BOSTON (AP) — A Massachusetts chemist accused of faking drug test results now finds herself in the same position as the accused drug dealers she testified against: charged with a crime and facing years in prison.

Annie Dookhan, 34, of Franklin, was arrested Friday in a burgeoning investigation that has already led to the shutdown of a state drug lab, the resignation of the state's public health commissioner and the potential upending of thousands of criminal cases.

"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 form a college or university.

Dookhan's alleged mishandling of drug samples prompted the shutdown of the Hinton State Laboratory Institute in Boston last month.

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

Since the lab closed, more than a dozen drug defendants are back on the street while their attorneys challenge the charges based on Dookhan's misconduct.

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

During Dookhan's arraignment in Boston Municipal Court, 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.

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Dookhan was charged with two counts of obstruction of justice, a felony count that carries up to 10 years in prison, and pretending to hold a degree, a misdemeanor punishable by as much as a year in jail.

She 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. Family members and Dookhan's attorney declined to comment after the brief hearing. 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 a master's degree in chemistry from the University of Massachusetts, Coakley said.

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 re-tested the sample 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.

"Her actions totally turned the system on its head," 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 between 50 and 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 allegedly admitted 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.

Defense attorneys for drug suspects were not surprised by Dookhan's arrest.

"I hope the system isn't treating the evidence against her the way she treated the evidence against several thousand defendants," said 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. AP writer Bridget Murphy contributed to this report.