LINGTON, Vt. (AP) – DNA from a blood sample taken from the pants of the prime suspect in the disappearance of University of Vermont student Michelle Gardner-Quinn has been found to match hers, the Associated Press has learned.

The blood was found on the blue jeans of Brian L. Rooney, 36, giving police at least one piece of physical evidence allegedly linking the man they call their prime suspect to the Oct. 7 disappearance of Gardner-Quinn.

Rooney, who has denied any involvement in the woman’s disappearance but is being held on unrelated sex charges, was ordered by Vermont District Court Judge Michael Kupersmith to submit to DNA testing during a closed-door hearing Thursday, according to David Sleigh, his court-appointed lawyer.

In an affidavit, prosecutors said a Vermont State Police analysis showed the DNA samples to match, according to Sleigh. Sleigh, who participated in the hearing via telephone and wasn’t present in the courtroom, disclosed the existence of the affidavit and described its findings in an interview afterward with the AP.

But he said later Thursday that when he gave the information, he was under the impression that the hearing at which it was discussed had been open to the public. He learned later that wasn’t the case, he said.

Deputy Chittenden County State’s Attorney Justin Jiron would not confirm or deny the DNA match when asked Thursday, saying the affidavit was under seal. “I’m not allowed to talk about the results,” Jiron said.

Neither Police Chief Thomas Tremblay nor Lt. Kathleen Stubbing would confirm it, either. District Court refused to release the affidavit, saying it was under seal.

Also Thursday, Rooney was ordered held without bail after entering not guilty pleas to two new sex charges filed based on information developed during the course of the investigation into Gardner-Quinn’s disappearance.

He was ordered held without bail pending an Oct. 24 bail hearing on the charges, which are aggravated sexual assault and inciting a felony.

Rooney, an unemployed construction worker already facing sex charges involving a 15-year-old girl, is believed to be the last person to see Gardner-Quinn alive. Gardner-Quinn, 21, of Arlington, Va., vanished Oct. 7, shortly after borrowing his cell phone. She was found dead in Huntington Gorge in what police now say was a homicide, but they have not given a cause of death.

In another unrelated case, Rooney is accused of sexual assault and lewd and lascivious conduct with a child. Those charges were filed as a result of information that came to light during the investigation into Gardner-Quinn’s disappearance, but they date to 1996 and 1998 and involve a teenage girl, not Gardner-Quinn.

The new charges that were the subject of Thursday’s arraignment involve a former girlfriend identified only as A.S., who Rooney was involved with for three years beginning when she was 17 and he was 31, according to an affidavit filed Thursday by Detective Ingrid Jonas of the Vermont State Police.

According to the affidavit:

• Rooney routinely sexually assaulted her in bed, sometimes when she was sleeping.

• Last November, the woman – now 22 – was told Rooney had asked a clerk at an Essex convenience store if she knew anyone who would be willing to kill her. Two other women interviewed by police testified that they heard Rooney say he wanted A.S. killed.

• A.S. reacted dramatically when told that Rooney had been described in the affidavit released Monday as having used a chemically treated rag to render women unconscious to sexually assault them. “Oh my God,” she told Jonas, before going on to say she remembered waking up to the smell of “starter fluid” more than once when she lived with Rooney in Underhill.

Once, she found a can under the bed they shared, and she saw a can in the living room and in a closet Rooney kept locked, she told Jonas.

• In a Monday search of Rooney’s parents’ home in Richmond, police found photographs and videotapes of naked women, one of which was labeled A.S. and showed a woman lying face down on a bed, making no movements as she was sexually assaulted.

The latest charges could put Rooney away for life.

William Norful, a public defender who represented him at Thursday’s arraignment, said he couldn’t address the allegations in the affidavit, having been retained as a substitute for Rooney’s court-appointed public defender, David Sleigh.

Sleigh didn’t return telephone calls seeking comment after the arraignment.

Rooney, who was granted $150,000 bail at Monday’s arraignment, now is being held without bail.

Police released no new information about the case Thursday.

“We still do not have any information to release on the Gardner-Quinn case, but we will notify you should that change,” police Lt. Kathleen Stubbing said in an e-mail message, responding to a query about new developments.