Single Nucleotide Polymorphisms Replaces the Short Tandem Repeat - Essay Example

Single Nucleotide Polymorphisms (SNPs) will replace STRs as the marker of choice in Forensic Genetics in the next 10 years” Discuss. STR (short tandem repeat) has been used for forensics and genetic testing since the mid 1990s, especially coming to the public attention through the OJ Simpson case in California. Some say OJ was acquitted because the jury did not understand STR DNA. STR are repeating sets of nucleotides or genetic markers. SNP (Single Nucleotide Polymorphisms) are changes to a single nucleotide in a DNA sequence. The differences and likelihood that SNP will replace STR in the next ten years will be discussed. The STR (short tandem repeat) are genetic markers that consist of repeating sets of nucleotides. These nucleotides are designated by a DYS number. The use of STR in genetic testing, forensic and paternity, has been for two reasons. The first is a small amount of DNA has to be present to do STR marker comparison. Secondly, “Y-STR markers exhibit much lower variability autosomal STR markers” (Gunn, 3006: 51). For these two reasons, forensic and paternity DNA tests have used the STR genetic markers. In DNA, the STR is a class of polymorphisms that occur within a pattern of two+ nucleotides which repeat and have repeated sequences that are directly next to each other. This pattern can be anywhere within the length from 2 to 10 base pairs. Through an examination of enough STR loci, then counting how many repeats of a STR sequence at a give locus, it is possible to create a profile of an individual. There are 10,000 known STR sequences in the human genome. In forensics, STR can create a genetic fingerprint. STR in forensics are all tetra-nucleotide or penta-nucleotides due to the high amount of error free data that is harvested, while having enough sample to survive degradation. Longer repeat sequences will suffer more highly from environmental degradation, plus do not amplify by PCR as well. Shorter repeat sequences tend to suffer from preferential amplification. This process is completed by gathering nuclear DNA, then enlarging certain polymorphic regions by the means of the polymerase chain reaction. After these sequences have been amplified, they are resolved either through gel electrophoresis or capillary electrophoresis. This allows the analyst to determine how many repeats of the STR sequence in question there are. If the DNA was resolved by gel electrophoresis, the DNA can be visualized either by silver staining, intercalating dye such as ethidium bromide, or as most modern forensics labs use, fluorescent dyes. SNP (Single Nucleotide Polymorphisms) are changes to a single nucleotide in a DNA sequence. Since the relative mutation rate is slow in SNP, it makes them good markers for the human genes. SNPs are labeled with a letter code and a number. The letters stand for the lab/researcher that discovered the SNP. The number is for the order in which the SNP was found. SNPs are used for disease detection and research. For example, “The aim is to access whether there is any association between the two nucleotides possessed by any individual for this SNP and that individuals disease status” (Ewens, 2004: 343). However, the SNP has been used within the forensic field. Single nucleotide polymorphisms can fall into coding sequences of genes, non-coding regions of genes, or in the intergenic regions between genes (Kieleczawa, 2005: 138). SNPs inside a coding sequence does not change the amino acid sequence of the protein that is created, due to degeneracy of the genetic code. A SNP in forms both lead to the same polypeptide sequence is termed synonymous, if a different polypeptide sequence is produced they are non-synonymous. SNPs that are not in protein-coding regions may still have consequences for gene splicing, transcription factor binding, or the sequence of non-coding RNA (Carracdo, 2005: 243). Variations in DNA sequences of humans can determine why and how humans develop diseases and respond to vaccines, drugs, and so forth. SNP can also be used to research and compare regions of genome between cohorts. SNP can also be used in farm programs, such as livestock breeding and crop development. The reason that SNP will replace STR in forensic science as the gene marker is SNP deals with one marker, instead of a sequence. This will mean a smaller sample of DNA can be utilized in order to profile. A smaller usable sample will be extremely useful in forensics, when samples at a crime scene are not left in quantity or in very good condition. Since an analyst is only looking at one marker, the time to analyze will be shorter. It can also provide more accuracy. Knowledge of SNP has been advancing in the past couple of years. Since technology is advancing, the more scientist understand the SNP, the more likelihood it will be used more than STR in the next ten years. SNP will prove to be easier in the long run than the sequencing in STR. SECTION B Below are listed the results from a paternity test. The alleles of the individuals tested are shown, use the allele frequencies in the table provided. Complete the table. You are advised to show your calculations. PI = paternity index. D3 vWA D16 D2 D8 D21 D18 D19 THO1 FGA Mother 14 15 15 16 8 9 19 20 12 12 28 29 14 15 15 16 6 6 23 23 Child 15 17 14 16 8 11 19 22 12 12 29 30 14 15 15 15 6 6 23 23 Tested man 16 17 14 14 8 11 22 22 12 13 27 30 14 15 15 15 6 6 23 24 PI Write a brief statement that could form part of a report for a civil case. The statement should include both the likelihood ratio and a probability of paternity. This man would be the father. Briefly (max 200 words) evaluate the use of SNPs and STRs for paternity testing. SNPs are being used by labs for paternity testing. Labs are favoring SNP over STR for several reasons. The first is a smaller sample of DNA can be used for SNP testing than can be used than in STR testing. SNP testing can also extract a genetic profile from a DNA sample that has not been preserved. This could help if the father is deceased or unavailable for a fresh DNA sample. If this was the case, then a DNA sample could be taken from a hairbrush or corpse. STR testing takes more of a DNA sample. Plus STR testing can only be used on a well preserved DNA sample. For these reasons, SNP is starting to be favored over STR. The more that is learned about SNP, the more accurate this testing will become. References Butler, J. M. (2005). Forensic DNA Typing, Second Edition: Biology, Technology, and Genetics of STR Markers. New York: Elsevier. Carracedo, A. (2005). Forensic DNA Typing Protocols (Methods in Molecular Biology). New Jersey: Humana Press. Ewens, W.J. (2004). Mathematical Population Genetics. USA: Springer Science and Math. Geberth, V. J. (2006). Practical Homicide Investigation: Tactics, Procedures, and Forensic Techniques, Fourth Edition. Boca Raton, Florida: Taylor and Francis Group. Gunn, A. (2006). Essential Forensic Biology. New York: John Wiley and Sons. Kieleczawa, J. (2005). DNA Sequencing: Optimizing the Process and Analysis. Canada: Jones and Bartlett. Read More