Vertex Pharmaceuticals' (Nasdaq: VRTX) VX-770 clearly helps the subset of cystic fibrosis patients with a rare mutation.

The combination of VX-770 and VX-809 in patients with the most common mutation? That's yet to be determined.

Vertex released phase 2 data today on the combination treatment in patients with the F508del mutation that occurs in nearly 90% of cystic fibrosis patients. The top-line results look like a success: At the largest dose, the combination treatment reduced sweat chloride levels by a statistically significant margin.

But no one actually cares about the level of chloride in cystic fibrosis patients' sweat. It's just a biomarker for the ability to remove salt from patients' lungs. The salt causes a buildup of mucus, which inhibits lung function.

The worry -- and the reason Vertex's shares are down substantially today -- is that the 9.1 millimoles-per-liter decrease in sweat chloride seen with the combination therapy might not be clinically meaningful. The FDA will want to see improvements in lung functions in a phase 3 trial, and a 9.1 mmol/L drop might not be enough to facilitate that.

Working in Vertex's favor, the current trial tested only the combination treatment for one week. The sweat chloride levels went down from a 4.2 mmol/L drop after two weeks on VX-809 alone to a 9.1 mmol/L drop after the addition of VX-770 for a week.

The bar may be fairly low in how much improvement in lung function the combination treatment really needs to show. Current cystic fibrosis treatments -- antibiotics Tobi from Novartis (NYSE: NVS) and Cayston from Gilead Sciences' (Nasdaq: GILD) -- only treat the symptoms.

Vertex plans to continue the phase 2 trial with higher and longer doses of the combination treatment. The additional dosing won't start until the fourth quarter, so expect data sometime next year.

There's little doubt VX-770 will be approved as a monotherapy, but the mutation it treats, G551D, occurs in just 4% of cystic fibrosis patients. The market to treat patients with F508del mutation is an order of magnitude larger.

In the short term, Vertex's hepatitis C battle with Merck (NYSE: MRK) will drive its valuation, but in the longer term, the number of patients Vertex can address with its cystic fibrosis drugs will play a major role in its valuation.

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