The Massachusetts justice system has been upended by allegations that a former state drug lab chemist, Annie Dookhan, 34, faked test results, forged paperwork, and sometimes mixed samples. Dookhan tested more than 60,000 samples covering about 34,000 defendants in her nine years at the lab, according to State Police.

Special court sessions are convening to handle drug cases tied to Dookhan’s work. Dookhan has pleaded not guilty to charges including obstruction of justice.

Here are some of the criminal defendants whose cases have been affected by Dookhan.Read more.

Jonathan Vaughan, 26, who was arrested after police allege he was drinking beer at a McDonald’s and refused to leave, was ordered held on $25,000 bail at his arraignment on Jan. 9.

Vaughan told arresting officers: “I just got out on Annie Dookhan and I ain’t going back to jail,” authorities said.

Police also allege that Vaughan had eight baggies of suspected crack cocaine in his belongings when he was arrested.

Read more.

Luis Quiles, 41, of Boston, was arrested in November on suspicion of theft after being released from custody in September because of the scandal at a now-closed state drug lab in Jamaica Plain.

A lawyer for Luigi Epifania, 29, of East Boston, asked a judge on Oct. 22 to rule that his arrest in 2010 in connection to a suspected drug deal should not be considered a probation violation. The judge denied the request, ruling that Epifania’s imprisonment for violating probation should remain in effect even if the suspected drugs cannot be used as evidence against him due to the drug lab scandal. Epifania was convicted in 2007 of killing a cat.

Read more.

Anthony Thames sought to have his drug case reviewed by a special court dealing with cases tied to the drug lab scandal on Oct. 22, but a judge refused to take up his case while he awaits trial in connection to a 2011 killing in the South End. Thames has pleaded not guilty to first-degree murder and is being held without bail.

Suffolk District Attorney Daniel F. Conley highlighted the cases of Thames and Luigi Epifania to try to refute claims by some defense attorneys that their clients are low-level dealers. Video.

Suffolk Superior Court Judge Christine McEvoy, pictured, granted bail on Oct. 17 to two drug defendants whose cases were tied to Annie Dookhan. The defendants, German Rios and Juan Cotilla, are both in the United States illegally and will be held by US Immigration and Customs Enforcement officials if they make bail, prosecutors said.

Rios’s attorney, Andrew Stockwell-Alpert said: “No juror in the Commonwealth will ever convict anyone on an Annie Dookhan case ever again.” Read more. Video.

A judge stayed a 2½-year sentence for Jose Rivera, pictured on the monitor, on Oct. 15 during a special session in Suffolk Superior Court for cases impacted by the drug lab scandal. Rivera’s bail was set at $500 and a curfew was imposed, according to court records. Read more.

Shawn Drumgold, 47, left, was acquitted of drug possession charges on Oct. 12 in a case in which former state chemist Annie Dookhan refused to testify. Drumgold’s lawyer sought to have the case dismissed on the grounds that Dookhan’s initials appeared on drug powder analysis forms in the case. A judge refused, and later acquitted Drumgold on the grounds that Boston police failed to link him to crack cocaine and heroin found in the kitchen of a Roxbury crack house in January 2011.

Drumgold spent 15 years in prison for the slaying he says he did not commit of a 12-year-old girl. Drumgold and defense attorney Rosemary Scapicchio insisted that his arrest was an act of harassment by officers who knew that Drumgold had won a $14 million federal jury verdict in 2009 against a former Boston detective for violating Drumgold’s civil rights when he was convicted of first-degree murder.

A judge on Oct. 12 stayed an 18-month sentence imposed on Anthony Craan, 30, for a drug offense because of Annie Dookhan’s ties to the evidence in his case, prosecutors said. His bail was set at $2,000 and a judge also imposed a curfew on him, according to prosecutors.

Craan is also under indictment in a separate drug case and is awaiting trial on an unrelated drug charge, prosecutors said. He is due back in court on Oct. 19.

Robert Jamison, 36, had his sentences stayed in two separate drug cases in which Annie Dookhan handled the evidence, prosecutors said. Jamison was serving a 2½-year prison term for a drug charge and had completed a separate prison term for a 2010 drug offense, prosecutors said.

A judge on Oct. 12 set bail for Jamison at $500 and imposed a curfew, prosecutors said.

David Otero, 47, was released on personal recognizance on Oct. 12 because of Annie Dookhan’s involvement in his drug case. He was serving a two-year drug sentence from a 2011 arrest in Boston, prosecutors said. He is due back in court on Dec. 21.

Richard Brown declined a stay of sentence because he’s serving another prison term conccurrently for a separate offense, according to the Suffolk district attorney’s office. He’s pictured here in court on Oct. 5.

A judge stayed the sentences imposed last year on Michael Wells, 24, of Dorchester, after Suffolk County prosecutors said they determined that Annie Dookhan handled drug evidence in his case.

He was released on personal recognizance on Oct. 5 and is schedule to return to court on Dec. 14 for a motion hearing. Read more.

A judge stayed a one-year sentence imposed on Carlos Colon, 22, of the South End, after Suffolk County prosecutors said they determined his case was handled by Annie Dookhan. He was released on $500 bail on Oct. 5, according to prosecutors. He is due back in court on Dec. 12 for a status hearing. Read more.

A judge dimissed drug charges on Oct. 5 against Jeffrey Banks, who is also known as Joseph Banks, because of allegations that Annie Dookhan doctored samples in his case. Her actions in Solomon’s case are the grounds for one of the obstruction of justice charges against her.

Solomon is serving a state prison sentence in an unrelated case in Middlesex County. Read more.

Officials arrested Marcus Pixley, 52, on Oct. 5 after he missed a court date following the reduction of his bail as part of the drug lab fallout.

A convicted rapist, Pixley ­appeared to have been among the first of the defendants freed because of the scandal to land in legal trouble again. He was arraigned and held on $2,000 cash bail. Read more.

Former state chemist Annie Dookhan was involved in testing drugs in a case involving Mylazia Johnson, 31, of Roxbury. A judge halted her 3½-year drug sentence on Sept. 28 and released her on personal recognizance. She is due back in court in January to determine the ultimate fate of her case, with the possibility that her conviction may be vacated. Read more.

A judge put on hold a seven-year prison sentence for David Huffman, 55, of Roxbury, on Sept. 24 at the request of his defense attorney, who said former state chemist Annie Dookhan signed or co-signed on cocaine seized in his case.

Huffman’s bail was set at $75,000. His case may be one of the first in which the problems with the drug evidence tested by Dookhan have affected more than just drug charges against the defendant. Huffman pleaded guilty to gun and drug charges in August. Read more.

A judge allowed David Danielli, right, to withdraw his guilty plea in a drug case on Sept. 19 after the scope of the drug lab scandal widened. Defense attorney John T. Martin said the evidence in Danielli’s case was tainted.

Quincy police arrested Danielli on March 26, 2011. He was accused of possessing oxycodone pills. Read more.

Video

Juan Irene, 51, was released on Sept. 6 at the request of the prosecution because of Annie Dookhan’s role in handling drug evidence against him. Irene had been jailed on charges that he sold heroin to an undercover officer. He still faces charges, but defense attorney Susan Rayburn said she doubts Irene’s case will come to trial. Read more.