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To clarify. I have been advised & persuaded that a blog under my real name is not advisable.

The hire car sampling.

This will be a shorter post and I hope quite easy to follow.

In the last post I showed how the existing DNA profile from the car sample could be used along with DNA profiles from McCann family & friends + a others to enhance our understanding of who might have contributed to the DNA profile and thus how likely it is that Maddy was one of those people.

Now I would like to consider what else should have been done in 2007 as soon as the DNA profile was known.

The whole of the carpet from the car boot should have been retained and sealed as evidence. It should have been cut into many (at least 100) small pieces in a grid like fashion ad each piece subjected to DNA extraction and LCN DNA analysis.

In addition random samples should have been taken from all interior areas of the car, seats, carpets, swabs from door handles, windows, floor (e.g.under car boot carpet) etc. Perhaps a further 100 samples. These should also have been subjected to LCN DNA analysis.

What would this sampling & testing reveal?

Had this been done several things might have been revealed including:-

1. Was it possible to get DNA profiles from any other parts of the vehicle?

2. Were the 15 (or more or less) Maddy markers present anywhere else in the vehicle?

3. Were there parts of the vehicle that gave single person DNA profiles? (I am aware of the Gerry McCann profile from the key fob I'm talking about the car itself.

4. Were the 15 Maddy markers present in other pieces of carpet from the boot? 

5. Were the 22 other markers from the car boot present in any other samples?

6. Were there samples that included markers not found among the 37 in the car boot sample?

7. Was there an area of the car boot carpet that gave significantly poor or zero DNA results?

What might any or these results indicate or prove?

1. If yes then these profiles might be used to show how the 15 Maddy markers could have come together in the single sample from the boot. 

2. If yes then the pattern of profiles seen would show whether the 15 Maddy markers were present in only one or a few areas of the car or were widespread. If they were present only in one area that would indicate her body could have been placed in the boot at some point. If widespread the chances are that these markers are coming from the DNA of others.

3. Any single person profiles would identify people who had definitely been in the vehicle (or their DNA transferred there. Clearly a single person profile that matched Maddy's would be significant, but others could also be used in a subtraction analysis on other samples.

4. If yes this would identify an area (or areas) that had Maddy's markers. The size and shape of any such areas would be very informative. e.g. a few drips spread out, a single small area consistent with a pool of liquid soaking into the carpet, a ring with a blank area in the center consistent with cleaning of a spill or leak etc

5. The presence of these other 22 markers in other samples, especially any single ID samples would permit subtraction analysis on the boot sample

6. This would show whether the car boot sample contained all the markers present in the car or not. Creating a complete picture of the amount of DNA contamination in the car.

7. This would indicate an area that had been specifically cleaned shortly before the car was seized as evidence.

Why weren't these things done?

I am at a complete loss to explain why these things or at least some of them were not done. The case was huge worldwide news at the time. The McCann's were being suspected of disposing of Maddy's body. The evidence from the single sample in the car boot suggested that could be the case but was inconclusive. Here was a great opportunity to either clear the McCann's or gather evidence that would help to prove they did dispose of Maddy's body. Why did no one.... NOT EVEN THE McCANN's themselves..... insist that this car was examined thoroughly and every scrap of evidence extracted?

Was Maddy's DNA in the hire car?

So we come to the all important question:- Was Maddy's DNA in the hire car?
Perhaps we need to phrase this question a little better before we move on. I prefer:- Was DNA from Maddy present in the sample taken from the boot of the McCann's hire car?

This question has already been answered in the FSS report >John Lowe said the answer was "I don't know."  (I've put that in "" for effect I'm not saying those were his precise words) It is an accurate answer as far as it goes, but as I will show here John Lowe could have said more, MUCH MORE.

Who's DNA could have been in the sample? 

(To be clear, in this post "the sample" always refers to the sample collected from the boot of the hire car)

APOLOGIES, BUT IT WILL START TO BE TOUGH GOING FOR SOME OF YOU NOW.

How many people? 3, 5 or more?

In my previous blog I explained that the sample contained DNA from several people. Lowe says at least three and possibly as many as five. He does not say how he arrives at this conclusion, but I can make a reasonable guess. The "at least three people" almost certainly comes from the observation that some loci contained five (or possibly six) different markers. The only way 5 markers can be found at one locus is if at least three peoples DNA is in the sample.This is because each individual person can contribute a maximum of two markers and minimum of one marker to each locus. Hence 5 markers requires at least three people (2 contributing 2 markers and 1 contributing 1 marker).
It appears that Lowe may have gone on to assume that because he never saw more than 5 markers at a single locus a maximum of 5 people's DNA was present (i.e. if each contributed 1 marker). This is possibly true, in a practical sense, as it is extremely unlikely that DNA from more than 5 people would produce a profile with a maximum of 5 markers at any locus, but in fact it is theoretically possible for the maximum number to be more than 5.

One question we might hope to answer is whether the number of people contributing to the profile was 3, 4, 5 or more than 5. Assuming that the most markers seen at any single locus was 5 I calculate that it is most likely that only three people contributed to the sample, but cannot rule out the possibility that it was more than three. The maths is complicated by several factors. 1. Each marker occurs at a different frequency within the population. 2. We don't know whether the contributors were related or how closely they were related. 3. We don't know how many loci had 5 markers present in the sample. Hence it is not possible to say any more than it was probably three people, but could have been more than three.

Which people have DNA in that sample?

It would be easy to say that the DNA could have belonged to anyone. This is simply not true. The DNA can only have come from a limited number of people who had been in contact with the car or the sample after it was collected from the car. It would have helped greatly if several samples had been taken from different parts of the vehicle & all subjected to LCN analysis. The fact that this was not done is a great pity as it might have allowed a simple subtraction analysis to have been performed. Here is how it works:-

The group would include people at the car hire company, McCann's (including Maddy) + friends & family and forensic scientists + others who had hired the car.

Anyone whose profile has a marker from the 8 loci that is NOT present in the sample can be eliminated. This would probably take care of most people. All of the people remaining would be potential donors to the sample. A potential breakthrough for the case could be made at this point. If it turns out that Kate & Gerry McCann are both potential donors to the sample it becomes highly probable that Maddy's DNA is not present. Their combined DNA would account for all the 15 markers from Maddy's profile. It would not rule out completely that Maddy's DNA was also present, but the odds on this being the case would fall dramatically. Furthermore if it was shown that Kate and Gerry McCann could NOT be contributors to the sample it would greatly increase the chance that Maddy's is in the sample along with all that that implies.

The group of people who are potential contributors could then be further analysed in a group inclusion analysis. Here is how it works:-

All possible combinations of three people are generated. This might be quite a large number of groups, but still possible to do by hand and easier with a computer. All combinations that do not recreate the exact profile seen can be rejected. Most combinations should be rejected by this process that is just a statistical fact. The FSS report is somewhat disingenuous about this when it says that many people are potential contributors to the sample including the report writer Lowe himself. This may be true, but what he does not say is that only a very few combinations of three people who had access to that vehicle or the sample would generate the EXACT profile that was obtained. 

Without access to the full profile obtained from the sample and the DNA profiles of people who are potential contributors to the sample (i.e. those who had access and who's DNA profile fits with the 37 observed markers) it is impossible to know how many groups of three people would be found. It is likely to be a very small number, possibly even zero and almost certainly no more than 5.

If there are no groups that can account for the sample profile it suggests that at least one individual is missing from the analysis or that the sample contained DNA from more than 3 people. The analysis can now be repeated looking at groups of 4 & 5 in fact this should be done regardless of the findings for groups of three.


If there are groups that can account for the sample profile their composition should be studied. There are three possibilities.

1. All the groups contain Maddy.
One key question is do all the groups that account for the sample profile contain Maddy? If the answer is yes then we have once again greatly increased the odds that Maddy's DNA IS present in that sample. Of course this is still some way short of proof, but it would be an indication that the parents should be considered suspects and the possibility that Maddy's body was moved using the hire car.

2. Some groups contain Maddy and some do not.
If there are groups of three people that can product the complete profile of 37 that do not contain Maddy as well as groups that do contain Maddy it would not rule out the possibility that Maddy's DNA was present in the sample, but it would provide a clear and obvious explanation for the presence of the 15 markers without Maddy's body ever having to be in the car thereby shifting suspicion away from the parents.

3. None of the groups contain Maddy.
The final possibility is that only groups not containing Maddy can account for the sample. This is highly unlikely, but if it were to happen it would strongly suggest that Maddy's DNA was not present in the sample.

As I said earlier the group inclusion analysis should be repeated for groups of 4 & 5 people in order to get a clear picture of which groups of people could have produced the observed profile. The composition and number of these groups should then be studied. For example if the only group that can account for the profile is Maddy + a Portuguese  forensic scientist + an FSS forensic scientist this would almost constitute proof that Maddy's DNA was present in the hire car. Alternatively if a group comprising Sean + Amelie + John McCann could account for the sample profile this would provide a strong indication that the sample from the car boot did not contain Maddy's DNA.

Could Maddy's DNA have been in the car without her body being there?

The simple answer to this question is "yes". It is theoretically possible that her DNA might have been transferred from luggage or clothing that she had used or worn to the car boot. However this is rather unlikely. It is also important to note that the DNA sample was obtained from the spot in the car boot to which the CSI dog alerted. So while DNA transfer cannot be ruled out it can be considered unlikely.

CONCLUSIONS

1. Analysis of individual DNA profiles and the profile of 37 markers found in the sample can ELIMINATE a large proportion of possible donors and IDENTIFY a smaller group as genuinely potential donors to the sample.

2. If Kate & Gerry McCann are eliminated as potential donors to the sample it greatly increases the probability that Maddy's DNA is present in the sample.

3. If Kate & Gerry McCann are identified as genuinely potential donors to the sample it greatly reduces the probability that Maddy's DNA is in the sample.

4. It should be possible to identify at least one group of 3,4or5 people whose DNA could have been on the car boot sample whose combined DNA profiles match exactly the profile obtained from the sample. The composition of this group or groups might greatly increase or decrease the probability that Maddy's DNA is present in the sample.

5. Most important is the fact that this type of analysis and conclusions is still possible today. The full 37 marker DNA profile from the sample should be available (if it has been destroyed someones head should roll). DNA samples could be obtained from all people who used that car while in the McCann's possession and earlier. Forensic scientist/tech DNA profiles should be on file. 

Next?

We are not quite finished with the car yet. My next post will consider what else could have been done in 2007 to confirm or not the presence of Maddy's DNA in the car.

15/19 or 15/37 & 100% or NOT 100%

There are people in the world who are convinced that Madeleine McCann was not abducted. They believe that Kate & Gerry McCann hid Madeleine's body following her death. One central plank of evidence in this hypothesis is the DNA that was found in the boot of the car hired by the McCann's about three weeks after Madeleine was reported missing. They argue that the only way her DNA could have been in the car is if they moved her body at some time after they hired the car.

There has been considerable debate about whether the DNA profile obtained contained Madeleine's DNA or not. The report by the now disbanded FSS (Forensic Science Service) says clearly that it is impossible to say for certain. Unfortunately it does not go on to say anything else about this sample. There is no attempt to say how likely it is that the DNA came from Madeleine or not. So we are left not knowing whether the chance it is Madeliene's DNA is 1%, 50%, or 99%. All we know is that according to John Lowe of the now defunked FSS that it is not 100%.

Perhaps that would be the end of the matter, but people have taken sides on this issue. Some say it was her DNA some say it wasn't. Both points of view are wrong because no one can say for certain either way. However it is possible to gain some understanding how likely it is that this sample does contain DNA from Madeleine McCann. This blog will attempt to do that over the next few weeks.

First of all some background about DNA identification.

The FSS test involves looking at 10 different loci (locations) in human DNA. Each location (locus) has two copies sometimes called markers or alleles. The two markers at a locus are often different to each other but can be identical. So by looking at 10 loci the FSS identify a maximum of 20 markers.
In Madeleine's case there are actually only 19 markers because at one locus the two markers are identical.

Each individual person has a unique combination of markers and this is called their DNA profile or fingerprint. Some elements of a DNA profile will be shared but the total combination of 20 markers is unique to an individual except in the case of identical twins who will share identical profiles.

You may find it helpful to think of the following analogy. Imagine that each marker is a coloured disc. Now imagine that each locus is a number from 1 to 10 and that one of these numbers is written on each disc. The discs can be any one of many different colours and they can have any number from 1 to 10. Each person gets two discs with the number 1, two discs with the number 2 and so on till they have 20 discs. Can you see how unlikely it is that any two people will get exactly the same set of discs?

In reality everyone gets 10 markers or coloured+numbered discs from their father and 10 from their mother. This means that everyone shares exactly half their DNA profile with their mother and the other half with their father. See the diagram below

The selection of discs from mother and father is completely random. This means that although two children (even twins though not identical twins) have the same parents they have very different DNA profiles. See diagram below:

The one exception is identical twins because they form from a single embryo identical twins will have identical DNA profiles to each other. As far as we know Maddy did not have an identical twin sister so there is no need to worry about this possibility.

15/19 OR 15/37 

Now we know the genetics behind DNA profiles we can push on to the next subject namely was it 15/19 or 15/37?

The answer is BOTH! Here is why.

Maddy has only 19 markers because at one locus she inherited exactly the same marker (numbered+coloured disc) from Kate as she did from Gerry. In the example above this happens at location 6 (child 1).

We have to assume that when the FSS tested the sample only 8 loci gave a positive response. That is to say they were not able to determine the colour of the discs at two loci. This can happen and I may deal with why in a later blog. For now all we need to know is that 8 loci gave a result (colours in our analogy) and 2 loci didn't. One of the eight that did give a result gave only one colour while the other seven gave two colours making a total of 15. This is exactly what you might expect if loci 1 to 8 gave a result and 9 & 10 didn't in the example above.

Great you say, that means 15 markers (out of a total of 19) all matching Maddy's DNA. So it's 15/19! Yes that is true. However the FSS say that they didn't just get one or two colours for each locus, they got more. This can happen if DNA from two or more people gets mixed in the sample. So if we take loci 1 to 8 from the sample above and count the number of markers we get from a mixture of Mum,Dad and Child 1 in the example above we get 31 markers. The exact number of markers obtained will depend on how many people's DNA is mixed and how many markers they share. In the McCann case FSS say they found a total of 37 markers at the 8 loci. It is not possible in a mixed DNA sample to say which marker came from which person unless you already know who the contributors were. So while we can say that 15/19 of Maddy's markers are present in the sample we must also say that 15/37 of the total number of markers in the sample match Maddy's DNA.

100% MATCH OR NOT

Once again the answer is BOTH! (Well sort of) 

We know that only 8 loci gave a result and we know that all 15 of Maddy's markers for those 8 loci were present so it is a 15/15 i.e. 100% match. If only 14 of Maddy's markers for those 8 loci had been present the match would be 14/15 i.e. 93.333% and we would be able to say with a high degree of certainty that Maddy's DNA is NOT present in the sample. 

However because it is a mixed sample it is not possible to say for sure (i.e. 100%) that all the markers that match Maddy's DNA came from the same person. So although the match IS 100% we cannot be certain that the DNA came from Maddy. This seems to be the bit that confuses many people. If you are confused perhaps thinking about the coloured+numbered counters can help. Here is another diagram to help.

This diagram clearly shows that it is theoretically possible for the same 37 marker profile to be produced from Maddie's DNA mixed with two strangers DNA or from Kate's DNA mixed with DNA from two strangers. (These are only representations of what Kate & Maddy's DNA profiles look like as numbered discs, but they provide an accurate illustration of principle).

In my next installment I will consider how likely it is that the 37 markers contain DNA from Maddy.