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Short Tandem Repeat (STR) DNA Analysis and the CODIS Database

Short tandem repeat (STR) is a molecular biology tool mainly exploited in forensic science in order to determine certain locations known as loci present on the nuclear material, DNA. STR sites exhibit remarkable polymorphism which offers a reliable platform for forensic investigations to differentiate the DNA profiles from one individual to the other. STR DNA analysis is made feasible through the utility of multiplex PCR (polymerase chain reaction) and fluorescent dye technology (Clayoton et al., 1998). This improved the automation of the process and accelerated the analytic determination of short tandem repeat loci (Clayoton et al., 1998). Ultimately, understanding the quality of types of alleles and quantity on the magnitude of band intensity has become easier (Clayoton et al., 1998). Hence, STR technology can be considered as the computing tool for assessing the extent of DNA amplification (Clayoton et al., 1998). STR DNA analysis has greatly permitted testing the identity in humans but on specific core regions of STR loci (John, 2006). These loci are reported to be extensively used for DNA typing (John, 2006).

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Today, many kits have been manufactured on a commercial basis to facilitate large-scale core STR loci amplification (John, 2006).

Markers specifically related to the core autosomal and Y-chromosomal STR are utilized (John, 2006). The genome that makes up humans will be studied to physically identify every each STR locus (John, 2006). The physical site of such locus is then elucidated and the range of alleles and their variations thus observed in the pool of individuals are summed up (John, 2006). With the advancements in web technology, several internet links are available in order to gain deeper insights on core STR loci (John, 2006). Much emphasis was given to dissecting the genetic relationship between disease contributing genes and STR loci, evaluating the samples for ethnicity, and additional required features for STR loci to modify the existing core loci (John, 2006).

The core STR loci developed provides a foundation for global databases of DNA and has future implications in the field of forensic science (John, 2006). Markers specific to STR were documented in the literature as indispensable tools for testing the identity in humans in the 1990s (John, 2006). Authorities such as Forensic Science Service (FSS) and the Royal Canadian Mounted Police (RCMP) were set up to investigate (John, 2006).FSS serves to identify novel loci and measure the variations among the population by employing several STRs as the candidates (John, 2006).

Multiplex technology of FSS exploited for forensic casework focused on four important loci such as TH01, VWA, FES/FPS, and F13A1. Similarly, the loci identified for second-generation multiplex (SGM) were loci TH01, VWA, FGA, D8S1179, D18S51, and D21S11(John, 2006).

STR projects were being set up and firms like Promega Corporation and Applied Biosystems. Promega Corporation has provided loci for FFFL multiplex (John, 2006). These include LPL, FES/FPS, F13 B, and F13 A1. Similarly, for the PowerPlex kit, the loci are D13S317, D5S818, D7S820, D16S539, VWA, TPOX, and CSF1PO (John, 2006). Applied Biosystems has provided an AmpFlSTR Blue kit. This includes sex-typing system amelogenin, CSF1POD3S1358, VWA, and FGA, and the AmpFlSTR Green I kit with TH01, TPOX, CSF1PO, and AmpFlSTR(John, 2006). Yellow multiplex has D5S818, D13S317, and D7S820 in combination with AmpFlSTR Green II multiplex that includes D8S1179, D21S11, and D18S51(John, 2006). The combination of the entire three firm’s products like AmpFlSTR Blue, Green I, and Yellow has resulted in the development of AmpFlSTR Profiler kit, whereas AmpFlSTR Profiler Plus kit comprises of Blue, Green II, and Yellow loci (John, 2006). This may indicate the interest shown in the production of loci by different firms for the smooth evaluation of STR data (John, 2006). Hence understanding the loci may play a vital role.

STR typing methodology was exploited by the Federal Bureau of Investigation (FBI) to set up the core STR loci that serves as the foundation for CODIS (Combined DNA Index System (John, 2006). This is considered as the U.S national database system (NDNAD) (John, 2006). FBI has selected 13 important STR loci that are customary for CODIS (www.dna.gov/basics). The main objective of setting up core STR loci is to guarantee that every forensic laboratory has a standardized DNA database system to facilitate the dissemination of the same common information (www.dna.gov/basics).

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The utility of the CODIS index for forensic or committed offense cases under mystery requires the production of DNA profiles with the help of STR technology and the important 13 core STR loci chosen by the FBI (www.dna.gov/basics). The 13 genetic markers of CODIS in various databases globally have made them pioneer the existing genetic repositories of humans gathered till the recent period (John, 2006).

There were nearly 5 million unique sketches in US and UK recorded in DNA databases, on criminal cases, which harbor the information about the core loci (John, 2006). Further, to determine parentage nearly 1 million samples are processed per year with core STR loci (John, 2006).

It is important to note the 13 CODIS loci most widely employed in the US. They are CSF1PO, FGA, TH01, TPOX, VWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11 (John, 2006). Whereas in the UK and most parts of Europe, 10 core loci are mainly used with other markers such as D2S1338 and D19S433 and 8 overlapping loci FGA, TH01, VWA, D3S1358, D8S1179, D16S539, D18S51, and D21S11(John, 2006). The above-mentioned loci are central in offering a common platform for the sharing of information (John, 2006). This applies both to human identity as well as paternity testing. In addition, information regarding lost individuals and those among the large-scale calamities can be obtained through STR markers (John, 2006).

The software developed for maintaining the CODIS database plays an important role. It helps the National DNA Index System (NDIS) by dealing out with automated DNA information and telecommunication (www.dna.gov). The CODIS database works based on the type of recorded DNA profile obtained from various forensic laboratories present in the local regions, throughout the state and country (www.dna.gov). The laboratories present in a local vicinity could establish and manage their unique database of forensic local DNA index systems (LDIS) and can send the permitted profiles to SDIS (www.dna.gov). SDIS stands for State DNA index system (www.dna.gov). It is a state-level database that has profiles collected from the laboratories of the local region and profiles of the state laboratory (www.dna.gov/basics).

SDIS has DNA profiles of victims who were arrested on the charges of offense or crime (www.dna.gov). The guidelines for maintaining profile types were set up by the states themselves and there is a need to get thorough knowledge for the analysis part as per the state policies (www.dna.gov). Here, the FBI also serves as an SDIS laboratory when it attempts to record its own forensic investigations into CODIS (www.dna.gov). The next aspect of the CODIS database is that of National. Forensic profiles obtained from various states along with the FBI are sent to National DNA Index System (NDIS) (www.dna.gov). Whether a given profile can be sent to NDIS depends on the criteria of Federal Law (www.dna.gov/basics). The profile needs to be in agreement with the Federal Justice For All Act 2004 in order to get qualified for NDIS (www.dna.gov). For example, if a patient or victim’s sample is falling short of DNA loci, it fails to become eligible for NDIS entry (www.dna.gov). Therefore, there is a need to develop in-depth knowledge of the CODIS database especially NDIS Board guidelines (www.dna.gov). There could be various types of profiles in the CODIS database like forensic, arrestee, suspect, human remnants’ under unidentified conditions, lost individuals, and their relatives(www.dna.gov/basics). With the ever-growing number of rape and murder cases, there is a high demand for CODIS software as revealed from extensive search hits (www.dna.gov).

References

STR Analysis. 2009. Web.

Clayton, T,M., Whitaker, J,P., Sparkes, R., Gill, P. (1998). Analysis and interpretation of mixed forensic stains using DNA STR profiling. Forensic Sci Int, 91, 55-70.

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John M Butler. (2006). Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing. J Forensic Sci, 51, 253 -2.

Combined DNA Index System. Web.

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StudyCorgi. 2022. "Short Tandem Repeat (STR) DNA Analysis and the CODIS Database." July 20, 2022. https://studycorgi.com/short-tandem-repeat-str-dna-analysis-and-the-codis-database/.

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