The Committee is a rogue organization within the American government and military. They were the power behind Manticore. Elizabeth Renfro, who worked for the committee, made an intentionally vague reference to their "other projects".
After Logan Cale exposed the location of Manticore's Washington base to the media, the committee had the Manticore program discontinued and the facility burned down. They subsequently arranged for federal agents such as Ames White to hunt down the surviving Transgenics and cover up their existence. White's public exposure of the existence of Transgenics was not in line with the committee's goals - but rather those of the Conclave he truly served.