AVEO Pharmaceuticals' (NASDAQ:AVEO) announced yesterday that the Food and Drug Administration rejected its kidney cancer drug tivozanib.

No surprise there. The briefing documents for the advisory panel meeting expressed the FDA reviewers' negative opinion, and tivozanib's fate was sealed when the committee voted 13-1, recommending against approving the drug.

What is a little surprising is that shares of AVEO jumped 8% on the news and are up another 6% today.

But only a little.

Call it a "cover the short on the news." Not as catchy as "sell the news," but it works in the other direction as well. After the advisory committee meeting, AVEO stock continued to fall, and the bump over the last two days puts it about where it traded after the meeting.

I certainly didn't see anything in the rejection announcement nor today's conference call  that would make AVEO worth more after the rejection. To get tivozanib approved for kidney cancer, the FDA wants a new clinical trial since the overall survival data was confounded -- to say the least -- by patients crossing over from the control group to take tivozanib as well.

But AVEO and its partner Astellas don't plan to fund any further trials in kidney cancer. Tivozanib is dead as a treatment for kidney cancer.

Long road
AVEO is currently trading substantially below the $192 million in cash and equivalents it had at the end of the first quarter because investors know AVEO has a long road ahead. It's going to burn through all of that cash and probably substantially more before tivozanib is approved.

The drug is in two phase 2 clinical trials, one for colon cancer and another for breast cancer. The colon cancer data is due next year but is a bit of a long shot since tivozanib inhibits VEGF pathway, which hasn't been a particularly good target in colon cancer.

More promising is the potential to treat triple negative breast cancer patients who are missing the estrogen receptor, progesterone receptor, and don't overexpress HER2. It's a small chunk of the breast cancer market, but there's an unmet need, so a small gain would be meaningful. Data from that trial aren't expected until the end of next year.

Confounding choices
There's an investment lesson here: Make sure your company is running the correct clinical trial.

AVEO's mistake seems to have been going head to head against the second-best drug for kidney cancer, Nexavar sold by Onyx Pharmaceuticals (UNKNOWN:ONXX.DL) and Bayer, rather than top-selling Sutent sold by Pfizer (NYSE:PFE). While progression-free survival was longer for the group taking tivozanib, once patients progressed, they wanted another drug. Lots of patients taking Nexavar crossed over to take tivozanib. Essentially some patients got two drugs while other only got one, confounding the overall survival data.

The most obvious solution would have been for AVEO to have gone after second-line patients that have already failed Sutent, like Pfizer did with its second-line drug Inlyta. In that scenario, comparison to placebo probably would have been sufficient, although the choice would have shrunk the potential market.

AVEO looks like it made better choices with its colon and breast cancer trials, but investors have awhile to wait to see if the better design results in better data.

Fool contributor Brian Orelli has no position in any stocks mentioned. The Motley Fool has no position in any of the stocks mentioned. Try any of our Foolish newsletter services free for 30 days. We Fools may not 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.