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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
Published on: September 3, 2009
Abundant human DNA contamination identified in non-primate genome databases
Mark S Longo1, Michael J O'Neill, Rachel J O'Neill
1Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America.
Plos One
|March 2, 2011
Summary
Extensive human DNA contamination was found in public databases across diverse species, from bacteria to plants. This discovery necessitates caution in genomic research and re-sequencing efforts.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Routine screening of NCBI databases using human repetitive elements revealed unexpected nucleotide identity across various phyla.
- Previous studies have not extensively documented the extent of human sequence contamination in non-human genomic databases.
Purpose of the Study:
- To investigate and quantify the contamination of public DNA sequence databases with human genetic material.
- To identify the prevalence and scope of human sequence contamination in non-human species across major genomic databases.
Main Methods:
- Screened 2,749 non-primate public databases (NCBI, Ensembl, JGI, UCSC) using AluY, a primate-specific SINE element.
- Performed in-depth searches for sequences of human origin within non-human species' DNA sequences, genome assemblies, and trace archive reads.
Main Results:
- Found 492 out of 2,749 databases contaminated with human sequences.
- Contamination spans a wide range of species, including bacteria (B. cereus), plants (Z. mays), and fish (D. rerio), across most phyla.
- Human sequence contamination was identified in DNA sequences, genome assemblies, and trace archive reads.
Conclusions:
- The extensive contamination of human sequences in public genomic databases warrants significant caution for the scientific community.
- Researchers should be vigilant about potential human sequence contamination in future sequencing projects, including human re-sequencing efforts.
- Understanding the mechanisms of this contamination is crucial for improving data integrity in genomics.
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