http://www.internationalskeptics.com/forums/showthread.php?postid=12878629#post12878629
A useful non-technical reference on the analysis of profiles of DNA mixtures:
https://www.nist.gov/featured-stories/dna-mixtures-forensic-science-explainer
Here is a quote from the above source with an analogy on DNA mixtures:
"UNCERTAINTY #2: Whose peak is it anyway?
When analyzing a DNA mixture, the alleles from all the contributors show up on the same chart. This can make it difficult to tease apart the DNA profiles of the individual contributors. To understand why this makes things complicated, recall that after amplifying the DNA, the forensic scientist has a test tube with millions of copies of the alleles in solution. Think of that test tube as a bowl of alphabet soup.
In this bowl of soup, each letter represents a different type of allele. Our suspect is named JOHN Q SUSPECT.
We analyze the soup and find that all the letters in the suspect’s name are present. Does that mean someone named JOHN Q SUSPECT contributed to the soup?
Not necessarily. There could have been two contributors named PATRICK QUEEN and JUSTIN OHR. In that case, the soup would have all the letters needed to spell JOHN Q SUSPECT, even though no person with that name contributed to the soup."
Here's some more information on DNA profiling using the STR - PCR method, the one used (and misused) by Stefanoni and the one generally used currently for forensic analysis. Note that STRs are also called microsatellites:
"A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. They have a higher mutation rate than other areas of DNA leading to high genetic diversity. Microsatellites are often referred to as short tandem repeats (STRs) by forensic geneticists and in genetic genealogy....
Forensic and medical fingerprinting
Microsatellite analysis became popular in the field of forensics in the 1990s. It is used for the genetic fingerprinting of individuals where it permits forensic identification (typically matching a crime stain to a victim or perpetrator). It is also used to follow up bone marrow transplant patients.
The microsatellites in use today for forensic analysis are all tetra- or penta-nucleotide repeats, as these give a high degree of error-free data while being short enough to survive degradation in non-ideal conditions. Even shorter repeat sequences would tend to suffer from artifacts such as PCR stutter and preferential amplification, while longer repeat sequences would suffer more highly from environmental degradation and would amplify less well by PCR. Another forensic consideration is that the person's medical privacy must be respected, so that forensic STRs are chosen which are non-coding, do not influence gene regulation, and are not usually trinucleotide STRs which could be involved in triplet expansion diseases such as Huntington's disease. Forensic STR profiles are stored in DNA databanks such as the UK National DNA Database (NDNAD), the American CODIS or the Australian NCIDD.
Amplification
Microsatellites can be amplified for identification by the polymerase chain reaction (PCR) process, using the unique sequences of flanking regions as primers. DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow annealing of primers and the extension of nucleotide sequences through the microsatellite. This process results in production of enough DNA to be visible on agarose or polyacrylamide gels; only small amounts of DNA are needed for amplification because in this way thermocycling creates an exponential increase in the replicated segment."
Source:
https://en.wikipedia.org/wiki/Microsatellite
"A Short Tandem Repeat (STR) analysis is a common method in molecular biology which is used to compare specific loci on DNA from two or more samples. A short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated several to dozens of times in a row on the DNA strand. STR analysis measures the exact number of repeating units. This method differs from restriction fragment length polymorphism analysis (RFLP) since STR analysis does not cut the DNA with restriction enzymes. Instead, polymerase chain reaction (PCR) is employed to discover the lengths of the short tandem repeats based on the length of the PCR product.
STR analysis is a tool in forensic analysis that evaluates specific STR regions found on nuclear DNA. The variable (polymorphic) nature of the STR regions that are analyzed for forensic testing intensifies the discrimination between one DNA profile and another. Scientific tools such as FBI approved STRmix incorporate this research technique. Forensic science takes advantage of the population's variability in STR lengths, enabling scientists to distinguish one DNA sample from another. The system of DNA profiling used today is based on PCR and uses simple sequences or short tandem repeats (STR). This method uses highly polymorphic regions that have short repeated sequences of DNA (the most common is 4 bases repeated, but there are other lengths in use, including 3 and 5 bases). Because unrelated people almost certainly have different numbers of repeat units, STRs can be used to discriminate between unrelated individuals. These STR loci (locations on a chromosome) are targeted with sequence-specific primers and amplified using PCR. The DNA fragments that result are then separated and detected using electrophoresis. There are two common methods of separation and detection, capillary electrophoresis (CE) and gel electrophoresis.
Each STR is polymorphic, but the number of alleles is very small. Typically each STR allele will be shared by around 5 - 20% of individuals. The power of STR analysis comes from looking at multiple STR loci simultaneously. The pattern of alleles can identify an individual quite accurately. Thus STR analysis provides an excellent identification tool. The more STR regions that are tested in an individual the more discriminating the test becomes.
From country to country, different STR-based DNA-profiling systems are in use. In North America, systems that amplify the CODIS 13 core loci are almost universal, whereas in the United Kingdom the DNA-17 17 loci system (which is compatible with The National DNA Database) is in use. Whichever system is used, many of the STR regions used are the same. These DNA-profiling systems are based on multiplex reactions, whereby many STR regions will be tested at the same time.
The true power of STR analysis is in its statistical power of discrimination. Because the 13 loci that are currently used for discrimination in CODIS are independently assorted (having a certain number of repeats at one locus does not change the likelihood of having any number of repeats at any other locus), the product rule for probabilities can be applied. This means that, if someone has the DNA type of ABC, where the three loci were independent, we can say that the probability of having that DNA type is the probability of having type A times the probability of having type B times the probability of having type C. This has resulted in the ability to generate match probabilities of 1 in a quintillion (1x1018) or more. However, DNA database searches showed much more frequent than expected false DNA profile matches. Moreover, since there are about 12 million monozygotic twins on Earth, the theoretical probability is not accurate.
In practice,
the risk of contaminated-matching is much greater than matching a distant relative, such as contamination of a sample from nearby objects, or from left-over cells transferred from a prior test. The risk is greater for matching the most common person in the samples: Everything collected from, or in contact with, a victim is a major source of contamination for any other samples brought into a lab. For that reason, multiple control-samples are typically tested in order to ensure that they stayed clean, when prepared during the same period as the actual test samples. Unexpected matches (or variations) in several control-samples indicates a high probability of contamination for the actual test samples."
Source:
https://en.wikipedia.org/wiki/STR_analysis
