Albym wrote:
Basic information on the establishment of DNA profiles.

DNA is a complex chemical that is found in the majority of cells in the human body, including cells in the blood, semen, saliva and hair roots. DNA carries genetic information that determines physical characteristics of a person and directs the processes involved in the functioning of an organism. This information exists in the form of a code, half of which is inherited from the father and [half] from the mother.

Except for truly identical twins, the DNA of each person is unique, although the technology currently available today does not permit the analysis of all the differences between persons. The techniques used by FSS analyses specific regions of DNA known as short tandem repeats (STRs), that are known to be amply variable from individual to individual. The techniques of establishing DNA profiles can, therefore, be used to exclude, conclusively, one person as the donor of an unknown DNA source, and can, frequently, provide convincing indications in terms of participation [contribution?], though not allowing, as yet, proof of identity.

The establishment of DNA profiles (STR) uses the technique of DNA amplification, through which specific DNA regions are selected and copied many times. This increases the quantity of DNA available for analysis and means that a DNA profile can be obtained from samples in which the initial quantity or quality of DNA is not adequate for other methods of establishing profiles.

In this way, DNA profiles are produced through amplification (copying) of eleven different areas of DNA. Ten of those areas contain STR. They are known as D3, VWA, D16, D2, D8, D21, D18, D19, THO1 and FGA. The eleventh, known as amelogenina, indicates the sex of the donor. The individual components of a DNA profile are represented by a series of peaks that can be measured, allowing them to be attributed a designation [labelled?]. One person will have two peaks in each STR, one inherited from each progenitor [parent], unless the same STR has been inherited from both progenitors, in which case only one peak will be observed.

If the DNA profiles relating to a stain, obtained from a crime [scene], and [that of] a suspect reveal no differences, it is said that they match. The estimation of the amount of the level of proof of DNA profiles that match between, for example, a stain of body fluid and a suspect, consists of calculating the probability of obtaining the match if, in reality, the stain was not from the suspect, but was from another individual with the same DNA profile. That is known as the probability of correspondence [matching].

The probability of matching depends upon the level of kinship [parental similarity] existing between the suspect and another individual. True identical twins have the same profile. But, due to the random manner in which DNA from the two progenitors combine to form the descendant, the probability of two siblings presenting a match in all ten STR regions is, approximately, one in ten thousand (1 in 10,000). The more distant the relationship becomes between two persons, the more reduced becomes the probability of matching in all ten STR regions.

For example, the probability of two first cousins having the same profile is of the order of one to one hundred million (1 to 100-million).

Where there exists no clear indication that a relative close to the suspect is involved, it is common practice to indicate a probability of matching relative to an unknown person who has no kinship with the suspect. With a complete profile this probability of matching is of the order of one to one thousand million (1 to 1,000-million) [or 1 to 1-billion using U.S. numbering].

In the case of a partial profile being obtained, the probability of matching is calculated using reference databases [tables] that contain calculated proportions of each DNA profile component present in the general population. These estimates are then combined in a manner that permits compensation for possible associations between DNA components in order to establish the calculation of the probability of matching relating to the partial DNA profile.

The calculations of probability of matching are done using three databases containing DNA profiles obtained previously from individuals of caucasian, afro-caribbean and asiatic descent of this country [namely, U.K.] When the racial origin of a person who left the biological material is not known, the result presented in the deposition will be the lowest of the results obtained.

Author: albym [ Mon Jun 01, 2009 2:38 am ]
Post subject: Re: FSS - The REAL Smoking Gun

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Going back over some of my notes on this, here are a few other observations to put into the mix starting with A.L.Palmer's report now at forum page: http://the3arguidos.net/forum/viewtopic ... 0#p1031140

EXTRACTS
Objects received
According to the lab records of 7 August and 6 September 2007 the objects referred to in this report entered the FSS laboratory in Birmingham, having been remitted by the Police Science Laboratory of Portugal and by the Leicestershire (UK) Police, respectively.
....
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.
END of extracts

Observations
1 - From the sample reference numbering it would seem that at least 36 samples/objects were handed over to the lab by Leics police on 6 SEPT 2007.

2 - We do not seem to know what items SJM/3 or SJM6 through SJM/35 were.

3 - Based on the reference SJM/1 this was also the pillowcase from which the MBM saliva was extracted, but there were no hairs on it. One might wonder whether the saliva search/extraction or the examination for hair occurred first - or perhaps I mis-translated the phrase 'fronha de almofada' only as 'pillowcase' when it should have been 'pillowcase of the pillow', i.e. there may have been two objects with the same reference, one going to Palmer the other to ....? [Answers to both these questions are observed below]

4 - The first Lowe report is dated 6 SEPT 2007, and it refers to the following:
I have received from my colleague, Sarah Vraitch, copies of the reference DNA profiles of Gerald McCann (CB/1), Kate Healy (CB/2), Amelie McCann (SBM/2) and Sean McCann (SBM/3). I have also received a copy of the DNA profile obtained from the possible saliva staining on the pillow case (SJM/1) which is assumed to be the DNA profile of Madeleine McCann.
No translation error here - the English report is posted - so it was a pillow case, but one might wonder what sample reference SBM/1 might have been.

5 - As one might expect the final report, attested to by JRL on 18 June 2008 (nine months later), the same references are used, and the same S.Vraitch information is given with one small but significant difference, namely that each reference sample is different from each other reference sample.

6 - On 28 June 2007 we have the two L.Denton reports abouts the reference samples (both on the same date). Note that they are both dated JUNE 2007, not 2008, and there is no mention of S.Vraitch nor any mention of L.Denton in the official reports.

Reference sets CB, SBM and SJM certainly appear to be UK references as opposed to anything from Portugal.
I asked the FSS some questions about the sample referencing and was, in effect, told to mind my own business.

So we have:
- L.Denton telling us that DNA profiling of reference samples (CB/1 and /2) from parents and (SBM/2 and /3) from the twins occurred before 28 June 2007.
- For any profiling to have occurred pre-28 June 2007 there had to be samples collected and delivered before that date.
- We don't appear to know when or by whom the CB and SBM sample sets were collected. The parents each gave written consent for themselves to PJ on 10 May, but there was no consent for the children in the file (that I recall seeing).
- Reportedly, hair samples from the children were denied by the parents until August/September.

- A.L.Palmer tells us that FSS records say that all SJM samples, including the MBM pillowcase, were received by them on 6 SEPT 2007.
- Reportedly, that pillowcase (and possibly everything else in that SJM forensic collection in UK) had occurred in MAY 2007 when the father went back to UK (and came back with the pink-shirted-one). If true, then what happened to them for 3-4 months?
- What else was happening on 6 September 2007?

Finally, the FSS profiling of the pillowcase SJM/1 was dated 22-23 MAY 2007 (depending on which date you take from which page of the documents in Apenso 1 Vol 1). It would seem, therefore, that the DNA profiling was done before the hair search - and that A.L.Palmer's report has at least one more question mark hanging over it.

For general information, it is also another coincidence that MBM's full profile had to be formally requested from Scotland Yard. The request was made on 1 October 2007 and the profile received by e-mail on 2 October 2007.
One must wonder if the investigation lead was slow in requesting or if the support operation was slow in being proactive on such a minor detail.

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Author: albym [ Mon Jun 01, 2009 2:46 am ]
Post subject: Re: FSS - The REAL Smoking Gun

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111, referring to your question back on page 15, I'll try to explain my limited understanding of how it works using a technology that we all understand.
After a DNA strand is extracted from the sample material it would all seem to be a set of string searches, e.g. FIND('this-string' inside 'that-string'). [Anyone for Google?]

A locus is a string of DNA components at a known location in the entire human DNA string. So the first 'FIND' is to locate the 'locus-string' inside the 'full-human-string'. [Find a subject web page inside the Internet]

An allele is a specific combination of components that are known to be somewhere between the beginning and the end of a given locus, i.e. the second FIND is actually a FIND-ALL 'allele-string' inside a particular 'locus-string'. [Find the subject words/phrase inside the web page]

In a single human this is expected to return one or two locations so, when three or more are found then there have to be two or more humans involved in the making of the 'locus-string' in the DNA pulled from the original forensic sample. [Multiple word/phrase hits]

In a very simple example, let's say we have a locus 1029384756748392019386273914 (28 numbers long), in which we know an allele with a known combination of '938' occurs.
The DNA 'processing' searches the locus for the '938' combination and finds it - in this example - starting at position 4 and again at position 19 - one allele contributed by the mother and one by the father.

This 4-19 location positioning is not unique to a single person, and may well be repeated in each offspring of the mother and father, but when 10 known alleles are looked for in 10 different loci the combinations of locations, when viewed as a pattern across all 10, are unique, even between ordinary siblings (but not between 'identical twins').

I say 'are unique' because, like fingerprints, I understand that researchers have not yet found two people with an identical set of location combinations except in identical twins, but even these have other variations that make them unique and separately identifiable.

Re: 'helix', 'ACGT', etc., I don't particularly care which pieces bond to which other pieces nor what labels are attached to what pieces by the genetic scientists, other than to differentiate between the three types of string.
All that stuff is in the literature and one doesn't need to know those things to understand that they are simply looking for small strings of characters inside bigger strings of characters, and writing down/displaying the starting positions of where they are found in the bigger strings. [just like using a more-refined kind of Google.

In a nutshell (as I understand it):
- The full pattern of 'allele' string locations across ten or more 'locus' strings is unique.
- In a known individual that pattern of locations is called a DNA 'profile'.
- When obtained from an unknown sample it is called a 'result'.
- An investigation wants to know if the 'result' matches the 'profile'.
- If the 'result' indicates more than one possible 'profile' then the FSS throws up its hands in horror and runs away.