Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples


Targeted genomic enrichment followed by next-generation DNA sequencing has dramatically increased efficiency of mutation-discovery efforts. We describe a protocol for genomic enrichment of pooled barcoded samples in a single assay that increases experimental flexibility and efficiency. We screened 770 genes (1.4 megabases) in thirty N-ethyl-N-nitrosourea (ENU)-mutagenized rats and identified known variants at >96% sensitivity as well as new mutations at a false positive rate < 1 in 8 megabases.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type



Prices may be subject to local taxes which are calculated during checkout

Figure 1: Mutation discovery strategy.

Accession codes


Gene Expression Omnibus


  1. Mamanova, L. et al. Nat. Methods 7, 111–118 (2010).

    Article  CAS  Google Scholar 

  2. Henikoff, S., Till, B.J. & Comai, L. Plant Physiol. 135, 630–636 (2004).

    Article  CAS  Google Scholar 

  3. Stemple, D.L. Nat. Rev. Genet. 5, 145–150 (2004).

    Article  CAS  Google Scholar 

  4. van Boxtel, R. et al. Pharmacogenomics J. advance online publication, doi:10.1038/tpj.2010.44 (8 June 2010).

    Article  Google Scholar 

  5. Moens, C.B., Donn, T.M., Wolf-Saxon, E.R. & Ma, T.P. Brief. Funct. Genomics Proteomics 7, 454–459 (2008).

    Article  CAS  Google Scholar 

  6. Till, B.J., Burtner, C., Comai, L. & Henikoff, S. Nucleic Acids Res. 32, 2632–2641 (2004).

    Article  CAS  Google Scholar 

  7. Mashimo, T. et al. Nat. Genet. 40, 514–515 (2008).

    Article  CAS  Google Scholar 

  8. Gady, A.L. et al. Plant Methods 5, 13 (2009).

    Article  Google Scholar 

  9. Cuppen, E. et al. Genome Res. 17, 649–658 (2007).

    Article  CAS  Google Scholar 

  10. van Boxtel, R. et al. BMC Genomics 9, 460 (2008).

    Article  Google Scholar 

  11. Mokry, M. et al. Nucleic Acids Res. 38, e116 (2010).

    Article  Google Scholar 

  12. Hodges, E. et al. Nat. Protoc. 4, 960–974 (2009).

    Article  CAS  Google Scholar 

  13. Okou, D.T. et al. Ann. Hum. Genet. 73, 502–513 (2009).

    Article  CAS  Google Scholar 

  14. Hoischen, A. et al. Hum. Mutat. 31, 494–499 (2010).

    Article  Google Scholar 

  15. Li, H., Ruan, J. & Durbin, R. Genome Res. 18, 1851–1858 (2008).

    Article  CAS  Google Scholar 

Download references


This work was supported by funds from the Cancer Genomics Centre, the award “Exploiting natural and induced genetic variation in the laboratory rat” to E.C. from the European Heads of Research Councils and European Science Foundation European Young Investigator Award scheme and the EU FP7 integrated project Euratrans.

Author information

Authors and Affiliations



R.v.B., I.J.N., M.M. and E.C. designed the experiments. R.v.B. and P.T. performed rat ENU mutagenesis. M.M. performed library preparation and genomic enrichments. E.d.B. performed SOLiD sequencing. I.J.N. analyzed the data. R.v.B. performed capillary sequencing reconfirmation experiments. I.J.N. and E.C. wrote the manuscript.

Corresponding author

Correspondence to Edwin Cuppen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2 and Supplementary Tables 2–5 (PDF 561 kb)

Supplementary Table 1

List of rat genes targeted in the next-generation reverse genetic. (XLS 2071 kb)

Supplementary Table 6

Complete list of polymorphic positions identified in the next-generation reverse genetics screen. (XLS 112 kb)

Supplementary Software

Custom SNP filtering PERL script. (ZIP 3 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Nijman, I., Mokry, M., van Boxtel, R. et al. Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nat Methods 7, 913–915 (2010).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing