Isis Pharmaceuticals (Nasdaq: ISIS) and Genzyme (Nasdaq: GENZ) have a clear path forward for their cholesterol drug mipomersen. Unfortunately, the Food and Drug Administration threw a fork in the road, and the companies will need to take two routes to a marketing approval.

Mipomersen has been tested in both homozygous familial hypercholesterolemia (HoFH) -- patients with two bad copies of genes that cause extremely high cholesterol levels -- and heterozygous familial hypercholesterolemia (HeFH), or those who have only one bad gene. The HoFH patients, who are fairly rare, are much sicker and usually end up with clogged arteries that result in heart attacks early in life.

Fortunately for Isis and Genzyme, there are a lot more HeFH patients than HoFH patients. Unfortunately, the larger potential treatment group means the FDA wants more data on mipomersen before it'll approve the drug for HeFH patients. The duo won't be able to file until after they run a 12-month trial in HeFH patients. The data for the HoFH patients looks like it's sufficient, although now that they're breaking up the two indications, it may take until the second half of the year to turn in the marketing application to the FDA.

Normally, one approval might be enough to gain some sales in the second indication. Doctors are allowed to prescribe drugs off label and might be willing to take the risk of prescribing it to HeFH patients even without the 12-month data. But given the small HoFH patient population, it seems likely that the companies will charge a fortune for mipomersen, which could limit reimbursement for off-label use.

Given the less-than-stellar side-effect profile and the fact that it's injected, I doubt mipomersen will ever compete against megablockbuster cholesterol drugs such as Pfizer's (NYSE: PFE) Lipitor or Merck's (NYSE: MRK) Vytorin. But it doesn't really have to; going after the FH patients who can't get their cholesterol under control with the current offerings should be enough to produce decent sales.

Investors just need to wait for Isis and Genzyme to finish their drug-development stroll down the FDA's newly cut path.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool has a disclosure policy.