Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing

National Institute of Standards and Technology, Gaithersburg, MD 20899-8311, USA.
Journal of Forensic Sciences (Impact Factor: 1.16). 04/2006; 51(2):253-65. DOI: 10.1111/j.1556-4029.2006.00046.x
Source: PubMed


Over the past decade, the human identity testing community has settled on a set of core short tandem repeat (STR) loci that are widely used for DNA typing applications. A variety of commercial kits enable robust amplification of these core STR loci. A brief history is presented regarding the selection of core autosomal and Y-chromosomal STR markers. The physical location of each STR locus in the human genome is delineated and allele ranges and variants observed in human populations are summarized as are mutation rates observed from parentage testing. Internet resources for additional information on core STR loci are reviewed. Additional topics are also discussed, including potential linkage of STR loci to genetic disease-causing genes, probabilistic predictions of sample ethnicity, and desirable characteristics for additional STR loci that may be added in the future to the current core loci. These core STR loci, which form the basis for DNA databases worldwide, will continue to play an important role in forensic science for many years to come.

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    • "DNA extracted from these hard tissues has been used extensively in missing persons investigations, disaster victim identification (DVI) projects, and human rights investigations. Its utility is particularly valuable when human remains are fragmentary, burned, commingled or otherwise compromised [1] [2] [17]. In such cases, DNA analysis may provide the only means to establish a positive identification. "
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    ABSTRACT: Identifying human remains often begins with cleaning and imaging the material. Hot water maceration is used to remove adherent soft tissue from bone and radiographs are taken to better visualize osseous details. Heat and radiation are known to have harmful effects on DNA, but their ability to degrade DNA when used for cleaning and imaging has not been well studied. To better understand their individual and combined effects on the recoverability of DNA from bone, skeletal samples were subjected to (1) hot water maceration (62°C for 45min); (2) CT scanning (0.6mm slices, 120kV, 10.4s); (3) X-ray (50kVp, 150mA, 0.03s, 40in); and (4) all 3 treatments combined. Forty-eight DNA samples were extracted, quantified and amplified with the AmpFLSTR(®) Identifiler(®) system. Nearly all of the processed samples had reduced RFU values relative to the unprocessed samples, indicating some amount of genetic loss. This loss did not always translate into loss of profile completeness, since only a few samples had a reduction in the number of loci detected after processing. DNA yields were not significantly reduced by any one of the processing methods, however the results indicate that the damaging effects are additive. It is possible that processing may reduce a bone's DNA reservoir and as more procedures are preformed, the pool of available genetic information might be diminished. Many intrinsic and extrinsic factors can affect the recoverability of DNA from bone. Collecting a DNA sample prior to processing avoids the negative effects from hot water maceration and radiological imaging.
    Forensic science international 09/2015; 257:189-195. DOI:10.1016/j.forsciint.2015.08.019 · 2.14 Impact Factor
    • ". Many forensic loci were chosen at a time when knowledge of the human genome in general, and STR loci in particular, was limited [11]. "

    Forensic Science International Genetics Supplement Series 09/2015; DOI:10.1016/j.fsigss.2015.09.181
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    • "Traditionally, these markers have been used in forensic genetics (Butler, 2006), which has resulted in the characterization of a large number of population groups worldwide. This allows us to compare our results with those obtained in other studies and integrate the information in a geographical context, and therefore to study population characteristics such as admixture, genetic structure, and migration (Wang et al., 2008). "
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    ABSTRACT: The present study aims to outline the genetic makeup of the current population of the town of Yanga (Veracruz State, Mexico), the first Latin American settlement founded by African slaves in Mexico. For this purpose, we carried out the genetic characterization of 60 individuals from Yanga, analysing 15 autosomal short tandem repeats (STRs) and interpreting the results in the context of the admixed population known as Mexican mestizos. The genetic contribution from the three most important human groups in the current admixed Yanga population was calculated using Structure software. We detected a high percentage of Amerindian (48%) and European inheritance (44.7%), and a much less important African contribution (7.3%). These results were then compared with 10 other Mexican mestizo populations. The results fit the tri-hybrid model for admixture characterized by a high genetic contribution from Europeans and Africans in the north—though the African influence is lower—and a decreasing contribution from these two populations to the south and southeast. Conversely, the Amerindian component presents maximum values in the south and minimum values in the north. The Amerindian and European genetic traces are related to their ancestral settlements, but the African contribution can be explained by other parameters. To understand the current African genetic traces, we have to assume that there was a redistribution of these population groups and an important admixture phenomenon which led to the dilution of the African ancestral genetic pool. Furthermore, admixture was favoured by conditions that allowed individuals who intermarried to ascend in social status. These reasons would explain why despite the fact that Yanga was founded by black slaves, high levels of African ancestry are not found in the current population.
    Anthropological Science 08/2015; 123(2). DOI:10.1537/ase.150422 · 0.61 Impact Factor
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