CC - DNA from mixed samples can be se...

CC - DNA from mixed samples can be separated

Posted in the JonBenet Ramsey Forum

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deb

Minneapolis, MN

#1 Feb 9, 2011
Abstract
With the advent of PCR-based STR typing systems, mixed samples can be separated into their individual DNA profiles. Quantitative peak information can help in this analysis. However, despite such advances, forensic mixture analysis still remains a laborious art, with the high cost and effort often precluding timely reporting. We introduce here a new automated approach to resolving forensic DNA mixtures. Our linear mixture analysis (LMA) is a straightforward mathematical approach that can integrate all the quantitative PCR data into a single rapid computation. LMA has application to diverse mixture problems. As demonstrated here on laboratory STR data, LMA can assess the quality and utility of its solutions. Such rapid and robust methods for computer-based analysis of DNA mixtures may help in reducing crime. http://www.ncbi.nlm.nih.gov/pubmed/11714147
deb

Minneapolis, MN

#2 Feb 9, 2011
Abstract
The use of multiplex PCR and fluorescent dye technology in the automated detection and analysis of short tandem repeat loci provides not only qualitative information about the profile--i.e. which alleles are present--but can also provide quantitative information on the relative intensities of the bands, and is therefore a measure of the amount of amplified DNA. The availability of this quantitative information allows for the interpretation of mixtures in a detailed way which has not been previously possible with many other human identification systems. In this paper we present a simple approach to the resolution and analysis of mixed STR profiles resulting from the testing of mixed biological stains in forensic casework and highlight factors which can affect it. This approach requires a detailed knowledge--gained through a mixture of experiments and validation studies--of the behaviour of each locus within the multiplex systems described. We summarise the available data from previously published experimental work and validation studies to examine the general principles underlying this approach.
http://www.ncbi.nlm.nih.gov/pubmed/9493345

Y-STR Human Chromosome, Forensic Value
Sometimes data cannot be obtained from autosome primers because of mixed female and male DNA (rape, sexual assault, mixed blood or other fluids at the crime scene). However, Y-STR typing enables detection and differentiation of male genetic indicators from the autosomal female genetic factors. Further, in mixed samples of female and male DNA, if the female DNA amount exceeds >10:1, and autosomal STR typing is done, the female genetic profile masks the male genetic profile. Of special interest is the fact Y-STR typing can detect multiple variations of the DNA when multiple assailants are involved in a rape (Kobilinsky et al., 2007).
DNA experts and forensic pathologists have selected several sites on the Y-chromosome where detailed base pair analysis is not needed. Instead, the lengths of the sites are determined, measured and compared, and this establishes prototypes for the Y haplotypehttp://www.suite101.c om/content/y-chromosome-forens ics-and-other-essential-facts- a199171

mixed samples -- this is the problem of mixed blood, common at crime scenes, between the victim and suspect. The autorad will show a superimposition of bands on top of one another, but PCR methods exist to screen out and amplify the different parts of the mixture if you have known samples from the contributors
http://www.drtomoconnor.com/3210/3210lect06.h...

C. Short Tandem Repeats (STR)
Short tandem repeats, as the name implies, are similar to VNTRs described above, except that the repeated units are much shorter. Those fragments chosen for forensic use generally have a tandem repeat unit of only three to four base-pairs, which may be repeated in the DNA molecule from a few to dozens of times. Clearly, units of only three to four base pairs are extremely small; this presents both an advantage and a problem in forensic-DNA work. The advantage is that only small amounts of even badly degraded DNA may be sufficient for forensic use. The problem is that a very small sample of very short DNA segments - the short tandem repeats - needs to be increased in size for analytical convenience and efficiency. This is done through the use of a relatively new technology known as the polymerase chain reaction.

With the advent of PCR-based STR typing systems, mixed samples can be separated
into their individual DNA profiles
http://www.trueallele.net/documents/publicati...
Charlie Chan

Lihue, HI

#3 Feb 10, 2011
deb wrote:
Abstract
With the advent of PCR-based STR typing systems, mixed samples can be separated into their individual DNA profiles. Quantitative peak information can help in this analysis. However, despite such advances, forensic mixture analysis still remains a laborious art, with the high cost and effort often precluding timely reporting. We introduce here a new automated approach to resolving forensic DNA mixtures. Our linear mixture analysis (LMA) is a straightforward mathematical approach that can integrate all the quantitative PCR data into a single rapid computation. LMA has application to diverse mixture problems. As demonstrated here on laboratory STR data, LMA can assess the quality and utility of its solutions. Such rapid and robust methods for computer-based analysis of DNA mixtures may help in reducing crime. http://www.ncbi.nlm.nih.gov/pubmed/11714147
Hi Deb,
Yes it can, and they have done it, but not always, and it is not common even today. However, you need enough of a quantity, and you actually need to be lucky. It could NOT be separated in 1997, and they do not have a DNA profile in the JB case from any of the mixtures they had.

One way they do it, is IF you have two different typs, say skin cells and blood cells, and enough of it, you can separate them using centriputal force, allowing the heavier cells to separate from the lighter cells.

The ONLY DNA profile they have in the JB case, is that of the Touch DNA, which is highly questionable, because they got it more than 10 years after the fact.

If you think that there is an unknown DNA profile in the JB case, please find us a source.

Again, in a mixture, or from a mixture, you can definitely eliminate a person as a possible contributor, but you CANNOT match a person's profile with a mixture and say his DNA is definitely in that mixture. In eliminating the Ramsey family from the mixture found, it is POSSIBLE, but highly unlikely because they are direct family members.
CC
deb

Minneapolis, MN

#4 Feb 10, 2011
Charlie Chan wrote:
<quoted text>
Hi Deb,
Yes it can, and they have done it, but not always, and it is not common even today. However, you need enough of a quantity, and you actually need to be lucky. It could NOT be separated in 1997, and they do not have a DNA profile in the JB case from any of the mixtures they had.
One way they do it, is IF you have two different typs, say skin cells and blood cells, and enough of it, you can separate them using centriputal force, allowing the heavier cells to separate from the lighter cells.
The ONLY DNA profile they have in the JB case, is that of the Touch DNA, which is highly questionable, because they got it more than 10 years after the fact.
If you think that there is an unknown DNA profile in the JB case, please find us a source.
Again, in a mixture, or from a mixture, you can definitely eliminate a person as a possible contributor, but you CANNOT match a person's profile with a mixture and say his DNA is definitely in that mixture. In eliminating the Ramsey family from the mixture found, it is POSSIBLE, but highly unlikely because they are direct family members.
CC
Believe what you want, but what you choose to believe is not factual - the DNA was entered in CODIS long before TDNA was found. Whether it was a mixture or not, it was entered.
Whether you care to believe it or not, it was entered.

Prove to me that it was not entered. Call Boulder DA's office.
This is a fact that is well known so if you can prove otherwise, let us know.

They had eliminated many suspects before the TDNA based on the DNA they had, including JMK. So how did they eliminate everyone without the DNA?

Prove it.

“WAX ON”

Since: Jul 10

WAX OFF

#5 Feb 10, 2011
10 markers Deb, not 13, and the 10th one was weak. I'm sure you know where to find this information since it was a news event when it happened and they finally got it in CODIS.
deb wrote:
<quoted text>
Believe what you want, but what you choose to believe is not factual - the DNA was entered in CODIS long before TDNA was found. Whether it was a mixture or not, it was entered.
Whether you care to believe it or not, it was entered.
Prove to me that it was not entered. Call Boulder DA's office.
This is a fact that is well known so if you can prove otherwise, let us know.
They had eliminated many suspects before the TDNA based on the DNA they had, including JMK. So how did they eliminate everyone without the DNA?
Prove it.
Biz

Brandon, FL

#6 Feb 10, 2011
DrSeussMd wrote:
10 markers Deb, not 13, and the 10th one was weak. I'm sure you know where to find this information since it was a news event when it happened and they finally got it in CODIS.
<quoted text>
It was reported back in 1995 that they had a full DNA profile. After the touch DNA analysis was compared there was absolutly no doubt....a full profile of the killer's DNA
Biz

Brandon, FL

#7 Feb 10, 2011
Correction on previous post, meant to type 2005, not 1995. ugh.
Here is the link. There was a full DNA profile back in 2005
http://www.cbsnews.com/stories/2004/12/16/48h...

“WAX ON”

Since: Jul 10

WAX OFF

#8 Feb 10, 2011
That was 9 years after the murder (2005). If they had had all 13 markers they wouldn't have had to wait 9 years to get it in the system, Deb. They originaly had 7, then as testing got more sophisticated they got 8 and 9, and then finally 10 in 2005, wjhen it was entered. Are you using 48 hours as a source?
Biz wrote:
<quoted text>
It was reported back in 1995 that they had a full DNA profile. After the touch DNA analysis was compared there was absolutly no doubt....a full profile of the killer's DNA
Biz

Brandon, FL

#9 Feb 10, 2011
DrSeussMd wrote:
That was 9 years after the murder (2005). If they had had all 13 markers they wouldn't have had to wait 9 years to get it in the system, Deb. They originaly had 7, then as testing got more sophisticated they got 8 and 9, and then finally 10 in 2005, wjhen it was entered. Are you using 48 hours as a source?
<quoted text>
Here is a source from Koldkase back in 2006
Originally Posted by KoldKase
During the Bode Tech media blitz, the woman who was the technician who processed the "touch" DNA said in an interview, when asked specifically about this, that they have a full 13 marker profile. She even said they didn't have to do the replicating process, as they found enough full strands without it.

“WAX ON”

Since: Jul 10

WAX OFF

#10 Feb 10, 2011
I wasn't disputing 'touch DNA'. We were talking when the original DNA acquired enough markers to meet the CODIS guidelines, when it was originally entered into CODIS, how many markers it had, and why it took 9 years IF they had 13 markers in 1996 to get it entered into CODIS. AND, touch DNA testing was in 2008, wasn't it?
Biz wrote:
<quoted text>
Here is a source from Koldkase back in 2006
Originally Posted by KoldKase
During the Bode Tech media blitz, the woman who was the technician who processed the "touch" DNA said in an interview, when asked specifically about this, that they have a full 13 marker profile. She even said they didn't have to do the replicating process, as they found enough full strands without it.
candy

East Lansing, MI

#11 Feb 10, 2011
What a bunch of idiots. That DNA has SAT AND SAT in CODIS for EIGHT LONG YEARS WITHOUT A MATCH, FOURTEEN YEARS IN TOTAL. And it sure is NOT the current DA who thinks that DNA belongs to "the real killer."
Charlie Chan

Lihue, HI

#12 Feb 10, 2011
deb wrote:
<quoted text>
Believe what you want, but what you choose to believe is not factual - the DNA was entered in CODIS long before TDNA was found. Whether it was a mixture or not, it was entered.
Whether you care to believe it or not, it was entered.
Prove to me that it was not entered. Call Boulder DA's office.
This is a fact that is well known so if you can prove otherwise, let us know.
They had eliminated many suspects before the TDNA based on the DNA they had, including JMK. So how did they eliminate everyone without the DNA?
Prove it.
Hi Deb,
Without the official DNA reports, there is nothing to prove. However, you CAN eliminate a suspect as a possible contributor from a mixture. What you CANNOT do from a mixture, is positively match a singular profile with a mixture.

As far as inputting the unknown DNA into CODIS, you must remember that it is unmatched, AND I am not sure if you have any UNKNOWN DNA in CODIS. I think what they did with CODIS, is try to find an existing DNA that matched the unknown mixture, but we will never know until they release the lab findings.

The statement made, that the Touch DNA matched the fingernail DNA and the bloodstain DNA must be false, because I really doubt that they got a profile from the mixture in the bloodstain, and they could not get a profile from the fingernails.
CC
Charlie Chan

Lihue, HI

#13 Feb 10, 2011
Biz wrote:
<quoted text>
It was reported back in 1995 that they had a full DNA profile. After the touch DNA analysis was compared there was absolutly no doubt....a full profile of the killer's DNA
IF it was the killer's DNA, then the DNA had to belong to a Ramsey. There were only four proven people in the home, and ONE was murdered. There is no credible evidence of any intruder.
PERRY

Maidenhead, UK

#14 Feb 10, 2011
Please provide the proof there were four people in the house when JB was murdered.
Charlie Chan wrote:
<quoted text>
IF it was the killer's DNA, then the DNA had to belong to a Ramsey. There were only four proven people in the home, and ONE was murdered. There is no credible evidence of any intruder.

“If life gives you melons”

Since: Nov 06

You might be dyslexic

#15 Feb 10, 2011
candy wrote:
What a bunch of idiots. That DNA has SAT AND SAT in CODIS for EIGHT LONG YEARS WITHOUT A MATCH, FOURTEEN YEARS IN TOTAL. And it sure is NOT the current DA who thinks that DNA belongs to "the real killer."
Amen Candy!
Charlie Chan

Lihue, HI

#16 Feb 10, 2011
deb wrote:
<quoted text>
Believe what you want, but what you choose to believe is not factual - the DNA was entered in CODIS long before TDNA was found. Whether it was a mixture or not, it was entered.
Whether you care to believe it or not, it was entered.
Prove to me that it was not entered. Call Boulder DA's office.
This is a fact that is well known so if you can prove otherwise, let us know.
They had eliminated many suspects before the TDNA based on the DNA they had, including JMK. So how did they eliminate everyone without the DNA?
Prove it.
Hi Deb,
On Codis, did you say the 1997 claimed profile in the JB case was put into CODIS? If so, can you provide a source of this information?

As I understand it, the ONLY profile they have is from the Touch DNA.

Now, IF they have a profile from the blood stain or under the fingernails that postively match the Touch DNA attained in 2005, there is a very good argument about a possible intruder.
CC
candy

East Lansing, MI

#17 Feb 10, 2011
That DNA was not put into CODIS until January, 2003.
Charlie Chan

Lihue, HI

#18 Feb 10, 2011
Hi Deb,
I have been using the google search engine, without any success. No DNA profile in 1996, 1997. No DNA profile that has been put into Codis. I am beginning to think your sources are not good. The only DNA profile I could find, is the questionable Touch DNA found 10 years later. So, if there is no profile, they could not match anything positively.
CC
candy

East Lansing, MI

#19 Feb 10, 2011
As soon as this DNA was identified in the underwear, they had only 9-10 markers. Not enough to enter it into CODIS in 1997, but enough with advances in replication to enter into CODIS in 2003 by Lacy.
Charlie Chan

Lihue, HI

#21 Feb 10, 2011
candy wrote:
As soon as this DNA was identified in the underwear, they had only 9-10 markers. Not enough to enter it into CODIS in 1997, but enough with advances in replication to enter into CODIS in 2003 by Lacy.
Hi Candy,
That is Lacy, and her credibility is about as bad as the JMK fiasco. I really doubt that the profile was attained from the blood stain. The reason is that the stain was a mixture.

Not only that, they did not release the official results of the tests like the official autopsy report. That tells me they are only blowing smoke and not telling the truth.

As I see it, the Touch DNA matches nothing but itself, and it was attained from contamination by somebody handling the long johns.

What would clear this matter one way or another, would be the official reports, but I really doubt that we will ever see it.
CC

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