APPLICATIONS OF DNA FORENSICS IN TODAY’S WORLD By: Patricia Beauzile, Meghan moore, Donald Hahn, Emily Hollens, Darwin O

1. APPLICATIONS OF DNA FORENSICS IN TODAY’S WORLD By: Patricia Beauzile, Meghan moore, Donald Hahn, Emily Hollens, Darwin Omar Larco Applications of DNA Forensics As the field of DNA forensics is ever increasing, the uses of DNA forensics are also increasing, and the current techniques are being refined. Some of the most common and important uses of DNA forensics are: Diagnosis of/ Development of cures for Inherited Diseases ~ diagnosis of cystic fibrosis, hemophilia, Huntington's disease, familial Alzheimer's, sickle cell anemia, thalassemia, and many others ~ education of prospective parents as to the risks of having an affected child ~ identification of DNA patterns associated with diseases to help establish treatment Biological Evidence ~ paternity/maternity testing ~ linkage of suspects to crime scenes Identification of Individuals ~ missing persons and casualties **ex. U.S. Armed Services Veterinary Applications ~ parentage testing of purebred animals ~ wildlife studies ~ identification of inheritance patterns of genetic diseases ~ identification of genetic patterns in populations ~ investigate genetic susceptibility of populations to diseases Agricultural Applications ~ breeding of dairy animals ~ cultivation of various crops The ability of scientists to use DNA fingerprinting to identify sequencing patterns in many different organisms is creating new possibilities every day, the extent of which is still not fully known.. History Forensic science is a developing field that owes its progression to the technical advancements made in the lab. This field was first coined as a science in 1936, but only recently has the area been recognized as an important asset in the fight against crime. This is due in large part to DNA fingerprinting. DNA fingerprinting was discovered accidentally by Alec Jeffreys in 1984 and published in Nature in 1985. This discovery revolutionized the area of molecular biology and became a gateway for many key developments in forensics, which let to the formation of DNA databases that store the DNA information of suspected criminals or already convicted criminals. The largest of such databases, UK’s National DNA Database, reported in 2004 that it contained 2,400,000 individual samples. In the United States there are similar databases, such as the National DNA Indexing System and Combined DNA Indexing System, which work directly with law enforcement agencies to match registered DNA samples to samples found at crime scenes. DNA fingerprinting was first used to provide evidence in a 1986 Pennsylvania case. Samples were extracted from corpses involved in the case, but much of the samples had been degraded. A technique called the Polymerase Chain Reaction (PCR) developed in the early 1980’s allowed for amplification of the limited samples, which were then used as evidence in the case. In this situation a limited supply of DNA would have been difficult to generate enough significant evidence since a technique developed in 1980 using restriction enzymes would have been the alternative. This shows the importance of developing techniques that enable scientists to help in the courtroom environment. Furthermore, refinement of these techniques allowed for the Human Genome Project to initiate in late 1980’s. Currently, the entire human genome has been sequenced, but there is still speculation as to the number of genes actually present. To the surprise of many scientists, current findings show that there are ~35,000 genes relative to original predictions, but as progress is made a much better understanding of the human genome can be established. The benefits of using DNA evidence have been made apparent with the increasing number of criminal cases that have been resolved in light of DNA findings. A man in Pittsburgh, PA was exonerated from a life sentence in May 2006 for a murder committed in 1989 as new DNA evidence established his innocence. Advancements in DNA matching have shown to be powerful tools in both the scientific society as well as the justice system. This particular area of forensics has evolved immensely within the last 2 decades, but there are still many issues that need to be addressed such as ethical questions and unexplained events in DNA science. There is no doubt that DNA fingerprinting will be a prominent area of research in the coming years. Special Cases DNA forensic science has recently been made popular because of its use in a number of high profile cases. In 1991, scientists exhumed the mass grave of the historical ruling Romanov family. The last generation of the ruling Romanov family, as well as their servants, were captured, murdered, and buried in a mass grave in Siberia in 1918. After the break up of the Soviet Union, scientists used DNA forensic evidence to identify the bodies in the mass grave. The forensics team collected DNA from dental remains, and skeletons. As a result, they discovered that of the 11 people who were reportedly executed and buried; only nine were found in the grave. In 1994, DNA forensic evidence was collected in form of blood, skin, and semen samples taken from the scene of the crime and was analyzed and compared to O.J. Simpson’s DNA taken from a cheek swab sample. Although the blood sample and the swab sample matched, this evidence was not used in court due to it nature. In this case, forensic evidence was considered circumstantial, and did not prove absolute guilt. In the 1998 Swissair Flight 111 disaster, short tandem repeat (STR) DNA was used to compare the DNA samples from the disaster sight with the DNA samples from searching family members. Scientists used the STR method as well as a computer algorithm to find similarity alignments between the victim DNA, and the victim’s family DNA. With the use DNA forensic tool, investigators were able track down the missing passengers on the flight, and identify lost loved ones. In 2001, after the attacks on the World Trade Center, DNA forensics was used to identify the missing victims of the bombings. Forensics team combed through the rubble to find any piece of remaining evidence to link the dead to their family members. Dental, blood, and hair samples were collected from ground zero, and compared to the DNA samples provided by family members in the form of hair brushes, tooth brushes, and other items that may have contained traces of biological tissue which DNA could have been extracted out of. References http://www.ornl.gov/sci/techresources/Human_Genome/elsi/forensics.shtml#6 http://www.universityscience.ie/pages/scimat_ethical_issues_dna.php http://jme.bmjjournals.com/cgi/content/full/26/4/266 http://www.le.ac.uk/ge/maj4/JoblingGill04.NRG.Forensics.pdf www.accessexcellence.org/RC/AB/BA/DNA_Fingerprinting_Basics.html http://en.wikipedia.org/wiki/DNA_testing www.news.ucdavis.edu/sources/ag_vet_DNA.lasso http://www.wesleyan.edu/synthesis/GROUP4/FINALVERSIONS/LASTD http://www.cambridgenetwork.co.uk/POOLED/ARTICLES/BF_NEWSART/VIEW.ASP?Q=BF_NEWSART_126943 http://www.ornl.gov/sci/techresources/Human_Genome/faq/genenumber.shtml Martin Paul, Johnson Paul, Williams Robin. Genetics and Forensics: Making the National DNA Database.Sci Stud. 2003 ; 16(2): 22–37. Clark, Michael. Forensic. The Lanclet. 2005; 366: 1351 Aronson Jay. DNA fingerprinting on trial: the dramatic early history of a new forensic technique. Endeavour 2005: 29(3): 126-131 McElfresh, Kevin C., Debbie Vining-Forde, and Ivan Balazs. 1993. "DNA-Based Identity Testing in Forensic Science." BioScience. Vol.43, No. 3, pp.149-157. Neufeld, Peter J. and Neville Colman. 1990. "When Science Takes the Witness Stand." Scientific American. Vol. 262, No.5, pp.46-53. Moody, Mark D. 1989. "DNA Analysis in Forensic Science." BioScience. Vol.39, No.1, pp.31-35. Marshal, Eliot. 1996. "Academy's About-Face on Forensic DNA." Science. Vol.272, pp.803-804. http://www.aic.gov.au/publications/tandi/ti26.pdf http://www.nature.com/embor/journal/v7/n4/full/7400669.html Lynch, Michael. The Discursive Production of Uncertainty: The OJ Simpson 'Dream Team' and the Sociology of Knowledge Machine Social Studies of Science, Vol. 28, No. 5/6, Special Issue on Contested Identities: Science, Law and Forensic Practice (Oct. - Dec., 1998) , pp. 829-868 Enhanced kinship analysis and STR-based DNA typing for human identification in mass fatality… http://www.astm.org/cgi-bin/SoftCart.exe/JOURNALS/FORENSIC/PAGES/JFS2003311.htm?E+mystore DNAi: http://www.dnai.org/romanovs/index.html Timeline: http://www.le.ac.uk/ge/maj4/JoblingGill04.NRG.Forensics.pdf Crime Scene Image:http://las.perkinelmer.com/Content/Images/smallImages/boodalcoholmontage.jpg PCR Image: http://www.dna-forensic.com/dna-str.html DNA background: http://www.ceul.ufms.br/semanabiologia2005/arquivos/dna.jpg Ethical Issues One of the major problems with DNA tests becoming common is the issue of privacy. Once a person’s DNA is sequenced, it is kept on record. Most states do not require that the DNA is destroyed after it is looked at, so the sample may be available at later times for evidence. Stored samples increase the possibility that someone could get a hold another human being genome. This is causing a stir because it’s increasing the likelihood that government, insurance companies, employers, schools, banks, could possibly get their hands on the information and use it in the future. These organizations could possibly use the information for genetic discrimination, not allowing people to obtain loans, work, or get health insurance if they found out that the person is predisposed to certain illness, or cancer. One place in the world where privacy is becoming a major issue is the UK. Police officials are allowed to obtain DNA samples from all suspects in a crime without permission. The UK has the largest DNA database in the world. The use of this database involves balancing between the rights of the individual versus the right of the state. The UK is having great success with finding criminals that match crimes, but in doing so many believe their tampering with an individual’s rights. Although DNA testing in the UK seems like a good idea, practically speaking it’s not, due to the fact that DNA sequencing takes a long time. There is a large build up of samples right now in the UK, so many cases have been dismissed, or trials ended before DNA is sequenced. Other countries such as Germany, Holland, France, Austria, have also turned to DNA samples for answers but only do testing when individuals are suspected of committing serious crimes. Here in the USA, police are unable to force suspects to give samples due to the 4th amendment. Measures must be taken to keep individuals right of dignity and freedom. As stated in the constitution, people should be given the choice, so many argue that consent should be obtained from each individual, before the DNA sample is taken. People being tested need to be aware of the consequences that will affect their lives, along with the lives of family members. Another point people are making is certain countries are also not allowing people to move around while being tested, and to object to DNA analysis of their sample. Problems Occurring in Analysis The beauty of the growing field of forensic science is the diversity in the methods of analyzing DNA samples. Given this diversity, if the nature of a sample does not allow it to be analyzed with one method then it is probably still useful to other techniques. The most common problem with DNA samples is usually caused by DNA degradation, which alters the structure of DNA so that it cannot be analyzed with the typical RFLP techniques. This can occur from exposure to heat, humidity, sunlight, etc. as well as contamination from bacteria and organic molecules from the environment from which the sample was withdrawn. Degradation causes longer regions of DNA to be interrupted. As a result, single tandem repeat assays work best for degraded DNA because it involves the amplification of a smaller amount of base pairs, about 150 or less. Using these mini STRs and amplifying them with 32 cycles of PCR has the advantage of increasing the likelihood of more DNA fragments of the desired alleles surviving. This, in turn, increases the chances of retrieving a complete DNA profile. Using longer numbers of base pairs can lead to an imbalance of the alleles during PCR amplification and even dropout of an allele in the results which, obviously, leads to invalid interpretations. Longer sequences have been shown to have significant dropout after two weeks of degradation, as opposed to 8 weeks for the STRs. Some alternatives to STRs have been in development. One of these methods is the use of single nucleotide polymorphisms, SNPs. These methods have found to be useful because they, based on the biochemistry mechanisms of extending primers, can genotype numerous SNPs in a single analysis. However, this requires a large amount of DNA template and PCR product, whose values are limited by sample amount. Another advantage of SNPs is that they, being single base sites, have much smaller amplicons, but the biallelic nature of these makes it difficult to interpret results from a mixed sample, thus requiring a well-balanced assay. One final problem with this method, because it is multiplex system, is that it contains several transfers of the sample which can lead to a higher chance of contamination. Once past the step of using PCR to retrieve a complete profile that has not been contaminated, the next issue arises in the discovery of a match. Forensics uses the probability of a match and the frequency of alleles in a population to determine the likelihood that the sample from the scene came from a suspect. Degraded DNA almost forces the use of mini STRs for forensic analysis because of its accuracy, but the smaller amount of base pairs and alleles used can mean that the probabilities of a match are higher than those for longer sequences. As a result PCR is used to remove a suspect form the scene of a crime rather than place him/her there. More problems exist with current forensic DNA analysis techniques outside of DNA degradation. One common problem, specifically with RFLP methods, is that of band shift on gels. Band shift is seen as DNA fragments moving across the gel at different speeds on the same gel. This can occur from problems with DNA concentration, faulty gel preparation, salt content in the sample, and contamination. When it comes to determining a match these band shifts could cause a problem because it seems difficult to defend two pieces of DNA as a match if the patterns are slightly different. However, scientists have concluded that this shift is just as likely to a match as away from it. Many problems can arise from the nature of the sample and the environment from which is withdrawn. Standardization of the techniques used to analyze the diversity of DNA samples will lead not only to consistent results but also consistent conclusions on the matching of two separate DNA samples. If error in an analysis occurs there is most likely no more of the sample left to use for a second round of analysis. Improving the methods used to analyze the various types of DNA will steer away from inconclusive results and lead to accurate conclusions in identifying the source of a DNA sample.