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Forensic DNA typing protocols

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... Not only samples from a crime scene, but also reference samples need to be taken in a proper way that is rapid and painless and least invasive for the person (suspect or victim). Typically, swabs are used for this purpose [4]. For the recovery of a sample from the crime scene, several different types of swabs can be used, with different structures, as shown in Figure 2. In contrast to what is common practice in forensics, most existing micro-devices use cell lysate or pure DNA in a buffer as input material, because microfluidic devices require samples in a liquid solution. ...
... Commonly present inhibitors in forensic samples are ethanol and sodium dodecyl sulfate (SDS) originating from the isolation technique, as well as hemoglobin, calcium-ions, melanin and urea, possibly present in biological samples. These inhibitors can result in a delay in the threshold cycle, reduction in the sensitivity of the detection (especially for larger amplicons) or even failure of PCR amplification [4]. ...
... Three main principles result in the occurrence of fluorescence: an (intercalating) dye to stain the DNA, fluorescently-labeled deoxynucleotides (dNTPs) and the incorporation of a fluorescent dye into the amplicon with a labeled oligonucleotide primer. An advantage of dye-labeled primers is that they can be used in multiplex assays, such as STR analysis [4]. Intercalating dyes, such as SYBR Green and EvaGreen, are sequence independent. ...
Article
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Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.
... Examples of these steps are northern blotting and microarray assays [72] . The addition of a µSPE chip is valuable for PCR chips since PCR needs DNA samples that are free of contaminants and inhibitors [73,74] . Crime scene samples are often collected from tissue, blood, food, or other environments. ...
... Examples of inhibitors with their corresponding forensic source are haemoglobin (blood), urea (urine), bile acids (faeces), humic acids (soil), polysaccharides (faeces), melanin (tissue and hair), and indigo dyes (denim clothes) [48,76,77] . These inhibitors can result in delayed threshold cycles, reduced density of detection for larger amplicons, or even complete PCR amplification failure [74] . The well-established DNA isolation and extraction procedures, for example those involving the phenol/chloroform/isoamyl alcohol (PCI) method [74] , the Chelex method [74] , and density gradient centrifugation [78] , have proven to be efficient in the removal of interfering species, but the main problem is that they require relatively large reagent volumes, making the concentration of DNA dilute. ...
... These inhibitors can result in delayed threshold cycles, reduced density of detection for larger amplicons, or even complete PCR amplification failure [74] . The well-established DNA isolation and extraction procedures, for example those involving the phenol/chloroform/isoamyl alcohol (PCI) method [74] , the Chelex method [74] , and density gradient centrifugation [78] , have proven to be efficient in the removal of interfering species, but the main problem is that they require relatively large reagent volumes, making the concentration of DNA dilute. These large volumes are not easily transferrable to microfluidic platforms [59] . ...
Thesis
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This Master's thesis describes the research that is done for the development of a plug-based microfluidic DNA extraction chip. The investigated method relies on a micro solid phase extraction method that is based on the electrostatic interaction between protonated amino groups and the negatively charged DNA.
... More than one-third of human genome consists of repetitive sequence region (Repeat Area) 1 Repeat (STR) with 2-6 bp repeat units [1,2]. Based on its short allele range 1,3 , STR can be used for the paternity testing 1,4 , it is often used also for the study of genetics disease, molecular archeology, as well as in forensic crime cases 1,4,5 . ...
... More than one-third of human genome consists of repetitive sequence region (Repeat Area) 1 Repeat (STR) with 2-6 bp repeat units [1,2]. Based on its short allele range 1,3 , STR can be used for the paternity testing 1,4 , it is often used also for the study of genetics disease, molecular archeology, as well as in forensic crime cases 1,4,5 . ...
... More than one-third of human genome consists of repetitive sequence region (Repeat Area) 1 Repeat (STR) with 2-6 bp repeat units [1,2]. Based on its short allele range 1,3 , STR can be used for the paternity testing 1,4 , it is often used also for the study of genetics disease, molecular archeology, as well as in forensic crime cases 1,4,5 . ...
Article
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Purpose: The purpose of this study is to identify genetic variability the family of Javanese married with Arab and their allele patterns for paternity testing. Material and Methods: We used human white blood cell from three generations of three families, consists of: 1 grandmother-mother, father-daughter 2 , grandfather-mother, father-daughter 3 , grandfather, grandmother – mother, father-son. DNA blood samples were isolated by salting out standard procedure, and amplified by PCR with applying 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and amelogenin primer. The Fingerprint profile was visualized by 8% polyacrylamide gel and took the picture by ChemiDoc gel Imaging and measure the intensity band pattern by Quantity One software Results: Our result showed that the genetic variability and heterozygote allele increasing by using the 13 CODIS markers from the first generation to the next generation with paternity testing from each family were matched. Conclusion: We can conclude that in a Javanese-Arab family ethnic seems stimulate the increasing genetic variation and allele heterozygote.
... El auge de este tipo de pruebas fue en aumento, eran aceptadas por los tribunales, pero pronto se empezaron a encontrar problemas. Los casos Castro (1987) y Simpson (1994) fueron dos referentes que pusieron de manifiesto algunos de los problemas de las pruebas de ADN en los tribunales (Butler, 2005;Michaelis et al., 2008;Kaye, 2010). Por ejemplo se detectó que la recogida y transporte de las muestras muchas veces no era cuidadosa, los análisis se realizaban en laboratorios sin suficientes garantías de control e incluso a veces los resultados que se obtenían con los marcadores genéticos primitivos no eran fáciles de interpretar. ...
... Por estas razones se empezaron a utilizar otros marcadores genéticos que mejoraban las características analíticas, los denominados STRs (short tandem repeats), es decir, repeticiones cortas en tándem, que también reciben el nombre de microsatélites (Mestres y Vives-Rego, 2009b). Aunque algunos de estos marcadores STRs fueron introducidos por el Forensic Science Service del Reino Unido y existía ya un kit comercial de laboratorio para su análisis en 1991 (Butler, 2005), el FBI definió en 1997 los 13 STRs que formarían el núcleo de marcadores para sus usos forenses (el denominado sistema CODIS, Combined DNA Index System). Además del laboratorio del propio FBI participaron prestigiosos científicos y el National DNA Advisory Board junto a la National Academy of Sciences fijaron una serie de características de tipo técnico y ético para la selección de estos marcadores, como por ejemplo que a partir de ellos no pudiese deducirse el origen étnico o características anatómico-fisiológicas de los individuos (Butler, 2005;Krimsky y Simoncelli, 2011;Mestres y Vives-Rego, 2012a). ...
... Aunque algunos de estos marcadores STRs fueron introducidos por el Forensic Science Service del Reino Unido y existía ya un kit comercial de laboratorio para su análisis en 1991 (Butler, 2005), el FBI definió en 1997 los 13 STRs que formarían el núcleo de marcadores para sus usos forenses (el denominado sistema CODIS, Combined DNA Index System). Además del laboratorio del propio FBI participaron prestigiosos científicos y el National DNA Advisory Board junto a la National Academy of Sciences fijaron una serie de características de tipo técnico y ético para la selección de estos marcadores, como por ejemplo que a partir de ellos no pudiese deducirse el origen étnico o características anatómico-fisiológicas de los individuos (Butler, 2005;Krimsky y Simoncelli, 2011;Mestres y Vives-Rego, 2012a). En el año 2000 el FBI abandonó finalmente los marcadores genéticos más antiguos (RFLP) y pasó a centrarse en la utilización de los STRs del sistema CODIS. ...
Article
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Justice and science are very different human activities. However, scientific knowledge has generated many disciplines that are useful in forensics and could be key elements to solve judicial cases. The first problem is to know whether a specialty is actually science and then, if it is enough reliable for being used in courtrooms. In this sense, DNA evidence is a good example of how its presence in the courts has been improved. Furthermore, laboratories where forensic analyses are carried out are properly accredited. Practitioners that work in them are professionals with an appropriate training that also has to be a continuous process. Finally, experts that present their testimony in the court have to be clear and understandable in their explanations. If they have to present a novel scientific approach as evidence, this must observe a series of requirements in order to be accepted by the court.
... When compared to techniques such as fingerprints and DNA, fibers do not have the same evidential value. Nuclear DNA profiles have been demonstrated to be unique to a particular person (excluding identical twins), meaning DNA evidence can be individualized (Butler, 2005). However, enough distinguishing characteristics can be observed so that a forensic examiner can testify that two fibers (a known fiber and a questioned fiber) may have originated from the same source. ...
... Even if DNA is present, fiber evidence can corroborate the DNA evidence and increase its evidentiary value, especially if the DNA evidence is not individualizing. Partial profiles and mitochondrial DNA are prime examples (Butler, 2005). ...
... Three primer sets for the amelogenin (AMEL) locus were designed including a conventional primer set (C-primer), a C-primer with additions of a 7-base GTGTCTT 5 -tail (TC-primer), and a TC-primer with an abasic site inserted between the conventional primer and the 7-base GTGTCTT 5 -tail (TaC-primer, Table 1). The 5 -tail is a non-template addition which has been proved to promote full adenylation of PCR products amplified with Taq [23]. All the forward primers were fluorescently labeled using 6-FAM dye. ...
Article
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Obtaining a full short tandem repeat (STR) profile from a low template DNA (LT-DNA) still presents a challenge for conventional methods due to significant stochastic effects and polymerase slippage. A novel amplification method with a lower cost and higher accuracy is required to improve the DNA amount. Previous studies suggested that DNA polymerases without bypass activity could not perform processive DNA synthesis beyond abasic sites in vitro and our results showed a lack of bypass activity for Phusion, Pfu and KAPA DNA polymerases in this study. Based on this feature, we developed a novel linear amplification method, termed Linear Aamplification for double-stranded DNA using primers with abasic sites near 3′ end (abLAFD), to limit the replication error. The amplification efficiency was evaluated by qPCR analysis with a result of approximately a 130-fold increase in target DNA. In a LT-DNA analysis, the abLAFD method can be employed as a pre-PCR. Similar to nested PCRs, primer sets used for the abLAFD method were designed as external primers suitable for commercial multiplex STR amplification assays. The practical performance of the abLAFD method was evaluated by coupling it to a routine PP21 STR analysis using 50 pg and 25 pg DNA. Compared to reference profiles, all abLAFD profiles showed significantly recovered alleles, increased average peak height and heterozygote balance with a comparable stutter ratio. Altogether, our results support the theory that the abLAFD method is a promising strategy coupled to STR typing for forensic LT-DNA analysis.
... Due to these limitations, scientists intend to develop more cutting-edge analytical methods coupled with chemometric techniques which are capable of resolving the aforesaid restrictions. With respect to this, conventional methods are now swapped for advanced technological methods such as DNA fingerprinting for biological exhibits 9 and more innovative and modern analytical instrument-based methods for chemical and physical evidence. ...
Chapter
Vibrational methods include Raman, terahertz, NIR, and FTIR spectroscopy, having some potential applications in the forensic science field. However, the use of FTIR and NIR spectroscopy is thriving around the globe in the forensic context. This is due to the non-destructive, inexpensive method and the accurate prediction potential of the technique. This chapter summarizes the application of FTIR and NIR spectroscopy in the chemical sensing of the relevant forensic exhibits. A detailed idea on infrared spectroscopy is mandatory to understand its working principals and parameters which ultimately assist the forensic professionals and other researchers working on it. However, the history of IR radiations, their mathematical theories, different modes of vibrations and the major IR instrumentation have been thoroughly discussed. Some examples are also summarized from the published literature which will aid in facilitating the practical applications of infrared spectroscopy. A quick statistic about the utilizations of spectroscopy in forensics has also been reviewed. The validation of results can be confirmed by applying chemometrics methods on spectral data sets. To sum up, the infrared spectroscopy is a robust and reliable technique for the discrimination and classification of relevant forensic evidence to their respective groups. The statistical methods contribute more objectivity to the outcomes.
... These alleles can be observed as a two-banded pattern, as seen in a heterozygote, or a single banded pattern as seen in a homozygote. In very rare instances, a three banded pattern may be observed at a single locus in a multiplex STR profile, which is not a result of a mixture [3]. ...
... It may be accomplished using primers directed at repetitive sequences that are interspersed throughout the genome, as in the case of the Repetitive Extragenic Palindromic (REP) sequence (1), the Enterobacterial Repetitive Intergenic Consensus (ERIC) sequence (1,2), or the BOX elements (3); it may also employ primers that anneal randomly in several locations along the genome, such as Random Amplified Polymorphic DNA (RAPD) (4)(5)(6)(7)(8) and Arbitrarily Primed PCR (AP-PCR) (9,10). When it comes to identifying human individuals through molecular means, primers that amplify hypervariable genomic regions, such as variable number tandem repeats (VNTR) and short tandem repeats (STR), are used (11). However, realistic molecular identification of human samples is impossible or tricky to perform in most undergraduate practical classes due to the fact that interindividual differences are very small and, as such, need capillary electrophoresis or at least polyacrylamide vertical gels to be revealed (12). ...
Article
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DNA fingerprinting is a major tool in identifying individuals and in evidence matching. However, this technique can be difficult to reproduce in practical classes. Here, we report on distinct PCR profiles obtained when amplifying saliva DNA of a score of distinct individuals with Random Amplified Polymorphic DNA (RAPD)-PCR primer BOXA1R. The RAPD-PCR method is simple and efficient for discrimination between bacterial strains and is used in this instance to obtain personalized fingerprints of each individual’s oral microbiota. We present real results with undergraduate students confirming that this procedure is easily feasible in practical classes. Based on the results presented, we suggest a laboratory activity for undergraduate Molecular Biology or Microbiology students.
... Three different multiplex assays were constructed following guidance of Butler [42], designated Light, Medium and Dark, and initially incorporating 27 loci. Primers designated "MS", developed by Jordan et al. [30], were included for cross-compatibility with previous studies. ...
Article
Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons.
... Thus, we consider that the artificial peaks were not dependent on the remaining template DNA because they were also detected in the no amplification controls with similar peak heights and data points. The artificial peaks had the following features: they were broad, similar to 'dye blobs' 14,15 and observed at almost coincident data points. Moreover, similar artefacts were also observed in autoclaved samples derived from control DNA 007 and ultrapure water using the AmpF'STR V R Yfiler V R PCR amplification kit. ...
Article
DNA contamination can result in false interpretation of short tandem repeat (STR) DNA typing. Proper decontamination is particularly required in forensic DNA laboratories where probative value of the evidence may be affected. The aim of this study was to establish an effective DNA decontamination procedure for amplified STR products focusing on laboratory-related contamination. We verified the effectiveness of thermally and temporally extended autoclaving and ultraviolet irradiation for the elimination of contaminating amplified STR products. STR amplification products were prepared using a control genomic DNA template and generated using the AmpFℓSTR® Identifiler® Plus and Yfiler® polymerase chain reaction amplification kits. In this study, the contaminants were dried before decontamination treatment, which resembles actual contamination situations. One microlitre of amplified STR products was eliminated by a combination of autoclaving (128°C, 420 min) and UV irradiation (60 J/cm²). Our results reveal that the combination treatment represents an effective DNA decontamination procedure and a practicable method in standard level laboratories. Finally, we propose a comprehensive approach for forensic DNA laboratories to implement to minimise contamination issues and guarantee provision of authentic results.
... Meanwhile, according to Mc Cord (2003) as for the success of the locus DNA sequence from small to large adal TPOX, THO1 and VWA. Besides, the use loci CSF1PO, THO1 and TPOX given that these loci is one of the first locus developed by the Forensic Science Service, as well as the loci that have a probability of a match with a ratio of 1 in 50 million (Butler 2003). ...
Article
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Accurate determination of personal identity is crucial for an investigation since any inaccuracy may lead to fatal consequences in the judicial process. Identification through DNA analysis involves somatic chromosomes and mtDNA. Each part of the human body can be taken as a specimen since every nucleated cell in the body of an individual has identical DNA sequence. To date, samples for identification through DNA analysis are obtained from blood stains, semen stains, bones, vaginal swab, buccal swab etc. In certain cases, urine stains on the clothing have frequently been overlooked. So far, personal identification through DNA analysis by the use of urine stains has not been commonly carried out. The present study detected bands in the loci CSF1PO, THO1, TPOX and 106bp-112bp amelogenin in all samples visualized from the results of Polymerase Chain Reaction (PCR) with Polyacrylamid Agarose Gel Electrophoreses-silver staining for exposure durations of 1, 7 and 14 days. However, for exposure duration of 20 days (the maximum in the study), bands were only detected in the loci THO1 and TPOX in all samples (100%), whereas the loci CSF1PO and 50% amelogenin exhibited obvious bands. This indicated that DNA analysis of urine stains through detection of the locus STR CSF1PO, THO1, TPOX exhibited different detection responses for different exposure durations assigned to the samples of urine stain. Successful detection of these loci was supported by the differences in amplicon product and GC content at each locus. Of the loci studied, the ratio of GC content of the primers, sorted from the lowest, were as follows: locus CSF1PO of 42.6 1%, TPOX of 56.25%, and THO1 of 63.83%. In conclusion, the loci THO1 and TPOX had the same probability of success in the STR examination compared with the locus CSF1PO.
... Genetic variation within a population can also be assessed. The simplest method of assessing genetic variability in a population is through the use of short tandem repeat (STR) typing and it is used for human as well as animal and plant populations (Butler, 2005). In STR typing, individual lineages can differ in the number of tandem repeats of a particular DNA sequence. ...
Article
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Chickens represent the most widely consumed meat in the world. Modern breeds are generally from a narrow genetic base. The genetic diversity of chickens consumed in urban areas of Malaysia has not been previously investigated. The aim of this study was to investigate the genetic diversity of chickens available for purchase in urban areas of Selangor adjacent to Kuala Lumpur. DNA of chickens were isolated from meats and livers. Seven microsatellite markers were selected and fluorescently labeled to allow the identification of each individual chicken from the seventeen populations based on the amplification of target DNA. A total of 52 different alleles was observed for the seven markers, giving a mean of 7.1 alleles per marker. The cumulative power of discrimination (CPd) of the seven microsatellites used was 0.999 based upon our population study. The data showed that most of the chickens consumed in the urban areas came from a very narrow genetic base. The supply is thus vulnerable to disruption caused by outbreaks of disease. Furthermore the data obtained illustrates the potential of this system to be used in chicken lineage identification. This would help to resolve uncertainties over the origin of the chickens. This system could be used for product assurance as well as safety.
... These data clearly indicate that the method used to concentrate low yield DNA samples prior to STR amplification can significantly affect the quality of the resulting STR profile. Work described herein suggests that the combined use of the QIAampâ DNA Investigator Kit followed by concentration using the Centri-Sep TM gel columns for processing of archived latent fingerprints will more likely lead to an STR profile sufficient for a human identification (≥8 loci) or for exclusionary purposes (45). ...
Article
DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases.
... This test is no longer used by the forensic community, because of the implication of radioactive probes, the need of large amounts of DNA and the limited accuracy for the analysis of degraded samples. The second generation of DNA fingerprinting was based on PCR and mainly involved DNA detection by gel silver-staining, slot blot, and reverse dot blots [4,5]. However, it was not suitable in the analysis of longer strands of DNA. ...
Article
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The use of DNA evidence in criminal investigations has gained worldwide acceptance in recent decades. During the last years in Mexico, reports of missing persons have increased dramatically due to the abrupt rise of violent crimes. The situation goes far beyond the current technological response capacity in the country and it exposed a second challenge in the form of increased social pressure on the government coming from the relatives of missing people: they seek to find any remaining of their beloved ones. Therefore, we implemented the FICHA project. Methods: A total of 190 blood samples from relatives of missing people in northeastern Mexico were genotyped and analyzed using a multiplex STR system. Results (statisticals) and conclusions: some of the profiles obtained served as an aid in the resolution of cold cases.
... The non-recombining portion of Y chromosome (NRY) is strictly inherited paternally and is therefore the best material to trace the paternal lineages of populations (Butler, 2011;Jobling and Tyler-Smith, 1995). The NRY has extensive use in the studies of human origins, population history, sex-biased admixture, male-female differences in migration, as well as in medical and clinical studies (Butler, 2005;Tyler-Smith, 2000, 2003). The two most important classes of Y-chromosomal markers are the short tandem repeats (Y-STRs) and single nucleotide polymorphisms (Y-SNPs) (Butler, 2011;de Knijff et al., 1997). ...
Article
Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assigned by the use of Y-chromosomal single nucleotide polymorphism (Y-SNP) markers. An increasingly popular and a less labor-intensive alternative approach has been Y-chromosomal haplogroup assignment based on already available Y-STR data using a variety of different algorithms. In the present study, such in silico haplogroup assignments were made based on 23-loci Y-STR data for 100 unrelated male individuals from the Tuzla Canton, Bosnia and Herzegovina (B&H) using the following four different algorithms: Whit Athey's Haplogroup Predictor, Jim Cullen's World Haplogroup & Haplogroup-I Subclade Predictor, Vadim Urasin's YPredictor and the NevGen Y-DNA Haplogroup Predictor. Prior in-house assessment of these four different algorithms using a previously published dataset (n = 132) from B&H with both Y-STR (12-loci) and Y-SNP data suggested haplogroup misassignment rates between 0.76% and 3.02%. Subsequent analyses with the Tuzla Canton population sample revealed only a few differences in the individual haplogroup assignments when using different algorithms. Nevertheless, the resultant Y-chromosomal haplogroup distribution by each method was very similar, where the most prevalent haplogroups observed were I, R and E with their sublineages I2a, R1a and E1b1b, respectively, which is also in accordance with the previously published Y-SNP data for the B&H population. In conclusion, results presented herein not only constitute a concordance study on the four most popular haplogroup assignment algorithms, but they also give a deeper insight into the inter-population differentiation in B&H on the basis of Y haplogroups for the first time.
... 3 Kelebihan metode ini yaitu cepat, tahapan singkat serta mengurangi kemungkinan sample to sample contamination. 3 Larutan Chelex yang digunakan terdiri dari styrene divinylbenzene copolymer yang berisi pasangan ion-ion iminodiacetate yang bertindak sebagai chelating group yang berikatan dengan ion Mg 2+ , bila chelating resin ini terlarut pada hasil ekstraksi DNA sehingga mengikat komponen Mg 2+ sebagai kofaktor enzim DNA polymerase, akibatnya tanpa ion ini enzim polymerase pada PCR tidak dapat bekerja. 4 Pemilihan subyek penelitian dilakukan secara acak tanpa kriteria tertentu serta telah menandatangani inform concont. Sampel bite marks didapatkan dengan mencetak gigi dengan alginat kemudian diirigasi dengan aquades steril (nuclease free water) menggunakan syringe 3 cc lalu dikumpulkan dalam tabung steril sampai 15 cc. ...
Article
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Background: In the case of crime often encountered evidence in bite marks form that was found on the victim’s body. Generally, bitemarks identification use standard techniques that compare the interpretation picture with the tooth model of suspected person. However, sometimes the techniques do not obtain accurate results. Therefore another technique is needed to support the identification process,such as DNA analysis that use the remaining epithelium attached in saliva to identify the DNA of the suspected person. In this processes a limited DNA material could be met, not only less in quantity but also less in quality. Chelex known as one of an effective DNA extraction method in DNA forensic case is needed to overcome this problem. Purpose: The study was aimed to examine the use of Chelex as DNA extraction method on a bitemarks sample models. Methods: The blood and bitemarks of 5 persons with were taken. The DNA of each subject was exctracted with Chelex and quantified the quantity with UV Spechtrophotometer. The DNA results was amplified by PCR at locus vWA and TH01 then vizualised by electrophoresis. Results: The electrophoresis’s results showed band at locus vWA and TH01 for blood sample and bite marks with no significant differences. Conclusion: The study showed that Chelex method could be use to extract DNA from bitemarks.Latar belakang: Dalam kasus kejahatan sering dijumpai bukti dalam bentuk bekas gigitan (bitemarks) yang ditemukan pada tubuh korban. Umumnya, untuk mengidentifikasi bite marks menggunakan teknik standar yaitu membandingkan foto interpretasi dengan model gigi dari orang yang dicurigai. Namun demikian teknik ini terkadang tidak mendapatkan hasil yang akurat, sehingga diperlukan teknik lain untuk menunjang keberhasilan proses identifikasi pelaku, yakni melalui analisis DNA bitemarks, yang diperoleh dari saliva yang mengandung sisa epitel tersangka pelaku. Sampel DNA yang berasal dari bitemarks umumnya terbatas, tidak hanya terbatas dalam kuantitas tetapi juga terbatas dalam kualitas. Hal ini seringkali menimbulkan kesulitan tersendiri dalam proses analisisnya. Chelex yang dikenal sebagai salah satu metode ekstraksi yang efektif di bidang forensik, sangat diperlukan untuk mengatasi kendala tersebut . Tujuan: Penelitian ini bertujuan untuk meneliti penggunaan metode ekstraksi DNA metode Chelex pada sampel bite marks. Metode: Darah dan cetakan gigi dari 5 subjek diambil, dan DNA di ekstraks dengan Chelex dan kemudian diuji kuantitas dengan UV Spechtrophotometer. Setelah itu hasil diamplifikasi dengan PCR pada lokus vWA dan TH01 kemudian divisualisasi dengan elektroforesis. Hasil: Hasil elektroforesis menunjukkan adanya band pada lokus vWA dan TH01 untuk sampel darah dan cetakan gigi tanpa perbedaan yang signifikan secara statistika. Simpulan: Penelitian ini menunjukkan bahwa metode Chelex dapat digunakan untuk mengekstraksi DNA dari bite marks.
... The percentage of observed stutter at STR locus was examined by calculating the ratio of the stutter peak height (in RFU) compared to the corresponding allele peak height [19]. On the other hand, the proportion of the less intense allele relative to the more intense allele at a given heterozygous genotype, i.e. peak height ratio (PHR), was calculated by dividing the peak height of the allele with the lower RFU value by the peak height of the allele with the higher value, and then multiplying this value by 100 to express the PHR as a percentage [20]. ...
Article
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Currently, two of the most widely used X-chromosome STR (X-STR) multiplexes are composed by 10 (GHEP-ISFG decaplex) and 12 markers (Investigator Argus X-12 Kit). The number of markers included is a drawback for complex relative testing cases, likewise the large size of some amplicons difficult their application to degraded samples. Here, we present a new multiplex of 17 X-STRs with the aim of increasing both the resolution power and forensic applicability. This newly proposed set includes the X-STRs of the GHEP-ISFG decaplex, three X-STRs from the Investigator Argus X-12 Kit, two of them also included in the decaplex, and six additional more. In order to ensure the allele designation, an allelic ladder was developed. The validation of the present multiplex was carried out according to the revised guidelines by the SWGDAM (Scientific Working Group on DNA Analysis Methods). A total of 488 unrelated individuals from four different continents were analyzed. The forensic efficiency evaluation showed high values of combined power of discrimination in males (≥0.999999996) and females (≥0.999999999999995) as well as combined paternity exclusion probabilities in trios (≥0.99999998) and duos (≥0.999996). The results presented herein have demonstrated that the new 17 X-STR set constitutes a high-resolution alternative to the current X-STR multiplexes. This article is protected by copyright. All rights reserved.
... One copy of the HER2 cDNA equals 6.96 × 10 −18 g of HER2 plasmid. For genomic DNA, the assumption used was that one genome copy is approximately 3 × 10 9 bp, with a resultant molecular mass of approximately 3 pg, and therefore, 1 ng of human genomic DNA would have approximately 333 copies of a single copy gene [27]. ...
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NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DCK, EIF5B, RPS27A, and PMM1. The ratios were measured using quantitative polymerase chain reaction and digital PCR, methods that gave similar ratios. The five components of SRM 2373 have certified HER2 amplification ratios that range from 1.3 to 17.7. The stability and homogeneity of the reference materials were shown by repeated measurements over a period of several years. SRM 2373 is a well characterized genomic DNA reference material that can be used to improve the confidence of the measurements of HER2 gene copy number.
... When a marker showed disbalanced peaks, we only considered as valid the highest peak unless the lowest one reached at least the 50% of the height of the highest one. Also we have taken into account the probability of allelic [3]. ...
... The human mtDNA is a 16569 np (nucleotide pair) closed, circular molecule located within the cytoplasmic mitochondria. mtDNA has a very high mutation rate, approximately 10-fold higher compared to nuclear DNA, probably as a result of poor repair mechanisms as well as a decreased proofreading efficiency of the mtDNA polymerase [4,5]. ...
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Today, mtDNA typing is utilized primarily in cases in which the nuclear DNA is too degraded or cannot be recovered in sufficient quantities to be typed. Laboratory of Genetic of Royal Gendarmerie in Morocco is actively involved in using mtDNA for forensic identifications of human skeletal remains. Reproducible results were obtained for bones and teeth up to 52 years old. The bone and tooth samples were pulverized to fine powder, decalcified and DNA was extracted. 341-bp fragment from HVI (hypervariable region I) and 267-bp fragment from HVII (hypervariable region II) of the mtDNA control region were amplified. After sequencing of the PCR products, mitotypes were compared to the rCRS (revised Cambridge Reference Sequence) and a phylogenetic tree was built.
... When a marker showed disbalanced peaks, we only considered as valid the highest peak unless the lowest one reached at least the 50% of the height of the highest one. Also we have taken into account the probability of allelic [3]. ...
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Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28% and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2 – 9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (R ST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
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The study of ancient human migration and peopling in Indonesia still raises debate until now, both from the perspective of biological anthropology, human genetics or archaeological. The debate was always open space again to do some research about that. We concentrated with samples of ancient Bali, the findings of human remains from Gilimanuk (Melaya, Jembrana) and Semawang (Sanur, Denpasar). Relatively, Bali is an island located in the centre of Indonesian Archipelago, which may represent a major pathway of human migration and distribution according to the outer arc islands. The research aimed to describe human genetic variation of the two archeological sites of ancient Bali. Based locus short tandem repeats (STR) combined DNA index system (CODIS), which CSF1PO, TH01 and TP0X, the research took a sample of six individual human ancient Bali, which includes each of the three individual from Semawang and Gilimanuk site. The process of genetic research has been done at the Institute of Tropical Disease Laboratory of Human Genetics, Airlangga University. Semawang and Gilimanuk derived from different populations based on the analysis of its CTT loci visualization. The results with reference to all possible aspects of archaeology and biological anthropology further enrich the wealth of knowledge about human migration events in Indonesia around the Neolithic period, the early times of increasingly massive mongoloid migrations to the Archipelago region. The results also further strengthen the results of previous genetic studies of Bali population. Balinese has undergone a genetic mixture of various immigrant populations since the Neolithic period.AbstrakPenelitian migrasi dan penghunian manusia kuno di Indonesia masih memunculkan perdebatan sampai kini, baik dari perspektif antropologi biologis, genetika manusia atau arkeologis. Perdebatan itu selalu membuka ruang lagi untuk melakukan penelitian perihal itu. Kali ini kami berkonsentrasi dengan sampel Bali Kuno, yakni temuan sisa-sisa manusia dari Gilimanuk (Melaya, Jembrana) dan Semawang (Sanur, Denpasar). Bali merupakan pulau yang relatif terletak di tengah gugusan kepulauan Indonesia, di mana dapat mewakili jalur besar migrasi dan persebaran manusia seturut rute pulau-pulau busur luarnya. Penelitian ini bertujuan untuk mendeskripsikan variasi genetik manusia kuno dari dua situs arkeologis Bali itu. Berdasarkan lokus short tandem repeats (STR) combined DNA index system (CODIS), yakni CSF1PO, TH01 dan TP0X, penelitian ini mengambil sampel enam individu manusia Bali Kuno, yang meliputi masing-masing tiga individu Semawang dan Gilimanuk. Proses penelitian genetik itu telah dikerjakan di Laboratory of Human Genetics, Institute of Tropical Disease, Universitas Airlangga. Sampel Semawang dan Gilimanuk berasal dari populasi yang berbeda berdasarkan analisis visualisasi lokus CTT-nya. Hasil penelitian ini dengan merujuk semua kemungkinan aspek arkeologis dan antropologi biologisnya makin memperkaya khazanah pengetahuan tentang peristiwa migrasi manusia di Indonesia sekitar masa Neolitik, yang menjadi masa awal makin masifnya migrasi Mongoloid ke kawasan Nusantara. Hasil penelitian ini juga makin menguatkan hasil-hasil penelitian genetika populasi Bali sebelumnya bahwa populasi Bali dari sejak Neolitik sampai sekitar masa yang lebih resen diturunkan oleh banyak leluhur atau banyak sumber gen. Penduduk Bali telah mengalami percampuran genetik dari berbagai populasi pendatang sejak Neolitik atau awal Tarikh Masehi.
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From a technical perspective, specimen identity determination in surgical pathology over the last several decades has primarily focused on analysis of repetitive DNA sequences, specifically microsatellite repeats. However, a number of techniques have recently been developed that have similar, if not greater, utility in surgical pathology, most notably analysis of single nucleotide polymorphism (SNPs) and gene panels by next generation sequencing (NGS). For cases with an extremely limited sample or a degraded sample, sequence analysis of mitochondrial DNA continues to be the method of choice. From a diagnostic perspective, interest in identity determination in surgical pathology is usually centered on resolving issues of specimen provenance due to specimen labeling/accessioning deficiencies and possible contamination, but is also frequently performed in cases for which the patient's clinical course following definitive therapy is remarkably atypical, in cases of an unexpected diagnosis, and by patient request for "peace of mind". However, the methods used for identity determination have a much broader range of applications in surgical pathology beyond tissue provenance analysis. The methods can be used to provide ancillary information for cases in which the histomorphology is not definitively diagnostic, as for example for tumors that have a virtually identical microscopic appearance but for which the differential diagnosis includes synchronous/metachronous tumors versus a metastasis, and for the diagnosis of hydropic early gestations versus hydatidiform molar pregnancies. The methods also have utility in several other clinical settings, for example to rule out a donor-transmitted malignancy in a transplant recipient, to monitor bone marrow transplant engraftment, and to evaluate natural chimerism.
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As criminal cases have become more complicated, Japan's law enforcement officials are promoting the use of more sophisticated technologies, such as DNA analysis, in the course of criminal investigations in order to verify facts with objective evidence. The primary DNA analysis method employed by law enforcement officials is short tandem repeat (STR) analysis, a method for identifying individuals utilizing individual differences in the number of repeat units of characteristic DNA sequences. Presently, STR analysis can discriminate between individuals with the probability of one in approximately 4.7 trillion, even when the DNA profile is the most common type among the Japanese population. In every prefectural police department, members of criminal investigation laboratories, who were trained and certified by the Training Center of Forensic Science at the National Research Institute of Police Science, perform STR analysis. Forensic DNA analysis plays an important role not only in criminal investigations but also following large-scale disasters, to aid in individual identification. The accuracy of DNA typing is increasing with the availability of STR typing kits that can examine more loci than conventional kits. However, it remains difficult for DNA analysis to identify individuals with only small amounts of samples, old samples, or mixed samples. New methods for handling these problematic samples are required. Here, we review current investigative techniques and challenges of DNA analysis, and focus on the latest research for solutions to these challenges.
Article
Short tandem repeat (STR) profiling is frequently carried out on biological stains in forensic casework, and the application of messenger RNA (mRNA) body fluid identification is becoming more prevalent. Increasing constraints on analysis time, resources, an increase in the number of samples for analysis, and a large backlog of cases creates significant demand for quicker methods that direct polymerase chain reaction (PCR) can help overcome. Direct PCR bypasses DNA and/or RNA extraction, and in some cases, quantification by adding the sample or substrate punch to the amplification reaction. This method is currently used in some laboratories on reference samples. Direct PCR is also a component of portable devices, which could improve efficiency even further by producing results at the scene, and enabling triaging of samples for further testing. Portable devices are currently used for STR profiling of reference samples but not for mRNA profiling. Various concerns regarding the reliability of the method and equipment (portable devices) must first be addressed before incorporation into forensic casework. This review discusses the limitations and factors that need to be considered for direct PCR to be used for the analysis of casework samples, including being used for mRNA body fluid identification. This article is categorized under: • Forensic Biology > Forensic DNA Technologies • Forensic Biology > Body Fluid Identification • Forensic Biology > Applications of RNA Abstract With advances in technology, direct PCR of DNA and RNA for forensic purposes is now a reality. While early progress has been made, there are still a number of factors that need to be considered. This review describes where direct PCR technology is at and what still requires attention before this technique can become a standard technique in forensic science.
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Identification include fingerprint, property, medical, dental, serologic and exclusion methods. In the development, identification methods led to molecular forensics, a new field of science evolving since the 1980s, known as DNA fingerprinting. Specimens widely used in DNA assay for identification are blood spots/bloods, semen spots, vaginal swabs, buccal swabs and bones. In addition to these specimens, the last objects often used by the perpetrators/victims can be used, such as hearing aids (headsets/earphones). In its use, earphones are attached to the outer ear skin; thus, the earwax is suspected to adhere to the device. To date, in Indonesia personal identification is performed through swabs of earphones/headsets using the DNA profiling method. In particular, mitochondrial DNA has not been widely used for identification. The present study was of laboratory experimental. Earphones which have been used for 3 days were placed in room temperature for 1, 7, 14 and 20 days. Results showed that the environmental factor of exposure duration had an effect of a significant decrease in the levels of DNA from day 1 to day 20. Only 126-bp mtDNA (HVS II) was detected on the samples of day 1 and continued with sequencing. Mitochondrial DNA has better durability and relatively higher number of copies than those of nuclear DNA. This leads to greater possibility of success in amplification, given the higher number of mitochondrial DNA copies and the fact that mitochondrial DNA is a single locus that allows recombination.
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Short tandem repeat (STR)-based DNA profiling is an exceptionally sensitive analytical technique that is often used to obtain results at the very limits of its sensitivity. The first step in the DNA profiling process, once PCR-amplification products are separated on the basis of their size, is to attempt to establish whether a bump on the graph is really a peak at all, and whether it is in the appropriate place to count as an allele—this is “allelic designation”. Deciding what is and is not a “real” peak, and where it lies on the graph, is often not a trivial exercise. Some peaks are visible but not very large or not of the expected shape. Many laboratories have subjective, “by eye”, methods to establish whether a peak is a true allele or not. These peaks, regardless of the uncertainty associated with their designation, are treated as if they are certainties for the purpose of generating match statistics.
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The European paternal lineage R-DF27 has been proposed as an haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27. Our results reveal frequencies over 35% of DF27 haplogroup in the four North Iberian populations analyzed and high frequencies for its subhaplogroups. Considering the low frequency of DF27 and its sublineages in most populations outside of the Iberian Peninsula, this haplogroup seems to have geographical significance; thus, indicating a possible Iberian patrilineal origin of vestiges bearing this haplogroup. The dataset presented here contributes with new data to better understand the complex genetic variability of the Y chromosome in the Iberian Peninsula, that can be applied in Forensic Genetics.
Conference Paper
Samples collected from 775 unrelated Chinese population in Taiwan were identified to obtain the allele frequencies for 20 DNA short tandem repeat (STR) loci (D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA) included in the Promega PowerPlex® 21 system amplification kit. The values of observed heterozygosity (Ho) ranged from 0.5290 for TPOX to 0.9058 for Penta E, expected heterozygosity (He) ranged from 0.5862 for TPOX to 0.9122 for Penta E, polymorphism information content (PIC) ranged from 0.5267 for TPOX to 0.9058 for Penta E, power of discrimination (PD) ranged from 0.5460 for TPOX to 0.9833 for Penta E, the duos probability of paternity exclusion (PEduos) ranged from 0.1826 for TPOX to 0.7001 for Penta E and the trios probability of paternity exclusion (PEtjios) ranged from 0.3327 for TPOX to 0.8236 for Penta E were calculated. The five new markers (D1S1656, D6S1043, Penta E, Penta D and D12S391) of the Promega PowerPlex® 21 system were different from the AmpFLSTR® IdentifilerTM kit, which were identified to decrease the random match probability and got the result for increasing the discrimination over 106 times than Identifiler system that were very useful for confirming the source of trace evidence identification.
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This article analyzes the relationship between Justice and Science. Both areas are certainly different, but their rapport can be of vital importance for the evolution of our societies. To the courts can properly evaluate the evidence based on forensic science is vital to understand how science works. We comment some areas where this relationship is quite fluid and others where it is still in the dawn. In particular, we will address the issues of Forensic genetics, environmental forensics and the worrying issue of food paradox. Finally, we discuss some requirements about the presentation of evidence in the courts.
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The evaluation of forensic evidence can occur at any level within the hierarchy of propositions depending on the question being asked and the amount and type of information that is taken into account within the evaluation. Commonly DNA evidence is reported given propositions that deal with the sub-source level in the hierarchy, which deals only with the possibility that a nominated individual is a source of DNA in a trace (or contributor to the DNA in the case of a mixed DNA trace). We explore the use of information obtained from examinations, presumptive and discriminating tests for body fluids, DNA concentrations and some case circumstances within a Bayesian network in order to provide assistance to the Courts that have to consider propositions at source level. We use a scenario in which the presence of blood is of interest as an exemplar and consider how DNA profiling results and the potential for laboratory error can be taken into account. We finish with examples of how the results of these reports could be presented in court using either numerical values or verbal descriptions of the results.
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This paper presents a comprehensive Y-chromosomal STR haplotype analysis in the Lithuanian population in order to evaluate Lithuanians’ Y chromosome diversity, to infer genetic relations between Lithuanian and other European neighbouring populations and to introduce population reference data for generation of reliable Y-STR haplotype frequency estimates to be used in the quantitative assessment of Y-STR haplotype match in the forensic casework. Data were collected from the peripheral blood samples of 194 unrelated males throughout various regions of Lithuania. The amplification of 17 Y-STRs was carried out in one multiplex PCR using an AmpFlSTR® YfilerTM PCR Amplication Kit according to the supplier’s protocol. The results indicated that the Y-chromosomal haplotype diversity in the Lithuanian population rises as the number of the analyzed Y-STRs is increased. However, all additional Y-STR loci are not hypervariable and only their whole makes a large diversity of Y-STR haplotypes in Lithuanian males. The analysis of molecular variance revealed low but significant interpopulation differences except the pair of Lithuanian and Latvian populations. The phylogenetic analysis showed that the clustered Y chromosome gene pool of Lithuanians and Latvians has a closer phylogenetic relation to Russian and Estonian populations and is less genetically related to other neighbouring populations of Belarus and Poland. Yet Y-STRs alleles and haplotypes differentiate effectively inside the Lithuanian population and between Lithuanians and its geographical neighbours excluding the Latvian population. Comparison of the Y-STR data suggests that Lithuanian and Latvian populations are closely related not only by geography and language but also by the Y chromosome gene pool represented by forensic Y-STR markers. Consequently, more forensic Y-STR markers should be included in the Y-STR haplotype in order to achieve a resolution between the Y chromosomes of Lithuanian and Latvian males. Lithuanian Y-STR haplotype data were submitted to the 34th release of the Y-STR Haplotype Reference Database 3.0 for match probability calculations in the forensic casework.
Article
The 3500xL Genetic Analyzer will be used for short tandem repeat (STR) analysis because 3130xl Genetic Analyzer has been discontinued. A validation study was performed for the 3500xL to carry out STR analysis of reference samples with Identifiler® Kit. Sensitivity test was performed with 0.125 ng, 0.5 ng, 1 ng and 3 ng DNA as PCR template. All alleles were detected with 0.5 ng, 1 ng and 3 ng DNA input. Any off scale data and noise over 175 RFU that is threshold value of 3500xL recommended by the manufacturer were not observed from 0.5 ng of input DNA. Thus the optimum input DNA for PCR template was 0.5 ng. We also examined Intra-color peak height ratio and heterozygote peak height ratio at 0.5 ng of template DNA. These results obtained by 3500xL showed similar validations with 310 and 3130xl previously reported. Spectral pull-up was examined by inspections of 240 injections data about each 0.5 ng, 1 ng and 3 ng DNA samples in the sensitivity study with a threshold value of 50 RFU. 1,011, 3,210, and 7,056 pull-up peaks were observed in 0.5 ng, 1 ng, and 3 ng, respectively. It was possible to remove all pull-up peaks using a global cut-off filter of 20%. We compared the profiles generated by the 3500xL and 3130xl using 84 samples with 0.5 ng DNA as PCR template. Both 3500xL and 3130xl detected peaks of all alleles contained in them. However, 3500xL also detected noise peaks and genotyping success rate were 71.4-88.1%. When the 3500xL run data were re-analyzed using the 20% filter, the genotyping results showed 100% concordance. The 20% filter is useful to obtain STR profiles with Identifiler® kit using 3500xL from reference samples because reference samples yield high-quality DNA and are collected from a single individual.
Article
Through this research we look for the best criterion to establish STR (Short Tandem Repeats) profiles from LTD (Low Template DNA) samples. Five different criteria have been proposed and evaluated for the interpretation of partial STR profiles from LTD samples, thus trying to establish the most reliable one. Specifically, 82 samples of 39 individuals from 6 different Chalcolithic and Bronze Age sites (3000 to 5000 years old) have been employed. The 5 different criteria have been established, taking into account information such as the height of the peaks and the reproducibility of the results. Secondly, the kinship analysis among individuals buried together has been carried out. In this second part, it has also been taken into account the mitochondrial DNA (mtDNA) analysis, to consolidate the STR results.
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