A new scandal at the San Francisco Police Department’s beleaguered crime lab may imperil hundreds of criminal cases based on DNA evidence, The Chronicle has learned.

Police confirmed Friday that “irregularities” at the lab’s DNA unit prompted them to reassign a technician and her supervisor while officials conduct an investigation into apparent violations of department testing standards.

According to testimony and evidence revealed in a trial late last year, the analyst allegedly filled in the gaps in poor-quality, incomplete genetic evidence. She generated two complete genetic profiles, and both were sent off as definitive test results to the state’s offender tracking database, something that would not have been allowed with the original, lower-quality DNA evidence.

State rules specify that only verified, complete samples from suspects or relevant genetic evidence drawn from crime scenes can be legally entered into its database to identify suspects in crimes.

The analyst’s alleged misconduct came to light in a trial in December of a child molestation suspect, Marco Hernandez. Citing the events of the trial, attorney Bicka Barlow, a DNA expert who has long advised the public defender’s office, lodged a complaint about the lab this month with the San Francisco police, the FBI and the national crime lab accrediting agency.

“I allege that serious misconduct, which substantially affects the integrity of forensic results, has occurred” at the lab, Barlow wrote in a March 6 letter to Police Chief Greg Suhr obtained by The Chronicle. She concluded that the lab’s improper analysis of genetic evidence “may have led police away from real perpetrators and resulted in the conviction of the innocent,” although she drew no conclusions on specific cases.

Lab analysts on leave

Suhr said Friday that the department’s review found the criminalist did not follow department standards and that her supervisor did not intervene.

“She was not doing her daily testing to the standards we expect from our criminalists,” Suhr said. “Whatever standard she was testing to, it was deemed to be incorrect and her supervisor should have caught it.”

Both lab analysts are on personal leave. “They will be administratively reassigned while we figure this out,” the chief said.

“We are undertaking an audit to determine how many cases, if any, this involved,” Suhr said. “We realize this is critical information to prosecutors, and we have briefed them” as to findings to date.

Suhr said he doesn’t know the exact number of cases the analyst processed, “but it is in the hundreds.”

The chief noted that the independent agency that certifies crime labs in the U.S. is auditing San Francisco’s lab.

“That has nothing to do with this — that certification is going well,” he said. “We take huge pride in our lab.”

In her letter, Barlow said that while it was in 2013 that the SFPD lab analyst generated two interpretations of problematic DNA evidence, the defense only learned at the trial in December that there were, in fact, two DNA profiles in the same case. One profile pointed to five suspects, while the other pointed to 28 suspects, including the defendant.

'Raises a big red flag’

Despite the apparent conflict, lab officials testified that the evidence did match the defendant’s DNA. The defendant, who had confessed to some elements of the crime, was ultimately found guilty.

Barlow argued that misinterpreting such vital evidence should have raised larger questions about the reliability of the lab and its testing processes to prosecutors. But there is no evidence that anyone did anything about the revelations that emerged from the trial, she said.

“This raises a big red flag, and the prosecutor’s office should be paying attention to this,” Barlow said. “They should not just accept this kind of evidence without more scrutiny. They need to educate themselves, and they are not doing it.”

District Attorney George Gascón said Friday that he only recently heard about the allegations in Barlow’s letter and immediately ordered an investigation.

“This raises tremendous concerns for us,” he said. “These are very serious cases involving DNA. A lot of them are sexual assault and murder. If these allegations are true, it could have a significant impact on the cases in the past and the ones we are currently handling.

“We are talking about the integrity of the entire trial process,” he said. “We have to be able to rely on the evidence that we present.”

The lab suffered a blow in 2010 when 29-year veteran employee Deborah Madden admitted she stole traces of cocaine seized as evidence for her personal use. The scandal led to the city farming out its drug lab work to other facilities and forced prosecutors to dismiss more than 1,000 cases.

Madden — who retired from the unit and said she used only cocaine left behind in testing to help her stop drinking — ultimately admitted in 2013 to misdemeanor drug possession charges after two federal prosecutions ended in mistrial.

D.A.’s concerns

Gascón, who was San Francisco’s police chief and ordered the lab shuttered during the first scandal, said it is premature to say if any cases are in jeopardy based on the new trouble at the lab.

“I don’t know how many cases may be impacted by this,” he said. “I want the public to know I take this very seriously — we are going to get to the bottom of this, because this is completely unacceptable.”

Jaxon Van Derbeken is a San Francisco Chronicle staff writer. E-mail: jvanderbeken@sfchronicle.com