"To the extent that we may have contributed in any way to the public perception that you might have been involved in this crime, I am deeply sorry," Boulder County District Attorney Mary Lacy wrote in a letter to the little girl's father, John Ramsey. "No innocent person should have to endure such an extensive trial in the court of public opinion."
Lacy said new "touch DNA" tests on skin cells that were left behind on JonBenet's long underwear point to an "unexplained third party" and not a member of the family.
John Ramsey, a software entrepreneur who now lives in Michigan, said Wednesday he is hopeful the killer will be found based on the DNA evidence.
"I think the people that are in charge of the investigation are focused on that, and that gives me a lot of comfort," he told KUSA-TV in Denver. He added: "Certainly we are grateful that they acknowledged that we, based on that, certainly could not have been involved."
For years after the slaying, tabloids and crime shows went after the couple, and Lacy's predecessor as district attorney, Alex Hunter, said in 1997 that the parents were under an "umbrella of suspicion." News reports also cast suspicion on JonBenet's older brother, Burke, who was 9 when his sister was killed.
The suspicions outlived Patsy, who died at age 49 in Atlanta, where the family moved after JonBenet's death.
"My first thought was obviously I wish Patsy Ramsey was here with us to be able to at least share vindication of her family," said L. Lin Wood, an attorney for the Ramsey family. "There are many people in this country, if not around the world, that also owe John and Patsy Ramsey and Burke Ramsey an apology."
Early in the investigation, police found male DNA in a drop of blood on JonBenet's underwear and determined it was not from anyone in her family. But Lacy said investigators were unable to say who it came from and whether that person was the killer.
Then, late last year, prosecutors turned over long underwear JonBenet was wearing to the Bode Technology Group near Washington, which looked for "touch DNA," or cells left behind where someone has touched something.
The lab has only been using this technology for about three years.
The laboratory found previously undiscovered genetic material on the sides of the girl's long underwear, where an attacker would have grasped the clothing to pull it down, authorities said. The DNA matched the genetic material found earlier.
Lacy said the presence of the same male DNA in three places on the girl's clothing convinced investigators it belonged to JonBenet's killer and had not been left accidentally by an innocent party.
"It is therefore the position of the Boulder District Attorney's Office that this profile belongs to the perpetrator of the homicide," she said in a statement. In her letter to the Ramseys, she said the DNA evidence "has vindicated your family."
She said investigators hope someday to find a DNA match in the ever-expanding national DNA databank.
Through a spokeswoman, Lacy declined to comment any further.
John Ramsey found his daughter's strangled and bludgeoned body in the basement of the family's home in Boulder on Dec. 26, 1996. Patsy Ramsey said she found a ransom note demanding $118,000 for her daughter.
Lacy had previously expressed doubts that the parents were involved. In 2003, a federal judge handling a defamation lawsuit in Atlanta involving the Ramseys said evidence in the case was more consistent with the theory that an intruder killed JonBenet, and Lacy said she agreed.
Less than two months after Patsy Ramsey died, the case appeared to blow wide open with the arrest in Thailand of John Mark Karr, a sometime teacher obsessed with the little girl's slaying. Karr made bizarre, detailed confessions to the killing, but authorities said DNA evidence showed he did not commit the crime.
