Caenorhabditis elegans mutant allele identification by whole-genome sequencing (original) (raw)

Nature Methods volume 5, pages 865–867 (2008)Cite this article

Abstract

Identification of the molecular lesion in Caenorhabditis elegans mutants isolated through forward genetic screens usually involves time-consuming genetic mapping. We used Illumina deep sequencing technology to sequence a complete, mutant C. elegans genome and thus pinpointed a single-nucleotide mutation in the genome that affects a neuronal cell fate decision. This constitutes a proof-of-principle for using whole-genome sequencing to analyze C. elegans mutants.

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References

  1. Brenner, S. Genetics 77, 71–94 (1974).
    CAS PubMed PubMed Central Google Scholar
  2. Sarin, S. et al. Genetics 176, 2109–2130 (2007).
    Article CAS PubMed PubMed Central Google Scholar
  3. Davis, M.W. et al. BMC Genomics 6, 118 (2005).
    Article PubMed PubMed Central Google Scholar
  4. Bentley, D.R. Curr. Opin. Genet. Dev. 16, 545–552 (2006).
    Article CAS PubMed Google Scholar
  5. Chang, S., Johnston, R.J. Jr. & Hobert, O. Genes Dev. 17, 2123–2137 (2003).
    Article CAS PubMed PubMed Central Google Scholar
  6. Hillier, L.W. et al. Nat. Methods 5, 183–188 (2008).
    Article CAS PubMed Google Scholar
  7. Lander, E.S. & Waterman, M.S. Genomics 2, 231–1239 (1988).
    Article CAS PubMed Google Scholar

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Acknowledgements

We thank C.T. Lawley (Illumina, Inc.) for generously producing the paired-end read data described in the manuscript, Q. Chen for performing microinjection, Hobert lab members for comments on the manuscript and the Caenorhabditis Genetics Center for providing the N2 strain. This work was funded by the Howard Hughes Medical Institute, the Muscular Dystrophy Association and the US National Institutes of Health (R01NS039996-05; R01NS050266-03 to O.H., F31 predoctoral grant NS054540-01 to S.S. and U54 CA121852-03 to I.P.).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, 701 W. 168th Street, New York, 10032, New York, USA
    Sumeet Sarin, M Maggie O'Meara & Oliver Hobert
  2. Department of Computer Science, Columbia University, 1214 Amsterdeam Avenue, New York, New York, 10027, USA
    Snehit Prabhu & Itsik Pe'er

Authors

  1. Sumeet Sarin
  2. Snehit Prabhu
  3. M Maggie O'Meara
  4. Itsik Pe'er
  5. Oliver Hobert

Contributions

S.S. isolated and mapped lsy-12(ot177), performed the manual resequencing analysis and the RNAi analysis; S.P. performed the bioinformatic analysis; I.P. designed, performed and supervised the bioinformatic analysis; M.M.O. performed complementation tests and rescue analysis; and O.H. initiated and supervised the project and wrote the paper.

Corresponding authors

Correspondence toItsik Pe'er or Oliver Hobert.

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Sarin, S., Prabhu, S., O'Meara, M. et al. Caenorhabditis elegans mutant allele identification by whole-genome sequencing.Nat Methods 5, 865–867 (2008). https://doi.org/10.1038/nmeth.1249

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