A chemist accused of lying about drug samples she tested at a state lab could face additional charges as prosecutors and defense attorneys sift through thousands of criminal cases that could be upended by her actions.

Annie Dookhan, 34, of Franklin, was arrested Friday in a burgeoning investigation that has already led to the shutdown of the lab, the resignation of the state's public health commissioner and the release of more than a dozen drug defendants.

Many more defendants are expected to be released. Authorities say more than 1,100 inmates are serving time in cases in which Dookhan was the primary or secondary chemist.

"Annie Dookhan's alleged actions corrupted the integrity of the entire criminal justice system," state Attorney General Martha Coakley said during a news conference after Dookhan's arrest. "There are many victims as a result of this."

Dookhan faces more than 20 years in prison on charges of obstruction of justice and falsely pretending to hold a degree from a college or university. She testified under oath that she holds a master's degree in chemistry from the University of Massachusetts, but school officials say they have no record of her receiving an advanced degree or taking graduate courses there.

State police say Dookhan tested more than 60,000 drug samples involving 34,000 defendants during her nine years at the Hinton State Laboratory Institute in Boston. Defense lawyers and prosecutors are scrambling to figure out how to deal with the fallout.

Assistant Attorney General John Verner called the charges against Dookhan "preliminary" and said a "much broader" investigation is being conducted.

Verner said state police learned of Dookhan's alleged actions in July after they interviewed a chemist at the lab who said he had observed "many irregularities" in Dookhan's work.

Verner said Dookhan later acknowledged to state police that she sometimes would take 15 to 25 samples and instead of testing them all, she would test only five of them, then list them all as positive. She said that sometimes, if a sample tested negative, she would take known cocaine from another sample and add it to the negative sample to make it test positive for cocaine, Verner said.

Dookhan pleaded not guilty and was later released on $10,000 bail. She was ordered to turn over her passport, submit to GPS monitoring, and not have contact with any former or current employees of the lab.

Dookhan's relatives and attorney declined to comment after the brief hearing in Boston Municipal Court. Her next court date is Dec. 3.

The obstruction charges accuse Dookhan of lying about drug samples she analyzed at the lab in March 2011 for a Suffolk County case, and for testifying under oath in August 2010 that she had an advanced degree from the University of Massachusetts, Attorney General Martha Coakley said at a news conference.

In one of the cases, Boston police had tested a substance as negative for cocaine, but when Dookhan tested it, she reported it as positive. Investigators later retested the cample and it came back negative, Verner said.

The only motive authorities have found so far is that Dookhan wanted to be seen as a good worker, Coakley said.

According to a state police report in August, Dookhan said she just wanted to get the work done and never meant to hurt anyone.

"I screwed up big-time," she is quoted as saying. "I messed up bad; it's my fault. I don't want the lab to get in trouble."

Dookhan's supervisors have faced harsh criticism for not removing her from lab duties after suspicions about her were first raised by her co-workers and for not alerting prosecutors and police. However, Coakley said, there is no indication so far of criminal activity by anyone else at the lab.

Co-workers began expressing concern about Dookhan's work habits several years ago, but her supervisors allowed her to continue working. Dookhan was the most productive chemist in the lab, routinely testing more than 500 samples a month, while others tested 50 to 150.

One co-worker told state police he never saw Dookhan in front of a microscope. A lab employee saw Dookhan weighing drug samples without doing a balance check on her scale.

In an interview with state police late last month, Dookhan acknowledged faking test results for two to three years. She told police she identified some drug samples as narcotics simply by looking at them instead of testing them, a process known as dry labbing. She also said she forged the initials of colleagues and deliberately turned a negative sample into a positive for narcotics a few times.

"I hope the system isn't treating the evidence against her the way she treated the evidence against several thousand defendants," said defense attorney John T. Martin, who has a client who was allowed to withdraw his guilty plea based on concerns over Dookhan's work.

Dookhan was suspended from lab duties after getting caught forging a colleague's initials on paperwork in June 2011. She resigned in March as the Department of Public Health investigated. The lab was run by the department until July 1, when state police took over as part of a state budget directive.

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Niedowski reported from Franklin. Associated Press writer Bridget Murphy contributed to this report.