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NCBI Appeased; Affy Takes Heat for Faults in Mouse Arrays

NEW YORK, March 9 – David Lipman, director of the National Center for Biotechnology Information, said Friday that he was looking forward to resuming a strong working relationship with Affymetrix after the company assured him that it was to blame for the recent problem with their U74 mouse arrays. 

“As far as I’m concerned this is resolved,” Lipman said. “They’ve been explicit that they made an error dealing with known ambiguities in the database.”

On Thursday Lipman said he felt that Affymetrix’s recent filing with the US Securities and Exchange Commission falsely accused the NCBI of having an error in its database that caused the fault in their arrays. In fact, it was a well-known inconsistency in the UniGene database that resulted in Affymetrix selecting sequence information from the wrong strand of DNA. 

The SEC document became the basis for several stories on the matter, including articles that appeared in the Wall Street Journal and on GenomeWeb.

In response to his concerns, Lipman said Affymetrix had indicated it would clarify the matter in a future SEC filing. An Affymetrix spokeswoman said she could not comment on the contents of any future regulatory documents.

Lipman noted that Affymetrix, a strong supporter of public databases, has historically provided the NCBI with useful feedback.

“They’ve been one of the best companies we’ve had to deal with,” Lipman said.

Affymetrix has said it would continue to support the public databases in the future and in no way intended to put the blame on the NCBI.
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