MADELEINE'S DNA - definitive study.

[Carana]

Well I never mentioned Amaral or 5 alleles, so I don't know where you got either of those. My information about swab 3A came from here;

Letter dated 11 September regarding FSS report received by PJ
on on 4 September from Leicester Police, citing 15/19 matches of Madeleine DNA
profile

This serves to add [to the case file] a laboratory examination report prepared
in England, written in English and translated into Portuguese, delivered to this
police force on 4 September 2007 by English police officer Stuart Prior.

This laboratory report tells about the examinations made of two trace evidence
recoveries, one behind the living room sofa in apartment 5A and the other in the
boot area of the vehicle used by the McCann family, hired [by them] from the end of May this year.

In some of these recoveries (samples) DNA was found whose components are also
found in the profile of Madeleine McCann.

With respect to the trace evidence recovered behind the sofa all the confirmed
DNA components coincide with corresponding components in the DNA profile of
Madeleine McCann.

In the sample collected in the boot area of the vehicle, 15 of the identified
DNA components coincide with the corresponding components in the DNA profile of
Madeleine McCann, this of [having] 19 components.

This was written by Joao Carlos on 11th September. Was it him or Prior who got it wrong, and not Amaral?

Ah.... That seems to be a summary of what João understood at the time from the English report.

But then, where did you get the swab 3A from? That was in the original Lowe report, which João Carlos didn't specify.

[Robittybob1]

I sort of understood this email.  http://www.mccannpjfiles.co.uk/PJ/MADELEINES_DNA.htm

"From: Lowe, Mr J R [mailto:John.Lowe@fss.pnn.police.uk
Sent: 03 September 2007 15:01
To: stuart.prior@leicestershire.pnn.police.uk
Subject: Op Task - In Confidence

Stuart

Firstly, here are the last three results you are expecting

An incomplete DNA result was obtained from cellular material on the swab 3a. The swab contained very little information and showed low level indications of DNA from more than one person. However, all of the confirmed DNA components within this result match the corresponding components in the DNA profile of Madeline McCann. LCN DNA profiling is highly sensitive it is not possible to attribute this DNA profile to a particular body fluid.

There is no evidence to support the view that Madeline MCCann contributed DNA to the swab 3B.

A complex LCN DNA result which appeared to have originated from at least three people was obtained from cellular material recovered from the luggage compartment section 286C 2007 CRL10 (2) area 2. Within the DNA profile of Madeline McCann there are 20 DNA components represented by 19 peaks on a chart. At one of the areas of DNA we routinely examine Madeleine has inherited the same DNA component from both parents; this appears therefore as 1 peak rather than 2, hence 19 rather than 20. Of these 19 components 15 are present within the result from this item; there are 37 components in total. There are 37 components because there are at least 3 contributors; but there could be up to five contributors. In my opinion therefore this result is too complex for meaningful interpretation/inclusion.

Why - ...

Well lets look at the question that is being asked

"Is there DNA from Madeline on the swab "

It would be very simple to say "yes" simply because of the number of components within the result that are also in her reference sample.

What we need to consider, as scientists, is whether the match is genuine and legitimate; because Madeline has deposited DNA as a result of being in the car or whether Madeline merely appears to match the result by chance. The individual components in Madeline's profile are not unique to her, it is the specific combination of 19 components that makes her profile unique above all others. Elements of Madeline's profile are also present within the the profiles of many of the scientists here in Birmingham, myself included. it's important to stress that 50% of Madeline's profile will be shared with each parent. It is not possible in a mixture of more than two people, to determine or evaluate which specific DNA components pair with each other. Namely, we cannot separate the components out into 3 individual DNA profiles.

Therefore, we cannot answer the question: is the match genuine or is it a chance match.

The same applies to any result that is quoted as being too complex for meaningful inclusion/interpretation

What questions will we never be able to answer with LCN DNA profiling -

When was the DNA deposited - 
How was the DNA deposited - 
What body fluid(s) does the DIVA originate from - 
Was a crime committed -

These, along with all other results, will be formalised in a final report

Please don't hesitate to contact me if you require any further assistance

kind regards
John

John Lowe Forensic Scientist
Major Incidents Team
Priory House
Inter Facility: 703 6973
External: 0121 607 6973
Fax: 0121 6221807


Please consider the environment before printing this e-mail

Forensic Science Service Ltd
...."

[Robittybob1]

I see those peaks are measured on a scale of 190 - 355 and to two decimal places so does that mean there could potentially be 13,500 peaks? (135 times 100)
If that was the case for a blood sample to have 5 identical peaks and none other is one chance in 4.48403E+20
 so that blood came from Madeleine  But if the peaks are  not found at each of those 13500 points then the chances will be somewhat less.

The alleles come in pairs one from the mother one from the father, and their weights are different but close so you get the two close peaks. So there is not going to be the vast number of peaks.

[Robittybob1]

".....it's important to stress that 50% of Madeline's profile will be shared with each parent."
 http://www.mccannpjfiles.co.uk/PJ/MADELEINES_DNA.htm


I'm not so sure that is correct.  If it was there was going to be no way to separate the three McCann children. 


LCN = Low copy number.
"The increased sensitivity of LCN also increases the risks posed by contamination of samples in the laboratory. Since LCN aims to amplify levels of DNA as low as 100 picograms, even breathing on a sample may contaminate it substantially enough to render the final profile unusable[citation needed]. Contamination is particularly problematic before the sample has undergone amplification because both the suspect's and the contaminator's DNA will be amplified, resulting in a mixed profile. Moreover, the small amounts of DNA that LCN aims to amplify also increase the probability of PCR artifacts appearing on profiles such as stochastic effects."

[jassi]

".....it's important to stress that 50% of Madeline's profile will be shared with each parent."
 http://www.mccannpjfiles.co.uk/PJ/MADELEINES_DNA.htm


I'm not so sure that is correct.  If it was the case there was going to be no way to separate the three McCann children by DNA testing. 


LCN = Low copy number.
"Low template DNA problems"
http://www2.le.ac.uk/departments/emfpu/genetics/explained/low-problems

"As LCN can be recovered from an area where no discrete stain (e.g. blood, semen, saliva) is visible, it can be hard to establish how an individual's DNA came to be there. An occurrence known as secondary transfer can mean that a person's DNA could be present at a scene when the person themselves was not."

It is.  The only DNA that is available is that which comes from the parents.
It all depends on how the  DNA combines at conception that determines an individual's DNA profile.
Even the twin's profiles might have significant differences because they are not identical twins.

[Robittybob1]

It is.  The only DNA that is available is that which comes from the parents.
It all depends on how the  DNA combines at conception that determines an individual's DNA profile.
Even the twin's profiles might have significant differences because they are not identical twins.

I see it now  - we say half from mum and half from dad but each time the parent's whole is divided up differently.  Each child does not receive  a similar half.  Thanks

[Carana]

I see it now  - we say half from mum and half from dad but each time the parent's whole is divided up differently.  Each child does not receive  a similar half.  Thanks

Yes - because mum and dad themselves inherited one allele from each of their parents at each locus. That means that a child could inherit one of two from mum and one of two from dad (i.e., a possibility of 4 combinations) at any locus. While some siblings may inherit the same allele base pair at some loci, there are a vast amount of loci, and at each there will 4 possible combinations.

Think of the sex gene, which is usually depicted as "XX (female) and "XY" (male).

So, you have:

Mother    Father
X X         XY

Child
X + X = a girl.

X + X = a girl.

X + Y = a boy.

X + Y = a boy.

The alleles at other loci are expressed as numbers (e.g. "6,9" or "11,15") because there are more possible variations
than simply an x or y value.

However, whichever of the 4 combinations a child inherits, it's still a matter of one bit from mummy and one bit from daddy, i.e. half or 50% from each.

Edited for clarification.

[Robittybob1]

I was thinking more in terms of the process of recombination during meiosis which mixes up the alleles before the gametes are produced.  It is a complicated process and it is more than just whole chromosomes as exampled by your post on "X and Y genes" (X and Y are actually chromosomes not genes). 
But I know you meant well.  Thanks

[Carana]

I was thinking more in terms of the process of recombination during meiosis which mixes up the alleles before the gametes are produced.  It is a complicated process and it is more than just whole chromosomes as exampled by your post on "X and Y genes" (X and Y are actually chromosomes not genes). 
But I know you meant well.  Thanks

What are you trying to work out as regards Madeleine?

NB: I didn't say that X and Y were genes. But that's ok. ;)

[Carana]

I see those peaks are measured on a scale of 190 - 355 and to two decimal places so does that mean there could potentially be 13,500 peaks? (135 times 100)
If that was the case for a blood sample to have 5 identical peaks and none other is one chance in 4.48403E+20
 so that blood came from Madeleine  But if the peaks are  not found at each of those 13500 points then the chances will be somewhat less.

The alleles come in pairs one from the mother one from the father, and their weights are different but close so you get the two close peaks. So there is not going to be the vast number of peaks.

Rob, I don't undestand what you're getting at...

From what I can gather (and I happily admit that it isn't an area that I was particularly interested in), the graph with peaks is apparently an electropherogram, measuring the "strength" of the amount of DNA present, and helps to determine whether the peaks represent a true allele or irrelevant background noise.

[Robittybob1]

Rob, I don't undestand what you're getting at...

From what I can gather (and I happily admit that it isn't an area that I was particularly interested in), the graph with peaks is apparently an electropherogram, measuring the "strength" of the amount of DNA present, and helps to determine whether the peaks represent a true allele or irrelevant background noise.

Yes when you look at the charts the peaks are spaced out but most times there is another peak real close (these are the two alleles of that gene.  They have similar length so they have a similar weight.  I read about the methods of LCN DNA analysis and I started to understand it.  Alleles can drop out (not copied) or drop in with contamination.  There can also be spluttering where the alleles don't copy perfectly and you get multiple peaks close together. 

[Robittybob1]

  I see 9 occasions where there are spaced out results with two peaks close together, e.g. the pair of alleles at (166.52) and (170.58).

There are two incidents of "Allele drop out" where there is a single peak and no allele pair at (103.07). and another later (186.04).

At 204.83 (top chart) there are 4 small peaks that look like "sputtering".
 

[Robittybob1]

What are you trying to work out as regards Madeleine?

NB: I didn't say that X and Y were genes. But that's ok. ;)

You said "Think of the sex gene, which is usually depicted as "XX (female) and "XY" (male). "   I think you meant to say the "sex chromosomes",
as in:
"Think of the sex chromosomes, which is usually depicted as "XX (female) and "XY" (male). "

http://www.biology-online.org/dictionary/Sex_chromosome
"A somatic cell contains a genome comprised of paired chromosomes: the autosomes and sex chromosomes. In humans, there are two forms of sex chromosomes: the X chromosome and Y chromosome. A pair of X and Y results in a male while a combination of X and X results in a female. This XX/XY sex-determination system is one of the most familiar sex-determination systems and is applicable in human beings and most other mammals. In this system, the sex of an organism is determined by the sex chromosomes since these chromosomes bear the genes that control the development of reproductive organs and other sexual characteristics of an organism."

[Carana]

You said "Think of the sex gene, which is usually depicted as "XX (female) and "XY" (male). "   I think you meant to say the "sex chromosomes",
as in:
"Think of the sex chromosomes, which is usually depicted as "XX (female) and "XY" (male). "

http://www.biology-online.org/dictionary/Sex_chromosome
"A somatic cell contains a genome comprised of paired chromosomes: the autosomes and sex chromosomes. In humans, there are two forms of sex chromosomes: the X chromosome and Y chromosome. A pair of X and Y results in a male while a combination of X and X results in a female. This XX/XY sex-determination system is one of the most familiar sex-determination systems and is applicable in human beings and most other mammals. In this system, the sex of an organism is determined by the sex chromosomes since these chromosomes bear the genes that control the development of reproductive organs and other sexual characteristics of an organism."

OK, I could have been clearer. X and Y are chromosomes, but I was thinking of the sex gene in terms of amelogenin.

https://www.homednadirect.com/knowledge-base/amelogenin-gene-in-paternity-dna-tests/

[Robittybob1]

OK, I could have been clearer. X and Y are chromosomes, but I was thinking of the sex gene in terms of amelogenin.

https://www.homednadirect.com/knowledge-base/amelogenin-gene-in-paternity-dna-tests/

I didn't know that.  amelogenin the paternity sex gene.  OK.