DNA Fingerprinting – a quick reference guide

Glossary of Terms

Does forensic science and DNA phrases leave you confused ?

Below is a brief description with working definitions of the processes used and what they mean. It is now some years old but the intention is to provide only an introduction to DNA terminology.

See also : http://www.bbc.co.uk/dna/h2g2/A639425

Caution: It is assumed, wrongly, that DNA testing is better and more reliable than fingerprints because it is more modern. It is not ‘more reliable.’ Fingerprints are unique (so far as we know) but DNA is not. In that context the phrase ‘DNA fingerprint’ is a misleading misnomer.

DNA, despite its fearsome reputation, is based not on an absolute but on a mathematical probability that the person in custody is the right person.  As such it puts into question the “beyond all reasonable doubt” standard

DNA ‘fingerprinting’ or profiling is a technique that identifies the DNA from a certain individual without examining the entire three billion letters in the full human genome. It can be used to track down suspects, test the parentage of children, and to follow the evolution of species.

DNA fingerprinting begins by extracting DNA from the cells in a sample of blood, saliva, semen, hair or other appropriate fluid or tissue.

Only two copies of nuclear DNA are present in human cells,  one copy from the biological mother and one copy from the biological father (see Mitochondrial DNA and LCN below).

Testing the nuclear DNA, i.e. the ‘normal’ way, is by far the most common analysis conducted in the United States and in other countries, but new advances (variations) are made every year.

The fingerprinting process uses enzymes to cut out specific sequences of DNA; these are then arranged in order of length and tagged with radioactive probes. These emit X-rays, so when the sample is photographed they show up. This produces the ‘fingerprint’ – a series of black lines corresponding to the DNA sequences present.

Big Brother Dimension (another caution)

The national DNA database being built up by government has ‘generational’ implications that are not fully appreciated by the public. Already DNA requests from Caribbean countries to the UK have been received to track down possible relatives of criminals living abroad. DNA taken from a petty criminal in this decade (2010) can be used 50 or 100 years hence to trace and imprison a descendent. Not only do most people not want to be the cause of a relatives’ imprisonment we have to assume that justice may not in fact be guaranteed 100 years hence. We cannot guarantee we shall not be ruled by a tyrannical dictator and that the limit/range of illegal acts will be the same in 100 years time as they are now.

DNA – Deoxyribonucleic Acid

Deoxyribonucleic Acid is a molecule found in the nucleus living cells that stores the genome of an organism, or the blueprint required to build proteins. It has a double helix backbone which supports the four bases labelled G, C, A and T; the sequence of these bases is the genetic code which characterises an organism. Although 99.9% of human DNA is identical for different individuals, only identical twins have exactly the same pattern. So in principle, given a single cell, we can identify the individual it came from. DNA fingerprinting works by screening for certain DNA sequences which are found in some individuals, but not others.

DNA Fingerprinting

The fingerprinting process uses enzymes to cut out specific sequences of DNA; these are then arranged in order of length and tagged with radioactive probes. These emit X- rays, so when the sample is photographed they show up. This produces the ‘fingerprint’ – a series of black lines corresponding to the DNA sequences present.

PCR – Polymerase Chain Reaction

PCR is a powerful technique which effectively ‘amplifies’ DNA. It can produce many copies of the DNA from a single cell, allowing the tiniest of samples to be tested. The process first heats the sample to unravel and split the double helix; primase and polymerase enzymes are then used to identify DNA sequences and produce a copy of them. The cycle is repeated a number of times, each time doubling the sequence samples.

PCR considerably increases the usefulness of DNA fingerprinting, however, it also increases the risk of contamination with DNA from laboratory staff or anyone who had handled a sample. This would be amplified along with the sample DNA.

MtDNAMitochondrial DNA

The emergence of mitochondrial DNA Testing (or mtDNA) is another recent forensic breakthrough – though it does have limitations. It is particularly useful for bone fragments and hair samples evidence where nuclear (normal) DNA may not be present. It is also helpful when the cell sample has deteriorated.  Where the sample consists of only a few cells and is not suitable to measure the short tandem repeats (STR analysis), mitochondrial DNA can be used (see also LCN).

The limitations for criminal forensic identification of mtDNA is that while it better withstands degradation, it is passed down through maternal lines, with all descendants in a given maternal line (only) sharing the same mtDNA sequence. Therefore, while mtDNA may conclusively prove that a particular person is related through maternal lineage to a specified woman, it does not serve the purpose of uniquely identifying the individual in question. Indeed, persons who would appear to be unrelated may in fact share a common maternal relative at some point in their lineage, and this would lead to the same mtDNA results. [1]

As a result, mtDNA testing can be used in criminal cases to positively include or exclude a person as a possible suspect, but does not provide the discriminatory power that the forensic community has come to expect from nuclear DNA analysis.

STR analysis  (Short ort Tandem Repeats)

The most prevalent method of DNA fingerprinting used today is based on PCR and uses short tandem repeats (STR). This method uses highly polymorphicregions 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 different people have different numbers of repeat units, these regions of DNA can be used to discriminate between individuals.

The polymorphisms displayed at each STR region are by themselves very common, typically each polymorphism will be shared by around 5 – 20% of individuals. The more STR regions that are tested in an individual the more discriminating the test becomes.

STR analysis is used by American police and FBI for their CODIS computer programme. For highly degraded samples, it is sometimes impossible to get a complete profile of the 13 STR srequired for entry into the CODIS database.

AmpFLP - Amplified Fragment Length Polymorphism

Another technique, AmpFLP, or amplified fragment length polymorphism was also put into practice during the early 1990s. This technique was also faster than RFLP analysis and used PCR to amplify DNA samples. It relies on ‘variable number tandemrepeat’ (VNTR) polymorphisms to distinguish various alleles.

“JUNK” DNA

In molecular biology,” junk” DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 80% -90% of the human genome has been designated as “junk”, including most sequences within introns and most intergenic DNA.

Some consider the “junk” label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term “non-coding DNA”.

LCN DNA  (Low Copy Number)

Frequently items contain an insufficient quantity of DNA (from sweat or skin cells) to obtain complete or even partial DNA profiles using standard forensic gentotyping techniques. LCN is used when the sample size shrinks from a tiny but visible sample to microscopic samples.

To increase the low amount of DNA (the number) a gel is used as a medium to multiplied itself. This is called ‘amplification’. The drawback is that normally the approach also multiplies any other DNA in the process and can distort readings.

Where an offender is thought to have transferred DNA through touch and the sample could be skin cells, sweat, or fingerprint residue, LCN is said to be the best technique. LCN, sometimes called LCC (Low Copy Count), is used whenever traditional DNA testing has failed to get a satisfactory result. However it is still a controversial technique with alleged suspect accuracy.

LCN is an extension of the routine SGM Plus® profiling technique. It enables DNA profiles to be produced from samples that contain very few cells. It is a useful tool for so-called “cold cases”.

LMD  (Laser Microdissection technique)

This technique was, the New Scientist reports first used in January 2007. Building on LCN technology it enables any sample of male cells to have the Y chromosome it contains extracted. When mounted onto a microscope slide the unique DNA sequences within cells can be highlighted by using FISH (fluorescence in-situ hybridisation).

It is calculated that this method will assist in about 90 sexual assault cases each year where it is just too difficult to get a usable DNA profile and particularly where no sperm can be found in the semen, either because of a medical condition or because the alleged male assailant has had a vasectomy. It should also assist where female DNA in any sample overwhelms the male trace.

END


[1] See BBC’s experiment of Kristy Wark’s DNA. According to Professor Brian Sykes, who analysed her DNA, 95% of European women are descended from seven “daughters of Eve” who lived more than 10,000 years ago. But Kristy has a unique set of genetic mutations not previously seen amongst the thousands of DNA samples Professor Sykes has on his database. http://www.bbc.co.uk/pressoffice/pressreleases/stories/2003/02_february/27/newsnight_dna.shtml

2 responses to “DNA Fingerprinting – a quick reference guide

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