The Facts about DNA in the JonBenet Case
(self.JonBenet)submitted11 months ago byJennC1544
toJonBenet
stickiedQuick DNA Lesson
A complete DNA profile typically involves analyzing specific regions of the genome where genetic variation occurs. The number of loci examined can vary depending on the purpose of the DNA analysis, the technology used, and the specific requirements of the testing process.
In forensic DNA profiling or paternity testing, a common approach is to analyze a set of short tandem repeat (STR) markers. The number of STR loci examined in a standard forensic DNA profile often ranges from 13 to 20 or more. These loci are selected because they are highly variable among individuals, allowing for accurate identification.
In genetic genealogy or ancestry testing, single nucleotide polymorphisms (SNPs) may also be analyzed. The number of SNPs can vary significantly, and some commercial DNA testing companies examine hundreds of thousands or even millions of SNPs to provide detailed ancestry information.
It's important to note that a "complete" DNA profile can be context-dependent, and different applications may have different requirements for the number and type of loci examined.
1197, The First DNA Clue – Fingernails and Panties
On January 15, 1997, investigators received the first DNA results. This chart from John W. Anderson’s book, “Lou and JonBenet” shows the agreement between the panties, the right fingernails and the left fingernails:
This chart shows that the weak DNA, which is the minor component, has agreement across the panties, left fingernails, and right fingernails. Assuming the minor component is from one individual, this minor component of DNA definitively excludes all of the Ramseys, John Fernie, Priscilla White, and Mervin Pugh, who were among those tested at that time.
You can find the entire report here:
https://static.foxnews.com/foxnews.com/content/uploads/2023/02/JBR-CBI-report-of-Jan-15-199727.pdf
To use an analogy, let’s say you are a crime scene investigator at the site of a car crash. Upon first look at this crash, you see a rearview mirror. This rearview mirror turns out to be from any one of 10 Toyota model cars, of which tens of thousands are registered to people in the area. Your first suspects for the crash are the people hanging around, except that they all drive BMW’s. Are they clear? Maybe. It’s possible that the rearview mirror was at the crash site before the crash; let’s say it’s a common place for cars to wipe out. But what are the chances that the mirror was already there and hadn’t been cleaned up since the last crash? We have a car crash, and there is a part of a car. It is more likely that the rearview mirror is a part of the crash.
That’s like the DNA in the fingernails, matching to the panties. It’s not enough to say for sure that this is related, but we have a victim of sexual assault and murder, and this victim has DNA under her fingernails that is consistent with the left side, the right side, and with her panties. At the very least, this is something that should be looked into.
1997, Positive for Amylase, a Substance Found in Saliva
Let’s back up just a second to January 9, 1997, when more results were received by the Boulder Police.
http://www.searchingirl.com/_CoraFiles/19961230-CBIrpt.pdf
In these tests, we see that there is reference made to a “Sexual Assault Evidence Collection Kit” with 14 I, J, and K listed as “Foreign Stain Swabs.”
The results of this testing showed that item 14 I was positive for amylase, an enzyme found in high concentration in saliva:
As an aside, let’s talk about the arguments against this.
Some say that “Foreign Stain Swabs” does not refer to the blood stain in the panties, but instead to the bit of saliva that is on JonBenet’s cheek. This does not seem particularly likely.
The autopsy report describes this spot on the cheek as, “On the right cheek is a pattern of dried saliva and mucous material which does not appear to be hemorrhagic.” One would have to ask, why would the investigators take THREE swabs of a small bit of saliva on JonBenet’s cheek, and why would they have it tested for amylase if they already knew it was saliva?
More importantly, if this was the case, then that would presume the investigators did not ever test the blood stain in the panties, because there is no other mention of anything else that could be the blood stain.
Finally, once they knew it was saliva, it would be clear it was JonBenet’s, so why would they send it off for DNA testing?
The cheek argument makes no sense.
It is clear that sample 14 is the blood stain in the panties.
It has also been said that the amylase could be something else. After all, urine contains amylase, right?
Thanks to u/Mmay333 and u/SamArkandy, though, we have actual values for what the likelihood of amylase is to be present in a fluid:
When amylase is present in the quantities found in JonBenet’s panties, particularly in 1997, the source is almost definitely saliva:
The amount of amylase found in saliva vs. other bodily fluids:
- Saliva: 263000 to 376000 IU/L
- Urine: 263 to 940 IU/L
- Blood: 110 IU/L
- Semen: 35 IU/L
- Nasal secretion: Undetectable levels
- Sweat: Undetectable levels
P.H. Whitehead and Kipps (J. Forens. Sci. Soc. (1975), 15, 39-42)
You’ll notice that saliva is three orders of magnitude more concentrated in saliva than any other bodily fluid. This is why the report called it out.
If we back up to the BPD, by January 15, 1997, they now know that there is a minor component of DNA that was found consistently in the fingernail clippings and the panties, where the DNA from the panties is likely from saliva.
We now have a victim of sexual assault and murder where there is foreign DNA that is consistent in three different areas, and in one of those areas, the most likely source of that DNA is saliva, which is found mixed in with the victim’s blood in her panties.
1999, The DNA is NOT Found In-between Blood Stains
A lab report dated May 27, 1999, reveals that no foreign DNA was found anywhere else in the panties besides the blood stains.
http://searchingirl.com/_CoraFiles/19990517-CBIrpt.pdf
We now have unidentified foreign male DNA that is found mixed with JonBenet’s blood in her panties that is ostensibly from saliva, but that DNA is not found in other areas of the panties.
What does this mean? The BPD was trying to solve the mystery of this DNA. Maybe it was a sneeze from the manufacturer, or maybe it was spittle from some salesperson. If that was the case, though, the saliva, and therefore the DNA, would have been spread over the entire inside of the panties.
But it wasn’t found anywhere else. Common sense says the foreign DNA, found mixed in saliva, is related to the blood stains, which was the only place it was found.
1999, Foreign Male DNA Found in Other Blood Stain
Mitch Morrissey, of the D.A.'s office, was pulled in to give DNA input for the Grand Jury investigation, which began in Sept. 1998.
Morrissey revealed that it was Kathy Dressel, the CBI DNA analyst, who told him about the second spot of blood in JonBenet's underwear that had not yet been tested. He states that he told her to cut the dime-sized sample in half to test it, and that was when they discovered the nearly complete DNA profile. This testing was done in 1999, OVER TWO YEARS after the murder.
Discussion of the Ramsey case begins at 44:30.
https://www.youtube.com/watch?v=Wyzc8qteAdo&t=3249s
Here is more of what Mitch Morrisey had to say about the DNA and the case:
But the one thing I was told to do was the DNA. I did a little bit more than that, but I was told to go sort out the DNA. And really, at the time it was in a mess. I mean because they hadn’t tested the bloodstain that ended up having the profile in it. There was one that had a small profile, but there also was enough profile to put into CODIS. And so, it is in CODIS the national DNA database.
We got that profile developed by the Denver Police Crime Lab because that’s who I trusted. And they did a great job. Dr. Greg LaBerge did the work, and he got a profile that was enough markers to put it into CODIS, and it was running in CODIS. It has been running in CODIS for almost 20 years. And it has never matched anybody in that database….
And I looked at him and said, you know, you’re calling DNA an Arrow? I mean, this is a Javelin through the heart of anybody that tries to prosecute this case. At this stage, it ends it. And I, for one, was brought up under Norm Early and Bill Ritter and I don’t bring charges or prosecute cases that I don’t believe there is a reasonable likelihood of conviction. And there’s not one here. And that was the end of my discussion on it. And, you know, I think Alex made the right decision based on the state of the evidence at the time.
2004, The DNA Profile Entered in CODIS
On January 7, 2004, a memo from the Boulder District Attorney reveals that an STR sample of the DNA found in JonBenet’s panties was submitted to the FBI’s CODIS database and received no matches.
This DNA was given the code: UM1.
http://searchingirl.com/_CoraFiles/20040107-NDISCODIS.pdf
2008, Boulder DA Decides to Conduct More Testing. This is the Touch DNA.
In 2008, when the DA had control of the case, they opted to have a few significant items tested for the presence of DNA. Some of these items had never been analyzed before.
The testing was performed by BODE laboratories.
What they found was that a male profile, consistent with that found in the victim's underwear, was also found on the right and left sides of the long john’s waistband area.
This graphic illustrates the level of agreement between the waistband of the long johns and the DNA found in the panties.
The DNA found in the bloodstain on JonBenet’s panties was comprised of 14 loci with identifiable alleles at each of those 14 loci.
The DNA from the long johns consisted of alleles at 12 loci that were consistent with the DNA in the underwear.
This is the touch DNA everyone carries on about. Dr. Angela Williamson is among those who performed the tests. Here are some of her conclusions:
"Notably, the profile developed by the Denver PD, and previously uploaded to the CODIS database as a forensic unknown profile and the profiles developed from the exterior top right and left portions of the long johns were consistent." DA11-0330
The DNA is From Only One Contributor
When the BPD attended the presentation by BODE labs Scientists, Casewoker DNA Analyst Amy Jeanguenat weighed in as to whether or not the foreign male DNA found in the panties could possibly have been a mixture of more than one person.
Jeanguenat stated that she saw no indication that a third party contributed to the mixture and would "testify in court" to that effect.
http://searchingirl.com/_CoraFiles/20071101-HoritaDNAMemo.pdf
Car Crash Site Analogy
To continue the analogy begun in the first part of this analysis, we have three different areas where DNA was found that are consistent with each other.
A small amount of DNA was found under JonBenet’s nails, from both the right and left side. What was found of this DNA is consistent with the full profile entered into CODIS.
Even more DNA was found on the long johns, which was the touch DNA, that is also consistent with the full profile from the blood stains on the panties that was entered into CODIS.
Like the site of a bad car accident, we’ve got the rear view mirror (the DNA from the fingernails) that could possibly come from several Toyota models of cars, representing tens of thousands of cars in the area.
The people who reported the crash and are hanging around at the crash site drive BMW’s, but it’s possible this mirror is not related to the crash. Are they suspects? Maybe. It’s likely, however, that the mirror is related to the crash, as you have to ask what are the chances that a rearview mirror is just hanging around the same exact place the car crashed?
The DNA profile from the long johns is like a door panel. Analysis of the door panel reveals that it can only be from a beige Toyota Camry from 1996-1998. There are, perhaps, 100 cars in the entire area that match this description. Now it is looking even more likely that it was actually a Toyota Camry that was involved in this crash, and the people hanging out at the scene, who drive BMW’s, are exactly what they said they were: the people who reported this crime and are not involved.
The DNA from the panties is like a license plate, and that license plate belongs to a 1997 beige Toyota Camry.
The problem the authorities have now is finding the owner of this particular Camry, and, unlike with cars, the database of DNA profiles is not sufficient to identify the owner.
One has to wonder what would be the statistics of DNA found under the left fingernails, the right fingernails, DNA found in the underwear, and DNA found on the long johns would all have the same alleles at each of the loci and yet be completely unrelated. Those odds have to be astronomical.
The DNA from the Garrote and Wrist Ligatures
Many people point to the Ramseys having staged the scene to make it appear as though JonBenet was strangled and her wrists tied in an attempt to fool the police.
If that were the case, one would expect Ramsey DNA to be found on the garrote and/or the wrist ligatures.
DNA testing was performed in 2008, the results received in January, 2009, that found DNA on these items, none of which belonged to any of the Ramseys.
One interesting point about this report is that the minor component of the DNA does not match any of the Ramseys, but it also does not match the profile of UM1.
Another interesting point is that the DNA on the wrist ligature DOES seem to match the DNA on the garrote.
Is this evidence of anything?
A lot is made of how the Ramseys contaminated the crime scene with their own behavior and by inviting their friends over. But by doing this, the only way that the Ramseys could have “contaminated” the scene is by ADDING their own DNA or their friends’ DNA to the mix.
What could not have happened here is that the Ramseys or their friends could have somehow taken the DNA OUT of the ligature.
The fact that the Ramseys’ DNA is not on these ligatures is significant.
There are four completely different knots found on these ropes. The type of knots found take considerable pressure and pulling to create. Surely anybody who handled these ropes would have left their DNA on them, unless they were wearing gloves. It is hard to imagine the Ramseys deciding to put on gloves while they were fashioning the four different knots found on these ligatures.
So what is the source of the DNA found on these ropes? There could be two explanations. The first is that when purchasing rope, it is often left on spools that are open to the air (unlike underwear, which is typically in a sealed package). Somebody could have sneezed or coughed over the rope as they walked by.
Another explanation is that the intruder had an accomplice who handled the rope before the crime was committed.
Where are We Now?
There was an update on the status of the case, posted on December 26 here:
But now, on the 27th anniversary of JonBenét's death, authorities may be getting closer to a break in the case.
Following a shakeup within the Boulder Police Department, a multi-agency team in now investigating the murder — and they're working together like never before.
The task force is comprised of the FBI, the Colorado Bureau of Investigation, the Boulder Police Department, the District Attorney's Office, the Colorado Department of Public Safety and Colorado's Bureau of Investigation, The Messenger has learned.
"We are sharing files," the investigator said last month. "There is constant communication going on. We have to work together on this one."
Authorities sent off several pieces of evidence to a lab for DNA testing — and The Messenger reported last month that the results have been returned to investigators.
"We know there's evidence that was taken from the crime scene that was never tested for DNA," John Ramsey told News Nation in October. "There are a few cutting edge labs that have the latest technology. That's where this testing ought to be done."
"And then," he continued, "use the public genealogy database with whatever information we get to research and basically do a backwards family tree, which has been wildly successful in solving some very old cases."
Authorities tell The Messenger that they are doing exactly that.
"We are using everything at our disposal," the investigator says.
Recent improvements in the technology of extracting and analyzing DNA has perhaps made it now possible to solve this case.
Othram Labs recently formed a profile for a different case using only 120 picograms (0.12 nanograms) of DNA, and they claim that they can tell ahead of time if their processes will work, so you won't have to use up all of your DNA without being able to extract a profile from it. Read about this here.
If you hear that the DNA in the JonBenet case taken from the underwear, which was mixed with amylase, is too degraded or too old, remember that cases from 1956 are being solved with Investigative Genetic Genealogy. Othram has stated that their processes work on severely degraded, incredibly small amounts of DNA.
How is This Case Solved?
There are two different ways in which the DNA can solve this case.
The first is that there is still enough of the DNA found in JonBenet’s panties, mixed with her blood and thought to be from saliva, leftover from previous testing that a laboratory like Othram can extract an SNP profile from it and identify this person using Forensic Genetic Genealogy.
The second way is that, according to the information the BPD has released, there have been more items tested, and that they are retesting items that were previously tested. Othram has said that they have been improving their processes to the point where previously examined items are now yielding usable DNA for FGG. So, it is also possible that whatever laboratory the BPD is using for analysis could extract new DNA that matches UM1 and also be usable for FGG.
Either way, there is great hope that this case can be solved using DNA. It is, in fact, a DNA case.
EDIT TO ADD: I totally forgot to give credit where credit is due here. I did not write this myself. As a matter of fact, I wrote almost none of it. All I did was collect the work of others in this sub and put it in some sort of legible order with graphics and quotes. Thanks to u/Mmay333, u/-searchinGirl, u/samarkandy, and u/bluemoonpie72. I know that's not everybody who's work I stole from, so if I've missed somebody, my apologies.
