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NCBI Fires Back at Affy Claim that Public Mouse Data was Corrupted

NEW YORK, March 8 – Affymetrix’s efforts to stem any negative fallout from the news that their mouse arrays contained faulty sequence data seemed to spin out of control on Thursday as the National Center for Biotechnology Information said that the company falsely accused them of causing the problem.

In response to the statement Affymetrix filed Wednesday with the US Securities and Exchange Commission, which indicated that the NCBI sequence data it used contained errors, David Lipman, director of the NCBI, said Affymetrix had told him that they had made a mistake while telling the SEC that the problem was with the NCBI.

“We’ve not been informed by Affymetrix of a database problem. We were told by them that they made an error,” David Lipman, director of NCBI, told GenomeWeb. “Unless something is pointed out that indicates there’s an error in the database, I think they should point our the error in their statement.”

In the SEC statement he was referring to, Affymetrix stated that: “The company has recently discovered errors in the UniGene U74 database build that was used in the design of the Murine Genome U74 Set of GeneChip arrays.”

On Thursday, following calls for clarification, Affymetrix executives said they were not pointing the finger at NCBI.

“Our position is certainly not that NCBI is at fault,” said Thane Kreiner, vice president of corporate operations and communications. “We’d like to work with David to discuss how we can resolve this.”

Affymetrix acknowledged that they misinterpreted the data based on ambiguities about the direction of the ESTs. The problem stems from the fact that different contributors submit data in different ways, both Affymetrix and the NCBI said. As a result, the orientation of the data may not be consistent.

Lipman, who admitted that ambiguities do exist in the database, noted that they have existed since the database was founded. But Lipman said he did not know whether the ambiguity was officially documented in the database.

Kreiner added that today more advanced tools, such as those Affymetrix acquired when it bought Neomorphic, would help the company to better interpret the data and catch inconsistencies.

Affymetrix, which has seen its share price drop 14.8 percent over the past two trading sessions to 47 11/16 as of Thursday’s close, has been trying to temper the damage by assuring customers that new arrays would be sent to them within the next six weeks.

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