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SNPs matter: impact on detection of differential expression

Nature Methods volume 4, pages 679–680 (2007)Cite this article

To the editor:

With the recent completion of the Perlegen–US National Institute of Environmental Health Sciences mouse resequencing project1, which adds 8 million single nucleotide polymorphisms (SNPs) to the more than 2 million SNPs already in the public databases, the genome-wide knowledge of variation among 16 of the most widely used mouse strains has increased dramatically. Given the proliferation of mouse genetic models (for example, knockout and transgenic models, selectively bred lines, heterogeneous stocks derived from standard inbred strains as well as wild mice) and the recent insurgence of sequence and microarray data using these models, we are now in a position to determine the impact of naturally occurring genetic polymorphisms on hybridization-based techniques.

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Figure 1: Acyp2 is an example of a false negative induced by SNPs.

References

  1. Frazer, K.A. et al. Genome Res. 14, 1493–1500 (2004).

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Acknowledgements

Supported by US National Institutes of Health grants AA010760, DA05228 and AA011114, and a Department of Veterans Affairs Merit Award.

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Authors and Affiliations

  1. Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, John K Belknap, Robert Hitzemann & Kari J Buck

  2. Portland Alcohol Research Center, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, Shannon K McWeeney, John K Belknap, Robert Hitzemann & Kari J Buck

  3. Division of Biostatistics, Oregon Health Sciences University Cancer Institute, Oregon Clinical and Translational Research Institute, Public Health and Prevention Medicine, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Shannon K McWeeney

  4. Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, 97239, Oregon, USA

    Sandra T Peters

  5. Portland Veterans Affairs Medical Center, 3710 SW US Veterans Hospital Road, Portland, 97239, Oregon, USA

    Nicole A R Walter, John K Belknap, Robert Hitzemann & Kari J Buck

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  1. Nicole A R Walter
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  2. Shannon K McWeeney
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  6. Kari J Buck
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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Tables 1–3, Supplementary Methods (PDF 221 kb)

Supplementary Data 1

SNP Mask file for the Affymetrix MOE 430 2.0 array (Mas 5.0 format) which incorporates all known SNPs between the B6 and D2 strains at the time of publication. (TXT 106 kb)

Supplementary Data 2

SNP Mask file for the Affymetrix MOE 430 2.0 array (RMA format) which incorporates all known SNPs between the B6 and D2 strains at the time of publication. (TXT 228 kb)

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Walter, N., McWeeney, S., Peters, S. et al. SNPs matter: impact on detection of differential expression. Nat Methods 4, 679–680 (2007). https://doi.org/10.1038/nmeth0907-679

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