NEW YORK, March 7 - After disclosing earlier that its U74 mouse arrays contain incorrect sequence information, Affymetrix said late Wednesday it expected to begin shipping customers free replacement chips in six weeks.
In the mean time, Affymetrix said it plans to send customers a CD-ROM that pinpoints the affected sequence on each array and provides them with bioinformatics tools that allow re-analysis of data generated from the original U74 chips, said Thane Kreiner, Affymetrix's vice president of corporate operations and communications.
"We want to provide customers with software analysis tools that allow them to go back, take already-generated data and remove all data generated by non-functioning probe sets," Kreiner said.
The U74 Array consists of three chips, A, B, and C. About 25 percent of the probes on chips A and B, and about 60 percent of the probes on chip C are non-functional, Kreiner said. The C chips are affected more substantially, Kreiner said, because they contain mostly ESTs, the primary target of the incorrectly assigned sequence directionality problem. Most of the probes on the A and B chips are full-length genes.
The replacement chips, which Affy is currently designing, will contain all of the original functional sequence, will have the non-functional sequence removed, and will contain functional replacements for this sequence when the company can provide it.
The errors in the chips derive from sequence information that was input into the publicly available UniGene sequence database with the directionality reversed. Affymetrix identified this error two weeks ago using bioinformatics tools provided by its new subsidiary Neomorphic. The company disclosed this information about the arrays in an 8-K statement filed with the Securities and Exchange Commission early Wednesday.
"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," Affymetrix wrote in the filing. "As a result, the company has begun the redesign of these arrays and has initiated discussions with its affected customers to address their individual needs."
Over the past two weeks, Affymetrix's product manager has talked to a number of the company's customers of the U74 Mouse arrays in order to figure out how to rectify the problem. Earlier, the company considered issuing new chips with only the replacement for the defective sequence, but customers said they wanted whole arrays, Kreiner said.
In the SEC filing on the matter, the company said replacement of the chips could cost as much as $4 million. "But this was calculated as a worst case scenario," said Kreiner. He said the specific financial impact of rectifying this error would not be known immediately, but in the SEC filing, the company stated, "sales of the Murine Genome U74 set of arrays may be impacted."
"Meanwhile, Affymetrix is employing the Neomorphic sequence analysis tools to avoid similar mistakes in the future," Kreiner said. "We're committed to analyzing and monitoring the public domain databases and getting them cleaned up."
The company is planning to release a revised set of human genome arrays in the second half of this year, using the completed draft sequence of the human genome. Affy will also provide a new mouse set in nine to twelve months based on sequence from the mouse sequencing consortium, in which it participates.
Affymetrix said its $4 million estimated costs in replacing the arrays was not final, and that depending on the outcome of its financial estimation, it might be required to take out additional product warranty accruals for the fourth quarter of 2000 and the first quarter of 2001