Madeleine McCann: Explanation of the DNA Analysis as detailed in the forensic report by John Lowe

This article was sent to me by a geneticist on facebewk:




Explanation of the DNA Analysis as detailed in the forensic report by John Lowe


Background

We all have 2 copies of every gene/stretch of DNA – 1 inherited maternally, the other paternally.

At some genetic sites, there are short, repetitive motifs called markers. Each marker will contain a variable number of repeated motifs. In diagrammatic form, a marker pair at any one site, could be represented like this, where the letters, ACGT, are the 4 bases which make up DNA (AAGTC is an arbitrary motif);

Maternally inherited marker AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC| 8
Paternally inherited marker AAGTC|AAGTC|AAGTC|AAGTC| 4

So, at this marker site, the repeat pair values would be read as 8,4
This would be shown as 2 peaks on a readout, at that site with relative heights on a compter-generated graph as 8 and 4.

A second site could be represented as follows (where CCGTCTA is an arbitrary motif);

Maternally inherited marker CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| 9

Paternally inherited marker CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| 5

So, at this second site, the computer readout would be 9,5

As you can see, the exact sequence of the DNA is irrelevant. It is just the number of motif repeats that is of significance. Therefore, any reference to a small chance of errors occurring during amplification of the DNA ie bulking up Low Copy Number (LCN) by copying a small amount of starting material, is irrelevant. The actual DNA code (ACGT) is of no interest, as long as the repeats of varying lengths, are present. Even if say a C is erroneously copied as an A, G or T (which is how errors can occur with individual letters) it does not affect the validity of this technique. It is akin to spelling the word “THERE” of 5 letters long and erroneously transcribing it as “THEIR”. The second spelling has a different meaning but all we are looking at here, is, how long is the word and how many times is it repeated? We don’t care about the meaning for this kind of analysis.





Creating profiles using the technique


Because the number of repeats each of us has at each of these sites is random, we can produce a unique profile, in terms of pairs of repeat values, over several sites.

If we were to look at 10 sites, with 2 values at each site, we will have 20 values, in pairs and that is an important thing to bear in mind. The power of the technique in terms of producing UNIQUE profiles is that we are not looking at 20 random sites giving 20 random values, but 10 pairs of values at 10 sites.
As touched on earlier, the computers that produce the data, do so by giving “peak heights” according to the length of the repeat. So a repeat length of 2, has a peak height of 2 units, a repeat value of 3, a peak height of 3 units etc., etc. These are the peaks referred to by Lowe.

The table below shows the way a unique profile of a child would be inherited from a given set of parental markers. The full set of 20 markers, in terms of 10 pairs of 2 values can be called the inherited genotype or genetic profile.
In the table below, the values I’ve listed at line “possible inherited marker sets at each site (child)”, are derived by combining each maternal value and with each paternal value in turn, resulting in 4 possible combinations. I have used arbitrary numbers for illustrative purposes.

NB at marker site no.8, I’ve shown how, if both parents possess the same number of repeats at a given site, there will be a 1 in 4 chance that a child could inherit the same number twice. A child inheriting the same number of repeats from both parents, in this case 9, will produce a profile that appears with only one peak at that site and in this example, it will have a height of 9 units. Cf the Lowe report where he explains that the DNA from the Rothley pillowcase (Madeleine’s control sample) yielded an apparent complete profile of 19 markers, not 20, because at one site, there was an inheritance of the same number of repeats from both Kate and Gerry. In fact, there would have been 2 peaks, superimposed on each other so appear as 1. Therefore, when Lowe says there were 19 markers this should strictly be described as 20 but 19 in terms of peaks.

               

Marker Site	1	2	3	4	5	6	7	8	9	10
Maternal repeat lengths (Maternal genotype)	8,4	5,9	6,8	3,7	5,6	8,4	4,7	9,4	3,8	5,4
Paternal repeat lengths (paternal genotype)	7,9	4,3	9,3	6,4	8,9	5,5	3,8	9,3	7,6	3,7
Possible inherited marker sets at each site (child)	8,7 8,9 4,7 4,9	5,4 5,3 9,4 9,3	6,9 6,3 8,9 8,3	3,6 3,4 7,6 7,4	5,8 5,9 6,8 6,9	8,5 8,5 4,5 4,5	4,3 4,8 7,3 7,8	9,9 9,3 4,9 4,3	3,7 3,6 8,7 6,8	5,3 5,7 4,3 4,7

Looking at the above, to produce a unique genetic profile for an offspring during reproduction, we randomly take 1 set of marker values (of the 4 we have to choose from) at each site. I’ve randomly taken one marker set at each site to produce an example of a profile shown below. It can then be seen that if we were to analyse these marker sets, we would get 2 peaks at each site on a readout, except site no. 8 in my example below, because of the inheritance pattern explained earlier. The probability of inheriting any one marker pair from a possibility of 4 options shown in the table above, is 1 in 4 or 0.25

         

Randomly inherited profile	4,7	9,3	6,9	3,4	6,8	4,5	4,8	9,9	8,6	5,7
Probability of inheriting that particular marker pair	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25

What is the probability that the crime scene DNA described as having a 15/19 marker match did or did not come from Madeleine?


The probability of inheritance of any single full genotype at all 10 sites, from one set of parents = 0.25 multiplied by 0.25, 10 times, so (0.25)¹⁰ = 0.00000095 which is just over 1 million to 1.

Therefore, there are just over 1 million permutations of inheritance of 10 pairs of markers from any 2 parents. It’s a very powerful technique because we look at marker PAIR values. Lowe says that we all share these repeats and if you were to look at any one person’s DNA, you would find a selection of these numbers. That is true, but the chances of any value represented along with its paired value at any single site is not at all likely. As you can see, even inheriting the same pair values at one site among siblings is a 1 in 4 chance. Looking at the population as a whole, variation in repeat values at each site is much larger.

According to Lowe, the profile of the crime scene DNA yielded 15 markers that were identical to that of Madeleine’s pillowcase DNA. He says 15/19 because 4 markers were missing due to the DNA being degraded. Because the analysis is done as pair values at each site and you can’t have half a site nor half a pair value, it should be 16/20. The pillowcase DNA did have 20 markers which looked like only 19 as described above. If you look along the profile in the table above, reading from site 1 to 8, you will see that in fact, by column 8, you have 16 markers even though 2 are identical.

In this case, the probability of inheriting those same 8 pairs of markers at those sites from the same parents is (0.25)⁸= 0.000015 or 66.66 thousand to 1 chance.

What is the probability that a random stranger, not related to Madeleine, deposited DNA with those exact same 16 marker pairs over the 8 sites with a complete match to Madeleine? Many million to 1.

Get'emGonçalo wrote:This article was sent to me by a geneticist on facebewk:




Explanation of the DNA Analysis as detailed in the forensic report by John Lowe


Background

We all have 2 copies of every gene/stretch of DNA – 1 inherited maternally, the other paternally.

At some genetic sites, there are short, repetitive motifs called markers. Each marker will contain a variable number of repeated motifs. In diagrammatic form, a marker pair at any one site, could be represented like this, where the letters, ACGT, are the 4 bases which make up DNA (AAGTC is an arbitrary motif);

Maternally inherited marker AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC|AAGTC| 8
Paternally inherited marker AAGTC|AAGTC|AAGTC|AAGTC| 4

So, at this marker site, the repeat pair values would be read as 8,4
This would be shown as 2 peaks on a readout, at that site with relative heights on a compter-generated graph as 8 and 4.

A second site could be represented as follows (where CCGTCTA is an arbitrary motif);

Maternally inherited marker CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| 9

Paternally inherited marker CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| CCGTCTA| 5

So, at this second site, the computer readout would be 9,5

As you can see, the exact sequence of the DNA is irrelevant. It is just the number of motif repeats that is of significance. Therefore, any reference to a small chance of errors occurring during amplification of the DNA ie bulking up Low Copy Number (LCN) by copying a small amount of starting material, is irrelevant. The actual DNA code (ACGT) is of no interest, as long as the repeats of varying lengths, are present. Even if say a C is erroneously copied as an A, G or T (which is how errors can occur with individual letters) it does not affect the validity of this technique. It is akin to spelling the word “THERE” of 5 letters long and erroneously transcribing it as “THEIR”. The second spelling has a different meaning but all we are looking at here, is, how long is the word and how many times is it repeated? We don’t care about the meaning for this kind of analysis.





Creating profiles using the technique


Because the number of repeats each of us has at each of these sites is random, we can produce a unique profile, in terms of pairs of repeat values, over several sites.

If we were to look at 10 sites, with 2 values at each site, we will have 20 values, in pairs and that is an important thing to bear in mind. The power of the technique in terms of producing UNIQUE profiles is that we are not looking at 20 random sites giving 20 random values, but 10 pairs of values at 10 sites.
As touched on earlier, the computers that produce the data, do so by giving “peak heights” according to the length of the repeat. So a repeat length of 2, has a peak height of 2 units, a repeat value of 3, a peak height of 3 units etc., etc. These are the peaks referred to by Lowe.

The table below shows the way a unique profile of a child would be inherited from a given set of parental markers. The full set of 20 markers, in terms of 10 pairs of 2 values can be called the inherited genotype or genetic profile.
In the table below, the values I’ve listed at line “possible inherited marker sets at each site (child)”, are derived by combining each maternal value and with each paternal value in turn, resulting in 4 possible combinations. I have used arbitrary numbers for illustrative purposes.

NB at marker site no.8, I’ve shown how, if both parents possess the same number of repeats at a given site, there will be a 1 in 4 chance that a child could inherit the same number twice. A child inheriting the same number of repeats from both parents, in this case 9, will produce a profile that appears with only one peak at that site and in this example, it will have a height of 9 units. Cf the Lowe report where he explains that the DNA from the Rothley pillowcase (Madeleine’s control sample) yielded an apparent complete profile of 19 markers, not 20, because at one site, there was an inheritance of the same number of repeats from both Kate and Gerry. In fact, there would have been 2 peaks, superimposed on each other so appear as 1. Therefore, when Lowe says there were 19 markers this should strictly be described as 20 but 19 in terms of peaks.

               

Marker Site	1	2	3	4	5	6	7	8	9	10
Maternal repeat lengths (Maternal genotype)	8,4	5,9	6,8	3,7	5,6	8,4	4,7	9,4	3,8	5,4
Paternal repeat lengths (paternal genotype)	7,9	4,3	9,3	6,4	8,9	5,5	3,8	9,3	7,6	3,7
Possible inherited marker sets at each site (child)	8,7 8,9 4,7 4,9	5,4 5,3 9,4 9,3	6,9 6,3 8,9 8,3	3,6 3,4 7,6 7,4	5,8 5,9 6,8 6,9	8,5 8,5 4,5 4,5	4,3 4,8 7,3 7,8	9,9 9,3 4,9 4,3	3,7 3,6 8,7 6,8	5,3 5,7 4,3 4,7

Looking at the above, to produce a unique genetic profile for an offspring during reproduction, we randomly take 1 set of marker values (of the 4 we have to choose from) at each site. I’ve randomly taken one marker set at each site to produce an example of a profile shown below. It can then be seen that if we were to analyse these marker sets, we would get 2 peaks at each site on a readout, except site no. 8 in my example below, because of the inheritance pattern explained earlier. The probability of inheriting any one marker pair from a possibility of 4 options shown in the table above, is 1 in 4 or 0.25

         

Randomly inherited profile	4,7	9,3	6,9	3,4	6,8	4,5	4,8	9,9	8,6	5,7
Probability of inheriting that particular marker pair	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25	0.25

What is the probability that the crime scene DNA described as having a 15/19 marker match did or did not come from Madeleine?


The probability of inheritance of any single full genotype at all 10 sites, from one set of parents = 0.25 multiplied by 0.25, 10 times, so (0.25)¹⁰ = 0.00000095 which is just over 1 million to 1.

Therefore, there are just over 1 million permutations of inheritance of 10 pairs of markers from any 2 parents. It’s a very powerful technique because we look at marker PAIR values. Lowe says that we all share these repeats and if you were to look at any one person’s DNA, you would find a selection of these numbers. That is true, but the chances of any value represented along with its paired value at any single site is not at all likely. As you can see, even inheriting the same pair values at one site among siblings is a 1 in 4 chance. Looking at the population as a whole, variation in repeat values at each site is much larger.

According to Lowe, the profile of the crime scene DNA yielded 15 markers that were identical to that of Madeleine’s pillowcase DNA. He says 15/19 because 4 markers were missing due to the DNA being degraded. Because the analysis is done as pair values at each site and you can’t have half a site nor half a pair value, it should be 16/20. The pillowcase DNA did have 20 markers which looked like only 19 as described above. If you look along the profile in the table above, reading from site 1 to 8, you will see that in fact, by column 8, you have 16 markers even though 2 are identical.

In this case, the probability of inheriting those same 8 pairs of markers at those sites from the same parents is (0.25)⁸= 0.000015 or 66.66 thousand to 1 chance.

What is the probability that a random stranger, not related to Madeleine, deposited DNA with those exact same 16 marker pairs over the 8 sites with a complete match to Madeleine? Many million to 1.

It must be trillions to one.

From the BBC

http://www.bbc.co.uk/science/0/20205874

The accuracy of DNA tests has big implications. DNA tests are sometimes the only evidence to prove that a suspect was involved in a crime, or free someone who has been wrongly convicted.
It is easy to tell if DNA from two biological samples does not match. But a match doesn't make you totally certain that the two samples come from the same person.
There is always a small chance that two different people's genetic markers could be the same, especially if they are related.
To reduce the chance of error, scientists test more than one genetic marker. The more identical markers there are in two samples, the more accurate the test.
However, testing more markers takes more time and is more expensive. Forensic DNA tests usually examine six to ten markers. The chances that two unrelated people have identical profiles is less than one in one billion.

Irrespective of all the other evidence ...this to my mind is damning on its own.

I'm not qualified to discuss forensic science in any detail, nor can I pretend to understand the minutiae.

Even without any technical knowledge of the science, I'm not oblivious to the summary of forensic results presented by John Lowes report.  It's very intriguing to note that, out of all the samples submitted for analysis, not one single element produced a meaningful result to move the investigation forward.

Funny that innit?

Nor have I ever seen a satisfactory explanation as to why the British laboratories were involved in the first place.  Because they are specialists in the particular field I hear it said - so much so that not one single meaningful result was possible?  Didn't I read also that there are other forensic laboratories throughout Europe with the same specialist methodology?

Maybe it was because Stuart 'call me Stu' Prior of Leicestershire Constabulary was coordinating the case in the UK - along side Philomena 'auntie' McCann.  Or maybe it was because of Glenfield Hospital's (home to Professor Gerald McCann) illustrious connections in the field of genetic fingerprinting?  Or maybe it was the most simple explanation - FFS were notorious for losing samples?

I've seen many an explanation from a number of self professed experts (?) that all seem to coincide with the conclusions of John Lowes report - confounded by technical jargon of course - confusion is good!  Personally, I have a general theory in life.  If you can't explain a subject in simple terms so as the layperson can understand, then you don't know the subject yourself!

I sent this article to PeterMac and this is his response:


I have a little residual knowledge of DNA, from a long time ago, . . .  and it looks OK to me.
Many million to 1 chance !


Now look at the chance of a dog getting an alert right / wrong.   notoriously unreliable, no better than chance !
Assume totally random, so the chance of alerting behind the sofa is 50%.  right or wrong
Chance of TWO dogs alerting is therefore 0.5 x 0.5 .  = 0.25.   or a I in 4 chance
If you are going to run this I will spell it out better,
 but we could have 
E right - K wrong 
E wrong - K right
E Wrong - K Wrong
E right - K right

Now apply this to another site, and the chances multiply to 0.25 x 0.25
Apply to just 10 sites, and the chances of both dogs being wrong all the time are now 1 in 1,048,576
One in a million, in fact.

Now multiply that by the number of Negative alerts  = found nothing, and we are into are the billions.

NOW use a dog which has a proven track record, but in training and in the field, of, say, 95% accuracy,  . . .  (Most would go for further training if they produced 1 in 20 FALSE positives - which would lead to 1 in 20 false arrests, and massive compensation . . .) and there are few numbers that can cope.   A pocket calculator doesn't have a screen wide enough to show the result.


Which is why police, customs, drugs, firearms, and the medical world use them.

P

This was a topic of discussion on The 3 Arguido's forum. The answer to the question comes from a former police officer.

QUOTE:
bomaris wrote:
I need some help on the DNA analysis.

Can anyone tell me the following:

1. Re the 15 out of 19 markers. Do we know if any other family member shares all 15 markers - not just in theory but in reality?

2. Do we know whether the analysis could determine if the DNA came from a living or a dead body? If so, do we know which it was?

3. If the 15 out of 19 markers are consistent with it being Madeleine, what are the odds of it being someone else? Are we talking 10 to 1, 100 to 1, 1000 to 1 or more?

4. Do we have a record yet of the initial FSS assessment?


Beachy's reply:

Bomaris, precise answers to some of your questions would be impossible without actually having the results of the DNA testing in front of us, but this is what I can tell you:

For the purposes of this discussion, let us call the sample of Madeleine's DNA that was obtained from her pillow in Rothley or wherever they got it the "known sample." The DNA found in the Scenic and the apartment would have been "questioned samples."

Regardless of the number of markers you are testing, if the DNA in ANY of the markers in a questioned sample does not match the DNA in the known sample, then the questioned sample does not come from the same person who was the donor of the known sample of DNA.

I have not seen anything in writing to date, but I have been assuming that the FSS was able to extract 15 markers from the sample of DNA found in the back of the Renault Scenic, and that the other four markers were so degraded (by heat, sunlight, efforts to clean them up, whatever) that they could not be analysed. If they had 4 out of 19 markers that clearly were NOT a match for Madeleine's DNA, that would have been the end of it, in my opinion; the DNA from the Scenic could not have been hers.

I have read that the Portuguese require 19 markers for a conclusive result on a DNA analysis because under their laws that is how many markers are required for a positive match on a paternity test. This is more markers than I have ever heard of being required anywhere for forensic purposes in a criminal case. In the UK, 10 markers are tested, plus the sex of the donor is determined, and a 10:10 match is considered conclusive. In America, the FBI CODIS database contains 13 markers. Individual states in America are allowed to pass their own laws about how many markers must be tested before evidence can be introduced in court, but most of the 50 states use 13 because there is so much interface with the FBI database. Therefore, in America, a 13:13 match is considered conclusive that the questioned DNA and the known DNA came from the same person. Neverthess, if Portuguese law requires analysis of 19 markers, then that's what must be done. Period.

Regarding your specific questions:

(1) Only identical twins are born with identical DNA, and even in that case, every individual on earth begins to accumulate mutations to his/her DNA that may make it possible to distinguish even between the DNA of identical twins. There is a laboratory in Texas called Orchid Cellmark that claims it already can do this, but so far as I know, this technique has never been used in court.

The DNA of everyone on earth is at least a 99% match. Yep, that's right. The DNA of the most profoundly mentally disabled person who ever lived was a 99% match for Albert Einstein's. The DNA of the poorest beggar on the streets of the poorest city in the world, whoever that unfortunate soul happens to be, is a 99% match for the Queen's. Rather humbling, isn't it? (Note: Studies published in 2001 indicated that the DNA of all human beings was about 99.9% alike. More recent information, obtained from the human genome project, indicates that the accurate figure is probably somewhere in the range of 99 - 99.5%.)

The DNA of siblings is even more alike than that of individuals selected at random, which makes sense, considering that they inherit their DNA from the same two people. Within that 1% or less variation, however, there are literally tens of thousands of different combinations that make the DNA of any one individual unique from that of everyone else, including his/her siblings.

The FBI's CODIS database, which contains the DNA profiles of approximately 6 million convicted criminals, has been extensively studied. No 13:13 match of genetic markers has ever been found except between identical twins. There was a widely reported case several years ago in which a forensics examiner for the state of Arizona in America found a 9:13 match between two unrelated individuals, and there has also been a report of a 10:13 match between two related individuals who were products of an incestuous relationship.

Given the experience with CODIS, I think it is highly, highly unlikely (as in, the odds in favour of it would be one in the tens of millions) that one would find a 15:15 match on genetic markers between two different members of the McCann family.

(2) As I have posted before, DNA cannot be used to determine whether a person was living or dead at the time the sample was taken. A DNA sample taken by swabbing the inside of the cheek of a living person one hour before death and another sample taken from the same person one hour after death would look identical under a microscope.

What MIGHT be possible, and it would depend on several different things, including the degree of experience and skill of the forensic examiner and the quantity of DNA available, would be that a forensic examiner asked to attempt to extract DNA from some object that appeared to contain a substance that might be a bodily fluid - a piece of clothing, say, or a piece of carpet from an automobile - MIGHT be able to recognise the type of fluid and therefore tell whether the donor had been alive or dead. There are certain types of fluids - one is an exudate from the lungs that is only seen after death - that might be recognisable as such. In Madeleine's case, however, with so little material available, I am virtually certain that this would not have been possible, i.e., it would not be possible to tell whether the donor of the questioned sample of DNA found in the back of the Scenic was alive or dead at the time the DNA was deposited there.

(3) If the forensic technicians were able to extract 15 markers from the material in the Scenic that were a match for the known sample of Madeleine's DNA and the other four markers could not be tested because they were degraded, there would be a high probability mathematically that the questioned sample of DNA came from Madeleine.

Just to give you an example, at the time the forensic examiner in Arizona found the 9:13 match on DNA markers, the FBI said that the chances of that happening would be 1 in 113 billion. Well, that obviously isn't right, because there WAS, in fact, a 9:13 match, and there are nowhere near 113 billion people in the world. There is something called the "prosecutor's fallacy," which is an example of mathematical analysis called "binary classification" which shows that even 10:10 or 13:13 DNA matches are subject to error rates much higher than prosecutors sometimes attribute to them. However, whilst saying that the chance of an incorrect finding is 1 in 113 billion is clearly ridiculous, my opinion would be that the chance of two DNA samples belonging to different people if the results of the forensic analysis shows a 15:19 match would be miniscule - at least 1 out of hundreds of thousands, if not millions. It would not, however, be a smoking gun. Any DNA scientist will tell you that DNA is only one piece of the puzzle in any case and should be viewed in the context of all the other evidence. However, if FSS got a 15:19 match between Madeleine's known DNA and the questioned sample from the hire car, and 4 other markers were too degraded to be tested, in my opinion, that would be a powerful piece of circumstantial evidence.

But in fact, I don't know exactly what they got. I don't understand what John Lowe is saying. This is the statement from him that I find so troubling: "Let's look at the question that is being asked: 'Is there DNA from Madeleine 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 - because Madeleine has deposited DNA as a result of being in the car or whether Madeleine merely appears to match the result by chance."

What is he saying? Um, Mr. Lowe, when the "components" (also known as "markers") within the result (AKA questioned sample) are the same as those in her reference sample (AKA known sample of Madeleine's DNA), then you're SUPPOSED to say "YES," or actually you're supposed to say the final results are inconclusive because 4 of the markers were too degraded to be tested, but all the others matched. How the stuff got where it was found is not the subject of DNA analysis. That's the kind of thing that an expert witness should be prepared to be asked about on the stand at a trial; could the questioned sample of the DNA have gotten where it was found by accidental transference, for example, from another object?

DNA analysis is just that - ANALYSIS. Either they were able to extract markers from the DNA found in the Renault Scenic that were not degraded and could be analysed, or they were not. Either those markers matched the markers in the known sample of Madeleine's DNA taken from her pillow in Rothley, or they did not. Was the gentleman quoted correctly? If so, why all this double-speak? If it's the case, why in heaven's name not just SAY, "There are limits to LCN DNA technology, and the sample from the automobile was too small for any analysis to be definitive." Or, "When we tried to analyse the questioned sample from the automobile, we discovered that the DNA of two or more people were mixed together, and given the minute amount of material we had to work with, we simply were unable to separate them. We cannot say for certain when this happened, but regrettably, it made it impossible for us to determine with any reasonable degree of certainty whether the DNA was Madeleine's."

My guess - and it is just a guess - is that no one leaned on the FSS. I don't think anyone had to. My personal opinion is that they were freaked out by what happened with the trial at Omagh and knew that if they came up with DNA results that didn't stand up in this case, they could kiss their cash cow of being one of the few labs in the world that can do LCN DNA analysis good-by. Trouble is where they are concerned, there is more than one thing that can cause police departments and other agencies the world over to doubt your results. One is to make mistakes and be wrong. Another is to be too afraid to call it when you see it.

One thing I CAN understand about the DNA is why Stuart Prior read somebody from the FSS the riot act over the telephone. Good on him. Wish I'd been there to hear it. END QUOTE

This was also posted by 'beachy' on The 3 Arguidos

Thanks to Joana Morais and Lilemor for alerting us to its existence, I located the actual PDF file on the FBI's forensic examination in the Caylee Anthony case (http://www.wftv.com/download/2008/1024/17794795.pdf) and read it. This is what jumped out at me:

"Results of examinations:

A Caucasian head hair found in specimen Q12 exhibits characteristics of APPARENT DECOMPOSITION [emphasis mine] at the proximal (root) end."

Now, before I lose it entirely, which I am definitely about to do, let me say that whilst this has evidentiary value, it is not a smoking gun.

Mitochondrial DNA analysis of another portion of the hair subsequently showed that it contained mitochondrial DNA which could have come from either Caylee Anthony or her mother, Casey. But Casey is sitting in jail in Orlando and isn't in a state of "apparent decomposition," is she? (Though she could be before too much longer, as she's been charged with first-degree, capital murder, and Florida is one of the states in America which does not mess around when it comes to executions.)

Caylee disappeared in mid-June. Casey's car was found abandoned in late June, approximately 15 days later. Gestalt, I love you, you've provided us with a lot of valuable information, but the situation with the hair in this case shows that it does NOT take 90 days or more for "corpse hairs" to show signs of decomposition, as you've told us. The article I've quoted again and again from timesonline in which Dr. Michael Baden says that changes indicating that a particular hair came from a corpse can show up as little as 5 days after death was correct. 15 days was long enough for it to show up in Caylee Anthony's hair found in her mum's car. 25 days certainly should have been long enough for signs of decomposition to appear in the hairs found in the back of the McCanns' hire car.

WHY IN HELL ISN'T THERE ANYTHING ANYWHERE - IN THE PJ REPORT, IN THE FSS REPORT, ANYWHERE TO INDICATE WHETHER THE HAIRS FOUND IN THE MCCANN'S HIRE CARE WERE CHECKED FOR SIGNS OF DECOMPOSITION? In the Caylee Anthony case they had one hair. ONE HAIR. And they checked it and found signs of decomposition AND mitochondrial DNA proving it could have come from Caylee. I don't know whether or not hairs were found in the McCanns' hire car in anything like the amount that press reports initially indicated, but they had more than one. Where is it? Was it checked for signs of decomposition? If not, why not? If it was, where's the report? The FSS supposedly determined that hair found in the McCanns' hire car contained Kate's (and also, therefore, Madeleine's DNA). They shouldn't have had to destroy a mass of hair to do that. Testing for mitochondrial DNA is not rocket science. A good university laboratory should be able to do it with a single hair, much less the most vaunted laboratory on the planet. SO WHERE IS THE REST OF THE HAIR, FSS?

There is no excuse for this. NONE. Every single hair found in the hire car should have been checked for (1) signs of decomposition; and (2) mitochondrial DNA. And if they determined that "corpse hairs" from a person with mtDNA identical to Madeleine's were found in that car, in my opinion the McCanns should have been ordered back to Portugal and thrown in the slammer whilst additional investigation was carried out.



Youtube video links:

Martin Brunt: DNA matches Maddie's

LVA 6.50 Analysis - McCann Sedatives Statement

Again, let's go back to what was being reported in 2007:

This is from the TELEGRAPH, 4:34PM BST 11 Sep 2007




Sponsored


Madeleine: 'Hair in car came from her body'

The police case against Kate and Gerry McCann was submitted to the public prosecutor today, amid conflicting reports about the nature of the DNA case against them.

 

According to police briefings given to Portuguese journalists, the samples found in the back of the McCanns' car were not blood but other "bodily fluids". These have provided an 88 per cent DNA match to Madeleine.

So much of Madeleine's hair was also found in the vehicle's boot that it must have come directly from her body, and not just been transferred from clothing or a toy, according to the briefing.

Link to full article:

 http://www.telegraph.co.uk/news/uknews/1562823/Madeleine-Hair-in-car-came-from-her-body.html

Steven Avery was exonerated for the wrongful conviction of rape on the strength of one single hair which was tested and matched to the real culprit. Now serving a life sentence for the murder of Teresa Halbach, his lawyer Kathleen Zellner has authorised advanced forensic testing which she is confident will free him for a second time. Science should be able to solve this, if the will is there.

I am not sure if the hair found in the hire car had roots or not.

With Caylee Anthony there were roots and the hairs showed corpse banding.

Despite all the evidence, the dumb jury decided they wanted fame and fortune from book deals and did not want to be sequestered for the penalty phase which is the only reason they found her not guilty.

As one juror  famously put it, they all knew she did it, the prosecutors didn't prove their case!!

Casey though is now leading a miserable life hated by everyone including her own family.

Her bella vita is non existent bar a cheap tattoo.

Hobs wrote:I am not sure if the hair found in the hire car had roots or not.

This is an extract from the FSS laboratory analysis of the hairs harvested from the hired Renault Scenic, contained in the PJ files.  For the benefit of the uniformed, like wot I am, I've excluded a lot of detail but for the purpose it matters not.

Objects from the Renault Scenic - licence plate 59-DA-27
The following objects recovered from the scenic were subjected to examination:
1A, 1B, 1C, 1D,
2A, 2B, 2C, 2D, 2E,
3,
4A, 4B, 4C,
5A, 5B, 5C,
6A, 6B, 6C,
7A, 7B, 7C,
8A, 8B, 8C,
9 and
11 (2 objects).

There were more than two hundred hairs, down or fragments of hair and down. The majority appeared to be different from the blonde reference hairs recovered from SJM2, 4 and 5. Furthermore, no blonde hair consistent with that seen in photographs of Madeleine McCann was found.

Approximately 15 hairs, down or fragments were blonde and fair, presenting a similarity with the reference material. All were of insufficient length to make a solid [definitive] comparison. Furthermore, they are too short to do mitocondrial DNA tests. Folicle root material is insufficient for standard DNA tests.

Four hairs - one from 7B and three from 7C - were sent for Low Copy Number DNA testing. The results of those tests will be presented by my colleague John Lowe.

Conclusion
In the objects recovered from the Scenic, there were around 15 blonde/fair hairs similar to the reference hairs from SJM2, 4 and 5. However, as it was not possible to do solid [definitive] or significant [forensically meaningful] tests it is not possible for me to determine if, or not, these could have been from Madeleine McCann.

The conclusions expressed in the present deposition are based on information available at the date of the examination. In the case that there are changes to that information, or additional information becomes available, it may be necessary to reconsider my interpretation and conclusions. That re-evaluation will be most effective when done immediately prior to any judgement.

A.L. Palmer
----------

Note: 

Examination and results

Reference objects

I received [obtained] information from the pillow-case SJM/1, the tops SJM2, 4 and 5, and the hairbrush SJM/36 belonging to Madeleine McCann or used by her. The hair found on these objects was used in substitution of [in place of] reference samples of her hair, [which were] not considered to be authentic samples of her hair.

No hair was recovered from the pillow-case SJM/1 nor the hairbrush SJM/36.

A total number of twelve [12] hairs or hair fragments were recovered from the tops SJM/2, SJM/4 and SJM/5. All of these appeared to be hair and not down, being mainly blonde in colour. One of the hairs was brown and distinctly darker than the other hairs, suggesting, at the least, that this was a hair from someone else.

The remaining eleven hairs/fragments varied in length from 4 millimetres to 45 millimetres [~1/8" to ~1,3/4"]. I could not conclude that all hairs were from the same person. If they had been from Madeleine McCann, then they are not representative/typical/characteristic of a sample of her hair, given the length of that seen in photographs of her.

So some of the hairs weren't blonde enough !

Some of the hairs weren't the right length !

They concluded this by looking at photos ?

Very scientific

I'm astonished that a renowned forensic science laboratory of the 21st century would partly base their analysis on photographs and/or the length of the hair..



Old hair growth?  New hair growth? The fringe?  As for hair colour, practically every image of Madeleine I've seen is different.

Something is amiss - pity I get bogged down by the technicalities.

ETA:  You beat me to it .

Verdi wrote:I'm astonished that a renowned forensic science laboratory of the 21st century would partly base their analysis on photographs and/or the length of the hair..



Old hair growth?  New hair growth? The fringe?  As for hair colour, practically every image of Madeleine I've seen is different.

Something is amiss - pity I get bogged down by the technicalities.

ETA:  You beat me to it .

I wonder which photos they went by ??   

There is a very good discussion of this on an old thread - what is suggested there is that it is the quality of the pillowcase sample that causes the problem and results in an inconclusive result. If I have understood it right, because the pillowcase sample is so poor (and because there is absolutely no other 'reference sample' then you cannot have a conclusive result. In other words, if the parents had provided a conclusive reference sample to compare the sample in the car to, then it would have been possible to make a conclusive match. Sadly, as Peter Mac says, we have evidence of absence here (not being able to provide a conclusive sample for comparison)  no adequate sample provided by the family in order to make a technically conclusive match, albeit this is a technicality because the reality is a probability of one in a billion it is not Maddie's hair. Hope that makes sense.

sandancer wrote:

Verdi wrote:I'm astonished that a renowned forensic science laboratory of the 21st century would partly base their analysis on photographs and/or the length of the hair..



Old hair growth?  New hair growth? The fringe?  As for hair colour, practically every image of Madeleine I've seen is different.

Something is amiss - pity I get bogged down by the technicalities.

ETA:  You beat me to it .

I wonder which photos they went by ??   

This one maybe?

,

What's_up_doc? wrote:There is a very good discussion of this on an old thread - what is suggested there is that it is the quality of the pillowcase sample that causes the problem and results in an inconclusive result. If I have understood it right, because the pillowcase sample is so poor (and because there is absolutely no other 'reference sample' then you cannot have a conclusive result. In other words, if the parents had provided a conclusive reference sample to compare the sample in the car to, then it would have been possible to make a conclusive match. Sadly, as Peter Mac says, we have evidence of absence here (not being able to provide a conclusive sample for comparison)  no adequate sample provided by the family in order to make a technically conclusive match, albeit this is a technicality because the reality is a probability of one in a billion it is not Maddie's hair. Hope that makes sense.

Don't get me on the subject of the ruddy pillowcase. 

Said to have been collected from chez Rothley by Gerry McCann on his trip back to the UK around the 21st May 2007.  The chain of custody I don't believe has ever been clarified, nor the actual circumstances of the collection.  It has also been suggest that an officer from Leicester police was with him when he collected to pillowcase but again I don't think it was ever confirmed.  In normal circumstances, correct me if I'm wrong, forensic evidence connected to a serious crime is harvested under clinical conditions and transported from the crime scene (or wherever else) to the forensic analysis laboratory in an appropriate sterilized sealed receptacle - for obvious reasons.

If I remember correctly, the PJ initially wanted a clean reference sample of Madeleine's DNA to prove parentage.  This suggests to me that the pillowcase was collected by Gerry McCann, with or without an officer of the law, then transported to Portugal - by Gerry McCann in his back-pack or by courier courtesy of Leicester police I know not.  The former seems most likely under the extraordinary circumstances.  I say extraordinary because there can be no guarantee that the pillowcase from Rothley was a clean reference sample any more than an item of Madeleine's clothing, tooth brush or bedding from apartment 5a.

Whatever, it didn't arrive at the UK Forensic Science Service laboratory until August/September/October 2007.  I'm being a bit vague but it's too late in the day to start searching for specifics.  I've been over this issue so many times in the past, not only have I forgotten the minute detail, I can't quickly locate the information I'm looking for at the moment - it seems to have disappeared.  Either that or my laptop's deleted it - it deletes everything else so why not!

Tomorrow is another day.

Verdi wrote:,

What's_up_doc? wrote:There is a very good discussion of this on an old thread - what is suggested there is that it is the quality of the pillowcase sample that causes the problem and results in an inconclusive result. If I have understood it right, because the pillowcase sample is so poor (and because there is absolutely no other 'reference sample' then you cannot have a conclusive result. In other words, if the parents had provided a conclusive reference sample to compare the sample in the car to, then it would have been possible to make a conclusive match. Sadly, as Peter Mac says, we have evidence of absence here (not being able to provide a conclusive sample for comparison)  no adequate sample provided by the family in order to make a technically conclusive match, albeit this is a technicality because the reality is a probability of one in a billion it is not Maddie's hair. Hope that makes sense.

Don't get me on the subject of the ruddy pillowcase. 

Said to have been collected from chez Rothley by Gerry McCann on his trip back to the UK around the 21st May 2007.  The chain of custody I don't believe has ever been clarified, nor the actual circumstances of the collection.  It has also been suggest that an officer from Leicester police was with him when he collected to pillowcase but again I don't think it was ever confirmed.  In normal circumstances, correct me if I'm wrong, forensic evidence connected to a serious crime is harvested under clinical conditions and transported from the crime scene (or wherever else) to the forensic analysis laboratory in an appropriate sterilized sealed receptacle - for obvious reasons.

If I remember correctly, the PJ initially wanted a clean reference sample of Madeleine's DNA to prove parentage.  This suggests to me that the pillowcase was collected by Gerry McCann, with or without an officer of the law, then transported to Portugal - by Gerry McCann in his back-pack or by courier courtesy of Leicester police I know not.  The former seems most likely under the extraordinary circumstances.  I say extraordinary because there can be no guarantee that the pillowcase from Rothley was a clean reference sample any more than an item of Madeleine's clothing, tooth brush or bedding from apartment 5a.

Whatever, it didn't arrive at the UK Forensic Science Service laboratory until August/September/October 2007.  I'm being a bit vague but it's too late in the day to start searching for specifics.  I've been over this issue so many times in the past, not only have I forgotten the minute detail, I can't quickly locate the information I'm looking for at the moment - it seems to have disappeared.  Either that or my laptop's deleted it - it deletes everything else so why not!

Tomorrow is another day.

Thanks you Verdi - what you have said here corroborates what the lab appear to have said which is that the quality of the reference sample, supplied by the parents, was of such a poor quality that it would be impossible to obtain a conclusive match to any subsequent  hairs found by the investigating team. The fact that GM had to provide a pillowcase from their home in the UK is the alarming thing here because no identifiable reference sample could be obtained from the crime scene. The reason the lab were forced to use length of hair to try and establish if hair provided as a reference sample was indeed Madeleine's is because, as far as I can tell, because they were unable to obtain a reliable reference sample from the crime scene. The question you have to ask here is why is that? Had the apartment been  forensically cleaned after the crime and if so, by whom? A second question, did a girl of nearly four not have her own hairbrush and why were there no hairs in the bed, on her favourite blanket and on her holiday clothes which could provide a reference sample of hair? Under normal circumstances, it should be possible to obtain an adequate reference sample but on this occasion it was not. Evidence of absence is recognised in law and as Peter Mac says, we have to look at not only what is there that shouldn't be but also what isn't there that should be and one of the things that should be there, is hair - enough of it to obtain a good reference sample and it wasn't. One of the many mysteries in this case...

Didn't Gerry come back with a pillow case and Clarence Mitchell?

Clarence Mitchell: I met them, errm... because of my role following the BBC, errm... I was with the BBC, as you rightly said, for around twenty years. I then joined the Cabinet Office, errm... as director of the media monitoring unit for, errr... the government which meant working at... with No. 10 and all of the major Departments of State and because of my existing media contacts, errm... whenever a big story came along, errr... I was considered, errm... as a possible, errr... press officer, if you like, for the government to go and assist the media on the ground. Now I thought it would be something like bird flu, or foot and mouth, or perhaps another terrorist incident where government press officers are... are sometimes sent out to assist the police or the emergency services on the ground deal with the media, errm... but as it was, errm... I was told that a... a child had gone missing in Portugal and, errr... the media interest was developing very rapidly and that the ambassador in Portugal had asked for assistance for his press office team, errm... So I was effectively seconded to the Foreign Office and sent out to Portugal. I actually met Gerry for the first time in Leicestershire. He came back to collect some belongings from home, errr... and he and I then flew back to Portugal in May 2007 and I met Kate out there for the first time. So that's... that's how it came about. I went out as a civil servant and met them through the... through the consular assistance that they were offered.

http://www.gerrymccannsblogs.co.uk/Nigel/id255.htm

I don't get the flying home for a DNA sample at all. 

It makes no sense.

Madeleine has supposedly been sleeping in that bed in 5A for 5 days.

What's_up_doc? wrote:

Verdi wrote: Had the apartment been  forensically cleaned after the crime 

 
Could I just ask, how would you do this? I'm not that well read about DNA, but I assume that my living room, for example, is full of my DNA. It's presumably on everything I touch, and I have no idea how you would get rid of it. So what do you have to do to forensically clean a place?

BlueBag wrote:Didn't Gerry come back with a pillow case and Clarence Mitchell?

Clarence Mitchell: I met them, errm... because of my role following the BBC, errm... I was with the BBC, as you rightly said, for around twenty years. I then joined the Cabinet Office, errm... as director of the media monitoring unit for, errr... the government which meant working at... with No. 10 and all of the major Departments of State and because of my existing media contacts, errm... whenever a big story came along, errr... I was considered, errm... as a possible, errr... press officer, if you like, for the government to go and assist the media on the ground. Now I thought it would be something like bird flu, or foot and mouth, or perhaps another terrorist incident where government press officers are... are sometimes sent out to assist the police or the emergency services on the ground deal with the media, errm... but as it was, errm... I was told that a... a child had gone missing in Portugal and, errr... the media interest was developing very rapidly and that the ambassador in Portugal had asked for assistance for his press office team, errm... So I was effectively seconded to the Foreign Office and sent out to Portugal. I actually met Gerry for the first time in Leicestershire. He came back to collect some belongings from home, errr... and he and I then flew back to Portugal in May 2007 and I met Kate out there for the first time. So that's... that's how it came about. I went out as a civil servant and met them through the... through the consular assistance that they were offered.

http://www.gerrymccannsblogs.co.uk/Nigel/id255.htm

I don't get the flying home for a DNA sample at all. 

It makes no sense.

Madeleine has supposedly been sleeping in that bed in 5A for 5 days.

And wearing her top and underclothes and the only mention of washing was a pj top with an unidentified stain which Kate said she hand washed. So by Thursday quite a heap of dna laden clothing. Although a whole load of clothing was sent to the Ocean club laundry withing a few hours of the supposed abduction.
http://www.mccannpjfiles.co.uk/PJ/SILVIA_CRAVINHO.htm

puzzled wrote:

What's_up_doc? wrote:

Verdi wrote: Had the apartment been  forensically cleaned after the crime 

 
Could I just ask, how would you do this? I'm not that well read about DNA, but I assume that my living room, for example, is full of my DNA. It's presumably on everything I touch, and I have no idea how you would get rid of it. So what do you have to do to forensically clean a place?

I didn't say that!

BlueBag wrote:Didn't Gerry come back with a pillow case and Clarence Mitchell?

Clarence Mitchell: I met them, errm... because of my role following the BBC, errm... I was with the BBC, as you rightly said, for around twenty years. I then joined the Cabinet Office, errm... as director of the media monitoring unit for, errr... the government which meant working at... with No. 10 and all of the major Departments of State and because of my existing media contacts, errm... whenever a big story came along, errr... I was considered, errm... as a possible, errr... press officer, if you like, for the government to go and assist the media on the ground. Now I thought it would be something like bird flu, or foot and mouth, or perhaps another terrorist incident where government press officers are... are sometimes sent out to assist the police or the emergency services on the ground deal with the media, errm... but as it was, errm... I was told that a... a child had gone missing in Portugal and, errr... the media interest was developing very rapidly and that the ambassador in Portugal had asked for assistance for his press office team, errm... So I was effectively seconded to the Foreign Office and sent out to Portugal. I actually met Gerry for the first time in Leicestershire. He came back to collect some belongings from home, errr... and he and I then flew back to Portugal in May 2007 and I met Kate out there for the first time. So that's... that's how it came about. I went out as a civil servant and met them through the... through the consular assistance that they were offered.

http://www.gerrymccannsblogs.co.uk/Nigel/id255.htm

I don't get the flying home for a DNA sample at all. 

It makes no sense.

Madeleine has supposedly been sleeping in that bed in 5A for 5 days.

That's how I understood it, yes.

It's a toss up though where Gerry met Clarrie - was it at the Foreign and Commonwealth Office or Westminster or Leicester Constabulary or Rothley House or Rothley war memorial?

Had to chuckle the first time I heard 'Rothley' mentioned on video.  It was pronounced 'Roeflee' whereas I thought it to be Rofley' .  How common!

Reminds me of years ago, when the upwardly mobile set invaded South London and tried to change the name of Streatham district to St. Reatham.

You 'ave to larf!

You have to be a bit careful here - there is understandly a tendency to misinterpret the forensic analysis report, although not disassociated, the hairs harvested were by no means the only samples provided to the FSS for analysis.

Firstly you need to seperate the primary reasons for identifying Madeleine's DNA profile..

a)  Required by the PJ to establish parenthood i.e. is Gerry McCann the blood father.
b)  For the process of elimination i.e. to identify the presence of DNA from an unknown person at the crime scene.
c)  Later in the investigation to compare Madeleine's DNA profile with samples harvested from the crime and other locations.

Of course you would expect Madeleine's DNA to be present at apartment 5a because she was there at some stage of the week, her DNA and sticky little fingerprints and other evidence would/should have been everywhere.  This is where the strong argument begins.  Understandably, for the purpose of forensic protocol, a clean reference sample is a must - as far as possible!  It could and has been argued that anything belonging to Madeleine at apartment 5a could/would be contaminated, so the obvious answer is to produce something from her usual residency.  This makes no sense at all to my simple mind - for one there is no guarantee that the sample from her home has not been contaminated and for two, how would this work if say, they were holidaying somewhere in the southern hemisphere.

I've argued this subject in the past till blue in the face.  When all aspects have been countered the experts then start the insults - 'your [sic] an idiot you don't know what your [sic] talking about you bleeeeeping bleeep' (as if I need teling:).  OK I don't understand the technicalities of forensic science but I do understand the basics and so far, my questions have never been satisfactorily answered - only confounded by jargon and abuse.

So, forgetting all the hairs, fluff, saliva stains, bodily fluids etc, still there remains..

a)  Why was the analysis of every sample submitted to the FSS not 'meaningful'
b)  Why did Gerry McCann collect a pillowcase from Rothley when visiting in May 2007
c)  How was the pillowcase conveyed to Praia da Luz
d)  Why was the pillowcase later sent to the FSS laboratories for further analysis

Is it really such a complication to locate a clean DNA reference sample?

The only simple explanation I can think of to cover all eventualities - Madeleine's DNA harvested from the crime scene might have identified some underlying clue as to her fate and the length of time she was in apartment 5a.