DNA Fingerprinting in the Criminal Justice System: An...

8
DNA AND CELL BIOLOGY Volume 25, Number 3, 2006 © Mary Ann Liebert, Inc. Pp. 181–188 DNA Fingerprinting in the Criminal Justice System: An Overview VARSHA ABSTRACT DNA fingerprinting is a powerful technology that has revolutionized forensic science. No two individuals can have an identical DNA pattern except identical twins. Such DNA-based technologies have enormous social im- plications and can help in the fight against crime. This technology has experienced many changes over time with many advancements occurring. DNA testing is a matter of serious concern as it involves ethical issues. This article describes various trends in DNA fingerprinting and the current technology used in DNA profil- ing, possible uses and misuses of DNA databanks and ethical issues involved in DNA testing. Limitations and problems prevailing in this field are highlighted. 181 INTRODUCTION K ING SOLOMONS STORY is well known for his famous de- cision in a maternity dispute, but today, parentage deci- sions are relatively easy with the assistance of DNA technol- ogy. DNA technology was first developed in England in 1985 by Sir Alec Jeffreys. This technology, so named because DNA is used for identification rather than latent physical fingerprints, gives a unique and specific profile similar to a thumb impres- sion (Jeffreys et al., 1985). DNA fingerprinting technology to- day has made it possible to identify the source of biological samples found at a crime scene and also to resolve disputes of paternity and other criminal cases. Ninety-five percent of the human genome is noncoding DNA, with only 5% coding for protein region. These noncod- ing regions are also called “junk” DNA, and are abundant where the number of repeats show variations among individuals. These DNA polymorphisms change the length of the DNA fragments produced by the digestion of restriction enzymes. A DNA fingerprint is constructed by first extracting a DNA sample from biological sample. The sample is then cut at spe- cific sites with restriction enzymes, and the segments are arranged by their molecular size using electrophoresis. The seg- ments are labeled with probes and exposed to X-ray film, where they form a characteristic pattern, that is, the DNA fingerprint. If the DNA fingerprints produced from two different sam- ples match, the two samples probably came from the same per- son. The exact number and size of the fragments produced by a specific restriction enzyme digestion varies from individual to individual. In 1985, police in the UK for the first time used forensic DNA profiling (http://www.crimtrac.gov.au/dnahistory.htm), and in the United States, the first criminal conviction based on DNA evidence occurred in 1988. In 1992, the National Re- search Council of the United States found that DNA testing was a reliable method for the identification of criminal suspects, and the technology rapidly entered the mainstream court system. The DNA evidence obtained is powerful, since it can implicate or exonerate a suspect. Currently, DNA testing is routinely used in civil and criminal cases. DNA ANALYSIS Early markers Karl Landsteiner, in 1901, discovered ABO blood grouping in humans (Landsteiner, 1901). A set of blood group markers (red cell antigens and serum protein) were also used to identify victims and suspects in crime cases. As the polymorphism was very limited in ABO blood grouping, it was neither informa- tive nor very suitable for excluding a person as a suspect in a criminal case. The advent of DNA-based markers has now rev- olutionized the field of forensic science, as it can measure an unlimited extent of polymorphisms sufficient to differentiate one individual from another. Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.

Transcript of DNA Fingerprinting in the Criminal Justice System: An...

DNA AND CELL BIOLOGYVolume 25, Number 3, 2006© Mary Ann Liebert, Inc.Pp. 181–188

DNA Fingerprinting in the Criminal Justice System: An Overview

VARSHA

ABSTRACT

DNA fingerprinting is a powerful technology that has revolutionized forensic science. No two individuals canhave an identical DNA pattern except identical twins. Such DNA-based technologies have enormous social im-plications and can help in the fight against crime. This technology has experienced many changes over timewith many advancements occurring. DNA testing is a matter of serious concern as it involves ethical issues.This article describes various trends in DNA fingerprinting and the current technology used in DNA profil-ing, possible uses and misuses of DNA databanks and ethical issues involved in DNA testing. Limitations andproblems prevailing in this field are highlighted.

181

INTRODUCTION

KING SOLOMON’S STORY is well known for his famous de-cision in a maternity dispute, but today, parentage deci-

sions are relatively easy with the assistance of DNA technol-ogy. DNA technology was first developed in England in 1985by Sir Alec Jeffreys. This technology, so named because DNAis used for identification rather than latent physical fingerprints,gives a unique and specific profile similar to a thumb impres-sion (Jeffreys et al., 1985). DNA fingerprinting technology to-day has made it possible to identify the source of biologicalsamples found at a crime scene and also to resolve disputes ofpaternity and other criminal cases.

Ninety-five percent of the human genome is noncodingDNA, with only 5% coding for protein region. These noncod-ing regions are also called “junk” DNA, and are abundant wherethe number of repeats show variations among individuals. TheseDNA polymorphisms change the length of the DNA fragmentsproduced by the digestion of restriction enzymes.

A DNA fingerprint is constructed by first extracting a DNAsample from biological sample. The sample is then cut at spe-cific sites with restriction enzymes, and the segments arearranged by their molecular size using electrophoresis. The seg-ments are labeled with probes and exposed to X-ray film, wherethey form a characteristic pattern, that is, the DNA fingerprint.

If the DNA fingerprints produced from two different sam-ples match, the two samples probably came from the same per-son. The exact number and size of the fragments produced by

a specific restriction enzyme digestion varies from individualto individual.

In 1985, police in the UK for the first time used forensicDNA profiling (http://www.crimtrac.gov.au/dnahistory.htm),and in the United States, the first criminal conviction based onDNA evidence occurred in 1988. In 1992, the National Re-search Council of the United States found that DNA testing wasa reliable method for the identification of criminal suspects, andthe technology rapidly entered the mainstream court system.The DNA evidence obtained is powerful, since it can implicateor exonerate a suspect. Currently, DNA testing is routinely usedin civil and criminal cases.

DNA ANALYSIS

Early markers

Karl Landsteiner, in 1901, discovered ABO blood groupingin humans (Landsteiner, 1901). A set of blood group markers(red cell antigens and serum protein) were also used to identifyvictims and suspects in crime cases. As the polymorphism wasvery limited in ABO blood grouping, it was neither informa-tive nor very suitable for excluding a person as a suspect in acriminal case. The advent of DNA-based markers has now rev-olutionized the field of forensic science, as it can measure anunlimited extent of polymorphisms sufficient to differentiateone individual from another.

Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.

Hybridization based multilocus and single locus DNAprofiling

The use of DNA fingerprinting in forensic science had beensuggested in the early 1980s by Prof. Alec Jeffreys using re-striction fragment-length polymorphism (RFLP). There wasgreat enthusiasm among the forensic science community for thediscovery of the minisatellite approach for specific identifica-tion (Wong et al., 1987).

Eukaryotic genomes contain a large number of repeatedDNA sequences. These regions are often referred to as satelliteDNA. The core repeat unit for a medium-length repeat, some-times referred to as a minisatellite or variable number of tan-dem repeats (VNTR) is in the range of approximately 10–100bases in length.

VNTR patterns are inherited and are unique (Weising, et al.,1995). The more VNTR probes used to analyze a person’sVNTR pattern, the more distinctive and individualized that pat-tern, or DNA fingerprint, will be. The children will inherit thedifferent combinations of paternal and maternal VNTRs, andtherefore their profile will be different from each other exceptidentical twins as shown in Figure 1.

DNA regions with repeat units that are 2–6 bp in length arecalled mcrosatellites, simple sequence repeats (SSRs) or shorttandem repeats (STRs). STRs consisted of microsatellites ofsmall repeating units, two to five bases in length, with a maxi-mum length of around 300 bases, which show a high degree ofpolymorphism. Specific microsatellites can be isolated using hy-bridized probes followed by their sequencing. SSRs can be de-tected by specific dyes or by radiolabeling using gel elec-trophoresis. The advantage of using SSRs as molecular markersis the extent of polymorphism shown, which enables the detec-tion of differences at multiple loci between strains (Butler, 2001).

Hybridization-based DNA fingerprinting involves the use oftwo types of probes called multilocus probes (MLP), which iden-tify repeating sequences in genomic DNA digested by restric-tion enzymes followed by Southern blot analysis at low strin-gency conditions. The radio labeled probes hybridize with aseries of tandemly repeated sequences with a size range greaterthan 20 kb. The resulting autoradiographs consist of a ladder-like series of bands that will be identical only for identical twinsas shown in Figure 2. The fact that DNA is a very stable mol-ecule makes this technology more effective, and even old cases

also can be reviewed. This is equally good for archived speci-mens. The MLP system, however, was not very successful. Themethod was demanding and the results were not suited for in-clusion in computer databases. After the advent of the single lo-cus probe (SLP) the technology substantially progressed. In theSLP system probes were isolated, which identified repeat se-quences in individual minisatellites using high stringency con-ditions to produce a maximum of two bands per probe. Althoughthe targeted minisatellites showed considerable variation in theirrepeat numbers, a single locus was not sufficient for individu-alization. A number of such loci were analyzed (Lalji, 1991).

PCR-based DNA profiling

In the early 1990s, the DNA fingerprinting technology tooka dramatic change with the advent of the polymerase chain re-action (PCR), a technique that enabled amplification from tinyamounts of template DNA. The method was fast, reliable, andwas efficient to work even with degraded samples. In the PCR-based technique the time required to analyze a sample was sig-nificantly reduced (Weber and May, 1989). It was found to bemore suitable than the previously used MLP and SLP systems.There was a period when both SLP and PCR-based methodswere used to identify a person in parallel. PCR technology wasused to type many VNTRs region for forensic purposes. Manypolymorphic loci like D1S80 and HLADQ� were used foranalysis. There were many reports claiming that it was not muchuseful for forensic purposes (Varsha et al., 1999).

In 1992, the use of a new compatible form of genetic pro-filing called STRs was proposed. Due to their small size theywere extremely stable, and could be detected even with old anddegraded samples.

In 1998, STR analysis became an established feature offorensic sciences, which basically involved study of a panel ofpolymorphic loci comprising THO1, VWA, FGA, D21S11,D8S1179, and D18S51, as well as D7S820, D13S317, D5S818,CSF1P0, D16S539, D2S1338, D19S433, TPOX, with recentlyintroduced Penta E and Penta D (Edwards et al., 1991).

A flow diagram (Fig. 3) and Table 1 show the progressiveadvancements in forensic genetics.

HOW IS DNA TYPING PERFORMED?

In criminal cases, samples obtained from crime scene evi-dence and a suspect are used for DNA extraction and analysisfor the presence of a set of specific DNA markers.

DNA markers are small DNA probes that bind to a comple-mentary sequence in the DNA sample. A distinctive pattern foran individual is created by a series of probes bound to a DNA

VARSHA182

FIG. 2. Multilocus DNA profiling of (a) Identical and (b)nonidentical twins.

FIG. 1. VNTR distribution in a family.

sample. Comparing such DNA profiles determines whether thesuspect’s sample matches the evidence sample. If the patternsmatch, the suspect may have contributed the evidence sample andif profiles do not match, the person is assumed innocent. Scien-tists believe that DNA evidence is far superior to eyewitness ac-counts, where the chance for correct identification is about 50:50.

A combination of probes used in DNA analysis, gives greaterreliability for profiling. Four to six probes are recommendedfor a good DNA profile. The recent new innovation in DNAchip technology (in which thousands of short DNA sequencesare embedded onto a tiny silicon chip) enables a more rapid,and less expensive analysis using many more probes (Linacreand Graham, 2002).

A flowchart is presented in Figure 4, which shows the stepsinvolved in DNA profiling.

DNA TECHNOLOGIES CURRENTLY USED INFORENSIC INVESTIGATION

RFLP is a technique for analyzing the variable lengths ofDNA fragments that result from digesting a DNA sample witha special kind of restriction endonucleases. Amplification frag-ment Length polymorphism (AFLP) is a PCR-based derivativemethod of RFLP in which sequences are selectively amplifiedusing primers. It is a reliable and efficient method of detectingmolecular markers. Random amplified polymorphic DNA(RAPD) is one of the most commonly used primary assays forscreening the differences in DNA sequences of two species ofplants. It involves random amplification (Cooper, 2000). HLA-DQ� analysis was also used for identification for quite longtime (Saiki et al., 1986). With the advancement, these tech-nologies became obsolete and were replaced by various tech-

niques like microsatellite analysis, single nucleotide polymor-phisms, etc.

Capillary electrophoresis

Capillary electrophoresis, or CE, is a group of techniques usedto separate a variety of samples. These analyses are performedin narrow tubes, and can result in the rapid separation of dif-ferent compounds. DNA typing with STR markers is now widelyused for a variety of applications including human identifica-tion. CE instruments, such as genetic analyzers, are the methodof choice for many laboratories which perform STR analysis.

The Genetic Analyzer (Applied Biosystems, Foster City,CA) is a fluorescence based DNA analysis system utilizing cap-illary electrophoresis. It has multiple color fluorescence detec-tion capability. This capillary machine is capable of running se-quence and fragment analysis (Butler et al., 2004) and is a verypopular method for STR typing. ABI 310 is a single-capillary

DNA FINGERPRINTING 183

TABLE 1. YEAR-WISE ADVANCEMENT IN FORENSIC

DNA TYPING

Year Developments

1985 RFLP approach was developed by Alec Jeffreys1986 Automated DNA sequencing was first described1988 FBI started using RFLP probes for case studies1989 TWGDAM (Technical Working Group on DNA

Analysis Methods) was established1995 O.J. Simpson case, which spread the awareness of

DNA; UK DNA database established1997 Y chromosome STR marker was first described

Source: http://www.denverda.org/legalResource/Overview.pdf.

FIG. 3. The progress in Forensic genetics. (Diagram reprinted by permission of Mark A. Jobling and Tanita Casci from paper“Encoded evidence: DNA in Forensic analysis, Mark A. Jobling, Nature reviews/Genetics, Vol 5, Oct 2004.)

instrument. Similarly ABI 3100 is a 16-capillary instrument andis used in large-scale applications.

Short tandem repeat analysis

STRs have discrete alleles. Variability in STR regions canbe used to distinguish one DNA profile from another (Edwardset al., 1991). The chance that two individuals will have the same13-loci DNA profile is about one in one billion. Microsatellitetyping can be multiplexed and semiautomated.

Sophisticated software has been developed for STR analysis totake sample electrophoretic data through the genotyping process(Ziegle et al., 1992). This is done in two steps by two differentsoftware programs. Genescan software (Applied Biosystems) isused to spectrally resolve the dye colors for each peak and to sizethe DNA fragments. The resulting pherograms are then importedinto the second software program, Genotyper. This program de-termines each samples genotype by comparing the sizes of alle-les observed in a standard allelic ladder sample to those obtainedat each locus in the DNA sample. Genotyping can be performedon the Genetic Analyzer with different available models (Ziegleet al., 1992). These are capillary electrophoresis systems.

A Genescan program was used to compare the individual’sprofile (Fig. 5). In genotyping the alleles are denoted by peaksrather than bands unlike Genescan and peak height is also takeninto consideration while analyzing the results (Fig. 6, Probabil-ity of paternity is 99.999%). The match probabilities obtainedwith STR multiplexes are very low, and is more than the worldpopulation. The preferred system for STR genetic typing was viafluorescent dye-labeled primers and automated DNA sequencers.Multiplexes are analyzed and typed using automated sequencingequipment. First multiplex used was quadruplex, which had fourSTR regions. The recent multiplex amplifies for 16 loci in a sin-gle reaction one out of that is Amelogenin, a gender marker. STRbase provides complete information about different STR mark-ers available (Butler, 2001). Simultaneous amplification and sep-aration of a number of STR loci in a single step is possible here.

Other methods include the use of single nucleotide poly-morphs (SNPs), DNA amplification fingerprinting (DAF) andtheir offshoots. DNA amplification fingerprinting (DAF) in-volves amplification of genomic DNA, which is directed by onlyone oligonucleotide primer of arbitrary sequence (Caetano-Anolles et al., 1991). While the major efforts were made for de-tecting markers in genomic DNA, there has also been a consid-erable effort expanded on methods for typing sequences withinthe mitochondrial DNA (mtDNA). Although these results arenot as discriminating as those of the STRs, they can be very use-ful in cases where skeletal remains, hairs, etc., are the only sam-ples available. There have also been advances in the use of mark-ers which are made specific (Y chromosome), and these havebeen used successfully particularly in cases of sexual assault.

Mitochondrial DNA analysis

Degraded samples such as hair, bones, and teeth quite oftenlack nucleated cellular material and cannot be analyzed withSTR and RFLP. Mitochondrial DNA analysis (mtDNA) can beused to examine such DNA samples. mtDNA is extremely valu-

VARSHA184

FIG. 4. Flowchart of DNA profiling.

FIG. 5. Genescan analysis of STR markers in a paternity case.Lane 1. DNA profile of the mother; Lane 2. DNA profile of thechild; Lane 3. DNA profile of the father.

able in such cases, as it has high copy number and has no re-combinational events.

Mitochondrial DNA is inherited maternally and does segre-gate independently. Therefore, it gives an excellent record ofmatrilineage. The father’s sperm contributes only nuclear DNA.Occurrence of heteroplasmy is the special feature of mtDNA.Comparing the mtDNA profile of unidentified remains with theprofile of a potential maternal relative can be an important tech-nique in investigations on missing persons. Simultaneously, itcan also be used as an important tool for matrilineage and evo-lutionary studies. Mitochondrial DNA can also help in studyingthe variety of human diseases, associated with mitochondrial dis-orders (Wallace, 1999). SNP outside the hypervariable segmentsalong with mtDNA can provide us a better tool for typing.

Y-chromosome analysis

Analysis of genetic markers on the Y chromosome is espe-cially useful for tracing relationships among males or for ana-lyzing biological evidence involving multiple male contributorsas in rape cases. There are a total of 219 useful STR markersavailable on Y chromosome (Kayser et al., 2004).

Single nucleotide polymorphism typing

SNP are DNA sequence variations that occur when a singlenucleotide (A, T, C, or G) in the genome sequence is changed.SNPs create mutations in human and can be used as markers.SNPs have lower heterozygosity compared to STR. It will benot of much use when the samples are mixed, as SNP is a bi-nary marker. Forensic SNP typing provides considerable assis-tance to forensic scientists in major disasters (Budowle et al.,2005). Many polymorphic sites need to be analyzed for the iden-tification of SNPs. Mutation analysis is one of the major thrustsof functional genomics. Validation of a 21-locus autosomalSNP multiplex has been performed for forensic identificationpurposes (Dixon et al., 2005). Microarrays are used very effi-

ciently for mutation analysis, which helps in monitoring thewhole genome on a single chip and for studying the interac-tions of thousands of genes simultaneously. In the scientific lit-erature various terminologies have been used to describe thistechnology as such as DNA chip, DNA microarray, etc.(Linacre and Graham, 2002).

Forensic studies are mainly done by commercially developedautosomal STR multiplexes, autosomal SNPs, and markers on theY chromosome and mitochondrial DNA (Jobling and Gill, 2004).

ESTABLISHMENT OF DATABANKS

DNA intelligence databases are modern tools for the execu-tive force investigating crime (Werret, 1997; Hoyle, 1998; Par-soh et al., 1998; Peeren boom, 1998; Schneider, 1998).

DNA forensics databases

The first of the national DNA databases involving STR datawas formed in the UK in 1995. The usefulness of such typesof databases was established during the first 5 years of use ofthis technology (Werrett and Sparkes, 1998). By 1998, threeother European countries, Austria, Germany, and The Nether-lands had introduced national DNA databases (Martin et al.,2001). The STR loci used to form these databases were THOI,VWA, FGA, D8S1179, D18S51, and D21S11. Finland and Nor-way have introduced a national database in 1999. Sweden hasalready a database of unknown crime samples. Belgium, Den-mark, Switzerland, France, Italy, Spain, and some east Euro-pean countries also took steps in this direction. In 1989, the FBIproposed a national DNA database for North America.

The Austrian DNA intelligence database was inaugurated in1997. In the United States, the Federal Bureau of Investigation(FBI) has created a national database of genetic informationcalled the National DNA Index System. The database contains

DNA FINGERPRINTING 185

FIG. 6. Electropherogram of genotype of STR markers in samples of a paternity case. 1. Genotype of the mother; 2. Genotypeof the child; 3. Genotype of the father.

DNA obtained from convicted criminals and from evidencefound at crime scenes.

National DNA databank: CODIS

The COmbined DNA Index System, CODIS, utilizes com-puter and DNA technologies together. All DNA profiles storedin CODIS are generated using STR analysis. The current ver-sion of CODIS uses two indexes where biological evidence isrecovered from the crime scene. The Convicted Offender in-dex contains DNA profiles of individuals convicted of sex of-fenses and other violent crimes. The Forensic index containsDNA profiles developed from crime scene evidence. A com-puter software will search these two indexes for matching DNAprofiles. Law enforcement agencies compare DNA from bio-logical evidence collected from crime scenes that have no sus-pect with the DNA profiles stored in the CODIS systems. If amatch is made between a sample and a stored profile, CODIScan identify the culprit.

This technology is authorized by the DNA Identification Actof 1994. As of January 2003, the database contained more thana million DNA profiles in its Convicted Offender Index andabout 48,000 DNA profiles collected from crime scenes butwhich have not been connected to a particular offender. Thisdatabase can also be used to identify criminals who are re-sponsible for crime in other countries. The FBI uses a standardset of 13 specific STR regions for CODIS (Budowle et al.,1998). CODIS is a software program that operates local, state,and national databases of DNA profiles from convicted crimi-nals and missing persons.

Advantages of DNA databanking

One advantage of a comprehensive and modern nationalDNA databank is the capability to perform DNA identificationtests of victims and missing persons in the case of disaster.

It is just a matter of comparison of the profile of the samplewith the databank, as the data is already available and the re-sults are more reliable. Time of investigation as well as cost isreduced. It is also beneficial to society as it helps the investi-gator to catch the criminal and exonerate the innocent person.

APPLICATIONS OF DNA FINGERPRINTINGTO PLANTS AND ANIMALS

Plant DNA fingerprinting is defined here as the applicationof molecular marker techniques to identify cultivars, but thisalso can be helpful in providing evidence in crime cases. RAPDcan be a better choice for identification of plant strains. DNAprofiling of plants can be used in solving civil disputes over theidentity of commercially important cultivars (Kumar et al.,2001).

The genotypic information is used for identification of ani-mals (Barallon, 1998), forensic analysis (Zehner et al., 1998)and for tracing specific animals to finished meat products (Var-sha et al., 2003), pedigree analysis, selection, and breeding pro-grams. Forensic analysis can be of immense help for poachingcases and to check the illegal trade of endangered species. Thecytochrome b region had been used for identification of the en-dangered animal species (Branicki et al., 2003). DNA typing inplants and animals is again a vast topic, and needs a separate

discussion. DNA fingerprinting has tremendous application es-pecially in forensic sciences, which is mentioned in Table 2.

ETHICAL, LEGAL, AND SOCIAL CONCERNSINVOLVING DNA FINGERPRINTING

The primary ethical, legal, and social issues concerning DNAfingerprinting is privacy. DNA profiles are different from latentfingerprints, which are useful only for identification. DNA canprovide insights into many aspects of a person and their familiesincluding susceptibility to particular genetic disorders, legitimacyof birth, and fertility. This increases the potential for genetic dis-crimination by government, society and others. Therefore, DNAtyping should be carried out in a very sophisticated way, andshould meet all the international standards and follow and abideall the ethical, legal, and social concerns involved with DNA typ-ing. Databanking also involves some ethical issues and requiresa balance between human rights and justice. Retention of sam-ples for long periods of time is also risky, since this providesconsiderable accessibility to private genetic information.

RELIABILITY OF DNA TECHNOLOGY

Generally, the legal system and courts have accepted the re-liability of DNA testing everywhere, and admitted DNA testresults as evidence. However, DNA fingerprinting is still con-troversial because of some important aspects. One is the accu-racy of the results, as result will always be in the form of someprobability value. Another aspect is the high cost associatedwith analysis. Some of the other important aspects such as thepossibility of misuse of the technique, chances of manual er-ror, and contamination cannot be ignored.

The accuracy of DNA fingerprinting has been challenged be-cause DNA segments rather than complete DNA strands are an-alyzed, which may not be necessarily unique. More researchwork is needed to confirm the uniqueness of DNA fingerprint-ing has not been conducted. In addition, DNA fingerprinting isoften performed in private laboratories that may not follow uni-form testing standards and quality controls. Therefore, humanerror could lead to false results. Awareness is still lacking aboutthis technology among law enforcing agencies and judiciaries,requiring a lot of interaction between these and forensic scien-tists. DNA identification can be quite effective if used intelli-

VARSHA186

TABLE 2. SOME EXAMPLES OF DNA USE FOR FORENSIC

IDENTIFICATION

Criminal identification.Exonerate persons wrongly accused of crimes.Identify crime and catastrophe victims in mass disasters.Establish paternity and other family relationships.Identify endangered species and can help in wild-life poach-

ing cases.Match organ donors with recipients in organ transplantation

as kidney transplantation.Determine pedigree for seed or livestock breeds.To identify different strains and cultivars and can help in pro-

tecting the rights of plant breeders.Personal Identification like identification cards, etc.

gently. Portions of the DNA sequence that vary the most amonghumans must be used; also, the number of loci studied shouldbe sufficient enough to make the results more reliable.

PROBLEMS WITH DNA FINGERPRINTING

DNA fingerprinting is not fully assured. The term DNA fin-gerprint is, in a true sense, a misnomer. We cannot compare itwith latent fingerprinting, as it is not as specific as fingerprints.Actually, a VNTR pattern gives a probability value that the per-son in question is indeed the person to whom the VNTR pat-tern (of the child, the criminal evidence, or whatever else) be-longs. The probability decides whether the person can bereasonably matched with the DNA fingerprint.

1. Generation and determination of high probability is a req-uisite for forensic cases. The probability of a DNA finger-print belonging to a specific person needs to be reasonablyhigh, particularly in criminal cases. High probability can beachieved by increasing the number of polymorphic loci an-alyzed. Population structure can cause variation in allele fre-quencies between subpopulations (Lander and Budowle,1994). VNTRs are not distributed evenly across all of hu-man population. A given VNTR does not have a stable prob-ability of occurrence, and not enough is known about theVNTR frequency distributions among ethnic groups to de-termine accurate probabilities for individuals within thosegroups. Some technical difficulties, like errors in the hy-bridization and probing process, will also affect the proba-bility. Population studies should be carried out and repro-ducibility of the results should be confirmed.

2. DNA testing faces important problem of impurities of the sam-ple. The sample collected from a crime scene most of the timeis mixed with soil and other potential contaminants and con-siderable time and effort in purification processes purificationon samples not directly amenable to analysis. Another impor-tant challenge to amplifying DNA samples from crime scenesis the fact that the PCR amplification process can be affectedby inhibitors present in the samples themselves. The sensitiv-ity of PCR with its ability to amplify low quantities of DNAcan be a problem if proper care is not taken. Mixed samplescan be challenging to detect and interpret. If mutation occursat the primer binding site it can result in failure to amplify,which is known as null allele or allele dropout. Sometimes,stutter bands are noted in the electropherogram of STR analy-sis, which is nothing but small peaks several bases smaller thanSTR allele peaks, which occurs because of strand slippage.These bands effect the interpretation of DNA profiles speciallyin mixed samples, which requires good understanding of thebehavior of stutter products (John M. Butler, forensic DNAtyping). Proper training, better understanding, extensive expe-rience, and careful analysis are required.

3. Very often investigators are not properly trained for samplecollection and encounter problems in identification and col-lection of proper DNA evidence from the scene of crime.Contamination of the samples and using the correct sample,proper labeling, etc., are a few important aspects, whichshould be taken into consideration. The DNA laboratoryshould follow the international standard and should be ac-credited.

4. Proper awareness about the subject is required among theinvestigators, but unfortunately, interaction and proper com-munication is lacking between law enforcement agencies andDNA laboratories.

5. Limited resources and poor infrastructure facility of differ-ent laboratories effects the efficiency of the DNA typing lab-oratories.

6. Risk of false or misleading results from DNA testing andchances of tampering with the evidence cannot be ignored.Strict confidentiality is required as far as identity of the sam-ple is concerned, and each sample should be tested by morethan one examiner to confirm the results. Irrespective of hav-ing all these limitations, DNA fingerprinting is a very reliabletechnique for identification if used efficiently and intelligently.

There are many international organizations, which are in-volved in quality control and uniformity of DNA fingerprint-ing such as the Technical Working Group on DNA AnalysisMethods, The DNA Advisory Board, National Institute of Stan-dards and Technology in United States, and International So-ciety for Forensic Genetics in Europe.

SOME HIGH-PROFILE CASES SOLVED BYDNA FINGERPRINTING

1. Identification of the remains of the last Russian Czar.2. O.J. Simpson case in Los Angeles.3. Clinton-Lewinsky affair.4. Thomas Jefferson-Sally Hemings affair.5. Identification of the bodies in World Trade Center attack: A

mass disaster.6. Assassination case of Sri Rajeev Gandhi, Prime Minister of

India.

CONCLUSION AND FUTURE DIRECTIONS

The power of DNA technology will be of immense help inthe future. The limitations of the technique have to be given se-rious thought. Forensic DNA testing will improve day by day,and will be benefited with the outcome of the Human GenomeProject. Microarray-based analysis will be in much use for itsmore reliability and fast analysis. This technology has the po-tential to review the cases, which were previously reported witholder methods. There is a real need for public awareness of thenew DNA technologies and their implications. For instance, thecollection of the correct sample and its proper preservation isvery crucial. Productive interactions are required between theforensic scientists and the law enforcement and other investiga-tors. It is necessary to make this technology more popular andcost effective so as to enable even developing and undevelopedthird world countries to take advantage of the technology as well.

ACKNOWLEDGMENTS

My special thanks to all those authors whose names are notquoted here because of space constraints, and those who havemade the information freely available on the internet. I am

DNA FINGERPRINTING 187

thankful to Dr. S. E. Hasnain and Dr. J. Nagaraju, for their con-stant support and encouragement. A draft of this manuscriptwas significantly improved through consultation with Dr. T.Ramasarma, Dr. Gayatri Ramakrishna, and the comments of theanonymous reviewer, and I thank them for their valuable sug-gestions. I am also thankful to Dr. Mark A. Jobling, author, andDr. Tanita Casci, senior editor, Nature Reviews Genetics forpermitting me to take Figure 3 from the published paper.

REFERENCES

BARALLON, R. (1998). Species determination by analysis of the Cy-tochrome b gene. In Forensic DNA Profiling Protocols. P.J. Lincolnand J. Thompson, ed. (Humana Press, Totowa, NJ).

BRANICKI, W., KUPIEC, T., and PAWLOWSKI, R. (2003).Valida-tion of cytochrome b sequence analysis as a method of species iden-tification. J. Forensic Sci. 48, 83–87.

BUDOWLE, B., BIEBER, F.R., and EISENBERG, A.J. (2005). Foren-sic aspects of mass disasters: Strategic considerations for DNA-basedhuman identification. Legal Med. 7, 230–243.

BUDOWLE, B., MORETTI, T.R., NIEZGODA, S.J., and BROWN,B.L. (1998). Proceedings of the Second European Symposium on Hu-man Identification. (Promega Corporation, Madison, WI), pp. 73–88.

BUTLER, J.M. (2001). Forensic DNA typing: Biology and technologybehind STR markers (Academic Press, New York).

BUTLER, J.M., BUEL, E., CRIVELLENTE, F., and MCCORD, B.R.(2004). Forensic DNA typing by capillary electrophoresis using theABI Prism 310 and 3100 genetic analyzers for STR analysis. Elec-trophoresis 25, 1397–1412.

CAETANO-ANOLLES, G., BASSAM, B.J., and GRESSHOFF, P.M.(1991). DNA amplification fingerprinting using very short arbitraryoligonucleotide primers. Biotechnology (NY) 9, 553–557.

COOPER, M.L. (2000). RAPD analysis of southern brown bandicoots(Isodon obesulus) populations in West Australia reveals genetic dif-ferentiation elated to environmental variables. Mol. Ecol. 9, 469–479.

DIXON, L.A., MURRAY, C.M., ARCHER, E.J., DOBBINS, A.F.,KOUMBI, P., and GILL, P. (2005). Validation of a 21-locus auto-somal SNP multiplex for forensic identification purposes. ForensicSci. Int. 154, 62–77.

EDWARDS, A., CIVITELLO, A., HAMMOND, H.A., and CASKEY,C.T. (1991). DNA typing & genetic mapping with trimeric &tetremeric tandem repeats. Am. J. Hum. Genet. 49, 746–756.

HOYLE, R. (1998). Forensics. The FBI’s national DNA database. Nat.Biotechnol. 16, 987.

JEFFREYS, A.J., WILSON, V., and THEIN, S.L. (1985). Individualspecific “fingerprints” of human DNA. Nature 316, 76–79.

JOBLING, M.A., and GILL, P. (2004). Encoded evidence: DNA inforensic analysis. Nat. Rev. 5, 739–751.

KAYSER, M., et al. (2004). A comprehensive survey of human Y chro-mosomal microsatellite. Am. J. Hum. Genet. 74, 1183–1197.

LALJI S. (1991). DNA profiling and its applications. Curr. Sci. 60,580–585.

KUMAR, L.D., KATHIRVEL, M., RAO, G.V., and NAGARAJU, J.2001. DNA profiling of disputed chilli samples (Capsicus annum)using ISSR-PCR and FISSR-PCR marker assays. Forensic Sci. Int.116, 63–68.

LANDER, E.S., and BUDOWLE, B. (1994). DNA Fingerprinting dis-pute laid to rest. Nature 371, 735–738.

LANDSTEINER, K. (1901). Uber agglutinationserscheinungen nor-malen menschlichen blutes. Wien Klin Wschr. 14, 1132–1134.

LINACRE, A., and GRAHAM, D. (2002). Role of molecular diagnos-tics in forensic science. Expert Rev. Mol. Diagn. 2, 346–353.

MARTIN, P.D., HERMANN, S., and SCHNEIDER, P.M. (2001). Abrief history of the formation of DNA database in forensic sciencewithin Europe. Forensic Sci. Int. 119, 225–231.

PARSOH, W., STEINLECHNER, M., SCHEITHAUER, R., andSCHNEIDER, D.M. (1998). National DNA intelligence database inEurope—Report on the current situation. In Proc 9th Symp Humanidentification (Promega Corporation, Madison, WI). pp. 52–54.

PEEREN BOOM, E. (1998). Central DNA database created in Ger-many. Nat. Biotechnol. 16, 510–511.

SAIKI, R.K., BUGAWAN, T.L., HORN, G.T., MULLIS, K.B., andERLICH, H.A. (1986). Analysis of enzymetically amplified �-glo-bin and HLA-DQ� DNA with allele–specific oligonucleotide probes.Nature 324, 163–166.

SCHNEIDER, P.M. (1998). DNA databases for offender identificationin Europe—The need for technical, legal & political harmonization.In Proc Europ 2nd Symp Human identification (Promega Corpora-tion, Madison, WI) pp. 40–44.

VARSHA, et al. (1999). D1S80 variation in random Indian popula-tions. Proceedings of X Intl. Symposium of Human Identification, FL,USA.

VARSHA, et al. (2003). Identification of cooked meat sample by 12Sr-RNA sequence analysis. Proceedings of 55th annual meeting ofAmerican Academy of Forensic Sciences, Chicago, IL.

WALLACE, D.C. (1999). Mitochondrial diseases in man and mouse.Science 283, 1482–1488.

WEBER, J.L., and MAY, P.E. (1989). Abundant class of human DNApolymorphisms which can be typed using polymerase chain reaction.Am. J. Hum. Genet. 44, 388–396.

WEISING, K., NYMBOM, H., WOLFF, K., and MAYER, W. (1995).DNA Fingerprinting in Plants and Fungi (CRL Press, Boco Raton,FL).

WERRET, D.J. (1997). The National DNA database. Forensic Sci. Int.88, 33–42.

WERRET, D.J., and SPARKES, R. (1998). Proceedings of Ninth In-ternational Symposium on Human Identification (Promega Corpora-tion, Madison, WI) pp. 55–62.

WONG, Z., WILSON, V., PATEL, I., POVEY, S., JEFFREYS, A.J.(1987). Characterization of a panel of highly variable mini-satellites,cloned from human DNA. Ann. Hum. Genet. 51, 269–288.

ZEHNER, R., ZIMMERMAN, S., and MEBS, D. (1998). RFLP and se-quence analysis of the cytochrome b gene of selected animals and man:Methodology and forensic application. Int. J. Legal Med. 111,323–327.

ZIEGLE, J.S., SU, Y., CORCORAN, K.P., NIE, L., MAYRAND, P.E.,HOFF, L.B., MCBRIDE, L.J., KRONICK, M.N., and DIEHL, S.R.(1992). Ligase-based detection of monoclonal repeat sequences. Ge-nomics 14, 1026–1031.

Address reprint requests to:Varsha

Laboratory of DNA Fingerprinting ServicesCentre for DNA Fingerprinting and Diagnostics

ECIL RoadNacharam, Hyderabad-76, AP, India

E-mail: [email protected]

Received for publication November 4, 2005; received in revisedform December 14, 2005; accepted December 15, 2005.

VARSHA188