Before you all jump to conclusions and start dreaming of buyouts, please understand. This has nothing to do with buyouts. This was an expected and almost necessary developement on the road to 108 approval.
AEZS-108 is a targeted drug, that is meant to attack cancer cells expressing LHRH receptors. In order to determine which patients will be best treated by 108, a rapid and fairly inexpensive test is needed to determine if a particular patient's endometrial, ovaria, bladder, or prostate tumor has these receptors in high concentrations. The current test is expensive and time consuming, and is not economically feasible for widespread use. As a result, AEZS has partnered with Ventana to develop a rapid test. This was totally expected. A recent NY Times article mentioned that the FDA has made this type of companion test almost a de facto requirement before approving highly targeted therapies. It just makes economic sense. Before Medicare and insurance companies will agree to pay for such expensive therapies, they want to make sure they have a high chance of success.
AEZS is only taking what is the logical next step in getting FDA approval for 108 by partnering to develop a companion test. The fact that Ventana, one of the worldwide leaders in this type of testing is a Roche affiliate is of no major consequence. It certainly does not mean that Roche is buying out the company at this point. In fact, I am willing to bet that the bigwigs at Roche had nothing to do with these partnership negotiations. I am sure it was all done by the Ventana people independently.
This is still important news, as it is one more step down the approval pathway. Unfortunately, for those dreaming of a buyout, I can only suggest you go back to sleep and continue dreaming.
Yosimi and Insidetrade,
This US PCAP patent issue you mention is not a loose end for AEZS in Europe and elsewhere that has, as mentioned, PCAP patents tied up to 2023. It would not be a concern anyway for Roche.
"Subsequent to quarter-end, on July 12, 2011, the European Patent Office granted a patent for the use of alkyl phosphocholines, and, more specifically for perifosine, in the preparation of a medicament for the treatment of benign and malignant tumors, prior to and/or during the treatment with approved antitumor antimetabolites including 5-FU ("fluorouracil") and capecitabine. This patent will expire on July 28, 2023."
Notice that European patent protection is not just the combination of P + CAP whereas the US patent application is specifically only for PCAP. This US constraint on P combinations could have ramifications conceivably (but not likely) mostly for KERX.
"Our composition of matter patent covering KRX-0401 (perifosine) expires in the second half of 2013 and we cannot assure you that we can obtain an extension"
Nonetheless, even thought the PCAP patent application in the US is still pending to the best of my knowledge, PCAP usage in the US is protected. Could there be an unexpected challenge from somewhere and the US application denied? I suppose so, but on what grounds? I do not see US PCAP patent protection as much of an issue for either company although IMO AEZS should have no concerns in the rest of the world.
If there were a challenge to the PCAP patent in the US, both companies would lose value of course, although AEZS would lose less comparatively. This patent issue is one of the main reasons from the get go that I preferred AEZS over KERX. Just keep in mind that PCAP patent protection in the US is on pretty solid grounds despite any concerns for excessive worriers like us about the remote possibility of the US PCAP application being turned down. About six months ago I wrote KERX about this concern and never got a reply.
If there even are US PCAP patent issues (I suspect there are not any meaningful ones), you can bet they would be too complex for lay people like us to understand. If there were an unexpected challenge it would almost cdertainly come from Roche. Just review the Mylan settlement with Roche to consider this argument seriously.
The Roche Xeloda patent expires in December 2013. That is the earliest predictable date that a generic version of Xeloda could become available. Roche would love to tie up as many Xeloda combinations as possible in order to extend its patent protection on Xeloda combinations. In a search I did months ago I found almost two dozen such combinations that Roche had tied up. You better believe Roche has a Pavlovian reflex response any time they think of the PCAP combination. Any concerns about the PCAP patent issue in the US would not be a concern to Roche.
Roche remains the most likely buyer of AEZS. IMO concerns about Quebec law or AEZS Bylaws preventing a takeover are over argued. I would bet that Roche attorneys have examined these issues carefully. The arguments that Roche would not make a tender offer because of Quebec law and AEZS Bylaws have made repeatedly on this M.B. Without going into specifics I think the arguments are specious. Again IMO patent issues would not be a concern to Roche. Nonetheless, because a friendly approach almost always works best, it would make sense for Roche to initiate collaboration with AEZS -- and collaboration with Roche is exactly what transpired with the Ventana deal.
I have just gone full circle in suggesting why the Ventana deal has meaningful ramifications vis a vis any patent concerns.
I understand the patent situation for PCAP. That's already been thoroughly explained and nicely reiterated by you. But I would think that a company interested in a buy out would want to fully control perifosine alone so that it can be more easily combined with other drugs for future indications without going through the patent process.
A single extension of the term of a patent may be obtained if the patent relates to the active ingredient of a human or animal drug product or a combination of such active ingredients, a medical device, a food additive or a color additive or to methods of manufacturing or using such products and the product is subject to regulation under the Food, Drug and Cosmetic Act. 
A patent relating to one of these regulated products is a candidate for an extension if the date of first marketing the product, or in the case of a process using recombinant DNA technology the first use of the process, was delayed as a result of regulatory review. Subject to a statutory maximum discussed below and subject to the applicant having been diligent in seeking regulatory approval, the extension shall be for the same period as marketing was delayed as a result of the regulatory review. 
The regulatory period is defined in different ways for the five different categories of product covered by this provision: (1) new drugs for human use, (2) new food or color additives, (3) new medical devices, (4) new animal drugs and (5) new veterinary biological products. The basis for the differences is that the approval procedures differ between these classes of products. By way of example, it may be noted that for new drugs for human use, the regulatory period is one half of the term starting on the date on which an investigational new drug exemption is granted, thereby permitting clinical testing in the United States, and ending on the date on which a request for marketing approval is filed plus the entire period during which the request for marketing approval is pending.  It may therefore be useful for those resident outside the United States to file an IND for a new drug earlier than might otherwise have been the case in order to maximize the benefits they may obtain from the law.
A petition for extension of the term of a patent must be filed within 60 days of the marketing approval being given and must be filed before the patent expires. 
Extensions of patents under the act are, however, subject to two types of limitation: a maximum duration of extension and a limitation on the scope of the patent during the extended period.
The limitations on the duration of the extension are twofold. First, the extension shall not result in the final expiration of the patent occurring more than 14 years after sale of the product is approved.  Second, the actual duration of the extension shall not exceed 5 years if the patent issued after the new law came into effect or no permitted clinical investigation prior to filing a formal request for approval of the new product was carried out before the new law came into effect.
The Ventana association announcement suggests to me that Roche is sniffing at the door. My guess is upper management is well aware of the association. Frankly, how could they not be if they have ever toyed with the idea of a buyout of AEZS? That would seem very unlikely to me. Management may even surmise that they can get a feel for another important member of the AEZS pipeline (i.e., 108), AEZS management and researchers before making a buyout offer. Now these thoughts are certainly speculations but I would not dismiss the announcement as having nothing whatsoever to do with a buyout down the road, especially when the association is with a Roche subsidiary. The collaboration may not be of major consequence although I suggest it is of some consequence. It is difficult for me to ignore the implications.