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Affymetrix Replacement Mouse Chips Arrive, But Some Users Demand More


As the promised replacements for Affymetrix’s defective batch of U74 mouse arrays arrive at labs around the world, some customers are now demanding to be compensated with additional reagents to make up for their lost time and expense.

“I’ve spoken with a number of people in our field who believe the one-to-one replacement [of chips] is not fair,” said J. Perren Cobb, director of the injury genomics group at Washington University-St. Louis. “It doesn’t replace the reagents or the tissue samples or all the work that went into generating the data from these chips.”

Cobb said a project in his lab that uses U74 chips has been delayed a month due to the need to replace the arrays.

Affymetrix disclosed in early March that its three-chip U74 murine set contained incorrect sequence on 25 to 60 percent of the genes, and told customers it would ship replacements within six weeks.

Most researchers report they have already received the replacement arrays for chip A, and many are now receiving chips B and C version 2, which Affymetrix said it began shipping several weeks ago. “The replacement program is progressing on schedule,” said Anne Bowdidge, Affymetrix’s director of investor relations.

Chandi Griffin, director of the Molecular Biology Core Laboratory at the University of California, San Francisco, said these replacements so far have been problem-free, but, like Cobb, Griffin would like more than chips in return for the inconvenience.

“With the discounts in academia, which are the norm now, there comes a point when the cost of the sample is actually equal or greater than the cost of the array itself,” said Griffin. “To just replace the array is partial payment.”

Affymetrix sells the Enzo BioArray HighYield RNA transcript labeling kit, as well as the Hybridization Control Kit for GeneChip arrays. Griffin suggested that the company give users the option of receiving free replacement kits as well as arrays.

But Affymetrix said it has no plans to offer additional compensation. Bowdidge pointed out that Affymetrix chose to replace the chips even though customers had already generated valuable data from experiments with the chips.

“The decision to offer a one for one replacement is a demonstration of our commitment to our customers to provide the highest standards of quality across our entire product line,” Bowdidge said.

Andrew Brooks, director of the Functional Genomics Center at the University of Rochester Medical Center, concurred with this sentiment, noting that many researchers are using the replacement arrays to run new experiments.

“If researchers choose to use the replacements Affymetrix is giving them to run a complete biological replicate, for 90 percent of the array that adds statistical power to the analysis,” Brooks said. “There’s no reason that Affymetrix has to pay for that.”

Brooks also said that re-running experiments originally performed on the defective slides requires little additional time or effort.

“If all people want to do is recover the data from the defective probe sets, all they have to do is pull their hybridization cocktails out of the freezer and run them over the replacement arrays,” Brooks said. “If people have not saved their biological materials that’s their problem.”

Meanwhile, Cobb said his lab was considering other options. “We are actually pursuing some of Affymetrix’s competition,” he said.


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