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Caenorhabditis elegans mutant allele identification by whole-genome sequencing

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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Figure 1: Variants found in whole-genome sequence analysis.
Figure 2: Physical location of the lsy-12 locus and its lesions.

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

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Correspondence to Itsik Pe'er or Oliver Hobert.

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Supplementary Tables 1–4 , Supplementary Methods (PDF 460 kb)

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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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