Assessment of Clone Identity and Sequence Fidelity
Within a Commercially Distributed Subset of IMAGE Clones

R.G. Halgren, M.R. Fielden, C.J. Fong, and T.R. Zacharewski.
Department of Biochemistry & Molecular Biology
National Food Safety & Toxicology Center and
Institute for Environmental Toxicology
Michigan State University
East Lansing, Michigan 48824-1319 USA

This report documents the error rate in a commercially distributed subset of the IMAGE Consortium mouse cDNA clone collection. After isolation of plasmid DNA from 1189 bacterial stock cultures, only 62.2 percent were uncontaminated and contained cDNA inserts that had significant sequence identity to published data for the ordered clones.

An agarose gel electrophoresis prescreening strategy identified 361 stock cultures that appeared to contain two or more plasmid species. Isolation of individual colonies from these stocks demonstrated that 7.1 percent of the original 1189 stocks contained both a correct and an incorrect plasmid. 5.9 percent of the original 1189 stocks contained multiple, distinct, incorrect plasmids, indicating the likelihood of multiple contaminating events.

While only 739 of the stocks purchased contained the desired cDNA clone, agarose gel prescreening, colony isolation, and similarity searching of dbEST allowed for the identification of an additional 420 clones that would have otherwise been discarded. Considering the high error rate in this subset of the IMAGE cDNA clone set, the use of sequence verified clones for cDNA microarray construction is warranted.

When this is not possible, prescreening non-sequence verified clones with agarose gel electrophoresis provides an inexpensive and efficient method to eliminate contaminated clones from the probe set.

These data accompany a published manuscript entitled "An Assessment of Clone Identity and Sequence Fidelity Within Commercially Distributed Clones From the IMAGE Collection" Halgren, R.G., Fielden, M.R., Fong, C.J. and Zacharewski, T.R., Nucleic Acids Research, 29(2), 582-588, 2001. This article was featured in April 19 issue of Nature (Vol 410, 860-1, 2001. When the Chips are Down). All of the clones described in the manuscript have been provided to Research Genetics and are available from Research Genetics. Collaborations or other joint efforts using these data and clones are appropriate and encouraged. Please contact Tim Zacharewski for further information.

Ideally, all the data you would want is available here. However, should you find that you require additional data or other file formats, please do not hesitate to ask. Due to space constraints, image files for electrophoresis assays are not presented, although they are archived off-line. Files are presented in either MS Excel or HTML format. Clicking on an HTML formatted file will open the page in a new window. Please note that the Excel files are commented in the headers for each sheet.