DNA

(Note: Public knowledge of the DNA testing is incomplete. Not all DNA testing documents have been released.)



Trace amounts of DNA were recovered from various items at the scene. The DNA overwhelmingly belonged to JonBenet Ramsey herself, however some mixed profiles contained unidentified components. Some argue that one or more of these identified profiles belongs to an intruder or intruders who were in the home on the night of JonBenet's death. This theory has been contested by Boulder Police and independent scientists consulted by the Boulder Daily Camera, however it has been supported by the Ramseys' lawyers and some investigators from the District Attorney's office.

Background
Early tests with CBI

The Colorado Bureau of Investigation lab discovered a semen stain after all on a blanket inside the suitcase that had been retrieved from the basement. DNA tests matched the specimen to John Andrew, and since we had cleared him, another trail ended where it started. Intruder theorists in the DA’s office would try to weave the semen stain, the blanket, and a Doctor Seuss book also found in the suitcase into a convoluted scenario in which JonBenét was lured from her bed with the book. The plan was then to stuff her in the suitcase and take it out through the window. When it was argued that the suitcase didn’t fit through the basement window, the theory simply changed to having her taken out through a door while the suitcase was used as a stairstep to the window. It was a convenient arrangement of these facts. We kept sending the CBI evidence to test, and they were moving us to the head of the line and doing solid work. The DA’s office decided that future DNA tests would be conducted by CellMark Diagnostic in Maryland, the largest independent testing lab in the country. In my opinion, the main reason was to placate Team Ramsey. The reason was painfully obvious. CBI director Carl Whiteside had banned Ramsey experts from observing the testing procedures, so they simply opened a new line of attack, and Trip DeMuth cleared the way for them. DeMuth gave CellMark orders not to begin testing without prior authorization from the Boulder County District Attorney’s office. “The reason for this restriction is that arrangements must be made to allow a representative from the Ramsey family to be present,” he wrote.

Lacy established herself as a strong supporter of the theory that an intruder killed JonBenét, dating back to her time as a chief deputy in the district attorney's office immediately following the murder. She had already issued one public "exoneration" of the Ramseys back in 2003.

As one example, then-DA's investigator Andy Horita wrote to the lab on March 12, 2008, that his bosses were "very excited" and "pleased" about the results that were being reported, and that "we're happy with what has been done and don't see the need for additional testing" unless strongly recommended by the lab.

An email one month earlier from Horita had alluded to the lab's assignment as an exercise "to validate the existing CODIS profile by eliminating point-of-manufacture controversies."

This, independent experts have said, runs contrary to the spirit of "double-blind" standards to which such testing should adhere.

Results Summary
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List of distinct contributors (or likely contributors) to DNA profiles recovered from the scene:

Limitations of DNA Analysis
Impossible to determine biological origin of touch DNA.

Impossible to determine when a piece of DNA was deposited.

The analysts who conducted the DNA testing

"Intruder" Explanation of the DNA
Proponents of this view concede that the majority of the unidentified DNA comes from transfer/contamination, but argue that one profile ("unidentified male 1") comes from an intruder.

Proponents of this theory believe the location of the DNA on the victim's underwear to be suspicious, and discount the possibility of a transfer before or after the crime.

The Ramseys' legal team has strongly endorsed this theory. District Attorney Mary Lacy claimed this was the only valid theory of the DNA and famously stated there was "no innocent explanation" for the DNA, though the Boulder Police Department and several scientists consulted by the Boudler Daily Camera disagreed with this conclusion.

Lin Wood: "DNA found on JonBenét’s underwear was from saliva, while the DNA found on her pajama bottoms was touch DNA". This is a simplification. Amylase testing ... initially inconclusive

Also, it cannot be proven that the DNA from the long johns was not also from saliva. the biological source of "touch dna"

"Transfer/Contamination" Explanation of the DNA
Proponents of this view point to


 * the minuscule quantity of the unidentified DNA, which is consistent with the amounts of foreign DNA found on clothing even immediately after laundering.


 * the lax handling of evidence at the crime scene and during the post-mortem, for example the use of unsterilized nail clippers in the morgue.

Generally two scenarios:


 * Before the crime


 * After the crime

James Kolar suggests that “Cloth to cloth” transfer could be responsible for [the transfer of genetic material from her underwear to the leggings.] (p. 427).

Dr Henry Lee also gave his support to this theory.

1997 CBI Testing
January 15, 1997 - CBI - (DNA Typing—DQα (DQA1)/ Polymarker)

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 * Bloodstains from shirt (Marked 5A) and white blanket (16A) consistent with JonBenet.


 * Bloodstains from panties (Marked 7) mixed profile, major component JonBenet. Unidentified minor component (1 allele identified at 1 locus).


 * Right Fingernails (14L) mixed profile, major component JonBenet. Unidentified minor component (1 allele identified at 2 loci). [According to Kolar, "The right fingernails indicated that two further unique profiles were present": an unidentified male, and a unique unidentified female profile.]


 * Left fingernails (14M) mixed profile, major component JonBenet. Unidentified minor component (1 allele identified at 4 loci). [According to Kolar the left fingernails indicated an unidentified male.]


 * Bloodstain from shirt (5B) matched JonBenet.


 * Swab with saliva (14I) matched JonBenet.


 * Samples from tape (15A and 15B) matched JonBenet.


 * Bloodstains from nightgown (17A and 17C) matched JonBenet.


 * Semen stains from black blanket (23A, 23B) - DNA profiles could not be developed from the sperm fractions. However, the results for the epithelial fractions was not visible in the excerpt. According to Thomas, these stains were matched to John Andrew Ramsey. [NOTE: semen stains contain fractions of both sperm cells and epithelial cells]

Summary
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1998
December 3, 1998 - "It’s learned that five Ramsey family members have been asked to provide DNA samples to authorities. The five are not considered suspects. Sources say authorities want the DNA to see if it can be linked to unmatched DNA found in the Ramsey home." - could this be the mitochondrial DNA testing of the axillary hair by the FBI?

1999 CBI Testing
January 5, 1999 - Photographs were taken of the underwear and the cutting taken from the crotch area of the underwear.

May 17, 1999 - CBI


 * Cuttings from panties (Marked 7-3 to 7-6) - 7-4 matched JonBenet Ramsey. No other interpretable profiles.


 * Cuttings from long johns (Marked 6-B1, 6-B2 and 6C) - No interpretable profiles.

2001
According to the Boulder Daily Camera, a round of DNA testing occurred in 2001 "after a legal battle in Colorado’s courts". According to the newspaper, "JonBenet’s underwear is analyzed again resulting in between one and two markers out of 13 being defined".

2002
Some time prior to 2002 - FBI extracts mitochondrial DNA profile from axillary hair. Consistent with Patsy Ramsey or a member of her maternal line.

December 10, 2002 - Andy Horita first contacts CBI about what would be needed to submit a profile to CODIS. He is informed that Boulder Police submitted a profile (via the Denver Crime Lab) "quite a while ago" to the CBI for comparison within Colorado (though not with the entire national database). According to CBI's guidelines " profiles with fewer than 5 autosomal loci should not be entered into CODIS as they would never be able to return matches". It is unclear if or when a profile was developed of sufficient quality to submit to the state database.

2003 Denver Crime Lab Testing
Laberge Denver Crime Lab deduces Unidentified Male 1 (report has never been made public)

2008 Bode Lab Testing
March 24, 2008 - Bode Laboratories

Touch DNA testing. Quantities much smaller.


 * Long Johns (top right exterior) (2S07-101-05A) - mixed profile including JonBenet and at least one male contributor. Unidentified male 1 was consistent but remaining component should not be considered single-source profile. Probability of randomly selecting an unrelated individual from the US population who would also be consistent: 1 in 6200.


 * (2S07-101-05B) - mixture including JonBenet and at least one male contributor. Unidentified male 1 "cannot be included or excluded".


 * (2S07-101-05C) - mixture including JonBenet and at least one other contributor. Minor contributor is "low level, contains allelic dropout and therefore is not suitable for comparison".


 * (2S07-101-05D) - mixture including JonBenet and at least two other contributors including one male. "Due to the complexity of this mixture it was deemed unsuitable for any further comparison purposes".


 * The cutting from the panties (2S07-101-06A, -06B, and -06C) - partial profile consistent with JonBenet.


 * Nightgown (bottom front) (2S07-101-07A) - mixture including JonBenet and at least one male contributor. Burke Ramsey and Patsy Ramsey cannot be excluded. Probability of randomly selecting an unrelated individual from the US population who would also be consistent: 1 in 50,000.


 * Nightgown (left shoulder, front and back) (2S07-101-07B) - mixture including JonBenet and at least one other contributor. Burke Ramsey and Patsy Ramsey cannot be included or excluded.


 * (2S07-101-07C) - mixture including JonBenet and at least one male contributor. Burke Ramsey and Patsy Ramsey cannot be included or excluded.


 * (2S07-101-07D) - mixture including JonBenet and at least one male contributor. Burke Ramsey cannot be included or excluded.
 * Other evidence received by Bode but "not processed at this time": ligature from neck, broken paintbrush handle, ligature from wrist, Wednesday panties,

2008 CBI Testing
June 26, 2008 - CBI - http://jonbenetramsey.pbworks.com/w/file/fetch/130877820/20080626-CBIrpt.pdf


 * Fingernails (14L and 14M) - could not be analyzed due to insufficient sample remaining.

(Miscellaneous items from suspects were also tested)

2009 CBI Testing
January 13, 2009 - CBI - http://jonbenetramsey.pbworks.com/w/file/fetch/130877823/20090113-CBIrpt.pdf


 * Neck ligature (Item 8) mixed profile, major component JonBenet. Unidentified minor component ("unidentified male 1" was excluded). According to Kolar this was a 7-marker male profile.


 * Wrist ligature (Item 166) mixed profile, JonBenet was consistent. Unidentified minor component ("unidentified male 1" was excluded). According to Kolar this was a 6-marker male profile.

(Miscellaneous items from suspects were also tested)

2018 CBI Testing
June 29, 2018 - Boulder Daily Camera reports "a new wave of DNA testing" has been completed, "although investigators are not talking about what was learned".

"We did meet with CBI and the district attorney's office, and we had a general discussion about evidence in the Ramsey case, including new technology and DNA testing," Testa said. "And we are going to take a look at the new technology, and see how they may help us further this investigation."

The testing would be conducted with new, more sensitive "kits" required of crime labs by the FBI - In 2017, the CODIS lab began requiring more sophisticated DNA tests that identify at least 20 individual points of comparison — as opposed to the standard of 13 required since 1997. All accredited DNA labs, including the one operated by the CBI, are required to use the new testing kits.

The underwear DNA
Timeline of DNA Testing of the underwear

1997 — DNA collected from a blood spot on JonBenet Ramsey’s underwear described as contaminated.

1999 — FBI releases new technology called Short Tandem Repeat to profile DNA. It uses 13 markers to raise the probability that a randomly selected individual would match it is one in 1 quintillion.

2001 — The new testing is allowed after a legal battle in Colorado’s courts, and JonBenet’s underwear is analyzed again resulting in between one and two markers out of 13 being defined.

2003 — Second blood spot on JonBenet’s underwear tested resulting in between nine and 10 markers on the spot to be defined. That genetic fingerprint meets the threshold to be placed into a national database, Combined DNA Indexing System or CODIS, which holds DNA profiles of those convicted in most states of certain crimes. No match has been made.

2008 - Bode Laboratories testing

Common Questions about the DNA

 * What is "Touch DNA"?

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 * Can Genealogical DNA Be used like with the Golden State Killer?

Unlikely.


 * If the DNA could be useless, why has it been used to clear people?

Police have repeatedly stated that no one has been cleared on the basis of DNA alone. Chief Mark Beckner specifically said: "Exonerating anyone based on a small piece of evidence that has not yet been proven to even be connected to the crime is absurd in my opinion. You must look at any case in the totality of all the evidence, circumstances, statements, etc. in coming to conclusions."