Guys, a few simple facts here, to clear up a bit of patent jargon that you have misunderstood. (Caveat: I do not know all the facts of the patents involved etc., so I am not making a call here on who will win the interference, or whether one or another of the involved patents is infringed by the other party. Please be careful when deciding infringement calls based on a summary in the press - that kind of statement often has little apparent relation to what the claims actually describe.)
An interference is declared when the PTO decides that there is overlapping material in the allowable claims of a patent application and those of either another application or an unexpired, issued patent. Often the PTO does not identify interfering applications at the right time to declare an interference. Since there are lots of reasons an applicant frequently prefers to have this settled in an interference rather than in court (technically literate PTO examiners as the decision makers, versus a jury that can't stand technical terms is just one of these), the parties involved often trigger the interference themselves. How? a device called "copying the claims." That means that the owner of the unissued application copies the claims of the issued patent. You can file claims in any words you like, including those used in someone else's patent claims, as long as the application you originally filed supports the material you are trying to claim. As long as the PTO agrees that AFFX in this case has an application that meets the patentability requirements for supporting those claims, the PTO has no choice but to hand the dispute over to the interference board. (Which has a several year backlog, so the PTO does not go out of its way to ID every potential interference.) In copying the claims, noone is saying that AFFX is admitting that INCY invented the subject matter first.
Cheers -
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