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DNA fingerprint |
Britannica Concise Encyclopedia:
DNA fingerprint |
For more information on DNA fingerprinting, visit Britannica.com.
Modern Science:
DNA 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.
World of the Body:
DNA fingerprinting |
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
See also genetics, human.
Dental Dictionary:
DNA fingerprinting |
The use of DNA analysis to identify a subject from blood or other suitable tissue.
Genetics Encyclopedia:
DNA Profiling |
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
Columbia Encyclopedia:
DNA fingerprinting |
Methods
A common procedure for DNA fingerprinting is restriction fragment length polymorphism (RFLP). In this method, DNA is extracted from a sample and cut into segments using special restriction enzymes. RFLP focuses on segments that contain sequences of repeated DNA bases, which vary widely from person to person. The segments are separated using a laboratory technique called electrophoresis, which sorts the fragments by length. The segments are radioactively tagged to produce a visual pattern known as an autoradiograph, or "DNA fingerprint," on X-ray film. A newer method known as short tandem repeats (STR) analyzes DNA segments for the number of repeats at 13 specific DNA sites. The chance of misidentification in this procedure is one in several billion. Yet another process, polymerase chain reaction, is used to produce multiple copies of segments from a very limited amount of DNA (as little as 50 molecules), enabling a DNA fingerprint to be made from a single hair. Once a sufficient sample has been produced, the pattern of the alleles (see genetics) from a limited number of genes is compared with the pattern from the reference sample. A nonmatch is conclusive, but the technique provides less certainty when a match occurs.
Applications
In criminal investigations, the DNA fingerprint of a suspect's blood or other body material is compared to that of the evidence from the crime scene to see how closely they match. The technique can also be used to establish paternity. First developed in the mid-1980s, DNA fingerprinting has been accepted in most courts in the United States, and has in several notable instances been used to exonerate or free persons convicted of crimes, but the Supreme Court has ruled (2009) that convicted criminals do not have a constitutional right to DNA testing. All states have established DNA fingerprint databases, and the Federal Bureau of Investigation has instituted a national DNA fingerprint database linking those of the states and including DNA collected in connection with federal offenses. DNA fingerprinting is generally regarded as a reliable forensic tool when properly done, but some scientists have called for wider sampling of human DNA to insure that the segments analyzed are indeed highly variable for all ethnic and racial groups. It is possible to create false genetic samples and use them to misdirect forensic investigators, but if those samples have been produced using gene amplification techniques they can be distinguished from normal DNA evidence.
The techniques used in DNA fingerprinting also have applications in paleontology, archaeology, various fields of biology, and medical diagnostics. It has, for example, been used to match the goatskin fragments of the Dead Sea Scrolls. In biological classification, it can help to show evolutionary change and relationships on the molecular level, and it has the advantage of being able to be used even when only very small samples, such as tiny pieces of preserved tissue from extinct animals, are available.
Science Q&A:
What is DNA fingerprinting? |
DNA, or genetic, fingerprinting is a method of determining identity, family relationships, etc. Formulated by Alec Jeffreys (1950- ), a British geneticist, the genetic fingerprint is based on the assumption that every person (except identical twins) has a unique sequence of DNA (deoxyribonucleic acid)-a substance present in the nucleus of every cell that determines individual characteristics.
Within the DNA molecule, the sequence of the genetic information is repeated many times along the DNA structure, which resembles a long twisting ladder. The length of the sequence, the number of repetitions, and its precise location within the DNA chain seems to be unique in all cases but identical twins, with the odds being 30 billion to one of a duplication. A process has been developed that translates these sequences into a visual record that resembles a series of bars on X-ray film. In this process the technician isolates the DNA from blood, saliva, hair follicles, or semen; then the DNA strand is separated into thousands of shorter pieces by placing the DNA into an enzyme solution. Finally, the fragments, which are placed in a gelatin-like material, are subjected to a strong electrical current that separates them according to size and electrical behavior.
In criminal investigations, hair, blood, and skin samples left by the criminal can yield a DNA fingerprint, which can be matched against any suspect's DNA fingerprint. DNA fingerprinting is also used to determine the father in paternity cases, since the infant's DNA strand contains the genetic coding of the parents.
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Intelligence Encyclopedia:
DNA Fingerprinting |
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).
Wine Lover's Companion:
DNA fingerprinting; DNA profiling; DNA typing |
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.
Wikipedia:
DNA profiling |
| Forensic science |
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| Forensic pathology Forensic dentistry Forensic anthropology Forensic entomology Forensic archaeology |
| Social sciences |
| Forensic psychology Forensic psychiatry |
| Other specializations |
| Fingerprint analysis Forensic accounting Ballistics Body identification DNA profiling Forensic arts Forensic toxicology Forensic footwear evidence Questioned document examination |
| Cybertechnology |
| Information forensics Computer forensics |
| Related disciplines |
| Forensic engineering Forensic linguistics Forensic materials engineering Forensic polymer engineering Fire investigation Vehicular accident reconstruction |
| People |
| Auguste Ambroise Tardieu Edmond Locard William M. Bass |
| Related articles |
| Crime scene CSI effect Trace evidence Skid mark Use of DNA in forensic entomology |
DNA profiling (also called DNA testing, DNA typing, or genetic fingerprinting) is a technique employed by forensic scientists to assist in the identification of individuals on the basis of their respective DNA profiles. DNA profiles are encrypted sets of numbers that reflect a person's DNA makeup, which can also be used as the person's identifier. DNA profiling should not be confused with full genome sequencing.[1] It is used in, for example, parental testing and rape investigation.
Although 99.9% of human DNA sequences are the same in every person, enough of the DNA is different to distinguish one individual from another.[2] DNA profiling uses repetitive ("repeat") sequences that are highly variable,[2] called variable number tandem repeats (VNTR). VNTRs loci are very similar between closely related humans, but so variable that unrelated individuals are extremely unlikely to have the same VNTRs.
The DNA profiling technique was first reported in 1984[3] by Sir Alec Jeffreys at the University of Leicester in England,[4] and is now the basis of several national DNA databases. Dr. Alec Jeffreys genetic fingerprinting was made commercially available in 1987, when a chemical company, ICI, started a blood-testing center in England.[5]
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Contents
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The process begins with a sample of an individual's DNA (typically called a "reference sample"). The most desirable method of collecting a reference sample is the use of a buccal swab, as this reduces the possibility of contamination. When this is not available (e.g. because a court order may be needed and not obtainable) other methods may need to be used to collect a sample of blood, saliva, semen, or other appropriate fluid or tissue from personal items (e.g. toothbrush, razor, etc) or from stored samples (e.g. banked sperm or biopsy tissue). Samples obtained from blood relatives (biological relative) can provide an indication of an individual's profile, as could human remains which had been previously profiled.
A reference sample is then analyzed to create the individual's DNA profile using one of a number of techniques, discussed below. The DNA profile is then compared against another sample to determine whether there is a genetic match.
The first methods for finding out genetics used for DNA profiling involved restriction enzyme digestion, followed by Southern blot analysis. Although polymorphisms can exist in the restriction enzyme cleavage sites, more commonly the enzymes and DNA probes were used to analyze VNTR loci. However, the Southern blot technique is laborious, and requires large amounts of undegraded sample DNA. Also, Karl Brown's original technique looked at many minisatellite loci at the same time, increasing the observed variability, but making it hard to discern individual alleles (and thereby precluding parental testing). These early techniques have been supplanted by PCR-based assays.
With the invention of the polymerase chain reaction (PCR) technique, DNA profiling took huge strides forward in both discriminating power and the ability to recover information from very small (or degraded) starting samples. PCR greatly amplifies the amounts of a specific region of DNA, using oligonucleotide primers and a thermostable DNA polymerase. Early assays 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.
Fortunately, the PCR method is readily adaptable for analyzing VNTR loci. In the United States the FBI has standardized a set of 13 VNTR assays for DNA typing, and has organized the CODIS database for forensic identification in criminal cases. Similar assays and databases have been set up in other countries. Also, commercial kits are available that analyze single nucleotide polymorphisms (SNPs). 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.
The method of DNA profiling 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 unrelated people have different numbers of repeat units, these regions of DNA can be used to discriminate between unrelated 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 combination 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, is 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.
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 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. However, since there are about 12 million monozygotic twins on Earth, that theoretical probability is useless. For example, the actual probability that 2 random persons have the same DNA depends on whether there were twins or triplets (etc.) in the family, and the number of loci used in the test. Where twins are common, the probability of matching the DNA is 22 in 1000, or about 2.2 in 100 will have matching DNA.
In practice, the risk of contaminated-matching is much greater than matching a distant relative, such as a sample being contaminated from nearby objects, or from left-over cells transferred from a prior test. Logically, 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, 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. In a relationship test, the full DNA profiles should differ (except for twins), to prove that a person wasn't actually matched as being related to their own DNA in another sample.
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.
Using PCR technology, DNA analysis is widely applied to determine genetic family relationships such as paternity, maternity, siblingship and other kinships.
During conception, the father’s sperm cell and the mother’s egg cell, each containing half the amount of DNA found in other body cells, meet and fuse to form a fertilized egg, called a zygote. The zygote contains a complete set of DNA molecules, a unique combination of DNA from both parents. This zygote divides and multiplies into an embryo and later, a full human being.
DNA does not change once it is formed at conception. At each stage of development, all the cells forming the body contain the same DNA—half from the father and half from the mother. This fact allows the relationship testing to use all types of all samples including loose cells from the cheeks collected using buccal swabs, blood or other types of samples.
While a lot of DNA contains information for a certain function, there is some called junk DNA, which is currently used for human identification. At some special locations (called loci) in the junk DNA, predictable inheritance patterns were found to be useful in determining biological relationships. These locations contain specific DNA markers that DNA scientists use to identify individuals. In a routine DNA paternity test, the markers used are Short Tandem Repeats (STRs), short pieces of DNA that occur in highly differential repeat patterns among individuals.
Each person’s DNA contains two copies of these markers—one copy inherited from the father and one from the mother. Within a population, the markers at each person’s DNA location could differ in length and sometimes sequence, depending on the markers inherited from the parents.
The combination of marker sizes found in each person makes up his/her unique genetic profile. When determining the relationship between two individuals, their genetic profiles are compared to see if they share the same inheritance patterns at a statistically conclusive rate.
For example, the following sample report from this commercial DNA paternity testing laboratory Universal Genetics [6] signifies how relatedness between parents and child is identified on those special markers:
| DNA Marker | Mother | Child | Alleged Father |
|---|---|---|---|
| D21S11 | 28, 30 | 28, 31 | 29, 31 |
| D7S820 | 9, 10 | 10, 11 | 11, 12 |
| TH01 | 14, 15 | 14, 16 | 15, 16 |
| D13S317 | 7, 8 | 7, 9 | 8, 9 |
| D19S433 | 14, 16.2 | 14, 15 | 15, 17 |
The partial results indicate that the child and the alleged father’s DNA match among these five markers. The complete test results show this correlation on 16 markers between the child and the tested man to draw a conclusion of whether or not the man is the biological father.
Scientifically, each marker is assigned with a Paternity Index (PI), which is a statistical measure of how powerfully a match at a particular marker indicates paternity. The PI of each marker is multiplied with each other to generate the Combined Paternity Index (CPI), which indicates the overall probability of an individual being the biological father of the tested child relative to any random man from the entire population of the same race. The CPI is then converted into a Probability of Paternity showing the degree of relatedness between the alleged father and child.
The DNA test report in other family relationship tests, such as grandparentage and siblingship tests, is similar to a paternity test report. Instead of the Combined Paternity Index, a different value, such as a Siblingship Index, is reported.
The report shows the genetic profiles of each tested person. If there are markers shared among the tested individuals, the probability of biological relationship is calculated to determine how likely the tested individuals share the same markers due to a blood relationship.
Recent innovations have included the creation of primers targeting polymorphic regions on the Y-chromosome (Y-STR), which allows resolution of a mixed DNA sample from a male and female and/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.
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 daughter'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 clear 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..
There are now several DNA databases in existence around the world. Some are private, but most of the largest databases are government controlled. The United States maintains the largest DNA database, with the Combined DNA Index System, holding over 5 million records as of 2007[7]. The United Kingdom maintains the National DNA Database (NDNAD), which is of similar size, despite the UK's smaller population. 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.[8]
The U.S. Patriot Act of the United States provides a means for the U.S. government to get DNA samples from other countries if they[clarification needed] are either a division of, or head office of, a company operating in the U.S. Under the act, the American offices of the company can't divulge to their subsidiaries/offices in other countries the reasons that these DNA samples are sought or by whom.[citation needed]
When a match is made from a National DNA Databank to link a crime scene to an offender who has provided a DNA Sample to a databank that link is often referred to as a cold hit. A cold hit is of value in referring the police agency to a specific suspect but is of less evidential value than a DNA match made from outside the DNA Databank.[9].
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 innocence 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), although the practical risk is actually 1 in 1000 because monozygotic twins are 0.2% of the human population. Moreover, 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[10]. 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 [11]. 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.
It's also possible to use DNA profiling as evidence of genetic relationship, but testing that shows no relationship isn't absolutely certain. While almost all individuals have a single and distinct set of genes, rare individuals, known as "chimeras", have at least two different sets of genes. There have been several cases of DNA profiling that falsely "proved" that a mother was unrelated to her children.[12]
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 raped one of his sedated patients in 1992 and left semen on her underwear. Police drew what they believed to be 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.
In a study conducted by the life science company Nucleix and published in the journal Forensic Science International, scientists found that an In vitro synthesized sample of DNA matching any desired genetic profile can be constructed using standard molecular biology techniques without obtaining any actual tissue from that person.
Familial searching is the use of family members' DNA to identify a closely related suspect in jurisdictions where large DNA databases exist, but no exact match has been found. The first successful use of the practice was in a UK case where a man was convicted of manslaughter when he threw a brick stained with his own blood into a moving car. Police could not get an exact match to the UK's DNA database because the man had no criminal convictions, but police implicated him using a close relative's DNA.[13]
Police forces may collect DNA samples without the suspects' knowledge, and use it as evidence. Legality of this mode of proceeding has been questioned in Australia.
In the United States, it has been accepted, courts often claiming that there was no expectation of privacy, citing California v. Greenwood (1985), during which the Supreme Court held that the Fourth Amendment does not prohibit the warrantless search and seizure of garbage left for collection outside the curtilage of a home. Critics of this practice underline the fact that this analogy ignores that "most people have no idea that they risk surrendering their genetic identity to the police by, for instance, failing to destroy a used coffee cup. Moreover, even if they do realize it, there is no way to avoid abandoning one’s DNA in public." [14]
In the UK, the Human Tissue Act of 2004 prohibited private individuals from covertly collecting biological samples (hair, fingernails, etc.) for DNA analysis, but excluded medical and criminal investigations from the offense.[15]
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.[16] The judge must ensure that the jury must understand the significance of DNA matches and mismatches in the profiles. The judge must also ensure that the jury does not confuse the 'match probability' (the probability that a person that is chosen 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".[17]
R v Bates (2006) EWCA Crim 1395 Moore-Bick LJ said:
There are state laws on DNA profiling in all 50 states of the United States.[19] Detailed information on database laws in each state can be found at the National Conference of State Legislatures website.[20]
In August 2009, scientists in Israel stunned the forensic sciences and raised serious questions concerning law enforcement's use of DNA matching as the ultimate method of identification. In a paper published in the journal Forensic Science International: Genetics, the Israeli researchers demonstrated that it is possible to manufacture DNA in a laboratory, and thus falsify DNA evidence. The scientists had fabricated saliva and blood samples, which originally contained DNA from a person other than the ostensible donor of the blood and saliva.[21]
Additionally, and perhaps more frighteningly, the same researchers showed that, using a DNA database, it is possible to take information from a profile and actually manufacture DNA to match it. Worse, this can done without access to any actual DNA from the person whose DNA they are duplicating. The synthetic DNA obligios required for the procedure are used in probably every molecular laboratory.[21]
Dr. Daniel Frumkin, lead author on the paper, was quoted in The New York Times as saying, "You can just engineer a crime scene...any biology undergraduate could perform this."[21]
Dr. Frumkin fortunately has perfected a test that can forensically differentiate real DNA samples from fake ones. His test uses epigenetic modifications, in particular, DNA methylation. Seventy percent of the DNA in any human genome is methylated, meaning it contains methyl group modifications within a CpG dinucleotide context. Methylation at the promoter region is associated with gene silencing. It appears that the synthetic DNA lacks this epigenetic modification, which allows the test to be used to distinguish manufactured DNA from original, genuine, DNA.[21]
The idea that DNA can be fabricated, and then planted at a crime scene, is now reality; fortunately Dr. Frumkin has developed the test to differentiate real from fake DNA. But it is unknown how many, if any, police departments currently use the test, which is distressing considering Frumkin’s claim that the DNA manufacturing procedure is within the grasp of any undergraduate biology student. No police lab has publicly announced that it is using the new test to verify DNA results, while FSI Genetics says that any forensic laboratory doing DNA identification should adopt this test to authenticate its results as "real" DNA.[22]
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| Dna Recognition Instruments | |
| Dna Sequences, Unique | |
| Fingerprint Analysis |
| Why do humans have unique DNA fingerprints? | |
| What A DNA fingerprint can be used to? | |
| What is't DNA fingerprint based on? |
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