Developments of DNA Profiles - Essay Example

The developments in the generation of DNA profiles using STR multiplex kits The developments in the generation of DNA profiles from highly compromised tissue samples originating from mass disasters for the purposes of human identification using STR multiplex kits. Introduction Advancements in DNA typing such as Multiplex PCR that involves targeting multiple genomic locations by using more than 1 set of PCR primers in the reaction as well as the typing and co-amplification of multiple STR systems have increased the possibility of obtaining the maximum amount of information from a DNA sample while limiting its consumption in instances where there is a limited availability (for example in the case of evidence collected from a crime scene). Multiplexing of STR (Short Tandem Repeats) and polymorphic loci through fluorescent labeling of the PCR primers are efficient and reliable forensic DNA analysis techniques as there is a inverse correlation between the number of polymorphic loci examined and the probability of identical alleles in two individuals. Developing DNA profiles for the identification of individuals who are unknown or identifiable or victims of accidents, calamities, crimes, and disasters using automated STR multiplex kits that rely on spectral resolution using different colored fluorescent dyes to label the overlapping loci due the presence of alleles that fall in the same size range has proven to be one of the most innovative methods. In fact, the polyacrylamide gels that are used in STR can resolve DNA fragments that differ by as little as 1 nucleotide in length and this precise allele designation eliminates the need for match guidelines and continuous allele distribution models that are usually needed in conventional DNA profiling methods The genes are the smaller portions of the DNA that produce a particular product, such as protein. They are particularly useful in the process for profiling. Other portions of the DNA whose functions are not determined yet are called “spacer or packer DNA between the genes” (DNA Profiling n.d., p. 2). These areas are called minisatellites while the smaller repetitive sequences are called as microsatellites (e.g. 4 base pairs). Short Tandem Repeats or STRs determine the number of times the sequence is repeated. Though identification is prohibitive in developing countries where the technology is quite expensive due to extensive processing, these countries usually send DNA samples to developed countries for analysis and profiling. (Lehman & Criscuolo 2009, p. 1). Short Tandem Repeat (STR) Profiling The Short Tandem Repeat or STR process of identification is said to be the new methodology is DNA profiling (DNA Profiling n.d., p. 3). The STR loci are said to be the “informative genetic markers” for DNA profiling currently in use, even for the degraded samples (Budowlea, Bieberb & Eisenberg 2005, p. 237). This process focuses on the microsatellite repeating regions, and is based on the PCR (Polymerase Chain Reaction). In a criminal investigation, it is common to encounter DNA samples that are highly degraded either due to oxidative damage or nucleases as a result of which the normal PCR amplification gives inconclusive results. Redesigned STR primers called “mini-STR” was introduced in 2003 to improve the success rate for degraded DNA where the primers were located closer to the repeat region to generate shorter amplicons. (Source: DNA Profiling n.d., p. 5) Research indicates that the PCR amplification of STR loci is a lot more advantageous due to the high level of sensitivity and degree of accuracy that this method offers when compared to the single locus profiling or SLP and this method. PCR based STR systems also can be used successfully for a wide range of different types of evidence where the forensic specimen is degraded, old, or poorly stored. The table below describes the type of repeated DNA sequences that are found in Satellite, Minisatellite, VNTR, and Microsatellite DNA. As seen from the length of the base pairs, the longest repeats are encountered in satellite DNA while the shortest repeats are seen in microsatellite DNA. Typically, Short Tandem Repeats (STR) are small and repetitive DNA sequences that are less than 20 base pairs long. Figure 2 Types of Repeated DNA Sequences (Source: Kloosterman 2003 p. 9) In most cases, a full genotype could be assigned across all the four STR loci and only a very small proportion of the samples generated partial profiles for either one or two or three loci. The generation of partial profiles was attributed to the quality of the individual DNA samples and the results obtained showed a converse relation between the extent of DNA degradation and the progressive gain or loss of higher molecular weight loci. Commercial autosomal STR multiplexes are now becoming widely used in forensics (Jobling & Gill 2004, p. 742). The first of autosomal multiplex profiling is the quadruplex (Kimpton CP et al., cited in Jobling & Gill 2004, p. 742) that comprised four Simple STRs. The match probability is ~1 in 10,000, too high that the process is used together with SLP (Single Locus Profiling). Adding two highly variable Complex STRs lessened the match probability to ~1 in 50 million. This approach called “second-generation multiplex” (SGM) also uses PCR assay that targets the XY-homologous amelogenin genes (Sullivan, Mannucci, Kimpton, & Gill 1993, cited in Jobling & Gill 2004, p. 743). The sensitivity of this system can reveal the sex of the source of the sample. The development of SGM Plus in 2000 added four more loci to the multiplex (Cotton et al., cited in Jobling & Gill 2004, p. 743). This has greatly reduced the match probability to below 10-13. Different countries though use different variations of the STR with US FBI CODIS having 13 STRs and amelogenin sex test, or Germany with eight loci and ACTBP2 locus. Improving the success rate of degraded DNA, the PCR primers for the STR loci are placed closer to the repeat region (Budowlea, Bieberb & Eisenberg 2005, p. 237). The amplified PCR or amplicon length is reduced, which allows genetic characterisation if it is “smaller than some of the fragmented DNA template molecules” (Budowlea, Bieberb & Eisenberg 2005, p. 237). The existence of reduced amplicon size STR multiplexes had greatly helped in the analysis of degraded DNA during the 9/11 attacks. STR Multiplex Kits for Mass Casualties during Disasters Mass casualties occur once in a while. The deaths resulting to disasters and calamities run from hundreds to thousands of individuals. Due to the huge quantity of deaths, the government, even with the assistance of the private sector, is burdened with proper disposition of the cadaver immediately. At times, the state of decomposition of the cadaver is so advanced that identification by relatives is not possible due to the change in physical appearance. DNA samples can be used in identification of victims of flood, plane crash and other terrorist attacks (Lehman & Criscuolo 2009, p. 1) and mass fatality incidents due to natural causes, accidents, as well as man-made occurrences (Lowe 2009, p. 1). Mass fatalities from intentional causes include gas poisoining (e.g. 1995 in Tokyo), car bombing and wars (Budowlea, Bieberb & Eisenberg 2005, p. 230). Flight disasters though can cause great fragmentation as well as degradation of remains (Budowlea, Bieberb & Eisenberg 2005, p. 230). Victims of the 2004 Southeast Asian Tsunami (Source: Lowe 2009, p. 13) During the early part of forensic identification, determination is based on fingerprint, dental record, X-ray, birthmark, skin tattoo and other physical traits (Lehman & Criscuolo 2009, p. 1). However, when the body has suffered severe trauma or decomposed, identification is restricted (Jennings et al. n.d., cited in Lehman & Criscuolo 2009, p. 1). The uniqueness of the genetic code of every person enables the identification in cases of mass casualties (DNA Initiative n.d., cited in Lehman & Criscuolo 2009, p. 3). Budowlea, Bieberb and Eisenberg (2005, p. 233) emphasised the importance of the collection of sample for DNA testing. The recovery of evidence or sample and preservation are critical steps in the identification process. The cadavers must be gathered immediately in a scientific manner. However, in cases where the disaster is relatively wide in scope, collection of human remains may take weeks to accomplish. Budowlea and his group presented the standard collection, packaging and transporting to maintain the integrity of the samples, together with the appropriate labeling. At the laboratory, analysis is first conducted on the unknown sample and the reference or known sample later (Budowlea, Bieberb & Eisenberg 2005, p. 235). Conclusion Over the past two decades, DNA profiling technology and other developments have truly revolutionized forensic science. One area of ongoing research is using biological traces at a crime scene in the form of only not only minute or degraded stain material to focus on and create an accurate physical description of an individual. While, DNA may be damaged by heat, temperature, humidity, pH, soil chemistry or other agents (Lehman & Criscuolo 2009, p. 1) with the rate of degradation being determined by time and environmental conditions (Burger, Hummel, Hermann, & Henke 1999 p.20), the short amplicon approaches that have recently been developed for the analysis of degraded DNAhold great promise. Moreover, when the mass casualty includes members of the same family, identification may pose some difficulty due to DNA similarity and it seems only budgetary restraints and the inertia of international legal change may limit the tempo at which these developments come into daily practice. During the 9/11 attacks, not all the remains were successfully identified due to their conditions (Lowe 2009, p. 10). The Southeast Asian tsunami, on the other hand, resulted to high degree of body fragmentation and degradation of DNA (Lowe 2009, p. 11). Thus, it is better, as suggested by Lehman and Criscuolo (2009, p. 1) that creation of DNA databases be made to anticipate mass fatalities, and that more specialists be trained in the field together with the funding of more research studies. Devices and innovations like these are currently in the development pipeline that would extract, amplify and sequence DNA materials immediately and on-site (Jobling & Gill 2004, p. 749) would greatly help in the profiling of mass casualty victims. The results of the robust and reliable quadruplex testing system for blood and tissue samples results generated highly reliable data for forensic identification using this analytical technique especially in cases where badly degraded and decomposed samples were encountered. PCR-based DNA technologies are the answer to successfully and completely identifying these remains with the highest level of accuracy. References Budowlea B, Bieberb FR & Eisenberg AJ 2005. Forensic Aspects of Mass Disasters: Strategic Considerations for DNA-based Human Identification. Legal Medicine, vol. 7, pp. 230–243. . [Accessed 1 December 2011]. Burger, J.; Hummel, S.; Hermann, B.; Henke, W. DNA preservation: a microsatellite-DNA study on ancient skeletal remains. Electrophoresis, 1999, 20, 1722-1728 Butler, J.M.; Shen, Y.; McCord, B.R. The development of reduced size STR amplicons as tools for analysis of degraded DNA. J. Forensic Sci., 2003, 48, 1054-1064. DNA Profiling in Forensic Science. n.d. XII-Biotech-D-DNA Profiling-1, pp. 1-6. . [Accessed 30 November 2011]. Jobling MA & Gill P 2004 October. Encoded Evidence: DNA in Forensic Analysis. Nature Reviews, vol. 5, pp. 739-752. . [Accessed 1 December 2011]. J.P. Whitaker, T.M. Clayton, A.J. Urquart, E.S. Millican, T.J. Downes, C.P. Kimpton and P. Gill. Short Tandem Repeat typing of bodies from a mass disaster: High success rate and characteristic amplification patterns in highly degraded samples. Biorechniques (in press). Kloosterman AD 2003 November- December. Current and Future Developments in Forensic DNA Typing. Universiteit van Amsterdam. . [Accessed 30 November 2011]. Lehman M & Criscuolo CL 2009 April 23. The Application of Deoxyribonucleic Acid in Victim Identification Following Catastrophic Events. . [Accessed 29 November 2011]. Lowe CM 2009 March 11. The Application of Forensic DNA Identification in Mass Disaster Investigations. . [Accessed 30 November 2011]. Read More