen, Alvis Brazma, Thomas Meitinger, Philip Rosenstiel, Roderic Guigó, Ivo G. Gut, Xavier Estivill, Emmanouil T. Dermitzakis, Transcriptome and genome sequencing uncovers functional variation in humans Nature. ,vol. 501, pp. 506- 511 ,(2013) , 10.1038/NATURE12531
K. D. Pruitt, T. Tatusova, G. R. Brown, D. R. Maglott, NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy Nucleic Acids Research. ,vol. 40, pp. 130- 135 ,(2012) , 10.1093/NAR/GKR1079
B. Xu, N. Zhi, G. Hu, Z. Wan, X. Zheng, X. Liu, S. Wong, S. Kajigaya, K. Zhao, Q. Mao, N. S. Young, Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing Proceedings of the National Academy of Sciences of the United States of America. ,vol. 110, pp. 10264- 10269 ,(2013) , 10.1073/PNAS.1303744110
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
N. Ohta, M. Sanders, A. Newton, Poly(adenylic acid) sequences in the RNA of Caulobacter crescenus. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 72, pp. 2343- 2346 ,(1975) , 10.1073/PNAS.72.6.2343
Peter AC't Hoen, Marc R Friedländer, Jonas Almlöf, Michael Sammeth, Irina Pulyakhina, Seyed Yahya Anvar, Jeroen FJ Laros, Henk PJ Buermans, Olof Karlberg, Mathias Brännvall, Gert-Jan B van Ommen, Xavier Estivill, Roderic Guigó, Ann-Christine Syvänen, Ivo G Gut, Emmanouil T Dermitzakis, Stylianos E Antonarakis, Alvis Brazma, Paul Flicek, Stefan Schreiber, Philip Rosenstiel, Thomas Meitinger, Tim M Strom, Hans Lehrach, Ralf Sudbrak, Angel Carracedo, Maarten Van Iterson, Jean Monlong, Esther Lizano, Gabrielle Bertier, Pedro G Ferreira, Paolo Ribeca, Thasso Griebel, Sergi Beltran, Marta Gut, Katja Kahlem, Tuuli Lappalainen, Thomas Giger, Halit Ongen, Ismael Padioleau, Helena Kilpinen, Mar Gonzàlez-Porta, Natalja Kurbatova, Andrew Tikhonov, Liliana Greger, Matthias Barann, Daniela Esser, Robert Häsler, Thomas Wieland, Thomas Schwarzmayr, Marc Sultan, Vyacheslav Amstislavskiy, Johan T Den Dunnen, GEUVADIS Consortium, Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories Nature Biotechnology. ,vol. 31, pp. 1015- 1022 ,(2013) , 10.1038/NBT.2702
N. Zhi, G. Hu, S. Wong, K. Zhao, Q. Mao, N. S. Young, Reply to Naccache et al: Viral sequences of NIH-CQV virus, a contamination of DNA extraction method Proceedings of the National Academy of Sciences of the United States of America. ,vol. 111, ,(2014) , 10.1073/PNAS.1318965111
Guorong Xu, Michael J. Strong, Michelle R. Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor, RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets PLoS ONE. ,vol. 9, pp. e89445- ,(2014) , 10.1371/JOURNAL.PONE.0089445