DNA fingerprint

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An individual's unique sequence of DNA base pairs, determined by exposing a sample of the person's DNA to molecular probes. DNA fingerprints are often used as evidence in criminal law cases. Also called genetic fingerprint.

A technique by which the DNA of an individual can be compared with that found in a sample or another individual. DNA fingerprinting is acepted by most courts as evidence for establishing paternity, and increasingly is being accepted as evidence in criminal trials.

DNA fingerprinting also known as DNA typing or genetic fingerprinting, is a method for identifying individuals by the particular structure of their DNA. It gained its name because the structure of the DNA of each person is different, and hence, just as each of us is unique with respect to the pattern of our fingerprints, so we can be identified from our DNA.

As well as containing the 100 000 or so genes that encode the structure of the thousands of proteins from which human beings are constructed, there are large regions of our DNA that do not consist of genes and appear to serve no useful purpose. Part of this functionless, ‘junk’ DNA is made up of long stretches of repeated sequences of the four nucleotide building blocks from which DNA is constructed. There is, however, some order in these repeats. For example, they may form what are called hypervariable regions, also known as mini-satellite DNA, which consist of blocks of tandem repeats of a short ‘core’ sequence. Nearly 100 of these hypervariable regions have been found in the human genome, many but not all of which are close to genes that encode different proteins. The number of copies in these different families of repeats varies widely between unrelated people and thus constitutes a unique genetic profile, or fingerprint. They are of particular value because they are apparently dispersed randomly throughout the genome and therefore are inherited independently of each other.

To produce a DNA fingerprint, DNA from a cell sample is digested with enzymes that cut it up into many different sized pieces and the mixture is placed in a gel. This is then exposed to an electric field and the fragments migrate to different positions by virtue of their size. In this way a pattern is obtained that reflects different numbers of repeats in different individuals; the length of a particular DNA fragment is a function of the number of repeats present.

After the separation of the fragments is complete, the DNA is transferred to a nitrocellulose filter, on which it is immobilized. The position of the fragments containing the repeats is identified by the use of a radioactively labelled DNA probe designed to bind to the core repeat sequences. The fingerprint is visualized by placing an X-ray plate over the filter and developing the film. Since mini-satellite DNA has a relatively high mutation rate, and this varies between different hypervariable regions, in practice it is important to ensure that the rates of mutation of the mini-satellites used for testing are not too great, so as to avoid false exclusions.

DNA fingerprinting is used for many purposes, particularly paternity testing and for forensic work. Of particular concern to the criminal fraternity is that DNA for fingerprinting can be obtained from whole blood, semen, vaginal fluid, hair roots, almost any tissue, and even from bones that have been buried for a long time. The probability that two unrelated individuals show exactly the same pattern varies depending on the particular hypervariable regions that are chosen. In one commonly used system the region analysed yields up to 36 different sized DNA bands, or alleles, for each individual. A band-sharing statistic is estimated at 0.25; that is, the probability of two unrelated individuals sharing the same pattern is 0.2536³⁶ or one in 5000 billion billion!

Because of its extreme sensitivity, and because appropriate hypervariable regions can be amplified from minute traces of DNA to produce diagnostic patterns, this technique has revolutionized forensic medicine over recent years.

— D. J. Weatherall

Bibliography

• Gill, P. (1994). DNA typing. In The enclycopaedia of molecular biology, pp. 286-8. Blackwell Science, Oxford.
• Jeffreys, A. J. et al. (1986). DNA fingerprinting and segregation analysis of multiple markers in human pedigrees. American Journal of Human Genetics, 39, 11-24

See also genetics, human.

The use of DNA analysis to identify a subject from blood or other suitable tissue.

DNA profiling is a molecular testing method used to uniquely identify people and other organisms. In many ways, it is similar to blood typing and fingerprinting, and it is sometimes called "DNA fingerprinting." Because every organism's DNA is unique, DNA can be examined to identify people who might be related to each other, to compare suspected criminals to DNA left at the scene of a crime, or even to identify certain strains of disease-causing bacteria.

Blood Typing and the Abo Groupings

Before the development of the molecular biology tools that make DNA testing possible, investigators identified people through blood typing. This method hails from 1900, when Karl Landsteiner first discovered that people inherited different blood types. Several decades later, researchers determined that the basis for those blood types was a set of proteins on the surface of red blood cells.

The main proteins on the surface of red blood cells used in blood typing come in two varieties: A and B. Every person inherits from their parents either the genes for the A protein, the B protein, both, or neither. Someone who inherits the A gene from one parent and neither gene from the other parent has blood type A. If a person inherits both genes, they are AB. A person who inherits neither is type O. Another protein group found on red blood cells is referred to collectively as the Rh factor. People either have the Rh factor or they do not, regardless of which of the A and B genes they inherited. To type a person's blood, antibodies against these various proteins (A, B, and Rh) are mixed with a blood sample. If the proteins are present, the blood cells will stick together and the sample will get cloudy.

Blood typing can be used to exclude the possibility that a blood sample came from a particular person, if the person's type does not match that of the sample. However, it cannot be used to claim that any particular person is the source of the sample, because there are so few blood types, and they are shared by so many people. About 45 percent of people in the United States are type O, and another 40 percent are type A. If four people were physically present at the scene of a murder, and the candlestick found nearby had type O blood spilled on it, chances are good that two of those individuals could be found guilty of the crime, based solely on the blood typing evidence. Most court cases, however, rely on more evidence than just blood or DNA typing, such as whose fingerprints are also found on the candlestick (see Statistics and the Prosecutor's Fallacy, below).

Dna Polymorphism Offers High Resolution

DNA is the molecule that contains all the genetic information of an individual. One person's DNA is made up of about three billion building blocks known as nucleotides or bases. Every organism in the world has a unique DNA sequence except for identical twins. Although identical twins accrue changes as they develop, they generally do not accumulate enough genetic differences for DNA typing to be useful. Portions of the DNA, called genes, encode proteins within the sequence of bases. Genes are separated by long stretches of noncoding DNA. Because these sequences do not have to code for functional proteins, they are free to accumulate more differences over time, and thus provide more variation than genes. Thus, they are more useful than gene sequences in distinguishing individuals.

Polymorphisms are differences between individuals that occur in DNA sequences which occupy the same locus in the chromosome. An individual will have only one sequence at a particular polymorphic locus in each chromosome, but if the population bears several to dozens of different possible sequences at the site in question, then the locus is considered "highly variable" within the population. DNA profiling determines which polymorphisms a person has at a small number of these highly variable loci. Because of this, DNA profiling can provide high resolution in distinguishing different individuals. The chances of one person having the same DNA profile as another are typically much less than the chances of winning a lottery.

Str Analysis

The technology of DNA profiling has advanced from its beginnings in the 1980s. Today, DNA profiling primarily examines "short tandem repeats," or STRs. STRs are repetitive DNA elements between two and six bases long that are repeated in tandem, like GATAGATAGATAGATA. These repeat sequences often exist in a chromosomal region called heterochromatin, a largely unused portion of DNA found in each chromosome.

Different STR sequences (also called genetic markers) occur at different loci. While their positions are fixed, the number of repeated units varies within the population, from four to forty depending on the STR. Therefore, one genetic marker may have between four and forty different variations, and each variation is referred to as an allele of that marker. Each person has at most two alleles of each marker, one inherited from each parent. The two alleles for a particular marker may be identical, if both parents had the same form.

The United States Federal Bureau of Investigation has designated thirteen of these sequences to use with STR analysis. These thirteen markers are all four-base repeats, and were chosen because multiple alleles of each exist throughout the population. The FBI system, called CODIS (Combined DNA Indexing System), has become the standard DNA profiling system in use today.

STR analysis begins with sample collection. Because of the often small samples involved and the legal weight that will be given to them, it is vital that the sample not be contaminated by other DNA. This may occur for instance if skin cells from the person collecting the sample are mixed with skin cells under the fingernails of a victim. Once the sample is collected, it must be kept secure at all times, to prevent any possibility of tampering.

In the laboratory, the DNA is isolated and purified, and then multiple copies of it are made using the polymerase chain reaction (PCR). Technicians can specify which DNA sequences to multiply, so that only the thirteen core STR sequences will be amplified (multiple copies produced), leaving the rest of the billions of irrelevant bases alone.

In order to specify which DNA to amplify, "primers" are used. The primers are DNA sequences that recognize a nonrepeated sequence in the genetic markers, and which are used by the DNA polymerase that does the actual copying. After the DNA has been copied, the new DNA molecules are separated by size, by gel electrophoresis. A fluorescent molecule previously attached to each primer will send a light signal to the machine that measures the length of the molecule, or allele.

Vntr Analysis

An early form of DNA profiling, rarely used today, is based on VNTRs, or "variable number of tandem repeats." VNTRs requires extensive sample processing: The DNA is chopped up with restriction enzymes, separated by size, and probes are applied to the fragmented DNA to view only the relevant DNA pieces. In the DNA of two different individuals, different spacing between two cut sites for the restriction enzymes gives a unique pattern of DNA size fragments, called "restriction fragment length polymorphisms," or RFLPs.

Making a Match

To understand how DNA profiling is used to identify a person, imagine a sample of blood collected at a crime scene that doesn't match the victim's blood, and is presumably from the unknown perpetrator. DNA from the blood is isolated and its set of STRs are analyzed. The results will be a list of the alleles found at each of the markers (for example, VWA-12, 13; TH01-6, 7, and so on), where the initial symbol is the abbreviation for the markers and the last two are the numbers of the alleles found in the sample for that marker. The full set of thirteen markers may or may not be analyzed in each case. When a suspect is identified, his or her DNA can be analyzed for these same markers. If the set of alleles are different, the investigators can be sure that the two DNAs came from different sources, and the suspect is not the source of the blood. Since the introduction of DNA profiling, an absence of matching DNA has been used to free dozens of wrongly convicted prisoners.

If the samples do match, the question becomes whether the blood is actually from the suspect, or from someone else with the same set of alleles. As with blood typing, this is a matter of statistics, and depends on how frequently each allele occurs in the population. This information has been tabulated and is kept on file in the FBI CODIS database. If two samples share a very rare allele, that increases the likelihood they came from the same source.

Matching multiple alleles increases the certainty they came from the same source. Since the thirteen STRs are inherited independently of each other, the likelihood that one person's DNA will include specific alleles of all thirteen STR sites is the product of the individual allele frequencies. For example, if each allele a person carries occurs in 25 percent of the population, then the probability that all thirteen alleles will occur in one individual is (0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25 × 0.25) or 1 in more than 67 million. This analysis can discriminate between millions of people, far better than is possible using the four blood groups. Since many alleles are even rarer than 25 percent, their presence in both samples further increases the probability that they came from the same source.

Statistics and the Prosecutor's Fallacy

Despite the persuasiveness of such figures, it is quite possible to misuse DNA evidence to incorrectly argue that an innocent suspect must be the perpetrator of the crime, or that a guilty suspect should go free. Both defense and prosecution attorneys can—accidentially or otherwise—misinterpret data to make a highly likely event seem improbable, or a highly unlikely event seem probable. Jurors can be confused because DNA testing reveals the probability that an innocent person's DNA profile matches the sample at the scene of the crime. Jurors must decide, however, what the probability is that a person is innocent, if his DNA matches that sample. The prosecutor's fallacy occurs when investigators focus on the existence of the match, rather than the possibility that the match could be a coincidence.

Let's assume the DNA profile found at the crime scene—and the matching DNA of the suspect—is expected to occur once in every million people. The correct statement of probability arising from these facts is, "If the suspect is innocent, there is a one-in-one-million chance of obtaining this DNA match." The fallacy is to reverse these clauses, and state, "If the DNA matches, there is a one in one million chance that the suspect is innocent." To understand the logical fallacy, imagine the statement, "If it's Tuesday, it must be a school day." The reverse is not true—there are other school days besides Tuesday.

Similarly, there are other ways of misusing statistics in DNA profiling. Let's assume the suspect in the above case is actually guilty. If the suspect hails from a city with a population of ten million, there are ten people in the city whose DNA matches the DNA at the crime scene. Therefore, his defense lawyers could argue there is a 90 percent chance that the suspect is innocent, because he is 1 out of 10 individuals with that same DNA profile. If the defense can convince the jury to ignore other incriminating evidence, such as the suspect's bloody glove left behind at the scene, then the attorney may introduce reasonable doubt. Only by considering DNA typing within the context of other evidence can the probability of a DNA match improve the integrity of the justice system.

Dna Profiling Comes of Age

Although DNA profiling was viewed with some skepticism when it first made its way into the courts, DNA typing is now used routinely, in and out of the courthouse. It is commonly used in rape and murder cases, where the assailant generally leaves behind some personal evidence such as hair, blood, or semen. In paternity tests, the child's DNA profile will be a combination of the profiles of both parents. DNA profiling has also been used to identify victims in disasters where large numbers of people died at once, such as in airplane crashes, large fires, or military conflicts.

DNA testing can also used in organisms other than humans. For instance, it has been used to type cattle in a cattle-stealing case. It can also be used to identify pathogenic strains of bacteria to track the outbreak of disease epidemics.

Bibliography

Bloom, Mark V., Greg A. Freyer, and David A. Micklos. Laboratory DNA Science: An Introduction to Recombinant DNA Techniques and Methods of Genome Analysis. Menlo Park, CA: Addison-Wesley, 1996.

Evert, Ian W., and Bruce S. Weir. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Sunderland, MA: Sinauer Associates, 1998.

Steward, Ian. "The Interrogator's Fallacy." Scientific American (September 1996): 172-175.

Internet Resources

"13 CODIS Core STR Loci with Chromosomal Positions." National Institute of Standards and Technology. http://www.cstl.nist.gov/biotech/strbase/images/codis.jpg.

The Biology Project. The University of Arizona. http://www.biology.arizona.edu/human_bio/activities/blackett2/gifs/sample2.gif.

FBI Core STR Markers.http://www.cstl.nist.gov/biotech/strbase/fbicore.htm.

The Innocence Project.http://www.innocenceproject.org/.

—Mary Beckman

For more information on DNA fingerprinting, visit Britannica.com.

DNA fingerprinting is the term applied to a range of techniques that are used to show similarities and dissimilarities between the DNA present in different individuals.

DNA fingerprinting is an important tool in the arsenal of forensic investigators and intelligence officers. In an era when plastic surgery can be used to alter a terrorist's appearance, DNA fingerprinting allows for positive identification not only of body remains, but also of suspects in custody. DNA fingerprinting can also link physical evidence from incidents that occur in different parts of the world.

Sir Alec Jeffreys at the University of Leicester developed DNA fingerprinting in the mid 1980s. The sequence of nucleotides in DNA is similar to a fingerprint, in that it is unique to each person. DNA fingerprinting is used for identifying people, studying populations, and forensic investigations.

Historical Uses of Dna Fingerprinting

Jeffreys was first given the opportunity to demonstrate the power of DNA fingerprinting in March of 1985 when he proved a boy was the son of a British citizen and should be allowed to enter the country. In 1986, DNA was first used in forensics. In a village near Jeffreys' home, a teenage girl was assaulted and strangled. No suspect was found, although body fluids were recovered at the crime scene. When another girl was strangled in the same way, a 19-year-old caterer confessed to one murder but not the other. DNA analysis showed that the same person committed both murders, and the caterer had falsely confessed. Blood samples of 4582 village men were taken, and eventually the killer was revealed when he attempted to bribe someone to take the test for him.

The first case to be tried in the United States using DNA fingerprinting evidence was of African-American Tommie Lee Edwards. In November 1987, a judge did not permit population genetics statistics that compared Edwards to a representative population. The judge feared the jury would be overwhelmed by the technical information. The trial ended in a mistrial. Three months later, Andrews was on trial for the assault of another woman. This time the judge did permit the evidence of population genetics statistics. The prosecutor showed that the probability that Edwards' DNA would not match the crime evidence was one in ten billion. Edwards was convicted.

DNA fingerprinting has been used repeatedly to identify human remains. In Cardiff, Wales, skeletal remains of a young woman were found, and a medical artist was able to make a model of the girl's face. She was recognized by a social worker as a local run-away. Comparing the DNA of the femur of the girl with samples from the presumptive parents, Jeffreys declared a match between the identified girl and her parents. In Brazil, Wolfgang Gerhard, who had drowned in a boating accident, was accused of being the notorious Nazi of Auschwitz, Josef Mengele. Disinterring the bones, Jeffreys and his team used DNA fingerprinting to conclude that the man actually was the missing Mengele.

In addition to forensics, DNA has been used to unite families. In 1976, a military junta in a South American country killed over 9000 people, and the orphaned children were given to military couples. After the regime was overthrown in 1983, Las Abuelas (The Grandmothers) determined to bring these children to their biological families. Using DNA fingerprinting, they found the families of over 200 children.

DNA has been used to solve several historical mysteries. On July 16, 1918, the czar of Russia and his family were shot, doused with sulfuric acid, and buried in a mass grave. In 1989, the site of burial was uncovered, and bone fragments of nine skeletons were assembled. DNA fingerprinting experts from all over the world pieced together the puzzle that ended in a proper burial to the Romanov royal family in Saint Petersburg in 1998.

The Mechanics of Dna Fingerprinting

The nucleus of every cell in the human body contains deoxyribonucleic acid or DNA, a biochemical molecule that is made up of nearly three-billion nucleotides. DNA consists of four different nucleotides, adenine (A), thymine (T), guanine (G), and cytosine (C), which are strung together in a sequence that is unique to every individual. The sequence of A, T, G, and C in human DNA can be found in more combinations or variations than there are humans. The technology of DNA fingerprinting is based on the assumption that no two people have the same DNA sequence.

The DNA from a small sample of human tissue can be extracted using biochemical techniques. Then the DNA can be digested using a series of enzymes known as restriction enzymes, or restriction endonucleases. These molecules can be thought of as chemical scissors, which cut the DNA into pieces. Different endonucleases cut DNA at different parts of the nucleotide sequence. For example, the endonuclease called SmaI cuts the sequence of nucleotides CCCGGG between the third cytosine (C) and the first guanine (G).

After being exposed to a group of different restriction enzymes, the digested DNA undergoes gel electrophoresis. In this biochemical analysis technique, test samples of digested DNA are placed in individual lanes on a sheet of an agarose gel that is made from seaweed. A separate lane contains control samples of DNA of known lengths. The loaded gel is then placed in a liquid bath and an electric current is passed through the system. The various fragments of DNA are of different sizes and different electrical charges. The pieces move according to their size and charge with the smaller and more polar ones traveling faster. As a result, the fragments migrate down the gel at different rates.

After a given amount of time, the electrical current in the gel electrophoresis instrumentation is shut off. The gel is removed from the bath and the DNA is blotted onto a piece of nitrocellulose paper. The DNA is then visualized by the application of radioactive probe that can be picked up on a piece of x-ray film. The result is a film that contains a series of lines showing where the fragments of DNA have migrated. Fragments of the same size in different lanes indicate the DNA has been broken into segments of the same size. This demonstrates a similarity between the sequences under test.

Different enzymes produce different banding patterns and normally several different endonucleases are used in conjunction to produce a high definition banding pattern on the gel. The greater the number of enzymes used in the digestion, the finer the resultant resolution.

In DNA fingerprinting, scientists focus on segments of DNA in which nucleotide sequences vary a great deal from one individual to another. For example, five to ten percent of the DNA molecule contains regions that repeat the same nucleotide sequence many times, although the number of repeats varies from person to person. Jeffreys targeted these long repeats called variable number of tandem repeats (VNTRs) when he first developed DNA fingerprinting. The DNA of each person also has different restriction fragment sizes, called restriction fragment length polymorphisms (RFLPs), which can be used as markers of differences in DNA sequences between people. Today, technicians also use short tandem repeats (STRs) for DNA fingerprinting. STRs are analyzed using polymerase chain reaction or PCR, a technique for mass-producing sequences of DNA. PCR allows scientists to work with degraded DNA.

Use as a forensic tool. DNA fingerprinting is now an important tool in the arsenal of forensic chemists. It is used in forensics to examine DNA samples taken from a crime scene and compare them to those of a suspect. Criminals almost always leave evidence of their identity that contains DNA at the crime scene—hair, blood, semen, or saliva. These materials can be carefully collected from the crime scene and fingerprinted

Although DNA fingerprinting is scientifically sound, the use of DNA fingerprinting in courtrooms remains controversial. There are several objections to its use. Lawyers who misrepresent the results of DNA fingerprints may confuse jurors. DNA fingerprinting relies on the probability that individuals will not produce the same banding pattern on a gel after their DNA has been fingerprinted. Establishing this probability relies on population statistics. Each digested fragment of DNA is given a probability value. The value is determined by a formula relating the combination of sequences occurring in the population. There is concern that not enough is known about the distribution of banding patterns of DNA in the population to express this formula correctly. Concerns also exist regarding the data collection and laboratory procedure associated with DNA fingerprinting procedures. For example, it is possible that cells from a laboratory technician could be inadvertently amplified and run on the gel. However, because each person has a unique DNA sequence and this sequence cannot be altered by surgery or physical manipulation, DNA fingerprinting is an important tool for solving criminal cases.

Further Reading

Books

Griffiths, A., et al. Introduction to Genetic Analysis, 7th ed. New York: W.H. Freeman and Co., 2000.

Jorde, L. B., J. C. Carey, M. J. Bamshad, and R. L. White. Medical Genetics, 2nd ed. Mosby-Year Book, Inc., 2000.

Klug, W., and M. Cummings. Concepts of Genetics, 6th ed. Upper Saddle River: Prentice Hall, 2000.

Watson, J. D., et al. Molecular Biology of the Gene, 4th ed. Menlo Park, CA: The Benjamin/Cummings Publishing Company, Inc., 1987.

Electronic

The University of Washington. "Basics of DNA fingerprinting." <http://www.biology.washington.edu/fingerprint/dnaintro.html,>(March 4, 2003).

DNA stands for deoxyribonucleic acid. Strands of DNA are long polymers composed of millions of nucleotides linked together. The sequence of nucleotides determines individual hereditary characteristics (the fingerprint) for all living matter, including grape vines. DNA fingerprinting (also called DNA profiling or DNA typing) allows small tissue samples of various grape varieties to be compared and analyzed to determine if they are similar or identical. In the United States, university of california, davis researchers have been at the forefront of DNA profiling. In the early 1990s, Davis researchers used DNA fingerprinting to establish a relationship between California's zinfandel and Italy's Primitivo. They established that some (but not all) examples of Primitivo were identical to Zinfandel, which caused speculation that Zinfandel might have originated in Italy. However, in late 2001, through collaborative efforts of researchers at UC Davis and the University of Zagreb in Croatia, DNA analysis determined that Crljenak (a little-known grape from Croatia) and Zinfandel had identical DNA profiles. Further analysis proved that a more popular Croatian grape, Plavac Mali, was a descendant of Crljenak (and therefore of Zinfandel). In 1997 researchers at UC Davis determined that cabernet sauvignon is an offspring of sauvignon blanc and cabernet franc. Since Cabernet Sauvignon appeared in the late seventeenth century prior to plant hybridization practices, UC Davis scientists believe that its origin was a natural occurrence rather than a planned cross of the two parents. This serendipitous union turned out to be viticulturally historical. Based on DNA profiling, Chardonnay's origins are believed to be from the Pinot family (pinot noir, pinot gris, pinot blanc) on one side and from Gouais Blanc (a mediocre variety) on the other. Gouais Blanc, which is no longer grown in France, appears to be identical to Heunischweiss, a variety once widely grown in eastern Europe. Information on these varieties has been added to the DNA profiles of about 700 grape varieties, a database developed in collaboration with UC Davis researchers' colleagues in Montpellier, France. These profiles will contribute to the efforts of the International Grape Genome Project-groups of research teams in ten countries that map the genetic material of grapes to better understand various characteristics of grapes.

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Trace evidence

Genetic fingerprinting, DNA testing, DNA typing, and DNA profiling are techniques used to distinguish between individuals of the same species using only samples of their DNA. Its invention by Sir Alec Jeffreys at the University of Leicester was announced in 1985. Two humans will have the vast majority of their DNA sequence in common. Genetic fingerprinting exploits highly variable repeating sequences called minisatellites. Two unrelated humans will be unlikely to have the same numbers of minisatellites at a given locus. In STR profiling, which is distinct from DNA fingerprinting, PCR is used to obtain enough DNA to then detect the number of repeats at several loci. It is possible to establish a match that is extremely unlikely to have arisen by coincidence, except in the case of identical twins, who will have identical genetic profiles. The chance of two people having the same DNA is one in a billion.

Genetic fingerprinting is used in forensic science, to match suspects to samples of blood, hair, saliva or semen. It has also led to several exonerations of formerly convicted suspects. It is also used in such applications as identifying human remains, paternity testing, matching organ donors, studying populations of wild animals, and establishing the province or composition of foods. It has also been used to generate hypotheses on the pattern of the human diaspora in prehistoric times.

Testing is subject to the legal code of the jurisdiction in which it is performed. Usually the testing is voluntary, but it can be made compulsory by such instruments as a search warrant or court order. Several jurisdictions have also begun to assemble databases containing DNA information of convicts.

The United States maintains the largest DNA database in the world: The Combined DNA Index System, with over 4.5 million records as of 2007. The United Kingdom, maintains the National DNA Database (NDNAD), which is of similar size. The size of this database,and its rate of growth, is giving concern to civil liberties groups in the UK, where police have wide-ranging powers to take samples and retain them even in the event of acquittal.

Reference samples

DNA identification must be done by an extraction of DNA from substances such as:

• Personal items (e.g. toothbrush, razor, ...)
• Banked samples (e.g. banked sperm or biopsy tissue)
• Blood kin (biological relative)
• Human remains previously identified

Reference samples are often collected using buccal swab.

DNA fingerprinting methods

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

RFLP analysis

Main article: Restriction fragment length polymorphism

One way to fingerprint DNA is by doing a Southern blot. This has several steps. First, the DNA being analyzed must be separated from other material. Next, it must be cut into a few different-sized pieces using restriction enzymes, proteins that can cut double-stranded DNA without damaging the bases. The pieces are sorted by size through gel electrophoresis. The pieces are poured into gel with a positive charge at the bottom. DNA has a natural slightly negative charge so it will be attracted to the bottom. The smaller pieces can move more quickly through the gel, therefore they will be further toward the bottom than the larger pieces. This will separate the pieces by size, with the larger ones higher up and the smaller ones further down. Next, alkaline solution or heat is applied to the gel so that the DNA denatures and separates into single strands. Nitrocellulose paper is pressed evenly against the gel and then baked so the DNA is permanently attached to it. The DNA is now ready to be analyzed using a radioactive probe in a hybridization reaction.

To make a radioactive probe, DNA polymerase is needed. The DNA that is going to be made radioactive should be put in a tube. Horizontal breaks should be made along the strand, while at the same time nucleotides should be added. The base C, or cytosine, should be radioactive. Next, the polymerase should be added to the tube. It will be attracted to the breaks and try to fix them. As the DNA polymerase fixes the DNA, it will break the existing bonds so that the existing nucleotides can be replaced by the new nucleotides in the tube. Whenever the lower strand has a G base, or guanine, the C put in will be radioactive. By repairing the strand of DNA, the polymerase is also making it radioactive. The DNA is heated so that the two strands split. Single-stranded pieces that might or might not be radioactive are made. The radioactive pieces are now probes ready for use. Now the radioactive probe can be used to create a hybridization reaction. Hybridization is when two genetic sequences bind together because of the hydrogen bonds that are in between the base pairs. There are two of these bonds between A, or adenine, and T, or thymine, and three between C and G. To make hybridization works, the DNA has to be denatured so it is single-stranded; like the Southern Blot that was made on the nitrocellulose paper. The denatured DNA and the radioactive probe should be put into a plastic bag with saline liquid, and then shaken. The probe will bond to the denatured DNA wherever it finds a fit. The probe and the DNA do not have to fit together precisely. The two will have sequences that can stick together even if the fit is poor, however there will be fewer hydrogen bonds. Probes that have low homology, or similarity, can bind to the DNA better if the temperature is varied or the amount of salt in the mixture is changed. Even if the fit is poor, the probe and the DNA are now hybridized. A way to make use of the whole process described above is by using it to determine a person’s VNTRs. VNTRs, or Variable Number Tandem Repeats, are repeated sequences of base pairs in someone’s genetic information. Every DNA strand contains exons, or sections that have genetic information, and introns, which have no discernible use other than containing VNTRs, or repeating sequences of base pairs. Every single human being has a few of these repeating sequences. To find out if somebody has a specific VNTR, a Southern Blot must be made, and then probed in a hybridization reaction, by a radioactive version of said VNTR. This process ends up making a pattern called a DNA fingerprint. Every person has VNTRs they have inherited genetically from one or both parents. It is impossible for somebody to have one that neither of their parents did. VNTR patterns are unique for each person, and they will be more exact if more VNTR probes are used.

PCR analysis

Main article: Polymerase chain reaction

With the invention of the polymerase chain reaction (PCR), DNA fingerprinting took huge strides forward in both discriminating power and ability to recover information from very small starting samples. PCR involves the amplification of specific regions of DNA using a cycling of temperature and a thermostable polymerase enzyme along with sequence specific primers of DNA. Commercial kits that used single nucleotide polymorphisms (SNPs) for discrimination became available. These kits use PCR to amplify specific regions with known variations and hybridize them to probes anchored on cards, which results in a colored spot corresponding to the particular sequence variation.

One of the primary complaints against RFLP was that it was slow and required large quantities of DNA to be used. This led to the development of PCR-based methods which required smaller amounts of DNA that could also be more degraded than those used in RFLP analysis. Systems such as the HLA-DQ alpha reverse dot blot strips grew to be very popular due to their ease of use and the speed with which a result could be obtained, however they were not as discriminating as RFLP. It was also difficult to determine a DNA profile for mixed samples, such as a vaginal swab from a sexual assault victim.

AmpFLP

Main article: 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 relied on variable number tandem repeat (VNTR) polymorphisms to distinguish various alleles, which were separated on a polyacrylamide gel using an allelic ladder (as opposed to a molecular weight ladder). Bands could be visualized by silver staining the gel. One popular locus for fingerprinting was the D1S80 locus. As with all PCR based methods, highly degraded DNA or very small amounts of DNA may cause allelic dropout (causing a mistake in thinking a heterozygote is a homozygote) or other stochastic effects. In addition, because the analysis is done on a gel, very high number repeats may bunch together at the top of the gel, making it difficult to resolve. AmpFLP analysis can be highly automated, and allows for easy creation of phylogenetic trees based on comparing individual samples of DNA. Due to its relatively low cost and ease of set-up and operation, AmpFLP remains popular in lower income countries.

STR analysis

Main article: Short 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 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 different people have different numbers of repeat units, these regions of DNA can be used to discriminate between individuals. These STR loci (locations) are targeted with sequence-specific primers and are 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.

The polymorphisms displayed at each STR region are by themselves very common, typically each polymorphism will be shared by around 5 - 20% of individuals. When looking at multiple loci, it is the unique combinations of these polymorphisms to an individual that makes this method discriminating as an 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 which amplify the CODIS 13 core loci are almost universal, while in the UK the SGM+ system, which is compatible with The National DNA Database in use. Whichever system is used, many of the STR regions under test are the same. These DNA profiling systems are based around multiplex reactions, whereby many STR regions will be under test at the same time.

Capillary electrophoresis works by electrokinetically (movement through the application of an electric field) injecting the DNA fragments into a thin glass tube (the capillary) filled with polymer. The DNA is pulled through the tube by the application of an electric field, separating the fragments such that the smaller fragments travel faster through the capillary. The fragments are then detected using fluorescent dyes that were attached to the primers used in PCR. This allows multiple fragments to be amplified and run simultaneously, something known as multiplexing. Sizes are assigned using labeled DNA size standards that are added to each sample, and the number of repeats are determined by comparing the size to an allelic ladder, a sample that contains all of the common possible repeat sizes. Although this method is expensive, larger capacity machines with higher throughput are being used to lower the cost/sample and reduce backlogs that exist in many government crime facilities.

Gel electrophoresis acts using similar principles as CE, but instead of using a capillary, a large polyacrylamide gel is used to separate the DNA fragments. An electric field is applied, as in CE, but instead of running all of the samples by a detector, the smallest fragments are run close to the bottom of the gel and the entire gel is scanned into a computer. This produces an image showing all of the bands corresponding to different repeat sizes and the allelic ladder. This approach does not require the use of size standards, since the allelic ladder is run alongside the samples and serves this purpose. Visualization can either be through the use of fluorescently tagged dyes in the primers or by silver staining the gel prior to scanning. Although it is cost effective and can be rather high throughput, silver staining kits for STRs are being discontinued. In addition, many labs are phasing out gels in favor of CE as the cost of machines becomes more manageable.

The true power of STR analysis is in its statistical power of discrimination. In the U.S.A., there are 13 core loci (DNA locations) that are currently used for discrimination in CODIS. Because these loci are independently assorted (having a certain number of repeats at one locus doesn't 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 (1 with 18 zeros after it) or more.

Y-chromosome analysis

Recent innovations have included the creation of primers targeting polymorphic regions on the Y-chromosome (Y-STR), which allows resolution of multiple male profiles, or cases in which a differential extraction is not possible. Y-chromosomes are paternally inherited, so Y-STR analysis can help in the identification of paternally related males. Y-STR analysis was performed in the Sally Hemings controversy to determine if Thomas Jefferson had sired a son with one of his slaves.

Mitochondrial analysis

Main article: Mitochondrial DNA

For highly degraded samples, it is sometimes impossible to get a complete profile of the 13 CODIS STRs. In these situations, mitochondrial DNA (mtDNA) is sometimes typed due to there being many copies of mtDNA in a cell, while there may only be 1-2 copies of the nuclear DNA. Forensic scientists amplify the HV1 and HV2 regions of the mtDNA, then sequence each region and compare single nucleotide differences to a reference. Because mtDNA is maternally inherited, directly linked maternal relatives can be used as match references, such as one's maternal grandmother's sister's son. A difference of two or more nucleotides is generally considered to be an exclusion. Heteroplasmy and poly-C differences may throw off straight sequence comparisons, so some expertise on the part of the analyst is required. mtDNA is useful in determining unclear identities, such as those of missing persons when a maternally linked relative can be found. mtDNA testing was used in determining that Anna Anderson was not the Russian princess she had claimed to be, Anastasia Romanov.

mtDNA can be obtained from such material as hair shafts and old bones/teeth.

Considerations when evaluating DNA evidence

In the early days of the use of genetic fingerprinting as criminal evidence, juries were often swayed by spurious statistical arguments by defense lawyers along these lines: given a match that had a 1 in 5 million probability of occurring by chance, the lawyer would argue that this meant that in a country of say 60 million people there were 12 people who would also match the profile. This was then translated to a 1 in 12 chance of the suspect being the guilty one. This argument is not sound unless the suspect was drawn at random from the population of the country. In fact, a jury should consider how likely it is that an individual matching the genetic profile would also have been a suspect in the case for other reasons. Another spurious statistical argument is based on the false assumption that a 1 in 5 million probability of a match automatically translates into a 1 in 5 million probability of guilt and is known as the prosecutor's fallacy.

When using RFLP, the theoretical risk of a coincidental match is 1 in 100 billion (100,000,000,000). However, the rate of laboratory error is almost certainly higher than this, and often actual laboratory procedures do not reflect the theory under which the coincidence probabilities were computed. For example, the coincidence probabilities may be calculated based on the probabilities that markers in two samples have bands in precisely the same location, but a laboratory worker may conclude that similar—but not precisely identical—band patterns result from identical genetic samples with some imperfection in the agarose gel. However, in this case, the laboratory worker increases the coincidence risk by expanding the criteria for declaring a match. Recent studies have quoted relatively high error rates which may be cause for concern [1]. In the early days of genetic fingerprinting, the necessary population data to accurately compute a match probability was sometimes unavailable. Between 1992 and 1996, arbitrary low ceilings were controversially put on match probabilities used in RFLP analysis rather than the higher theoretically computed ones [2]. Today, RFLP has become widely disused due to the advent of more discriminating, sensitive and easier technologies.

STRs do not suffer from such subjectivity and provide similar power of discrimination (1 in 10^13 for unrelated individuals if using a full SGM+ profile) It should be noted that figures of this magnitude are not considered to be statistically supportable by scientists in the UK, for unrelated individuals with full matching DNA profiles a match probability of 1 in a billion (one thousand million) is considered statistically supportable (Since 1998 the DNA profiling system supported by The National DNA Database in the UK is the SGM+ DNA profiling system which includes 10 STR regions and a sex indicating test. However, with any DNA technique, the cautious juror should not convict on genetic fingerprint evidence alone if other factors raise doubt. Contamination with other evidence (secondary transfer) is a key source of incorrect DNA profiles and raising doubts as to whether a sample has been adulterated is a favorite defense technique. More rarely, Chimerism is one such instance where the lack of a genetic match may unfairly exclude a suspect.

When evaluating a DNA match, the following questions should be asked:

• Could it be an accidental random match?
• If not, could the DNA sample have been planted?
• If not, did the accused leave the DNA sample at the exact time of the crime?
• If yes, does that mean that the accused is guilty of the crime?

Fake DNA evidence

The value of DNA evidence has to be seen in light of recent cases where criminals planted fake DNA samples at crime scenes. In one case, a criminal even planted fake DNA evidence in his own body: Dr. John Schneeberger of Canada raped one of his sedated patients in 1992 and left semen on her underwear. Police drew Schneeberger's blood and compared its DNA against the crime scene semen DNA on three occasions, never showing a match. It turned out that he had surgically inserted a Penrose drain into his arm and filled it with foreign blood and anticoagulants.

DNA Evidence as Evidence in Criminal Trials

England

Evidence from an expert who has compared DNA samples must be accompanied by evidence as to the sources of the samples and the procedures for obtaining the DNA profiles.^[1] The judge must ensure that the jury understand the significance of matches and mismatches in the profiles. The judge must also ensure that the jury do not confuse the 'match probability' (the probability that a person picked at random has a matching DNA profile to the sample from the scene) with the 'likelihood ratio' (the probability that a person with matching DNA committed the crime). In R v. Doheny,  EWCA Crim 728 (1996) Phillips LJ gave this example of a summing up, which should be carefully tailored to the particular facts in each case:

Members of the Jury, if you accept the scientific evidence called by the Crown, this indicates that there are probably only four or five white males in the United Kingdom from whom that semen stain could have come. The Defendant is one of them. If that is the position, the decision you have to reach, on all the evidence, is whether you are sure that it was the Defendant who left that stain or whether it is possible that it was one of that other small group of men who share the same DNA characteristics.

Juries should weigh up conflicting and corroborative evidence, using their own common sense and not by using mathematical formulae, such as Bayes' theorem, so as to avoid "confusion, misunderstanding and misjudgment"^[2].

Cases

In the 1920s, Anna Anderson claimed that she was Princess Anastasia Romanov of Russia; in the 1980s after her death, samples of her tissue that had been stored at a Charlottesville, Virginia hospital following a medical procedure were tested using DNA fingerprinting and showed that she bore no relation to the Romanovs.

In 1987, British baker Colin Pitchfork was the first criminal caught using DNA fingerprinting in Leicester, the city where it was first discovered.

In 1987, Florida rapist Tommie Lee Andrews was the first person in the United States to be convicted as a result of DNA evidence, for raping a woman during a burglary; he was convicted on 6 November 1987 and sentenced to 22 years in prison. [3] [4]

In 1988, Timothy Spencer was the first man in the United States to be sentenced to death through DNA Testing for several rape and murder charges, He was dubbed "The South Side Strangler" Because he killed all his victims on the southside of Richmond, Virginia. He was later charged with rape and 1st degree murder and was sentenced to death. He was executed on April 27, 1994.

In 1989, Chicago man Gary Dotson was the first person whose conviction was overturned using DNA evidence.

In 1991, Allan Legere was the first Canadian to be convicted as a result of DNA evidence, for four murders he had committed while an escaped prisoner in 1989. During his trial, his defense argued that the relatively shallow gene pool of the region could lead to false positives.

In 1992, DNA evidence was used to prove that Nazi doctor Josef Mengele was buried in Brazil under the name Wolfgang Gerhard.

In 1993, Kirk Bloodsworth was the first person to have been convicted of murder and sentenced to death, whose conviction was overturned using DNA evidence.

The science was made famous in the United States in 1994 when prosecutors heavily relied on — and through expert witnesses exhaustively presented and explained — DNA evidence allegedly linking O.J. Simpson to a double murder. The case also brought to light the laboratory difficulties and handling procedure mishaps which can cause such evidence to be significantly doubted.

In 1994, RCMP detectives successfully tested hairs from a cat known as Snowball, and used the test to link a man to the murder of his wife, thus marking for the first time in forensic history the use of non-human DNA to identify a criminal.

In 1998, Dr. Richard J. Schmidt was convicted of attempted second-degree murder when it was shown that there was a link between the viral DNA of the human immunodeficiency virus (HIV) he had been accused of injecting in his girlfriend and viral DNA from one of his patients with full-blown AIDS. This was the first time viral DNA fingerprinting had been used as evidence in a criminal trial.

In 2002, DNA testing was used to exonerate Douglas Echols, a man who was wrongfully convicted in a 1986 rape case. Echols was the 114th person to be exonerated through post-conviction DNA testing.

In August 2002 Annalisa Vincenzi was shot dead in Tuscany. Some time later, Bartender Peter Hamkin, 23, was arrested in Merseyside in March 2003 on an extradition warrant heard at Bow Street Magistrates' Court in London to establish whether he should be taken to Italy to face a murder charge. DNA "proved" he shot her, but he was cleared on other evidence.[5]

In 2003, Welshman Jeffrey Gafoor was convicted of the 1988 murder of Lynette White, when crime scene evidence collected 12 years earlier was re-examined using STR techniques, resulting in a match with his nephew.[6] This may be the first known example of the DNA of an innocent yet related individual being used to identify the actual criminal, via "familial searching".

In June of 2003, because of new DNA evidence, Dennis Halstead, John Kogut and John Restivo won a re-trial on their murder conviction. The three men had already served eighteen years of their thirty plus year sentences.

The trial of Robert Pickton is notable in that DNA evidence is being used primarily to identify the victims, and in many cases to prove their existence.

In March 2003, Josiah Sutton was released from prison after serving four years of a twelve year sentence for a sexual assault charge. Questionable DNA samples taken from Sutton were retested in the wake of the Houston Police Department's crime lab scandal of mishandling DNA evidence.

In December 2005, Evan Simmons was proven innocent of a 1981 attack on an Atlanta woman after serving twenty four years in prison. Mr Clark is the 164th person in United States and the fifth in Georgia to be freed using post-conviction DNA testing.

References

1. ^ R v. Loveridge,   EWCA Crim 734 (2001)
2. ^ R v. Adams,  EWCA Crim 2474 (1997)

See also

• National DNA database
• restriction fragment length polymorphism (RFLP)
• paternity test
• genealogical DNA test
• short tandem repeat (STR)
• capillary electrophoresis (CE)
• Gene mapping
• Harvey v. Horan
• ribotyping

External links

• How to make a DNA (genetic) Fingerprint and applications of DNA Fingerprinting
• Create a DNA Fingerprint
• Forensic genetics and ethical, legal and social implications beyond the clinic

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