Forensics

Abstract

BioTechniquesVol. 39, No. 1 Technology NewsOpen AccessForensicsLynne LedermanLynne LedermanSearch for more papers by this authorPublished Online:30 May 2018https://doi.org/10.2144/05391TN01AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit DNA Bears WitnessFor most, the term “forensics” conjures up the macabre, given its use in identification of victims of natural disasters or crimes, whether large scale (e.g., the World Trade Center attacks or the tsunami of December 2004) or not so large—for the victims and their loved ones, no disaster or crime is small. DNA forensics is one of the three major means for identifying humans, along with fingerprints and odontology. For these to be of use, comparators are needed, whether a known DNA sample, previously archived fingerprints, or an authenticated antemortem dental record.Image 1. The steps in DNA analysis include sample collection and storage, extraction and quantitation of DNA, genotyping to generate an individual pattern of short tandem repeat (STR) loci, and interpretation and storage of the results.Beyond the obvious applications of identifying victims and perpetrators, or at least potential suspects, in crimes, DNA forensic identification is also used to establish paternity or other familial relationships, to trace migratory patterns of human populations, and to determine the relationship of ancient remains (e.g., the so-called ice men and maidens of Europe and South America) to modern humans. Other applications of DNA forensics include tagging products with synthetic DNA to prevent counterfeiting, determining whether an animal product is from an endangered species, and determining the origin of agriculturally important plants such as wine grape cultivars, to name but a few.DNA DatabasesIn the U.S., the FBI's Combined DNA Index System (CODIS), contains DNA profiles generated using short tandem repeats (STR) from 13 loci. The STRs are repetitive DNA sequences (microsatellites) in noncoding regions, with very high variability among individuals due mainly to differences in the number of repeats. These are amplified using PCR, with the usual cautions to avoid contamination. Other countries use systems based on a different number of STRs, may include different sequences from those in CODIS, and can include blood types or other genetic markers.State laws determine which offenders must have their profile stored in CODIS or other databases, and the data uploaded to CODIS must meet set standards. State and local databases containing data that differ from those meeting CODIS standards can be used on a local level. There is a backlog of samples awaiting entry into CODIS, and the statute of limitations may have expired for cases where DNA analysis would have proved useful. For those crimes where a perpetrator has not been identified, some communities have enacted Jane or John Doe laws, which allow an arrest warrant to be issued for the DNA profile before the statute of limitations runs out. In the UK, all suspects and all persons arrested can be forced to provide a DNA sample, whereas in the U.S., Fourth Amendment rights may be invoked to prevent DNA sampling without strong probable cause. DNA profiles, of course, can be used not only to convict, but to exonerate.From Fingerprints to DNA ProfileAs mentioned, fingerprints have been one of the mainstays of human identification. In situations where fingerprints can be found, they may be incomplete and often may be too smudged to be useful. Theresa Caragine, Forensic Scientist (Criminalist IV), at the Office of the Chief Medical Examiner (OCME) of the City of New York, expects their High Sensitivity Laboratory to open this summer to process and generate DNA profiles from low copy number (LCN) DNA samples such as fingerprints. The LCN protocols grew out of lessons derived from their experience in optimizing protocols for the World Trade Center identification efforts. Current protocols in use for DNA profiles require a minimum sample of approximately 150 pg of DNA. A fingerprint may have only a couple of cells stuck to it, and each cell contains about 6 pg of DNA. In the research setting, they have been able to amplify 6 pg of DNA, but are setting the lower limit at 20 pg. Caragine expects their methodology will be presented at a meeting and be published this fall. The OCME will be the first laboratory in the U.S. to be performing such LCN, or as they prefer to call it, high sensitivity, detection, although Caragine acknowledges the British already have a low copy number laboratory as part of their privately run Forensic Science Service (FSS).The OCME team will need to get both state and national approval of the LCN protocols in order to enter profiles generated using them into state and national databases. The number of amplifications and the way the loci are confirmed differ from those used in conventional case work. Caragine says they will measure the amount of DNA in all samples, and if there is enough for conventional analysis, that will be used. If not, they will use their high sensitivity protocol. “If the profile doesn't get into the national database, that's OK, because if the amount of DNA was too low to run by conventional means, it wouldn't have been amplified anyway,” she observes. “If nothing else, the information derived from a touched object can provide an investigational lead (for local law enforcement) whether it is probative or not.”Image 2. Variability in the number of repeats in short tandem repeat (STR) regions, detected with PCR, is used to distinguish DNA profiles.Image 3. The FBI's Combined DNA Index System (CODIS) includes 13 STR loci.The individual's DNA profile shown is highly unlikely to match that of any other individual.Meeting the Challenges“The biggest challenge in the World Trade Center investigation,” says Caragine, “was degraded samples.” Brian McCord, Associate Professor of Chemistry, Florida International University, and Staff, International Forensic Research Institute, Miami, and John Butler, Project Leader, Human Identity DNA Technologies Group, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland, have a grant from the National Institute of Justice to develop technology using mini STRs for analysis of DNA in degraded samples. The kits used for analyzing STRs for CODIS require DNA in a size range of 100 to 300 or 400 base pairs. Degraded DNA samples include those that might be obtained from a specimen that is old or that has been exposed to fire, chemicals, or harsh environmental conditions. Like LCN, mini STR technology will need to be validated before data obtained will be able to be uploaded to CODIS. “The main problems in using mini STR technology on degraded samples,” says McCord, “are that the DNA may not amplify, something might inhibit amplification, or DNA is simply not there to begin with.” Mini STR analysis, notes Caragine, is performed on samples below 100 bp, and 16 loci are examined.The problems of working with degraded samples may also be solved by the use of single-nucleotide polymorphisms (SNPs), which, according to Timothy McMahon, Supervisor of Validation and Quality Control, Armed Forces DNA Identification Laboratory, Armed Forces Institute of Pathology, Washington, D.C., is the “hot new field.” Due to the smaller number of variants per SNP, most often two, a larger number must be analyzed to be as informative as STRs, in the range of 50 to 100 autoso-mal SNPs; however, SNP typing can be performed on shorter DNA fragments than are required for STR analysis, making SNP analysis more useful for degraded DNA samples. Privacy and insurance coverage may become an issue with the use of SNPs if the first and second positions in each codon, rather than just the wobble position, are used, because these sequences may reveal disease susceptibility, unlike the CODIS STRs, which were chosen from noncoding regions and don't identify disease states.Usable mitochondrial DNA, which is maternally inherited, can sometimes be obtained from degraded samples. McCord says this is frequently used for identifying soldiers repatriated from previous theaters of operation, such as World War II battlefields, Korea, and Southeast Asia. Ira R. Titunik, Adjunct Assistant Professor of Forensic Science Research, John Jay College of Criminal Justice, New York City, and a forensic odontologist, notes that starting with Operation Desert Shield, DNA samples (blood cards) and dental scans have been obtained from all active and reserve military personnel, which will facilitate identification.The use of Y chromosome DNA is another area gaining importance in the courts. Male-specific STR regions on the Y chromosome (Y-STRs) are particularly useful in the processing of rape kits, because female DNA, even in large quantities, is non-interfering.Future DirectionsMcCord observes that the problem of the backlog of samples waiting to be analyzed is compounded by lack of personnel and funding, particularly for research. Both he and Caragine feel that automation will be a key to handling large amounts of evidence. McMahon sees getting LCN data accepted as the “biggest fight in the field; that FSS has shown it works will help.” McCord notes that, contrary to conjecture, there is no evidence that DNA sequences will one day reliably predict what a person looks like, so generating a picture of a suspect from DNA left at the scene remains in the realm of science fiction.FiguresReferencesRelatedDetails Vol. 39, No. 1 Follow us on social media for the latest updates Metrics History Published online 30 May 2018 Published in print July 2005 Information© 2005 Author(s)PDF download