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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Fool contributor Brian Orelli holds no position in any company mentioned. See his holdings and a short bio. Motley Fool newsletter services have recommended buying shares of Novartis, Vertex Pharmaceuticals, and Gilead Sciences. Try any of our Foolish newsletter services free for 30 days. We Fools don't all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.