One of the most serious accusations came during a "60 Minutes" interview last May when former teammate Tyler Hamilton said he saw Armstrong use EPO during the 1999 Tour de France and in preparation for the 2000 and 2001 tours.
The report also said Armstrong loyalist George Hincapie, another ex-teammate, told federal authorities that he and Armstrong supplied each other with PEDs and discussed them. Hincapie released a statement after the segment aired, saying he did not speak with the show and didn't know where it got its information.
U.S. anti-doping officials said Friday they will not be dissuaded by the government's decision to close the Armstrong probe.
"Unlike the U.S. Attorney, USADA's job is to protect clean sport rather than enforce specific criminal laws," said Travis Tygart, chief executive officer of the U.S. Anti-Doping Agency. "Our investigation into doping in the sport of cycling is continuing and we look forward to obtaining the information developed during the federal investigation."
As the investigation progressed, Armstrong assembled a legal team, hired a spokesman and briefly created a website to address any of the allegations reported by the media.
Frustrated by a slew of news articles about the investigation, Armstrong's attorneys filed a motion in July, asking a judge to order federal agents to testify about their contacts with reporters.
Armstrong consciously maintained a high profile throughout the investigation, raising money for his cancer charity, Livestrong, and racing in events such as off-road triathlons. He had no reason to hide, he said.
A spokeswoman for Livestrong, Katherine McLane, said the group was "very glad to hear this news." She called Armstrong an inspiration to millions of cancer survivors.
That could have played a role in prosecutors' decision, one expert said.
"The government always has a tremendous amount of prosecutorial discretion regarding whether or not to bring an indictment. In this case it appears that they have acted judiciously and likely considered all of the good works of Lance Armstrong and his foundation," said Mathew Rosengart, a former federal prosecutor who is not involved in the case.
Associated Press writers Pete Yost in Washington, Anthony McCartney in Los Angeles and Eddie Pells in Las Vegas contributed to this report.
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