Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones

This report documents the error rate in a commercially distributed subset o f the IMAGE Consortium mouse cDNA clone collection, After isolation of plas mid DNA from 1189 bacterial stock cultures, only 62.2% were uncontaminated and contained cDNA inserts that had significant sequence identity to publis hed data for the ordered clones. An agarose gel electrophoresis pre-screeni ng strategy identified 361 stock cultures that appeared to contain two or m ore plasmid species, Isolation of individual colonies from these stocks dem onstrated that 7.1% of the original 1189 stocks contained both a correct an d an incorrect plasmid, 5.9% of the original 1189 stocks contained multiple , distinct, incorrect plasmids, indicating the likelihood of multiple conta minating events, While only 739 of the stocks purchased contained the desir ed cDNA clone, agarose gel prescreening, colony isolation end similarity se arching 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 cl ones for cDNA microarray construction is warranted, When this is not possib le, pre-screening non-sequence verified clones with agarose gel electrophor esis provides an inexpensive and efficient method to eliminate contaminated clones from the probe set.