The drugmaker took the move after data raised concerns about dosages used in some patient groups. This is certain to raise investor anxiety, because the blood thinner is the most widely anticipated drug in Lilly’s pipeline. Although Wall Street has been waiting for new data to be reported on Nov. 4 at the American Heart Association meeting, Lilly has been hoping prasugrel will generate at least $1 billion annually and compete with Plavix, which is marketed by Bristol-Myers Squibb and Sanofi-Aventis.

“We are suspending enrollment in these two small pharmacodynamic trials so that we can amend current protocols,” J. Anthony Ware, Lilly’s cardiovascular platform leader for prasugrel, in a statement. “These amendments are strictly protocol-related and do not provide a basis for inferring overall outcomes of other prasugrel trials.”

The larger study due next month, called Triton, was completed over the summer. But as The Wall Street Journal notes, Lilly has been tallying that and relied, in part, on Triton data in deciding to suspend the continuing studies, casting doubt on whether some dosages in that study were appropriate. Earlier today, Cowen analyst Steve Scala downgraded Lilly stock on concerns over the Triton data.

The data “could be the biggest binary event in pharma in 2007,” he wrote in an investor note. “In preclinical, Phase I and II studies, prasugrel appeared to be more potent than…Plavix. This potency could translate into superior benefit/risk and $2B in 2012 sales to Lilly. But if superior efficacy increases serious bleeds, 2012 prasugrel sales could be zero. A mixed outcome may generate modest sales; this is our expectation.”