Presence of 3rd person's genetic markers never before revealed 
 
 John Ramsey looks on as his wife Patsy Ramsey holds an ad promising a reward for information leading to the conviction of the killer of their 6-year-old daughter, JonBenet, during a television interview on May 1, 1997. Eleven years later, Boulder's top prosecutor exonerated the Ramseys — but a new independent analysis of DNA evidence in the case calls that into question. ( Patrick Davison / Rocky Mountain News via AP ) 
 
 The DNA evidence in the JonBenet Ramsey case doesn't support a pivotal and controversial development in Colorado's most vexing unsolved murder — a former Boulder prosecutor's decision to clear the girl's family from all suspicion in her death, a joint Daily Camera/9NEWS investigation has found. 
 
 Forensic experts who examined the results of DNA tests obtained exclusively by the two news organizations disputed former District Attorney Mary Lacy's conclusion that a DNA profile found in one place on JonBenet's underpants and two locations on her long johns was necessarily the killer's — which Lacy had asserted in clearing JonBenet's family of suspicion. 
 
 In fact, those experts said the evidence showed that the DNA samples recovered from the long johns came from at least two people in addition to JonBenet — something Lacy's office was told, according to documents obtained by the Camera and 9NEWS, but that she made no mention of in clearing the Ramseys. 
 
 The presence of a third person's genetic markers has never before been publicly revealed. 
 
 Additionally, the independent experts raised the possibility that the original DNA sample recovered from JonBenet's underwear — long used to identify or exclude potential suspects — could be a composite and not that of a single individual. 
 
 About this story Charlie Brennan of the Daily Camera and Kevin Vaughan of 9NEWS exclusively obtained laboratory test results and reports from the JonBenet Ramsey case on which then-Boulder County District Attorney Mary Lacy based her decision to exonerate members of the Ramsey family. The reporters sought a review of that evidence by independent experts. This is the result of their investigation. 
 
 More from 9NEWS See additional coverage of the DNA evidence in the JonBenet Ramsey case at 9 and 10 p.m. Thursday and Friday on KUSA-Channel 9, or watch the full report at 9NEWS.com. 
 
 "It's a rather obvious point, but I mean, if you're looking for someone that doesn't exist, because actually it's several people, it's a problem," said Troy Eid, a former U.S. Attorney for Colorado. 
 
 The documents obtained by the Camera and 9NEWS included results from the actual DNA testing process on the long johns and summary reports sent to Lacy's office in the months leading up her July 9, 2008, letter exonerating the Ramseys. 
 
 The experts who examined the laboratory results at the request of the Camera and 9NEWS reached similar conclusions on multiple points: 
 
 • Two of the three samples that led Lacy to declare publicly that no one in the Ramsey family could be responsible for the murder actually appear to include genetic material from at least three people: JonBenet, the person whose DNA profile originally was located in JonBenet's underwear during testing in the late 1990s and early 2000s, plus at least one additional as-yet-unidentified person or persons. Consequently, its meaning is far from clear. 
 
 • The DNA profile referred to as Unknown Male 1 — first identified during testing on the panties — may not be the DNA of a single person at all, but, rather, a composite of genetic material from multiple individuals. As a result, it may be worthless as evidence. 
 
 • The presence of that DNA on JonBenet's underwear and long johns, be it from one or multiple people, may very well be innocent; the profiles were developed from minute samples that could have been the result of inconsequential contact with other people, or transferred from another piece of clothing. If true, it would contradict the assertions that DNA will be key to finding JonBenet's killer. 
 
 A Boulder police officer sits in her cruiser on Jan. 3, 1997, outside the 15th Street home in which 6-year-old JonBenet Ramsey was found dead on Dec. 26, 1996. The murder remains unsolved nearly 20 years later. (David Zalubowski / Associated Press) 
 
 This represents the first time independent experts have reviewed the DNA evidence on which Lacy based her widely questioned exoneration of the family. 
 
 And the findings could cut both ways. 
 
 "It's certainly possible that an intruder was responsible for the murder, but I don't think that the DNA evidence proves it," said William C. Thompson, a professor in the Department of Criminology, Law and Society at the University of California-Irvine and an internationally respected authority on DNA evidence and its applications in the criminal justice system. 
 
 Similarly, the findings don't implicate or exonerate anyone in the family. 
 
 Ramsey lawyer Lin Wood, who has not reviewed the documents or the work of the experts consulted by the Camera and 9NEWS, said, however, "I have absolute and total confidence in the integrity of former District Attorney Mary Lacy, and I am also aware of internet comments by former Boulder police Chief Mark Beckner where he, within the last several months, affirmed that the Ramsey case was a DNA case. 
 
 "So I know what Chief Beckner has said publicly in recent months, I know what ... former District Attorney Mary Lacy has said, and until someone impugns her integrity, or contradicts former Chief Beckner's statement, I continue to believe, as I have said before, that this is a DNA case and that the best chance for solving the case will be a hit and match on the DNA in the future. I hope that day comes." 
 
 'The silver bullet misfired' 
 
 Lacy was long known as a believer in the Ramseys' innocence, something others noticed as early as June 1998, when Boulder police detectives put on a detailed two-day presentation of the evidence and sought either charges against John and Patsy Ramsey or a grand jury investigation. 
 
 "My impression of her response to that was that she was among the very, very skeptical," said former Adams County District Attorney Bob Grant, who attended the police presentation in his role as adviser to then-Boulder County District Attorney Alex Hunter. 
 
 The experts consulted by the Camera and 9NEWS suggested that Lacy may have been guilty of "confirmation bias," a phenomenon in which investigators become so blinded by their own theories that they give extra credence to evidence that supports them, and ignore evidence that does not. 
 
 The lab that performed the DNA testing, for example, told Lacy in March 2008 that it was "likely" the two samples found on JonBenet's long johns came from "more than two people" and "should not be considered a single-source profile," according to the documents obtained by the Camera and 9NEWS. 
 
 But in exonerating the Ramseys with a three-page letter made public July 9, 2008, Lacy failed to disclose any of that, writing that "the previously identified profile from the crotch of the underwear worn by JonBenet at the time of the murder matched the DNA recovered from the long johns." 
 
 The word "match" actually never appears in the reports from Bode Technology, which conducted the testing in March through June of 2008. 
 
 Similarly, the Camera and 9NEWS have learned that investigators in Lacy's office suggested no additional testing was needed once they learned male DNA had been located on the long johns that she later labeled as a "match" to the DNA found in JonBenet's panties. 
 
 Correspondence from an investigator on Lacy's staff indicated that "my bosses" were "very excited" and "pleased" about the purported match, "and don't see the need for additional testing (unless you strongly recommend otherwise)." 
 
 The twin realities pointed to by the experts — that the genetic profile may not be from a single individual and that DNA on the girl's clothing may have landed there innocently — turn on its head Lacy's assertion that investigators had identified the killer's genetic fingerprint and that it was the key critical to solving the case. 
 
 Thompson, the UC-Irvine professor, noted that many people have come to see DNA evidence as a foolproof "silver bullet" to solving many crimes. 
 
 "Here, the silver bullet misfired," said Thompson, one of the experts who reviewed the evidence at the news organizations' request. 
 
 'Something I can't explain' 
 
 Former Colorado Gov. Bill Owens, who called for a review of the Ramsey case in October 1999 to determine whether it merited the attention of a statewide grand jury — his panel of advisers told him it did not — said Lacy's exoneration made no sense to him at the time and is even more troubling now. 
 
 "This is an important development. This is new information," Owens said. 
 
 "She knew, based on your investigation, that this DNA wasn't necessarily from one person and that it, in fact, was potentially accumulated DNA," Owens said. "She knew it at the time, and why she used this evidence to clear the Ramsey family ... is something I can't explain. And she should explain." 
 
 Lacy did not respond to repeated requests for comment on this story, sent to her by email, U.S. mail and left at her home. 
 
 Donald R. Von Hagen, a spokesman for Virginia-based Bode Cellmark Forensics, as the lab is now known, said in an email that the company's report "stands on its own" and that he would not have further comment. 
 
 The murder of JonBenet exploded into the national consciousness within days of the discovery of her body on Dec. 26, 1996, in the sprawling home she shared with her parents, John and Patsy Ramsey, and older brother, Burke, on 15th Street in Boulder. The 6-year-old's skull was fractured by a blow to the head, and her killer cinched a garrote around her neck, placed duct tape over her mouth and bound her wrists. 
 
 Everyone from seasoned investigators to amateur sleuths to talk show hosts quickly settled on one of two theories: That JonBenet was slain by someone in her family, either accidentally or in a fit of rage, and that the killer then tried to make it look like a botched kidnapping; or, that she was the victim of a cunning intruder who intended to spirit the child out of the house, but ended up committing murder instead. 
 
 John Ramsey, the girl's father, declined a request for an interview. 
 
 "I think we have said all that can be said and I need to get back to my job!" Ramsey wrote in an email. 
 
 'We don't actually have to live with it' 
 
 The implications of the conclusions reached by the experts consulted by the Camera and 9NEWS could, if considered by investigators still working the state's most famous cold case, dramatically impact the future direction of their work. At the time the Bode results were returned, Lacy's office had control of the Ramsey investigation, and Boulder police did not reclaim responsibility for the probe until Lacy left office the following year. 
 
 On one hand, it could lead detectives to consider anew the possibility that someone in JonBenet's family was responsible for her death. And it could also lead them to take a new look at dozens of potential suspects who were ruled out because their DNA didn't match the profile known as Unknown Male 1. 
 
 Eid, who served as Owens' chief counsel and was on the governor's statewide panel that reviewed the case in 1999, said in a recent interview he had suspected in 2008 that Lacy's exoneration was, at the very least, misleading. 
 
 "But now, it really looks wrong in the scheme of things," Eid said. "And it's not one of these instances where you think, in hindsight, she made a tough call, but we've got to live with it. No, we actually don't have to live with it anymore. Right?" 
 
 Lacy's successor as Boulder's district attorney, Stan Garnett, remembers exactly where he was when he learned of Lacy's decision to exonerate the Ramseys: sitting at LaGuardia Airport in New York waiting for a flight home when news of Lacy's letter crawled across a television screen. Although he called Lacy "an honorable person" and an "honest district attorney," he also said he was — and is — puzzled by her decision. 
 
 The job of a district attorney is to file charges in cases where the evidence warrants it, Garnett said. 
 
 "Our role is not to issue random exonerations of people in cases, and it's very confusing when that happens," Garnett added. 
 
 Although Garnett said he is not bound by Lacy's decision, it has lasting ramifications for countless people beyond John Ramsey and Burke Ramsey, now 29. Patsy Ramsey succumbed to ovarian cancer in June 2006. 
 
 Boulder police investigators continue to use the problematic DNA profile known as Unknown Male 1 to clear others who might potentially have been involved in the killing. A case investigator said dozens of suspects have been cleared that way. 
 
 Boulder police Chief Greg Testa declined this week to comment on the DNA evidence. But in a video statement released to all media on Sept. 1, Testa said detectives in the department had submitted more than 200 DNA samples in the case for analysis. 
 
 'This could easily be a composite profile' 
 
 At the crux of the evidence is the DNA profile referred to as Unknown Male 1. 
 
 That profile was first developed in late 1998 and early 1999 from tests on JonBenet's panties — but analysts couldn't at that time identify sufficient genetic markers. Sending it to the FBI's Combined DNA Index System — the national genetic database commonly known as CODIS — requires at least 10 markers. 
 
 Further lab work in 2003 yielded an additional marker, and the profile, featuring the required minimum of 10 genetic markers, was entered into CODIS that December. 
 
 "People believed back in those days almost all mixtures are two-person mixtures — that was like gospel truth," said Phillip Danielson, a professor of molecular biology at the University of Denver and science adviser to the National Law Enforcement and Corrections Technology Center. 
 
 In the ensuing years, as the "kits" used to detect DNA became ever more sensitive, scientists came to realize that many mixtures contained genetic markers from more than two people. 
 
 "You know," Danielson said, "looking at the profiles in this case, it seems pretty clear that their idea of this 'unknown male' — this could easily be a composite profile. Meaning that we have multiple contributors. But because of the low sensitivity of the kit, they interpreted those multiple contributors as being just one extra person." 
 
 However, Lacy — and others — concluded that profile must belong to JonBenet's killer. 
 
 Against that backdrop, an investigator in Lacy's office submitted JonBenet's panties, long johns, nightgown and other items for further testing at Bode's lab in Lorton, Va., in late 2007 and early 2008. 
 
 The Bode scientists could not replicate the profile found in JonBenet's panties, which bothered Danielson as he examined the materials obtained by the two news organizations. 
 
 "Reproducibility and repeatability is a hallmark of science," Danielson said. "To me, as a scientist, that does raise concern. If there was this unknown male DNA on the underwear, you would expect that Bode would have been able to reproduce that. Now, are there any possible explanations why they would not be? Sure." 
 
 The sample could have been degraded, though Danielson said that's not likely given the way evidence is handled and stored. Another possibility is that the original tests consumed all of the foreign genetic material in the panties. It's also possible that variations in the way the original tests were done could account for the failure to find the same profile in the panties during the 2008 tests. 
 
 'Should not be considered a single source profile' 
 
 When analysts at Bode tested the long johns, they focused on four distinct areas: the inside and outside of both the upper left and upper right sides of the garment. The tests on the two spots on the inside of the long johns yielded too little DNA to be useful. 
 
 But on the outside of the long johns, Bode analysts found much more DNA. 
 
 According to a March 24, 2008, report from Bode, a copy of which was obtained by the Camera and 9NEWS, the sample from the right side, labeled as 2S07-101-05A, included DNA containing "a mixture of at least two individuals including the victim and at least one male contributor." They got the same results on the left side, which was labeled 2S07-101-05B. 
 
 But in notes included with the report, it's clear the Bode analysts concluded that those two samples contained genetic material from at least three people. After assuming that JonBenet was one of those people, the analysts were left with the "remaining DNA contribution." 
 
 "Based on the results," according to the report, "it is likely more than two people contributed to the mixtures observed in 2S07-101-05A and 2S07-101-05B therefore, the remaining DNA contribution should not be considered a single source profile." 
 
 Christopher McKee, a former public defender in both Atlanta and Washington, D.C., and now director of the Schaden Experiential Learning & Public Service Programs at the University of Colorado Law School, concurred. 
 
 "My own personal review of the material and looking at the allele information at the various loci is that it looks and appears to me to be at least three individuals," McKee said. McKee also teaches an advanced course on Forensic Science in the Courts at the CU Law School, teaches on the subject around the country and has been recognized by courts and nationally as an expert on the topic. 
 
 Danielson also said, "There are too many alleles to be accounted for by only JonBenet and this alleged Unknown Male No. 1 profile." 
 
 An allele is a specific genetic marker. 
 
 Lacy's investigator asked Bode's analysts to compare the DNA from the two spots on the outside of the long johns with the Unknown Male 1 profile. 
 
 Bode's analysts concluded that Unknown Male 1 "could not be excluded as a possible contributor to the mixture DNA profile" obtained from the outside of the long johns on the right side, according to a June 20, 2008, report obtained by the Camera and 9NEWS. On the left side, the Unknown Male 1 profile "cannot be included or excluded from the mixture DNA profile." 
 
 In other words, the link between the two spots on the long johns and the DNA in the underwear is tenuous at best, according to analysts at the lab Lacy used for the testing. 
 
 'There is no innocent explanation' 
 
 But a little more than two weeks later, Lacy wrote the letter clearing members of the Ramsey family of suspicion. However, she included none of the caveats spelled out in the Bode reports and used language suggesting the lab work was ironclad. 
 
 "The Bode Technology laboratory was able to develop a profile from DNA recovered from the two sides of the long johns," Lacy wrote. "The previously identified profile from the crotch of the underwear worn by JonBenet at the time of the murder matched the DNA recovered from the long johns at Bode. 
 
 "Despite substantial efforts over the years to identify the source of this DNA, there is no innocent explanation for its incriminating presence at three sites on those two different items of clothing that JonBenet was wearing at the time of her murder." 
 
 The experts consulted by the news organizations disagreed, to varying degrees, on both assertions — that the Unknown Male 1 profile "matched" the DNA found on the outside of the long johns, and that there was "no innocent explanation" for the presence of that DNA on JonBenet's clothing. 
 
 "You have to understand a match is an analyst's judgment that the two samples fall into the 'included' category," Thompson said. "A match doesn't mean that the material examined is necessarily identical — just that there's a sufficient consistency to think that it might have come from the same source." 
 
 Thompson said his analysis found "a strong level of consistency" between the two long johns samples and the Unknown Male 1 profile. 
 
 "But," he said, "there are also some genetic characteristics that could not be accounted for by either JonBenet Ramsey or Unknown Male 1, thus suggesting there could be DNA from other people." 
 
 Danielson and another expert consulted by the Camera and 9NEWS offered similar opinions. 
 
 "To simply state that there's no innocent way that this DNA could have arrived at separate sites on JonBenet's underwear ... there's simply no scientific justification to make such a statement," Danielson said. "It's just simply not true." 
 
 Danielson offered a hypothetical: Say JonBenet had physical contact with other kids she was recently playing with, or had contact at a party on Christmas night, or say she touched anything bearing others' DNA; she could have then transferred that genetic material to her own clothes simply while getting dressed. 
 
 McKee, based on his review of the evidence, called Lacy's actions based on the lab reports "a cautionary tale." 
 
 "I don't think her letter at all reflects an appreciation or understanding for what that said in the report," McKee said. "You know, as I read the (Lacy) letter, it seems to suggest that there's just one single profile that was found here." 
 
 'False logic of declaring this as exonerating' 
 
 Michael Kane, who served as lead counsel to the Ramsey grand jury, is now senior legal counsel to the Judiciary Committee in the Pennsylvania House of Representatives. He expressed little surprise that Lacy's decision had been thrown into serious doubt. 
 
 "Until you ID who that (unknown sample) is, you can't make that kind of statement (that Lacy made)," Kane said in an email. "There may be circumstances where male DNA is discovered on or in the body of a victim of a sexual assault where you can say with a degree of certainty that had to have been from the perpetrator and from that, draw the conclusion that someone who doesn't meet that profile is excluded. 
 
 "But in a case like this, where the DNA is not from sperm, is only on the clothing and not her body, until you know whose it is, you can't say how it got there. And until you can say how it got there, you can't connect it to the crime and conclude it excludes anyone else as the perpetrator. And that's the false logic of declaring this as exonerating. It seems to me to be pretty self-evident." 
 
 As for potentially innocent explanations to the presence of DNA on the clothes JonBenet was wearing when she died, all three experts said they are numerous. 
 
 "There have been some very intriguing studies where they had people hold hands for a very short period of time and then touch a knife handle," Danielson said. 
 
 In some cases, subsequent tests found DNA from both people on the knife. In others, DNA from only the person who actually touched the knife. And in still others, no DNA was found from the person who actually touched the knife, yet DNA from the other person was found. 
 
 Thompson recently testified in a case involving sex toys. Analysts located DNA on the sex toys, Thompson said, in "quantities comparable" to that found on JonBenet's long johns — but it turned out to have no link to the crime. 
 
 "The DNA came from a person who had carried the wrapped items from the crime scene to a truck to take to the crime lab," Thompson said. "So somebody who had never touched the items, but had touched the exterior of the wrappers of the items, that person's DNA was apparently transferred onto the wrappers. Then when the wrapped items got back to the crime lab and were unwrapped, the analyst apparently touched the wrappers and then touched the items, transferring it onto the items — in a way that made it indistinguishable from DNA that would have been deposited there during that crime. 
 
 "So if that can happen in this sexual assault case that I worked on, it's easy to imagine similar scenarios that could have gotten the DNA found on JonBenet Ramsey's clothing to where it was found. And I think the fact that DNA can be transferred so easily in small quantities is a weakness of the technology at this time." 
 
 'Can't get my arms around that one' 
 
 Lacy established herself as a supporter of the intruder theory in the Ramsey case when she was still Mary Keenan, a chief deputy specializing in sexual assault cases under the man she would soon succeed, then-District Attorney Alex Hunter. 
 
 In June 1998, JonBenet's parents were questioned at length for the second time — Patsy Ramsey by Denver district attorney's investigator Tom Haney and Boulder prosecutor Trip DeMuth, and John Ramsey by retired El Paso County homicide detective Lou Smit and Kane, the attorney who directed the grand jury investigation. 
 
 Lacy wasn't directly involved in the interrogations. But Haney recalls that after she saw videotape of the interview with Patsy Ramsey, Lacy chided him for being hard on JonBenet's mother. 
 
 Haney said Lacy volunteering such an opinion seemed odd to him at the time. And, he said in a recent interview, "It still does." 
 
 Lacy took other steps that left many to believe she ruled out the Ramseys as suspects long before she issued her letter in 2008. 
 
 Lacy succeeded Hunter as Boulder County's elected district attorney in 2001. It was in that role that, in 2003, she made her first public proclamation on her belief in the Ramseys' innocence. 
 
 A federal judge in Atlanta — in dismissing a libel case filed against the Ramseys by a journalist they named as a potential suspect in their 2000 book "The Death of Innocence" — ruled that exhibits in the case led her to believe an intruder was more likely to have killed JonBenet than Patsy Ramsey. 
 
 Although Lacy had not been a party to that suit, she nevertheless volunteered a public statement in support of the federal judge's ruling, saying, "I agree with the conclusion that the weight of the evidence is more consistent with the theory that an intruder murdered JonBenet than it is with a theory that Mrs. Ramsey did so." 
 
 After Patsy Ramsey succumbed to ovarian cancer in 2006 following a 13-year battle, she was buried alongside JonBenet in St. James Episcopal Cemetery in Marietta, Ga. Lacy attended her funeral. 
 
 Former Boulder police detective Steve Thomas, who had investigated the case in its first years, said that stunned him. 
 
 "I know of no other case in which a sitting district attorney or prosecutor attended the funeral of a person whom she knew a grand jury had voted to criminally indict, and traveled across the country to do so, as Mary Lacy did in the case of Patsy Ramsey," he wrote in an email. 
 
 "I can't get my arms around that one. I can assure you that many in law enforcement were also distressed by it." 
 
 Thomas quit the investigation in August 1998 over multiple frustrations, including Hunter's reluctance at that time to take the case to a grand jury. He later wrote a book about the case and was sued by the Ramseys. That suit resulted in an undisclosed settlement. 
 
 'Culmination of what she wanted' 
 
 Lacy also presided over what is widely seen as one of the greatest debacles in a case marred by numerous missteps: the high-profile 2006 arrest of John Mark Karr, a suspect unearthed by University of Colorado journalism professor Michael Tracey, followed almost immediately by an about-face. 
 
 Karr was arrested in Thailand and brought back to Boulder with a sea of photographers recording virtually every moment of his transport — only to be abruptly cut loose a few days after arriving in Colorado when his DNA was found not to match the Unknown Male 1 sample. 
 
 Numerous experts have cautioned about the importance of maintaining objectivity, both that of the scientists examining forensic samples, and those who are evaluating the results. They also underscored the importance of severely limiting what is termed contextual information, which is supplied to a laboratory along with items to be tested. 
 
 In the case of testing done by Bode Technology for Lacy's office, the Bode staff was provided not only a PowerPoint presentation on the case, but a six-page Nov. 7, 2007, letter providing background so extensive that it even made mention that John Ramsey was president of Access Graphics, a Lockheed Martin subsidiary that had just cleared $1 billion in sales at the time of JonBenet's murder. 
 
 "Just as they need to make sure that evidence is not physically contaminated, you want to make sure that they're not cognitively contaminated, so that they're not aware and influenced by irrelevant contextual information that biases how they perceive and interpret the information, the judgments they make," said Itiel Dror, senior cognitive neuroscience researcher at University College London. He has presented training at the Colorado Bureau of Investigation, the California Department of Justice and elsewhere on objectivity in forensic examination. 
 
 "The investigators, the lawyers and everybody else need to stay emotionally disconnected from the case as much as humanly possible, so they keep as objective as possible and not fall into a lot of cognitive problems, wishful thinking, self-fulfilling prophecy," Dror said. 
 
 Grant, the former Adams County district attorney, was skeptical about the Karr arrest at the time as he watched it unfold from a distance. 
 
 "Just listening to him, and seeing the televised interviews, it just struck me as improbable that he had anything to do with it," Grant said. 
 
 Lacy, he said, "was one of the folks that was more skeptical of the someone-in-the-house theory from the beginning. When she agreed — I thought, hastily — to bring Mr. Karr back on the flimsiest of non-evidence, it kind of cemented for me that she was looking for some way to bolster the intruder theory." 
 
 And alluding to the exoneration letter of July 2008, Grant said, "That was the culmination of what she wanted to do all along." 
 
 Not a DNA case 'pure and simple' 
 
 The ramifications for the case in the wake of Lacy's letter were considerable, and continue to reverberate to this day. 
 
 The day Lacy issued the letter, John Ramsey hailed the news in an exclusive interview with 9NEWS. 
 
 "The most significant thing to me was the fact that we now have pretty irrefutable DNA evidence, according to the DA's office," Ramsey said. "And that's the most significant thing to me. And certainly we are grateful that they acknowledged that we, you know based on that, certainly could not have been involved. But the most important thing was we now have very, very solid evidence." 
 
 It was first reported by the Camera in January 2013 that the grand jury that heard the Ramsey case from September 1998 to October 1999 had signed indictments against both John and Patsy Ramsey, charging both with child abuse resulting in death. 
 
 Hunter declined to file those indictments with the court and prosecute the case at trial. While the standard for filing of charges is that of probable cause, the hurdle for conviction is proof beyond a reasonable doubt, and Hunter didn't believe the evidence was strong enough for him to do so. 
 
 A lawsuit filed against Garnett in September 2013 led to the unsealing the following month of the 1999 indictments, confirming the child abuse charges as well as charges against both parents for accessory to first-degree murder. 
 
 But still, the subsequent Lacy exoneration held sway for many, coming, as it did, nearly 10 years later, from the very same office that had secured those indictments. 
 
 As recently as September, Wood, the lawyer for the Ramsey family, cited the DNA-based exoneration in a tweet in the wake of national television broadcasts that had raised anew the question of whether someone in JonBenet's family was involved in her murder. 
 
 "In 2008, Boulder DA publicly exonerated them and apologized. DNA evidence conclusive. End of story," Wood tweeted. 
 
 And the same day, Wood tweeted, " This is a DNA case plain and simple." 
 
 That contention is flatly refuted by the independent experts consulted by the Camera and 9NEWS. 
 
 "No, it is not," Danielson said. "It's clearly not. We have a questioned profile that is very low level in terms of the amount of DNA. The quantity of DNA is very small, the profile is extremely complex. The one thing this case is not, it is not a 'DNA case pure and simple.'" 
 
 McKee, at the University of Colorado, agreed. 
 
 "I don't think any case is just a DNA case. And laboratories across the country operate, and their analysts are trained, not to talk in terms like that," said McKee, emphasizing that genetic evidence should be considered an investigative thread that is part of a larger fabric to be considered in its entirety. 
 
 "I think it would be a big mistake to say that, you know, DNA is the only thing that you're going to look at," McKee said. "And certainly, in this case, I don't think it is the only thing to look at." 
 
 They were echoed by Thompson, the UC-Irvine professor. 
 
 "I would say that the DNA evidence is not conclusive," Thompson said. "I would say that the DNA evidence is indeterminate, leaving us uncertain as to what really happened in this case, and who really killed this little girl." 
 
 Thompson added, "I mean, wasn't there other evidence in this case as well? I heard something about a ransom note, and handwriting analysis, and so on." 
 
 Wood, in an interview, said his tweets were based on Lacy's official statements, and on comments by former Boulder police Chief Beckner, made in a Reddit conversation on Feb. 24, 2015. 
 
 "My statements are 100 percent supported by the public statements of the Boulder district attorney and the former Boulder police chief," Wood said. "They're almost verbatim." 
 
 But those waiting for nearly 13 years for a match in the CODIS database to the Unknown Male 1 profile could wait forever for something that is never going to happen, Danielson said. 
 
 Although the unknown male sample had been entered into CODIS, it has never been matched to any of the other DNA profiles in the system. According to the FBI, as of August that included 12,517,059 offender profiles, 2,462,335 arrestee profiles and 726,709 forensic profiles of unknown individuals, such as the one submitted from the Ramsey case. 
 
 One possible answer to the question of why a match has never occurred is that the profile is a composite containing genetic material from multiple people. 
 
 "As I looked at this case, the more I looked, I was just like, 'Oh, OK, that would explain why no database hits,'" Danielson said. 
 
 A call for new testing 
 
 The JonBenet Ramsey investigation remains under the control of the Boulder Police Department, which has been in command of the case since Garnett passed it back to the department's detectives when he became DA in 2009. 
 
 Revelations about the questioned value of the DNA evidence as it now stands is stirring calls for renewed action on the case. 
 
 Owens hesitated to be telling others what should happen now, but said he was unsurprised to have his longtime suspicions that the DNA cited by Lacy could, in fact, be innocently explained — and may even be insignificant to the investigation — confirmed. 
 
 "And it would be very good to hear from Mary Lacy or from others involved, in terms of what this new evidence should show them in terms of where we should go," Owens said. 
 
 Eid, his former chief counsel who was part of the governor's October 1999 case review, hopes it will prod new action in the investigation, possibly employing the latest in DNA technology, which has evolved by quantum leaps since Lacy's letter was issued. 
 
 No new DNA testing in the Ramsey case has been conducted since 2008. 
 
 "And there ought to be a process to reevaluate this in light of what you have brought forward. That's my view," Eid said. "And you shouldn't feel locked in because some person who is no longer an elected official made a decision and said something. How many people have said things about this case that turned out to not be very relevant, or very accurate?" 
 
 One important step in the evolution of DNA testing, which was available in 2008 but has matured considerably since then, is known as Y-STR testing, which looks exclusively at male-inherited Y chromosome DNA. 
 
 Testing in this manner on key pieces of evidence, such as JonBenet's underwear, long johns and perhaps the cord on the garotte used to strangle her or other items associated with the crime scene, would not pick up any of JonBenet's genetic markers. That would enable analysts to focus with greater accuracy on only male contributors to the mixed samples. 
 
 "If you are able to ignore, completely, the female contribution, and can focus just on the male, you are able to then get much more robust results," McKee said. "I don't really see a reason why it hasn't been done, or why you couldn't do it." 
 
 Danielson agreed, saying, "With the Y-STR testing, you eliminate all of the female DNA. So you can amplify male DNA, even if the male DNA is a fraction of 1 percent of the DNA of the females' on the samples. So that's, if I were going to do any additional testing, that's the additional testing that I would do. It would help to at least answer some of the questions." 
 
 Grant, the former Adams County district attorney and one-time adviser to Boulder prosecutors, also pointed out that if Lacy truly had faith in the profile on which she based her exoneration, she could have done far more than simply write a letter. 
 
 "A prosecutor can file a John Doe warrant identifying the suspect by that DNA profile," Grant said. "If then-District Attorney Lacy was convinced that that suspect, that DNA profile, was the killer, and she was going to exonerate somebody else, then that's what she should have done. 
 
 "The fact that she didn't do that tells me something — tells me something about how strong she thinks the DNA evidence may or may not be." 
 
 Garnett expressed faith in the work of the Boulder Police Department, and also said his own office remains committed to doing whatever can be done to solve a case that he sees as still severely compromised by mistakes made in the past. 
 
 "I'm not going to talk publicly about what we're doing or what we would do," Garnett said. "But what I can tell you is that DNA evidence and the theory behind DNA work is changing almost daily, and I have excellent people on staff who review those issues and handle that, and we will make sure that any appropriate testing that can be done to update the theories of the evidence is done." 
 
 Garnett said Lacy's 2008 decision was "legally insignificant" and "has no meaning," largely due to the fact that the evidence she cited in her letter was never subjected to the rigorous scrutiny and cross-examination that all evidence in any case goes through in a courtroom. 
 
 "None of that happened with the bits and pieces of evidence that was the basis of the exoneration," Garnett said. "And so it's just not significant." 
 
 Eid observed that "it's incredible the number of cases that get solved later. And also as DNA testing gets better, it sometimes removes doubt and sometimes adds doubt." 
 
 Eid remains convinced that, "It's not too late for justice." 
 
 Charlie Brennan: 303-473-1327, brennanc@dailycamera.com or twitter.com/chasbrennan 
 
 Kevin Vaughan: 303-871-1862, kevin.vaughan@9news.com or twitter.com/writerkev ||||| Mary Lacy was one of a team of four who walked through the home of JonBenet Ramsey just days after the 6-year-old beauty contestant was discovered dead in the house's basement in Boulder, Colorado, on Dec. 26, 1996. 
 
 Interested in Jon Benet Ramsey? Add Jon Benet Ramsey as an interest to stay up to date on the latest Jon Benet Ramsey news, video, and analysis from ABC News. Add Interest 
 
 Just around the corner from JonBenet's room on the second floor, an indentation in the carpet was spotted and chills ran down her spine, she told ABC News. "It was a butt print. We all saw it. The entire area was undisturbed except for that place in the rug," Lacy, who was then the chief deputy district attorney heading up the Sexual Assault Unit under Boulder County DA Alex Hunter, said. "Whoever did this sat outside of her room and waited until everyone was asleep to kill her." 
 
 The apparent presence of that indentation went on to help form a theory that Lacy believes to this day. 
 
 The morning after Christmas in 1996, JonBenet was reported missing by her parents after they said a ransom note was found in their home. Her body bound and her mouth covered with duct tape, JonBenet was later discovered in the basement. An autopsy concluded that the cause of death was asphyxiation due to strangulation. The coroner's report stated that a blunt object had hit her so hard, there was an 8-inch fracture to her tiny skull. The report also showed some damage to JonBenet's hymen, indicating possible sexual assault. 
 
 John and Patsy Ramsey, as well as JonBenet's brother, Burke Ramsey, were the only other people known to be in the house at the time of the slaying, and for years after her death, they were each trailed by a cloud of suspicion. John and Patsy Ramsey were at one point considered persons of interest in the case by authorities. 
 
 But in 2008, Lacy -- who by then had been named Boulder County DA and taken over the investigation -- surprised even some of the most seasoned of her fellow prosecutors by exonerating the family. 
 
 Now, for the first time in eight years, the former prosecutor is speaking out to ABC News about her decision to clear the Ramsey family as her exoneration letter has now come under scrutiny following a joint investigation by the Boulder Daily Camera and Denver's KUSA-TV/9News. 
 
 Helen Davis/AP Photo 
 
 'Trying to Prevent a Horrible Travesty of Justice' 
 
 Former Adams County DA Bob Grant, one of a number of consultants on the case brought in early on by the Boulder County DA at the time, Hunter, told ABC News he was confounded by Lacy's 2008 decision. "This is craziness," he said. "This is not what prosecutors do. If prosecutors are going to exonerate someone they do it by charging someone else." 
 
 But Lacy didn't charge anyone else in the murder. Instead, armed with newly discovered DNA evidence found on JonBenet's long johns that Lacy said she believes belongs to JonBenet's unknown murderer, she sent the Ramseys a letter of apology. It read, in part, "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." The letter made international news. 
 
 The DNA evidence was discovered after Lacy sent the long johns to Bode Cellmark Forensics to be tested for touch DNA. She had attended a seminar in the summer of 2007 that explained the relatively new process. She felt it could advance the seemingly stalled case, she said. 
 
 Some Boulder Police Department detectives who had long worked on the investigation and still considered the Ramseys persons of interests were furious. 
 
 "Here’s what I was doing with the exoneration letter," Lacy explained. "I was trying to prevent a horrible travesty of justice. I was scared to death that despite the fact that there was no evidence, no psychopathy and no motive, the case was a train going down the track and the Ramseys were tied to that track." 
 
 In the 2008 letter, Lacy hung her hat on newly discovered touch DNA found on JonBenet's long johns, which she said was found to belong to an unknown male. Lacy argued that this unknown male DNA matched DNA found in two spots of blood in the crotch of JonBenet's panties. The unknown male DNA, reasoned Lacy, was the smoking gun that pointed to JonBenet's killer and that killer was not anyone in her family. Family members and 200 other potential suspects were excluded from the unknown male DNA found on the panties and long johns, she said. 
 
 Lacy's theory? When the Ramseys left to have Christmas night dinner with friends, they left the front door unlocked, and a male intruder simply walked inside and waited for hours for the family to come home. During that time, Lacy believes, he wrote the rambling two-and-a-half page ransom note. 
 
 That note referenced several lines from movies. "The Boulder police should have checked all of the video stores to see who was renting those movies and they never did," said Lacy. 
 
 However, the Boulder Daily Camera's investigation published Thursday found the DNA results in the Bode report are not necessarily as clear cut as Lacy concluded they were. According to the Daily Camera, they showed the Bode report to independent experts who say that the DNA samples from both the underwear and long johns may be composite samples from multiple people: JonBenet, an unknown male and, in one sample, a third unidentified person. To the extent composites were used in the search to identify the killer, the investigation states that the DNA profile "may be worthless as evidence." According to the paper, the possible presence of a third individual's DNA on the long johns has never been publicly revealed. 
 
 The experts also stated that the presence of the DNA on JonBenet's undergarments could have an innocent explanation because the "profiles were developed from minute samples that could have been the result of inconsequential contact with other people or transferred from another piece of clothing." 
 
 According to the paper, these opinions "cut both ways" on the competing theories of the case. They neither disprove the intruder theory nor "implicate or exonerate anyone in the family." 
 
 When asked about the impending Daily Camera report ahead of its publication Thursday, Lacy said she has taken criticism for her decision to write the exoneration letter in the past. "I've withstood worse than this," she said. "And it's nothing compared to what the Ramsey family has gone through targeted as suspects in their own daughter's murder." Lacy has not responded to ABC News' request for comment since the Daily Camera report was published. 
 
 Is JonBenet's Murder a DNA Case or Not? 
 
 There have been conflicting views over whether the mystery of JonBenet's murder can be solved by DNA alone. 
 
 Former Boulder Police Chief Mark Beckner, who headed up the department from 1998 to 2014, said in an "Ask Me Anything" session on Reddit last year that the investigation considered the DNA important, but that there was other crucial evidence in the case that couldn't be ignored. 
 
 "Mary Lacy, the DA who said the DNA exonerated them, made up her mind years before that a mother could not do that to a child, thus the family was innocent," Beckner wrote. 
 
 Stan Garnett, the current Boulder County DA, told ABC News that no case is ever solely reliant on DNA. "DNA is a part of the case," he said. "But you have to account for everything else. There were problems with crime scene, you have the ransom note ... you have debates about the cause of death -- to solve this case we have to account for all of that." 
 
 But forensic pathologist Lawrence Kobilinsky with the John Jay College of Criminal Justice, who has not worked on the case but who reviewed a summary of the Bode report put together by Boulder County investigator Andy Horita prior to the publication of the Daily Camera report, told ABC News that ignoring the unknown male DNA would be a huge mistake. "This is definitely a DNA case," he said. Kobilinsky said the markers found on the long johns are not enough of a profile to "match" those found in the panties, as Lacy wrote in her letter exonerating the Ramseys, but he would describe the markers from both the long johns and the panties as being "consistent" and noted that the DNA does belong to an unknown male. "Lacy did the right thing [in clearing the Ramsey family]," he said. 
 
 When questioned about hanging her hat on the DNA in her exoneration letter, Lacy said that she only did that because the DNA was "something tangible people could understand." The truth is, she said, she cleared the Ramseys not just based on the DNA, but also from looking at the totality of the evidence. 
 
 "There was no motive [for the parents], and no psychopathy," Lacy said. She added that she is one of only two people who have read the entire transcripts of Patsy Ramsey's psychiatric interviews, in which Lacy said she saw no indication of jealousy toward JonBenet or any violent tendencies. In 2006 when Patsy Ramsey was dying of cancer and even on her deathbed, Lacy said the distraught mother was trying to solve the death of her daughter. 
 
 Lacy, who was the Boulder County DA from 2001 until 2009, said the Boulder police investigation had ignored important evidence that pointed away from the Ramseys and instead focused on them while "trying to get the death penalty." 
 
 "They were running around the country looking for something negative on that family," Lacy said. But the Ramseys, she said, were clean. 
 
 The case is currently cold, but Boulder police say they are continuing to investigate any lead that comes in. It's recently attracted new attention this fall as the 20th anniversary of JonBenet's death approaches, and police have received hundreds of new tips. 
 
 Ed Andrieski-Pool/Getty Images 
 
 A Lacy 'Apology Tour' 
 
 People who worked with Lacy remember her bringing John Ramsey into the Boulder County prosecutor's office around the time she exonerated the family. "She wanted us all to shake hands with him. We didn't know what to say ... it was like an apology tour," said one of Lacy's former DA investigators, Gordon Coombes. 
 
 Coombes, who worked in the Boulder prosecutor's office from 2008 to 2011, said he feels Lacy got too close to the family and lost her objectivity. "It was understood that if you didn't fall in line with the intruder theory, you were out," he said. 
 
 Another investigator who worked under Lacy, Ruth Aten-Shearwood, who is now a social worker in England, said that apart from a tight network of advisers, Lacy did not allow other investigators to work on the Ramsey case. Aten-Shearwood said she found out about the exoneration letter from watching the news. Said Aten-Shearwood, "I had to pick my jaw up off the floor." 
 
 Garnett, the current Boulder County DA, is running unopposed for his third term. Of Lacy's exoneration letter, he said, "This letter is not legally binding. It's a good-faith opinion and has no legal importance but the opinion of the person who had the job before I did, whom I respect." 
 
 When asked about the Ramseys, he said, "They, like everyone else, are presumed innocent. There's not enough admissible evidence beyond a reasonable doubt to charge anyone with this crime." 
 
 The Ramseys have always maintained their innocence. Burke Ramsey, now 29, recently filed a $150 million defamation suit against a forensic pathologist who claimed he was involved in the murder on CBS’ "The Case of: JonBenet Ramsey." Burke's attorney, Lin Wood, told ABC News that Burke was falsely accused of being responsible for the death of his sister. 
 
 Wood told ABC News he has tremendous respect for Lacy and the work she did during her time as DA. "This was a one-side, unfounded and brutal attack on Lacy who served well the citizens of Boulder for eight years," he said of the Daily Camera report. 
 
 Later, he added that he is encouraged that the DNA is being called into question because "now maybe all of those other suspects who were excluded will have to be reinvestigated." 
 
 Lacy told ABC News she stands by her decision to exonerate the Ramseys, insisting that "if the evidence had been there [to prosecute them], I'd have gone for it."
– After just short of 20 years, the murder of JonBenet Ramsey is as much of a mystery as ever—especially in light of a new examination of DNA evidence. A joint investigation by the Boulder Daily Camera and 9News calls into question former District Attorney Mary Lacy's decision to exonerate the Ramsey family. At the time, Lacy concluded that DNA evidence found on JonBenet's underwear and long johns belonged to a male intruder who was not part of the Ramsey family. But now three forensic experts who examined the DNA test results and lab reports used by Lacy say they do not support her conclusion. For one thing, a sample on her underwear identified as coming from "Unknown Male 1" may in fact be a composite from multiple people and thus "worthless as evidence," says the news report. Another revelation that further muddles the picture: DNA samples on her long johns appear to come from JonBenet and at least two other people, not one, a fact that has never been revealed before. What's more, the independent experts say all of the unknown DNA may be the result of "inconsequential contact with other people," reports the Camera. With the exoneration, "I was trying to prevent a horrible travesty of justice," Lacy tells ABC. (The interview was done before these latest revelations.) "I was scared to death that despite the fact that there was no evidence, no psychopathy, and no motive, the case was a train going down the track and the Ramseys were tied to that track." Comparison to the DNA profile now in doubt was used to exonerate dozens of other potential suspects. (JonBenet's older brother is suing a pathologist who accused him of the killing.)