Chromosome as Markers in Forensics and Short Tandem Repeats Advantages and Disadvantages - Assignment Example

Genetics assignment Name: Instructor: Course: Date of submission: Q.1. SNP as a forensic marker SNP refers to a single nucleotide polymorphism. It is a variation occurring in a single point of a DNA sequence among different individuals. It is worth noting that DNA sequence is made up of four nucleotide bases i.e.: A, T, G and C. If a population exceeding 1% lack in similar nucleotide at a certain position in their DNA sequence, then the variation is referred to as SNP. If SNP appears within a certain gene or rather gene location, then the gene is said to be having more than single allele. In such situations, SNPs results to production of different amino acids sequences. It is also worth noting that SNPs occurs not only in coding regions but also in non-coding regions of DNA sequence. Even if some of SNP doesn’t result into disorders, some SNPs are linked to particular genetic diseases. This therefore guides the scientists into identifying the SNP so as to examine the genetic predisposition of an individual to that particular genetic-based disease (Cardon & Bell 2001, pg 93). Another point worth noting is that SNPs are associated with certain peculiar traits in individuals whose DNA is present. In this respect therefore, scientist may study the DNA stretches bordering these SNPs on the verge of pinpointing the very gene or genes linked to that particular trait. The aim of doing so can be in case of disputed parentage, removing a tussle in case of a lost person, identification of criminals in case of a crime scene and so on. Genetic polymorphism typing at the DNA (molecular level) helps to see to it that these objectives are attained. It is able to attain the objectives due to the facts that: there exist numerous variations at DNA level. These variations are therefore exploited to ascertain the identity of the individual in question. A second point to note here is that any nucleated cell/ biological material is likely to contain DNA polymorphism and can be types for the same as well. Lastly, DNA material is more stable in forensic samples in comparison to when it is in natural proteins hence making the typing process easy and applicable. It is also worth noting that typing of human polymorphisms at the DNA level is more specific, sensitive and informative as opposed to conventional application of protein markers makes it more preferable than the later. SNP has the ability of lowering the number of the individuals to be identified and hence narrow the suspects to a small group which includes the actual character being sought. It is under these attributes that SNP are very important as forensic markers since they enable easy comparative narrowing of the individuals in question to the very culprit. Samples employed here can be cell debris from saliva, serum semen, hair and other potential sources of DNA of the suspects. The main principle exploited in this case is the rarity of variations among individuals in terms of SNP and hence ease in application. This marks the very importance of Single Nucleotide polymorphism as a vital forensic marker. Q.2. Y-Chromosome as markers in forensics In the field of forensic science, the analysis of Y-Chromosome has three main applications. These applications are what make it peculiar/different from other techniques employed in the same field. These applications includes: male lineage identification, identification of male sex from the females and lastly identification of geo-geographical origin human paternal lineage. Male individual can be identified via this technique through DNA technique by pinpointing samples of Y-Chromosome from the scene of crime. On the other hand, the patrilineal identification of males with their respective male relatives alongside their pedigree of their male parent, grandparent and so on. This is done by picking and then typing the samples of male DNA for male-specific polymorphism found in Y-chromosome. After this, the typed polymorphism is then compared to the known profiles of the suspect at hand (Reid, 2003 pg 1). The genetic lineage or geographic origin of males is determined by application of Y-Chromosome polymorphism markers that exhibit specific pattern of distribution among males originating from a certain geographical region. This is established through the use of data base of already known geographical distributions of these polymorphisms. The magnitude of the importance of the application of Y-Chromosome markers in forensic science is based on the fact that a big percentage of the violent crimes have males as the probable perpetrators. This can be backed by the fact that almost all cases involving sexual assaultinvolve males as the probable culprits. It was in 1959 when it was determined that human sex was determined by X and Y chromosome with a combination of XX resulting to female and XY resulting to male. Later in 1990s SRY (Sex determination Region) of the Y chromosome as determined. Due to the fact that offspring inherit no Y chromosome from their mothers, and then the inheritance of Y chromosome is solely from the paternal side. This therefore means that one’s paternal lineage can be comfortably established without interruptions from ones maternal genes. This technique has therefore proved to be very effective in cases of disputed paternal parentage, rape and the likes. The use of STR referred to as ‘minimal haplotype’ is very commonly used and recommended for forensic purposes. It is advantageous over other genetic markers in the rest of the chromosomes is that single marker info can be incorporated as haplotype info plus the male-specific sequence of Y-Chromosome is completely inherited from the father down to his sons. Therefore for the forensic purposes, this translates to; for the replication of allele in single locus, the rate of getting combined DNA profile matching probabilities is not applicable to Y-Chromosome markers. To conclude this question, it is worth noting that Y-Chromosome are very useful as markers in forensic science especially in cases that involves male-only culprits. A good number of multi-copies of Y-STR markers are found in varying regions of Y-chromosome and hence coherently manifest male-specific alleles that exceed one when it comes to number. There has been a dramatic increase in the genetically known number of male-specific STR due to increasing research based on the usefulness that encompasses this technique. Q3. PCR and tits processes in forensic science Polymerase Chain Reaction (PCR) refers to a technology in molecular biology in which a few or single copy of DNA fragment is magnified via numerous magnitude resulting to millions of copies (replicas) of a certain DNA sequences. These fragments of certain DNA sequences are employed for a number of applications for instance: functional gene analysis, sequencing for DNA cloning; diagnosis of infectious and hereditary diseases and also in forensics for genetic fingerprinting in case of disputed parentage or identification of culprits in criminal justice (Cardon & Bell 2001, pg 95). Components and processes PCR technique is basically based on the tenet of thermal cycling. Thermal cycling process consists of recurrent phases of heating and cooling DNA melting coupled with enzymatic replication of short DNA sequences (primers) with complimentary sequences to the region of target using DNA polymerase (Enzyme) for targeted and recurrent replications. In almost all the process in PCR involves thermo-stable DNA polymerases for instance Taq polymerases. Taq polymerase enzyme gathers the new DNA strand from the nucleotides (building blocks of DNA) by the use of single stranded DNA template and DNA primers (DNA oligonucleotides) required in initiating the process of DNA synthesis (Saiki et al. 1988, pg 486). Step I (DNA denaturation) The initial step in this technique entails physical separation of double stranded DNA at high temperature. The enzyme helicase is used to separate the Hydrogen bonds between two complementary strands of a double helix DNA strands at the base-paring region. Since helicase might be expensive, the use of temperature (DNA melting) is applied to break the H-bond between the base-pairs and hence achieve the same effect at a cost-effective manner. One heats the temperature of the solution to a level slightly below the boiling point of the PCR solution. This breaks all the H-bonds between all, the base-pairs. Human polymerase is avoided in this process and instead Taq polymerase is used since human polymerase could destroy the proteins as it is not fit to work at these temperatures. Taq polymerase is initially derived from thermophilic bacteria hence fit to work in these high temperatures (Saiki et al. 1988, pg 488). Step II (Annealing Step) This refers to a step in which the primers are attached to the DNA template at hand. Within the course of replication, RNA primase (enzyme) forms primer nucleotide-by-nucleotide on the DNA template at hand (Saiki et al. 1988, pg 487). Step III (Elongation/extension step) It is worth noting that the PCR technique replicates (amplifies) a certain section of the DNA sequence as opposed to the overall DNA template. A primer serves as the initiation point to enable elongation. In this step, Taq polymerase attaches to every DNA primers and then continues with unidirectional addition of the nucleotides. This explains the need for two primers for opposite sides of the regions to be amplified. Every primer replicates one of the complementary DNA strands and thereby elongating them. This process is referred to as elongation phase basically it entails elongation of the sequence to be cloned. This three-step process is repeated until the required amount of the DNA replicas is attained. Below are the illustrations for the PCR technique (Pavlov et al. 2004, pg 250). Illustrative fig of PCR (Pavlov et al. 2004, pg 263). Q.4. Short Tandem Repeats, advantages and disadvantages Short tandem repeats refers to small DNA fragments that are repeated in a manner that results to a certain pattern in a double helical DNA strands. It is notable that these short sequences naturally occur in varying sizes. Due to this, their classification is based on the lengths of the basic repeat units, the overall size of the repeating region and also the specific number of the contiguous recurring units. The DNA regions characterized by short repeating sequences (basically between 2 and 6 base pairs) are referred to as STR (Short tandem repeats). In most cases STR are found around the centromere of the chromosomes (Pavlov et al. 2004, pg 253). STRs have proved to possess various benefits that make them very fit for human identification. This therefore explains their application in forensic science. They have been employed as crucial DNA markers since they can be multiplied via the use of PCR without any technical bottlenecks when it comes to differential replication. This means that after PCR, the products from STRs are basically the same in terms of quantity. This subsequently makes the analysis very applicable. It has been proven that an offspring inherits one copy of STR from both the mother and the father. This means that these copies may have similar repeat sizes or otherwise. There can be a very high variability between STRs among individuals. This variability is the one that is employed for the purpose of human identification in forensics. In cases that require human identification, DNA markers exhibiting the highest possible variations is needed for easy segregation of individuals in question. In most cases, it is so difficult to get PCR amplification results from the forensic samples of the suspects owing in mind that the DNA in those samples is likely to be mixed or degraded for instance in case of rape (Dittmar et al.2010, pg 57). The smaller the STR allele sizes, the better it becomes when it comes to forensic analysis. In addition, PCR replication of degraded samples of DNA is achieved easily when one employs smaller final product sizes. Due to the small sizes that characterises STR alleles, it is easier to separate them from their locations within the chromosome. This also ensures that closely coupled loci are not picked. This is important owing to the fact that closely coupled loci are unlikely to conform to any pattern characterizing any natural population. Otherwise, this would shut the doors for the application of statistical analysis (Dittmar et al.2010, pg 58). STR alleles are characterized by lower rates of mutation; therefore their data is more predictable and stable. It is on these basis that, STR with higher discrimination power are recommended in identifying missing persons, perpetrators and/ any other mission in forensic science. Q.5. Alleles frequency Since we are told to assume that HWE and biallelic focus The number of alleles =2. Let the dominant Allele be A while the recessive one will be a. Taking the biallelic locus and HWE holds, the genotypes frequency are represented by: PA, PAa, PAA, Pa and Paa For HWE to hold PAA=P2A ; PAa =2PAPa; paa = P2a (Wigginton et al. 2005 pg 890). Therefore estimated frequency = PA= nA/ (2n) = (Naa + ½ nAa) X2 = (1/4- 1/5)2/ 1/5 Frequency or X2= 1/5 Q.6. RFLP results and Chi-squared test Chi-squared test Chi squared test is another method used to identify thee equilibrium of different alleles in the same loci. It is relatively faster when the value of n in the equation is larger. In this instance the following equation is employed as test statistic: 2 (Wigginton et al. 2005, pg 890). This expectation must not be linked to both alleles Therefore: pA = nA = (2n) = (nAA = ½ nAa) = n While estimated coeff. Of disequilibrium = DA = nAA / N- (nA= (2n)) 2 (Wigginton et al. 2005 pg 898). From these equations: p= (36/140) / (2x 36/140) =2 If it’s at equilibrium 2 should be equal to [(53/140+ 102/140)] 36/140 Since they are not equal, then this population is not at population is not in Hardy Weinberg equilibrium at this gene locus. References list Cardon and Bell (2001) Association study designs for complex diseases. Nat. Rev.s Gen. 2:92-99 Saiki, R.; Gelfand, D.; Scharf, S.; Stoffel, S.; Horn, G.; Higuchi, R.; Erlich, H.; Mullis, K.; (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Sci 239: 486–490 Pavlov, A. R.; Kozyavkin, S. A.; Slesarev, A. I; Pavlova, N. V.; (2004). Recent developments in the optimization of thermostable DNA polymerases for efficient applications. Trends in Biotech 22 (6): 240–270 Dittmar et al., (2010) Quality of cell products: authenticity, identity, genomic stability and status of differentiation. ; 36:54– 69. Tewari, (2000). History and development of forensic science in India and the rest of the world. J. Postgrad Med (47): 300–309. Reid, L. (2003). Dr. Henry Faulds - Beith Commemorative Societ y. Journ of For. Identif. 53 (1) Wigginton et al. (2005) A note on exact tests of Hardy -Weinberg equilibrium. Am J Hum Genet 76: 887-905 Read More