JonBenét Ramsey Case Encyclopedia 

DNA in JBR Case

• Where DNA Was Found. DNA originally was collected from JBR's underwear and fingernails and it later was determined to be male DNA, but not to include sperm. Because it was "degraded" it originally was not placed into the FBI Combined DNA Index System (CODIS). Subsequently, however, in December 2003 the DNA was put into CODIS. However, as technology evolved, new DNA tests were performed. We now know (paragraphs 188-197):
• DNA Under Fingernails. The DNA of an unidentified male was found under JonBenét’s fingernails. The DNA found under JonBenét’s nails does not match John, Patsy, or Burke’s DNA.
• DNA in Crotch of Underwear Likely From Saliva. The DNA of an unidentified male was found in the crotch of JonBenét’s underwear. The DNA found in JonBenét’s underwear does not match John, Patsy, or Burke’s DNA. The DNA found in JonBenét’s underwear was likely from saliva.
• Touch DNA on Pajama Bottoms. The DNA of an unidentified male was found on the left and right sides of the waistband of the pajama bottoms worn by JonBenét at the time of her death. The DNA found on JonBenét’s pajama bottoms does not match John, Patsy, or Burke’s DNA. The DNA found on JonBenét’s pajama bottoms was touch DNA.
• DNA on Underwear Consistent With DNA on Pajama Bottoms. The saliva DNA found on JonBenét’s underwear is consistent with the touch DNA found on JonBenét’s pajama bottoms. 
• Key Issues. The existing evidence about the DNA in this case is here. But there are two outstanding issues. First, is the DNA even related to the death of JBR or did it instead come from contamination by some innocent outside source? Second, even if the DNA is related to the perp, is its nature and quality such that a future perp could be convicted based on this evidence?  
• News Coverage. See the Daily Camera's index of 20 headlines/stories related to forensic analysis in this case.   
• On-Line Discussion. See Day 8: The DNA by u/AtticusWigmore at Reddit.

General Information on DNA Testing

• Primer. DNA Testing: An Introduction For Non-Scientists provides a primer on how DNA testing is done and the limitations of partial samples. DNA Forensics also provides a good overview of the technologies used for DNA testing.
• What is "Degraded" DNA? Internet poster Margoo provides a good explanation at Starting Over-JonBenet. It is particularly worth noting that degraded does not necessarily mean the DNA is old. Even fresh DNA can become degraded for a variety of reasons.
• Touch DNA.  Touch DNA, can link perpetrators to a particular crime if the perpetrator leaves enough skin cells behind on an item at the crime scene.

Legal Issues Regarding DNA

• Individuals May Legally Refuse to Provide DNA. According to CBS News, "It's perfectly legal, the police say, to ask for a DNA sample – but the sample must be given voluntarily. If you decide not to volunteer, Maddox says you may become a suspect: 'For them not to cooperate with us in solving her case, it leaves an open end out there for us to look at.'"
• DNA Evidence May Be Obtained With or Without a Search Warrant. According to Findlaw.com, "It is now settled that such evidentiary items as fingerprints, 131 blood, 132 urine samples, 133 fingernail and skin scrapings, 134 voice and handwriting exemplars, 135 conversations, 136 and other demonstrative evidence may be obtained through the warrant process or without a warrant where special needs of government are shown."
• Non-Suspects Subject to Search Warrants. According to Findlaw.com,"Another important result of Warden v. Hayden is that third parties not suspected of culpability in crime are subject to the issuance and execution of warrants for searches and seizures of evidence. Zurcher v. Stanford Daily, 436 U.S. 547, 553 -60 (1978)."
• Suspects Have Rights to Review DNA Evidence. According to a 1996 National Research Council report "The 1992 National Research Council (NRC) report stated that 'all data and laboratory records generated by analysis of DNA samples should be made freely available to all parties,' and it explained that 'all relevant information . . . can include original materials, data sheets, software protocols, and information about unpublished databanks' (NRC 1992, p 150, 148)."
• Suspects May Plea Bargain to Lesser Charges To Avoid Being Included in CODIS. A recent study showed "Estimates provide evidence that database eligible offenders are more likely to accept charge bargains and less likely to accept sentence bargains relative to defendants that do not face database collection, indicating that plea bargaining may help parties involved in plea negotiations to assist offenders in avoiding DNA database registration.

Can Race Be Inferred from DNA?

• Genetic Variation Within Races is Too Great. Some have stated that with current technology, race cannot be deduced from DNA. Specifically, "race is minor at the DNA level. The genetic differences between any two randomly selected individuals in one socially recognized population account for 85 percent of the variation one might find between people of separate populations. Put another way, the genetic difference between two individuals of the same race can be greater than those between individuals of different races--table sugar may look like salt, but it has more similarities with corn syrup." Further discussion is here, here, and here.
• 1996 Technology. Identification of race using DNA was not possible at the time of JBR killing.
• JBR DNA Not Shown to be Caucasion. Although some on the Internet claim that the DNA is "Caucasian" the arrest warrant (p. 82) in the John Mark Karr case did not state that the DNA was "caucasian" - merely that it contained a male fraction. Since Karr was caucasian, law enforcement would have had a strong motivation to include in the arrest warrant the fact that the DNA was caucasian since this would have provided a very important additional justification for making the arrest; this suggests that for whatever reason, BDA has not yet tested the JBR DNA for race even though BPD has done so in the 1997 Susannah Chase case (see below).
• 1998 Technology. But in 2003 it was reported "Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA. "It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks."
• 2003 Technology. In June, 2003, it was reported "Authorities hunting the Louisiana serial killer started focusing on black men after a DNA test indicated the killer's race, the company that did the test said yesterday. It was apparently the first such use of a test in a criminal investigation [emphasis added]. A crime-scene DNA sample was found to have come from an African-American individual of average skin tone for the African-American group, said Tony Frudakis, chief scientific officer of DNAPrint Genomics Inc. of Sarasota, Fla.....Frudakis said the test his company performed determines how much of a person's ancestry comes from each of four groups: sub-Saharan African, East Asian, Indo-European, and Native American. It indicated that the ancestry of whoever left the DNA sample from the serial killer investigation was 85 percent sub-Saharan African and 15 percent Native American, he said. From that mix, the company was able to estimate the individual's skin tone, he said."
• 2004 Technology.
• By early 2004, technology reportedly could determine race within a 3.8% margin of error. "The Boulder District Attorney's Office is reportedly looking into using this technology in the JonBenet Ramsey investigation."
• DNAPrint Genomics in Sarasota, FL has used this technology to determine the race of the suspect in the Susannah Chase murder, based on DNA collected from semen. "A representative of the Boulder Police Department has stated, “DNAPrint reported that the DNA investigators submitted is indicative of someone exhibiting features that are common to Hispanics or Native Americans. This information will assist detectives with prioritizing tips and possibly generate more investigative leads.”"
• However, it also has been reported that "DNAPrint's DNAWITNESS™ product for the law enforcement forensics market is a presumptive (investigative) genetic test, rather than confirmatory test such as human ID tests. The difference between the two is that while the former is used to help an investigator prioritize leads and make decisions, only the latter can be used to incriminate a suspect in a crime by matching a person with a crime scene sample."
• 2005 Technology. In 2005, it was reported "Researchers on Risch’s team examined the genetic signposts of white, African-American, East Asian and Hispanic subjects using a computer program that groups relevant results into clusters. Only four clearly distinguishable clusters appeared. In all but five cases, individuals within each cluster were of the same race, Risch said. “Socially defined categories of race-ethnicity correspond extremely closely to genetically defined categories,” he added.
• 2006 Technology.
• Growing Consumer Use. By early 2006, commercial use of this technology was growing, according to the New York Times: "Driving the pursuit of genetic bounty are start-up testing companies with names like DNA Tribes and Ethnoancestry. For $99 to $250, they promise to satisfy the human hunger to learn about one's origins — and sometimes much more. On its Web site, a leader in this cottage industry, DNA Print Genomics, once urged people to use it "whether your goal is to validate your eligibility for race-based college admissions or government entitlements.""
• Residual Skepticism. However, Internet poster Jayelles posted that this latest evidence has not been subjected to peer review. 
•  

Evidence of a DNA Case 

• Former BPD Police Chief Beckner's View. In 2015, former BPD police chief Mark Beckner stated "I think the only thing I would emphasize is that the unknown DNA (from JonBenet's clothing) is very important. And I'm not involved any more, but that has got to be the focus of the investigation. In my opinion, at this point, that's your suspect. The suspect is the donator [sic] of that unknown DNA, and until you can prove otherwise, I think that's the way you've got to look at it."
• Former DA Mary Lacy's View. Lacy publicly exonerated the Ramseys in 2008 based on DNA evidence. As summarized by the DailyBeast, "in 2008, a few months before she left office, Lacy apologized to the Ramseys, saying:"
• “I believe it is important and appropriate to provide you with our opinion that your family was not responsible for this crime.”
• She cited the “unknown” male DNA found in JonBenet’s underwear, consistent with that found on the waistband of her leggings. “The match of male DNA on two separate items of clothing worn by the victim at the time of the murder makes it clear to us that an unknown male handled these items,” she wrote.
• “Based on the DNA results and our serious consideration of all the other evidence, we are comfortable that the profile now in CODIS (the Combined DNA Index System) is the profile of the perpetrator of this murder.”
• DA Stan Garnett. Garnett has recently ordered additional DNA testing; it would make no sense to undertake this expense if he did not believe it would facilitate solving the case. Details reported:
• CBI To Conduct Tests. The Colorado Bureau of Investigation plans to test specific pieces of evidence according to Boulder District Attorney Stan Garnett, based on “rapidly developing area of forensic investigation. 
• YFiler Plus Testing. It is believed he was referring to a highly sensitive form of testing now available called “YFiler Plus,” and it focuses specifically on the Y chromosome.  The technique greatly enhances the resolution of trace evidence and sex assault mixtures of small quantities of male DNA amidst a much greater quantity of female DNA.  
• Items to be Tested. Analysis of the case suggests the evidence to be retested is a flashlight found in the home, duct tape on JonBenet’s mouth, ligatures on her wrists and the garrote ostensibly used to strangle her."
• Lin Wood's motion in Burke Ramsey's 2016 defamation case against CBS includes a thorough refutation of the claim that the DNA evidence is worthless (detailed in pp. 82-86).

Other Cases With An Intruder But No DNA

• Skepticism The DNA in the panties is "degraded" and hence possibly could be explained by an "Asian factory worker's sneeze" (see below). If this were genuinely a sexual assault, shouldn't there have been more DNA?
• Van Dam Case. "The prosecution could not present any evidence that directly linked Westerfield to Danielle. There were no traces of evidence that he had been in her house (as his lawyers told jurors, "not hair, not fingerprints, not fiber, not nothing"); no one saw them together; and none of his DNA was found on her body. For the prosecution a trio of criminalists linked microscopic fibers found on the body of Danielle Van Dam to hundreds found in Westerfield's home." He had been arrested because "two small stains of her blood were found on his clothing and in his motor home." (Wikipedia). Even apart from his conviction by a jury, there seems little doubt Westerfield committed this crime since "Westerfield offered to lead them to Danielle's dead body in exchange for a plea deal" (CourtTV).

Other Old Cases Recently Solved With DNA

• In a recent case of a girl murdered 12/2/96, a DNA profile was not developed and submitted to CODIS until 2005, but led to the arrest of a suspect still on probation. The Connecticut governor reported "I asked why the match wasn't made sooner. But they had tested sooner with old DNA technology, and it wasn't until new DNA testing that they were able to get a match."
• On October 4, 2006 it was announced that an English firm, The Forensic Science Service (FSS) "today begins a pilot of new technology that could revolutionise high volume crime detection by separating out mixed or poor quality samples of DNA....Where more than one individual has touched a surface – a chair arm, for instance - previous technology had a low success rate in distinguishing one person from another, particularly where only small amounts of DNA have been left behind, or the material found is of poor quality. Breakthrough new techniques developed at the FSS are set to boost crime detection rates by upward of 15%."
• Although the technology is not yet available, scientists are working on being able to reconstruct someone's face based on DNA evidence.

Skepticism

• Mary Lacy Comments. In the press conference announcing that John Mark Karr would not be charged, Mary Lacy stated: "The DNA could be an artifact. It isn’t necessarily the killer’s. In all…there’s a probability that it’s the killer’s, but it could be something else." (Transcript by Internet poster Jayelles (see Tape 3)).
• Here's what one of the investigators had to say about the DNA "evidence": "We certainly don't think it is attributable to an assailant. That's our belief. When you take everything else in total, it doesn't make sense. I've always said this is not a DNA case. It's not hinging on DNA evidence." (Rocky Mountain News, November 19, 2002.).
• Barry Scheck commented on the DNA for CNN in October 2006 (document undated).
• DocG Critique.  Internet poster DocG has critiqued the DNA evidence in detail: Hot Off the Press:Doubtful DNA The Problem with DNA  
• Limitations of CODIS Internet poster Margoo has stated the requirements for inclusion in CODIS: "Conviction is a prerequisite, but the Justice For All Act (signed into law in 2004) states: "Qualifying federal offenses now include any felony, crimes of sexual abuse as set out in 18 U.S.C. § 4221 et seq., any crime of violence, as defined in 18 U.S.C. § 16, as well as any attempt or conspiracy to commit any of these offenses. Qualifying military offenses formerly limited to felony or sex offenses, now include any offense under the Uniform Code of Military Justice for which a sentence of confinement for more than one year may be imposed." Prior to the signing of this Act, 31 states included ALL convicted felons in their eligibility requirements."
• Databank However, in Virginia, which had the nation's first and most extensive DNA databank, "the databank is supposed to contain DNA samples from anyone 14 or older convicted of a felony or punished as juveniles for felony-level crimes since July 1, 1990. Since 2003, the databank also has included anyone arrested for violent felonies." However, it was recently reported that despite this long-standing requirement, as many as one fifth of felony DNA samples may be missing statewide.
• Panty DNA May be from Manufacturing Plant. According to the same article, investigators did some tests on similar panties from the same plant and found that some also contained DNA. Since the bits of DNA molecule found mixed with JonBenet's blood were fragmented and degraded to the point that they couldn't even be sourced to any particular type of cell, contamination from the plant is the most likely explanation for its presence -- and the fact that it was never sourced to anyone connected to the family or anyone in the CODIS database. Similarly, in a book about a completely different case, it was stated: "Mandros said renowned forensics expert Dr. Henry Lee told him that he once conducted a test to see how easy it is for DNA to be transferred to an object. Doctor Lee said he bought a package of men's underwear from a department store, opened it in his laboratory, and tested for DNA evidence immediately - and he found some." (quote provided by Internet poster Freespirit).
• Reliability of DNA Tests. DNA tests can result in false positives (an individual's DNA sample is found incorrectly to "match" crime scene DNA) or false negatives for several reasons.
• DNA May Not Be Unique. "Some lawyers and experts are questioning the belief that DNA profiles are unique and can only belong to one person" according to a recent report.
• DNA Testing Errors. DNA testing errors can result in false positives and false negatives Discovery Magazine.
• Chimeras. Some individuals have 2 sets of DNA caused by the fusion of non-identical twin cells early in pregnancy. In such individuals, blood DNA may be different than skin DNA. "Twins researcher Charles Boklage, a biologist at East Carolina University, says chimerism is underdiagnosed: "The great majority of people who are spontaneous chimeras will never be detected by any means whatever. It's a spooky thing. It's very difficult to find when it's there." He estimates that about 15 percent of people were conceived alongside a twin who was then lost. As multiple conceptions grow with the rising popularity of fertility drugs, the percent of the population with double DNA may increase" Discovery Magazine.