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Related Experiment Videos

Corruption of genomic databases with anomalous sequence.

E D Lamperti1, J M Kittelberger, T F Smith

  • 1Department of Neurology, Children's Hospital, Harvard Medical School, Boston, MA 02115.

Nucleic Acids Research
|June 11, 1992
PubMed
Summary
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Accidental DNA vector sequences are appearing in the GenBank database, impacting data accuracy. This contamination issue is growing, potentially compromising scientific research and database integrity.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • The GenBank database serves as a critical repository for genetic sequences.
  • Ensuring the accuracy and integrity of DNA sequence data is paramount for scientific research.
  • Vector DNA contamination in genomic databases has been a recognized, though historically minor, issue.

Purpose of the Study:

  • To investigate the extent and nature of accidental DNA vector sequence incorporation into eukaryotic GenBank entries.
  • To assess the increasing prevalence of this contamination.
  • To evaluate the potential impact on data interpretation and database management.

Main Methods:

  • Analysis of 20,000 eukaryotic sequences from GenBank Release 63.
  • Identification of DNA sequences matching known cloning and sequencing vectors.

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  • Examination of incorporation mechanisms, including simple errors, contamination, and unusual rearrangements.

    • Main Results:

    • Vector sequences were found in 0.23% of analyzed GenBank entries.
    • Incorporation varied from minor editing errors to large blocks of vector DNA.
    • Identities to vector sequences ranged from 94.8% to 96.8% in matching regions.
    • Evidence suggests the problem is increasing at a rate faster than database growth.

    Conclusions:

    • Accidental incorporation of vector DNA is a significant and growing issue in the GenBank database.
    • This contamination poses risks to the accurate interpretation of genetic data and impacts database utility.
    • The findings highlight the need for improved quality control measures in sequence databases.