Because it had initiated a phase 3 trial for its cholesterol-lowering drug, mipomersen, I figured that Isis Pharmaceuticals (Nasdaq: ISIS) would wait until after the phase 3 results were announced before deciding on a partner. But with the offer it received from Genzyme (Nasdaq: GENZ), how could it not accept?

The deal announced on Monday includes a $325 million up-front payment to Isis -- including purchasing 5 million shares of Isis -- and more than $1.5 billion in potential development, regulatory, and sales milestone payments. That's some serious cash being thrown around.

Isis didn't even have to give up the farm to get it. The company was able to retain a 30% revenue share of the drug that goes gradually up to 50% until sales surpass $2 billion. Genzyme does get rights to any backup drugs developed using the same target, as well as preferential treatment for any drugs Isis develops for "CNS and certain rare diseases." With a partner that generous, I'd give them preferential treatment as well.

The companies are hoping to file a marketing application with the FDA in 2009 for patients with familial hypercholesterolemia (FH), a rare genetic mutation that causes ultra-high cholesterol levels. From there, the two plan to move the drug into a more general population of patients who aren't responding to their current treatment. The drug is injected, so it's unlikely that it will ever compete against statins such as Pfizer's (NYSE: PFE) Lipitor or Merck's (NYSE: MRK) Zocor, which are taken orally.

As if its partnerships with Novartis (NYSE: NVS) and Johnson & Johnson (NYSE: JNJ), among others, weren't enough of a sign that Isis' RNA antisense drugs are sought after, there were reportedly more than 10 other companies vying to get the rights to mipomersen. Even if Genzyme wasn't offering the largest upfront payment, the company was probably a good choice, since it has loads of experience with drugs for unmet medical needs.

Then again, that experience probably helped it know how much it can get away with charging for the drug, so perhaps this deal isn't as overblown as it sounds. I guess we'll all find out in 2010 or so.

More Foolishness on DNA's long lost cousin:

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. Pfizer is a pick of the Inside Value newsletter. Johnson & Johnson is a selection of the Income Investor newsletter. The Fool has a disclosure policy.