Autosomal Short Tandem Repeat Research Articles

An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing

In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (N = 371). The findings were then compared to a larger Norwegian population dataset (N = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.

Studying the Role of Soil Factors on Degree of Degradation of DNA of Human Remains

Generating a DNA profile using autosomal Short Tandem Repeat (STR) DNA allele from skeletal remains is a crucial step in the identification process for mass disaster and unidentified person situations. The capacity to extract substantial amounts of relevant DNA from bones, which were highly durable biological components that can withstand soil elements and climatic conditions over long periods of time, would be advantageous. 70 femur male bone samples were collected from two different environmental mass graves (Al-Mahaweel massgrave) in Babil governorate and (Al-Saqlawiya massgrave) in Al-Anbar governorate in Iraq. The DNA from bone samples extracts were assessed by capillary electrophoresis and a standardized set of short tandem repeat (STR) loci are analyzed using Mutiplex 21 STR loci System to allow human identification by matching the profile of the dead individuals with their relatives. From these two different sites; soil samples were collected to analyze and study the different environmental factors and find a relation between the degree of preservation or degradation with these factors like temperature, humidity, salinity, PH and texture of soil and find how these factors can affect on pattern of degradation of DNA profiles. The average of the percentage of the detected alleles in each locus in the two sites; were 87\% for Al-Mahaweel site and 32\% for Al- Saqlawiya site. we found that clay soil, low salt concentration, PH slightly alkaline and low humidity for Al-Mahaweel site; all participate in DNA preservation while the chalky and very high salt concentration of Al- Saqlawiya site soil; all participate in DNA degradation. Predicting the effect of these factors on the quality of the DNA profiles can be helpful in finding better solutions for many complications that may face the process of analyzing samples and finding sufficient informative profiles.

Anthropogenetic study of the Arabic - speaking population of Chaouia Ouardigha (Morocco) based on autosomal STRs

BackgroundThe Chaouia - Ouradigha is a historical and ethno-geographic region of Morocco. Despite its historical relevance, this region has not received sufficient attention in terms of population genetic exploration. The present study aims to provide new data on the genetic background of the Chaouia-Ouardigha population, the Arabic-speaking North African population in the western center of Morocco, and to examine the relationship between this population and other reference populations based on our dataset as well as previously published population data. Genetic exploration will enable the reconstruction of past gene flows that have influenced the genetic makeup of this particular population. We utilized the Investigator® IDplex Plus PCR amplification kit (Qiagen, Germany) to establish the allelic frequencies and forensic statistical parameters of 15 autosomal Short Tandem Repeats (STRs) included in the kit in 153 random healthy unrelated individuals from the Chaouia-Ourdigha region.ResultsThe Chaouia-Ouardigha population, which speaks Arabic, exhibits a high degree of genetic diversity with heterozygosity values ranging from 0.670 to 0.879. The loci with the highest allele frequencies, namely D7S820 and TPOX, have the lowest heterozygosity values (0.670 and 0.672, respectively), resulting in lower exclusion power (PE) and typical relatedness index (TPI) values (PE = 0.427 and TPI = 1.66 for TPOX; PE = 0.442 and TPI = 1.72 for D7S820). Phylogenetic analysis showed that the Arabic-speaking population of Chaouia-Ouardigha was found to be distinct from Sub-Saharan, East Asian, and Latin American populations.ConclusionsOur study provides insights into the genetic connections of the Chaouia Ouardigha population, highlighting how historical events, socio-cultural influences, and geographical proximity have contributed to shaping their genetic structure. It demonstrates the substantial impact of historical events and geographical closeness in fostering affinities between the Chaouia Ouardigha community and neighboring populations in North Africa, Southern Europe, and the Middle East. Additionally, the study has generated valuable data confirming the effectiveness of these 15 genetic markers for forensic applications across the broader population.

Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population

This study aimed to estimate A-STR mutation rates in 2,317 Korean parent–child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39–1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38–1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.

Forensic efficiency and genetic polymorphisms of 12 X-chromosomal STR loci in Northeastern Thai populations.

Northeastern Thailand comprises one-third of the country and is home to various populations, with Lao Isan constituting the majority, while others are considered minority groups. Previous studies on forensic short tandem repeats (STRs) in Thailand predominantly focused on autosomal STRs but there was a paucity of X-STRs, exclusively reported from the North and Central regions of the country. In this study, we have newly established a 12 X-STRs from a total of 896 samples from Northeastern Thailand, encompassing Lao Isan as the major group in the region, alongside nine minor populations (Khmer, Mon, Nyahkur, Bru, Kuy, Phutai, Kalueang, Nyaw, and Saek). Across all ten populations, the combined powers of discrimination in both genders were high and the combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were also high (> 0.99999). DXS10148 emerged as the most informative marker, while DXS7423 was identified as the least informative. Genetic comparison based on X-STRs frequency supported genetic distinction of cerain minor groups such as Kuy, Saek and Nyahkur from other northeastern Thai groups as well as genetic differences according to the geographic region of Thai groups (Northeast, North and Central). In sum, the overall results on population genetics are in agreement with earlier reports on other genetic systems, indicating the informativeness of X-STRs for use in anthropological genetics studies. From a forensic perspective, despite the limitations of small sample sizes for minority groups, the present results contribute to filling the gap in the reference X-STRs database of the major group Lao Isan, providing valuable frequency data for forensic applications in Thailand and neighboring countries.

Analysis of 26 STR loci (PowerPlex® Fusion 6C System) in a mestizo population from Mexico city.

Short tandem repeats (STRs) are the most widely used genetic markers in forensic genetics. Therefore, it is essential to document genetic population data of new kits designed for human identification purposes to enable laboratories to use these genetic systems to interpret and solve forensic casework. However, in Mexico, there are no studies with the PowerPlex Fusion 6C System, which includes 26 STRs (23 autosomal STRs and 3 Y-STRs). 600 DNA samples from Mexico City were subjected to genotyping using the PowerPlex Fusion 6C System. For autosomal STRs, 312 different alleles were observed. Combined PE and PD were 99.999999809866% and 99.99999999999999999999999818795%, respectively. Genetic distances and AMOVA test showed low but significant differentiation between Mexican populations. The results reported in this work demonstrate the efficacy of this system for human identification purposes in the population studied and justify its possible application in other Mexican Mestizo populations.

Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit.

Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.

A rare case of type II tri-allelic inheritance at vWA, SE33, D8S1179, and D13S317 loci demonstrated by STR analysis in paternity testing.

Short tandem repeat (STR) typing has been regularly used in paternity disputes and forensic human identification linked caseworks. Occasionally, forensic scientists come across aberrant allele patterns during STR typing because of mutations, genetic variations, and other abnormalities. The tri-allelic pattern of STR is rare, particularly, the case where this pattern exists at 4 loci. Here, we report the type II tri-allelic patterns observed at vWA, SE33, D8S1179, and D13S317 loci in the product of conception (POC) sample during the course of our regular paternity case investigation. The DNA extracted from the blood samples and tissue of POC were subjected to STR typing for autosomal and sex STR loci using the commercial QIAGEN's Investigator® IDplex Plus Kit and QIAGEN's Investigator® 24plex QS Kit. Capillary electrophoresis was carried out in 3500 and 3500xL Genetic Analyzer Applied Biosystems and genotyped using GeneMapper ID-X Software v1.5 and v1.6. In this case of paternity inclusion, the POC sample displayed type II tri-allelic patterns at vWA (16, 19, 20), SE33 (19, 28.2, 29.2), D13S317 (16, 19, 20), and D8S1179 (10, 13, 17) loci. In addition, the POC displayed an abnormal genotype with a heterozygous peak imbalance (type II-B) of (1:2) pattern at D3S1358, D21S11, and D16S539 loci, of (2:1) pattern at D1S1656, D12S391, D10S1248, D2S1338, D2S441, D18S317, FGA, CSF1PO, and D5S818 loci, and type II-C allelic pattern (one single peak with triplicate height) at D19S433 and DS7820 loci. Understanding of such anomalous genotypes improves the knowledge about tri-allelic pattern of CODIS loci and helps in the appropriate interpretation of the results in STR typing.

Utilizing Massively Parallel Sequencing (MPS) of Human Leukocyte Antigen (HLA) Gene Polymorphism to Assess Relatedness in Deficiency Parentage Testing.

In the realm of DNA testing with legal implications, the reliability and precision of genetic markers play a pivotal role in confirming or negating paternity claims. This study aimed to assess the potential utility of human leukocyte antigen (HLA) gene polymorphism through massively parallel sequencing (MPS) technology as robust forensic markers for parentage testing involving genetic deficiencies. It sought to redefine the significance of HLA genes in this context. Data on autosomal short tandem repeat (aSTR) mutational events across 18 paternity cases involving 16 commonly employed microsatellite loci were presented. In instances where traditional aSTR analysis failed to establish statistical certainty, kinship determination was pursued via HLA genotyping, encompassing the amplification of 17 linked HLA loci. Within the framework of this investigation, phase-resolved genotypes for HLA genes were meticulously generated, resulting in the definition of 34 inherited HLA haplotypes. An impressive total of 274 unique HLA alleles, which were classified at either the field 3 or 4 level, were identified, including the discovery of four novel HLA alleles. Likelihood ratio (LR) values, which indicated the likelihood of the observed data under a true biological relationship versus no relationship, were subsequently calculated. The analysis of the LR values demonstrated that the HLA genes significantly enhanced kinship determination compared with the aSTR analysis. Combining LR values from aSTR markers and HLA loci yielded conclusive outcomes in duo paternity cases, showcasing the potential of HLA genes and MPS technology for deeper insights and diversity in genetic testing. Comprehensive reference databases and high-resolution HLA typing across diverse populations are essential. Reintegrating HLA alleles into forensic identification complements existing markers, creating a potent method for future forensic analysis.

Forensic parameters and population analysis of 21 autosomal STR loci in the Wuhu Han population from Anhui Province, East China

Background At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. Aim This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. Subjects and methods Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. Results In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni’s correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. Conclusion The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.

日本人集団において個人を識別するのに必要なSTRとSNPの最小座位数

For this study, we investigated the minimum number of short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci sufficient for personal identification in the Japanese population. A guidance for the data volume that should be treated as personal information was presented here. The uniqueness of individual genotypes was evaluated according to the Scientific Working Group on DNA Analysis Methods interpretation guideline, using the probability that another individual would have the same genotype by chance. In the Japanese population, the threshold of random match probability sufficient for personal identification was 8.15×10－11. In STR, it was considered that when 9 or more of the 21 autosomal STR loci of the GlobalFiler system were combined, they should correspond to personal information. For SNP, a total of 112 loci should be required for identification when cumulating the number of loci at the minor allele frequency interval of 0.01. However, based on the median of allele distribution, a total of 47 loci were necessary to reach below the threshold. Furthermore, we simulated the number of the required loci when the size of the population was variable. Since genome data is already widely used in society, we need to recognize that strict management of genome data are essential from the viewpoint of protecting personal information.

Tri-Allelic Autosomal STR Patterns Observed in Pakistani Population during Forensic Case Work

The tri-allelic pattern is a genotyping abnormality that can be observed during routine short tandem repeat (STR) profiling in the field of forensic science. Fourteen tri-allelic patterns have been observed in nine different loci during routine forensic casework consisting of 20,000 STR profiles. All these 20,000 STR unrelated profiles were profiled using AmpFlSTR Identifiler Plus® and Global Filer® kits. Tri-allelic patterns can be divided into two types based on RFUs (relative fluorescent units) in peaks of three component alleles. Unequal RFUs of all three peaks are observed in the Type-I pattern, whereas in the Type-II pattern, RFUs of all three peaks are nearly equal. A total of nine novel tri-allelic genotypes were observed out of 20,000 unrelated individuals in the Pakistani population. All of these forensic cases belonged to the Type-I pattern which means that the sum of the height of two smaller peaks is nearly equal to the height of the third larger peak. The frequency of occurrence for all these patterns was compared with already reported data. In this study, eight novel tri-allelic patterns have been reported which are not listed in the National Institute of Standards and Technology (NIST) database as well as in any published article.

Effect of uniparental disomy in parentage testing

Uniparental disomy (UPD) is a rare type of chromosomal aberration that may hinder the analysis of kinship during forensic identification. Here, we investigated these genetic findings to avoid false exclusions during parentage testing. Thirty-nine fluorescently labeled, autosomal short tandem repeats (STR) were amplified in three cases, to detect parent–child relationships. Twenty-three fluorescently labeled Y-chromosome STRs were also employed. These were subjected to capillary electrophoresis. The parentage index was calculated by the bipartite or tripartite model. Single nucleotide polymorphism (SNP) microarrays were performed to further investigate the genetic mechanisms. The conclusions supported the biological mother–child relationship in three cases. However, in all cases, the alleged father and child had three autosomal STR markers, constrained to a single chromosome, which did not conform to Mendelian inheritance rules. The genotyping of 23 Y-chromosome STRs did not reveal any violations of Mendelian law. The combination of STR profiling and SNP microarrays suggested that two children had maternal UPD of chromosome 7, whilst one had UPD of chromosome 2. After excluding the three incompatible loci, the conclusions supported the biological father-child relationship in all cases. The same results were obtained when parentage testing of trios was used. Uniparental disomy may complicate the judgment of kinship in parentage testing. The possibility of UPD should be considered when incompatible STR loci are found on the same chromosome. Genetic evidence obtained through additional molecular techniques can provide better interpretation of kinship in the presence of UPD and avoid false exclusions of biological relationships.

Sequence variations of 58 STRs and 94 SNPs in Northeastern Xibe with ForenSeq™ DNA signature prep kit

Abstract Massively parallel sequencing (MPS) technology has already shown many advantages in forensic DNA typing. In this study, the repeat region (RR) and flanking region (FR) variations were detected at 58 short tandem repeats (STRs) by MPS, which could increase allelic diversity (34.59%) and gene diversity (3.95%) compared with the capillary electrophoresis (CE) method. Six novel RR variants were identified at 5 STRs, and eleven FR variants were found at 8 STRs. Concordance amounted to 99.96% (4598 out of 4600 alleles) between ForenSeq DNA Signature Prep Kit and CE kits, and discordance was due to bioinformatic misinterpretation at DXS7132. Additionally, allele frequencies and forensic parameters of 94 identity-informative single nucleotide polymorphisms (iiSNPs) provided a reference dataset, which held a higher power of discrimination (1–3.4825 × 10−35). A total of 29 FR variants were found at 24 target iiSNPs. The power of the system effectiveness with the combined 27 autosomal STRs by sequence and 94 iiSNPs was added more substantially than that of a single type of marker alone, such as the combined power of discrimination (CPD) and the combined power of exclusion (CPE) achieving 1–7.1358 × 10−65 and 1–4.4803 × 10−21, respectively. Population structure analyses with iiSNPs and additional ancestry-informative SNPs (aiSNPs) demonstrated that Chinese Xibe in the northeast was one of the East Asian populations. At the genetic level, Northeastern Xibe is close to populations where they live, such as Han Chinese and other ethnic minority groups.

A Tibetan group from Ngawa Tibetan and Qiang Autonomous Prefecture, southwest China, is rich in genetic polymorphisms at 36 autosomal STR loci and shares a complex genetic structure with other Chinese populations

The Tibetan people are ancient and populous, constituting the seventh-largest of the fifty-five ethnic minority groups in China. The Ngawa Tibetan and Qiang Autonomous Prefecture (NTQAP), situated on the border of northwest and southwest China, has its distinct group relationships. Short tandem repeat (STR) is extremely polymorphic and extensively used in the application of forensic medicine and population genetics. However, it is not clear the genetic information including linkage disequilibrium (LD) by 36 autosomal STR (A-STR) markers in the Tibetan group from NTQAP. The Tibetan population from NTQAP of southwest China was examined for 36 A-STR loci in the research. Every marker across the 36 A-STR loci was consistent with Hardy–Weinberg equilibrium (HWE). The results of the calculation revealed that the total discrimination power (TDP) is 1–2.2552 × 10−42 and the cumulative probability of exclusion (CPE) is 1–1.3031 × 10−16. Subsequently, a total of 345 alleles with allelic frequencies ranging from 0.00382 to 0.55343 were identified, and the allelic numbers varied from 5 in both the TH01 and TPOX markers to 28 in the SE33 locus. The Ngawa Tibetan population, along with other Chinese populations, exhibited influences from historical factors and regional distribution, as indicated by the results of population genetics analysis. We thus first explored the genetic characteristics and correlated forensic parameters of the 36 A-STR markers in NTQAP to fill the gap in the Tibetan population. It was discovered that these 36 autosomal STR markers supplemented forensic STR databases and offered extremely valuable polymorphisms for Chinese forensic applications, such as parentage testing and personal identification. Moreover, the study would contribute additional information regarding the substructure and diversity in the Chinese population.

Processing biological samples from simulated radiological terrorist events using Rapid DNA instruments

Two commercially available portable Rapid DNA instruments were evaluated for their ability to process 1 µL and 10 µL saliva samples deposited on metal and plastic surfaces and contaminated with surrogates of cesium (Cs)-137, strontium (Sr)-90 and cobalt (Co)-60; radioactive materials potentially released during a nuclear weapon accident or a radiological dispersal device detonation. A comparable success rate was noted for both Rapid DNA instruments when considering the number of complete and balanced DNA profiles, the number of profiles with a minimum of 10 autosomal STR loci (out of 23 [FlexPlex™ 27] or 21 [GlobalFiler™ Express]), and the possibility to search a national DNA database in Canada and the United States. Cobalt had an adverse impact on the quality of the megaplex short tandem repeat (STR) DNA profiles derived on each instrument for two of the three contamination levels tested in this study, i.e., 0.05 M and 0.1 M as reflected by a reduced number of detected alleles and decreased profile peak heights. Strontium exhibited some adverse effect on the Rapid DNA results when used at the highest contamination level (0.1 M) whereas cesium had none. No new artifacts were observed in the Rapid DNA profiles of samples spiked with the non-radiogenic surrogates. Importantly, in the context of a radiological/nuclear (RN) event, the ANDE™ 6C offers the possibility to dispose of all radioactive materials associated with contaminated samples quickly using a chip on which all steps of the Rapid DNA process are performed whereas the RapidHIT™ ID accumulates radioactive materials for many days before disposal. An individual handling 25 samples in a week (5 per day) on the RapidHIT™ ID at a 30.5 cm distance with a 5 min exposure to the radioactive source estimated at every run would exceed the 0.042 µSv/5 min limit with gamma dose rates for Cs at 0.13 mSv and for Co at 3.8 mSv. Beta dose rates calculated for the surrogate isotopes at the three concentrations tested were also above the recommended radiation exposure limit of 1 mSv/yr (0.042 µSv/5 min). Various potential mechanisms of action behind the interference noted for Sr and Co at high concentrations are presented. These elements may play a role in the steps prior to PCR (at the DNA molecule by binding to bases or to phosphate groups), during PCR (at the DNA polymerase as cofactors for catalytic sites), or even during amplified DNA fragment detection (as fluorescence quenchers).

The Autosomal Short Tandem Repeat Polymorphisms Are Potentially Associated with Cardiovascular Disease Predisposition in the Latin American Population: A Mini Review.

According to the World Health Organization, cardiovascular diseases (CVDs) are the leading cause of death worldwide across nearly all ethnic groups. Inherited cardiac conditions comprise a wide spectrum of diseases that affect the heart, including abnormal structural features and functional impairments. In Latin America, CVDs are the leading cause of death within the region. Factors such as population aging, unhealthy diet, obesity, smoking, and a sedentary lifestyle have increased the risk of CVD. The Latin American population is characterized by its diverse ethnic composition with varying percentages of each ancestral component (African, European, and Native American ancestry). Short tandem repeats (STRs) are DNA sequences with 2-6 base pair repetitions and constitute ~3% of the human genome. Importantly, significant allele frequency variations exist between different populations. While studies have described that STRs are in noncoding regions of the DNA, increasing evidence suggests that simple sequence repeat variations may be critical for proper gene activity and regulation. Furthermore, several STRs have been identified as potential disease predisposition markers. The present review is aimed at comparing and describing the frequencies of autosomal STR polymorphisms potentially associated with cardiovascular disease predisposition in Latin America compared with other populations.

Determination of allele frequencies in 15 autosomal short tandem repeat (STR) loci of Arab residents in Iraq

Determination of allele frequencies in 15 autosomal short tandem repeat (STR) loci of Arab residents in Iraq

Internal validation of the GA118-24B Genetic Analyzer, a stable capillary electrophoresis system for forensic DNA identification.

The GA118-24B Genetic Analyzer (hereafter, "GA118-24B") is an independently developed capillary electrophoresis instrument. In the present research, we designed a series of validation experiments to test its performance at detecting DNA fragments compared to the Applied Biosystems 3500 Genetic Analyzer (hereafter, "3500"). Three commercially available autosomal short tandem repeat multiplex kits were used in this validation. The results showed that GA118-24B had acceptable spectral calibration for three kits. The results of accuracy and concordance studies were also satisfactory. GA118-24B showed excellent precision, with a standard deviation of less than 0.1 bp. Sensitivity and mixture studies indicated that GA118-24B could detect low-template DNA and complex mixtures as well as the results generated by 3500 in parallel experiments. Based on the experimental results, we set specific analytical and stochastic thresholds. Besides, GA118-24B showed superiority than 3500 within certain size ranges in the resolution study. Instead of conventional commercial multiplex kits, GA118-24B performed stably on a self-developed eight-dye multiplex system, which were not performed on 3500 Genetic Analyzer. We compared our validation results with those of previous research and found our results to be convincing. Overall, we conclude that GA118-24B is a stable and reliable genetic analyzer for forensic DNA identification.

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

BackgroundMassively Parallel Sequencing (MPS) allowed an increased number of information to be retrieved from short tandem repeat (STR) analysis, expanding them not only to the size, as already performed in Capillary Electrophoresis (CE), but also to the sequence. MPS requires constant development and validation of the analytical parameters to ensure that the genotyping results of STRs correspond to those obtained by CE. Given the increased frequency of usage of Y-STRs as supplementary markers to the autosomal STRs analysis, it is urgent to validate the concordance of the typing results between CE and MPS analyses.Methods and resultsDNA extracted from 125 saliva samples of unrelated males was genotyped using Yfiler™ Plus PCR Amplification Kit and ForenSeq™ DNA Signature Prep Kit, which were analyzed by SeqStudio™ Genetic Analyzer for HID and MiSeq™ FGx Forensic Genomics System, respectively. For each shared Y-STR, allele designation, number of length- and sequence-based alleles per locus, stutter percentage, and the intra-locus balance of multicopy Y-STRs were screened.ConclusionsAlthough the number of forensic genetics laboratories that are applying the MPS technique in routine analysis is small and does not allow a global assessment of MPS limitations, this comparative study highlights the ability of MPS to produce reliable profiles despite the generation of large amounts of raw data.