A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits

Nucleic Acids Research

Volumn 43, Issue 22, 2015, Pages

  Karamitros, Timokratis ^a   Magiorkinis, Gkikas ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GENOMIC DNA;

ARTICLE; BACTERIAL STRAIN; BIOTINYLATION; CONTROLLED STUDY; ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI; GENE SEQUENCE; GENE TARGETING; MOLECULAR LIBRARY; NEXT GENERATION SEQUENCING; NONHUMAN; OPERON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS GENOME; DNA SEQUENCE; EVALUATION STUDY; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; RNA GENE;

BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI; GENE LIBRARY; GENES, RRNA; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OPERON; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84964599878     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv773     Document Type: Article

References (19)

1. Kasianowicz, J.J., Brandin, E., Branton, D. and Deamer, D.W. (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A., 93, 13770-13773.
2. Branton, D., Deamer, D.W., Marziali, A., Bayley, H., Benner, S.A., Butler, T., Di Ventra, M., Garaj, S., Hibbs, A., Huang, X. et al. (2008) The potential and challenges of nanopore sequencing. Nat. Biotechnol., 26, 1146-1153.
3. Stoddart, D., Heron, A.J., Mikhailova, E., Maglia, G. and Bayley, H. (2009) Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore. Proc. Natl. Acad. Sci. U. S. A., 106, 7702-7707.
4. Cherf, G.M., Lieberman, K.R., Rashid, H., Lam, C.E., Karplus, K. and Akeson, M. (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat. Biotechnol., 30, 344-348.
5. Ashton, P.M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., Wain, J. and O'Grady, J. (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol., 33, 296-300.
6. Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., Kumar, A., Howard, E., Shendure, J. and Turner, D.J. (2010) Target-enrichment strategies for next-generation sequencing. Nat. Methods, 7, 111-118.
7. Briggs, A.W., Good, J.M., Green, R.E., Krause, J., Maricic, T., Stenzel, U., Lalueza-Fox, C., Rudan, P., Brajkovic, D., Kucan, Z. et al. (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science, 325, 318-321.
8. Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M.N., Smith, S.W., Middle, C.M., Rodesch, M.J., Albert, T.J., Hannon, G.J. et al. (2007) Genome-wide in situ exon capture for selective resequencing. Nat. Genet., 39, 1522-1527.
9. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C. et al. (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol., 27, 182-189.
10. Maricic, T., Whitten, M. and Paabo, S. (2010) Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PloS One, 5, e14004.
11. Duncavage, E.J., Magrini, V., Becker, N., Armstrong, J.R., Demeter, R.T., Wylie, T., Abel, H.J. and Pfeifer, J.D. (2011) Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. J. Mol. Diag., 13, 325-333.
12. Xing, M., Shen, H., Zhao, W., Liu, Y., Du, Y., Yu, Z. and Chen, X. (2011) dsDNA-coated quantum dots. Biotechniques, 50, 259-261.
13. Quail, M.A., Smith, M., Coupland, P., Otto, T.D., Harris, S.R., Connor, T.R., Bertoni, A., Swerdlow, H.P. and Gu, Y. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics, 13, e341.
14. Hedges, D.J., Guettouche, T., Yang, S., Bademci, G., Diaz, A., Andersen, A., Hulme, W.F., Linker, S., Mehta, A., Edwards, Y.J. et al. (2011) Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PloS One, 6, e18595.
15. Caruccio, N. (2011) Preparation of next-generation sequencing libraries using Nextera technology: simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods Mol. Biol., 733, 241-255.
16. Picelli, S., Bjorklund, A.K., Reinius, B., Sagasser, S., Winberg, G. and Sandberg, R. (2014) Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res., 24, 2033-2040.
17. Marine, R., Polson, S.W., Ravel, J., Hatfull, G., Russell, D., Sullivan, M., Syed, F., Dumas, M. and Wommack, K.E. (2011) Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl. Environ. Microbiol., 77, 8071-8079.
18. Tsangaras, K., Wales, N., Sicheritz-Ponten, T., Rasmussen, S., Michaux, J., Ishida, Y., Morand, S., Kampmann, M.L., Gilbert, M.T. and Greenwood, A.D. (2014) Hybridization capture using short PCR products enriches small genomes by capturing flanking sequences (CapFlank). PloS One, 9, e109101.
19. Quick, J., Quinlan, A.R. and Loman, N.J. (2014) A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer. Gigascience, 3, e22.