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Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?

Nature Biotechnology volume 24, pages 1068–1070 (2006)Cite this article

To the editor:

Single-nucleotide polymorphisms (SNPs) are the most frequent type of human genetic variation. They are the major basis of our phenotypic individuality, particularly with respect to heritable differences in disease susceptibility. Large collections of mapped SNPs, public and private, are powerful tools for genetic studies1. The most comprehensive public SNP database, dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP), currently contains more than 12 million human SNPs (version 126). This wealth of data is extensively used by a broad community, including clinical, experimental and computational scientists, for both locus-specific and genome-wide studies. Therefore, the quality and completeness of dbSNP is of paramount importance and a recent meta-analysis of four confirmation studies estimated a false-positive rate of ∼15–17%2.

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Figure 1: RefSNPs and sequence confidence.

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Author information

Authors and Affiliations

  1. Genome Analysis, Leibniz Institute for Age Research–Fritz Lipmann Institute, Beutenbergstr. 11, Jena, 07745, Germany

    Matthias Platzer, Karol Szafranski, Niels Jahn & Klaus Huse

  2. Institute of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, Freiburg, 79110, Germany

    Michael Hiller & Rolf Backofen

  3. Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstr. 12, Kiel, 24105, Germany

    Jochen Hampe & Stefan Schreiber

Authors
  1. Matthias Platzer
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  2. Michael Hiller
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  3. Karol Szafranski
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  4. Niels Jahn
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  5. Jochen Hampe
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  7. Rolf Backofen
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  8. Klaus Huse
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Supplementary information

Supplementary Table 1

Error estimation for trace data supported RefSNPs at splice acceptor position -2. (PDF 33 kb)

Supplementary Table 2

Error estimation for trace data supported RefSNPs at splice acceptor position -1. (PDF 39 kb)

Supplementary Table 3

Error estimation for trace data supported RefSNPs at splice acceptor position +1. (PDF 36 kb)

Supplementary Notes (PDF 51 kb)

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Platzer, M., Hiller, M., Szafranski, K. et al. Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?. Nat Biotechnol 24, 1068–1070 (2006). https://doi.org/10.1038/nbt0906-1068b

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