STR Loci Research Articles

Prevalence of cases of amebic liver abscess in a tertiary care centre in India: A study on risk factors, associated microflora and strain variation of Entamoeba histolytica.

BackgroundAmebiasis, caused by Entamoeba histolytica (E. histolytica), is a significant cause of morbidity and mortality in developing countries. Mortality due to amebiasis is mostly by extra intestinal infections, amebic liver abscess being the most common one. This study was conducted to determine the current epidemiological status, risk factors, associated microflora and strain variation of E. histolytica causing liver abscesses.Methods/FindingsA total of 115 liver abscess cases comprising of 107 (93%) males and 8 (6.9%) females were included in the study. Microscopic examination of pus samples from the abscesses and species discrimination using nested multiplex PCR showed the presence of E. histolytica in 101 (87.5%) cases. Data collected by face to face interviews using a pre tested questionnaire suggested intake of untreated drinking water (ORs: 6.4, p = 0.002), habit of alcohol consumption (ORs: 4.0, p = 0.019) and lack of urban services (ORs: 0.08, p = 0.017) to be major risk factors associated with E. histolytica infections. The study of associated bacterial flora through aerobic culture of liver aspirates and conventional PCR for detection of anaerobes revealed the presence of Fusobacterium (19, 25.5%), Peptococcus (19, 25.5%), Prevotella (18, 24.3%), Bacteroides (8, 10.8%), Staphylococcus aureus (3, 4%), Escherichia coli (2, 2.7%), Peptostreptococcus (2, 2.7%), Clostridium (2, 2.7%) and Klebsiella pneumoniae (1, 1.3%). Further to study the clonality, genotyping of E. histolytica targeting six tRNA-linked polymorphic STR loci (A-L, D-A, N-K, R-R, STGA -D and S-Q) was carried out which showed the presence of 89 different genotypes in the liver aspirate samples.ConclusionThe findings highlight the high prevalence of genetically diverse E. histolytica from the liver abscess cases in this geographical region. Low socio-economic status and habit of alcohol consumption were important predictors of amebic liver abscess.

Detection of a new allele variation in Chinese Han population at the STR locus SE33 (ACTBP2)

In order to apply a useful STR system in DNA database construction, we performed a population study in China. Allele and genotype frequencies for STR SE33 were obtained for a sample of 213 random Chinese in view of application in personal identification. And we observed a new structural variation of 21.2 allele at SE33 locus which is described here for the first time.

Allele frequencies for 15 forensic STR loci in a population sample from the Kyiv region, Ukraine

ABSTRACT In this study we characterized allele frequencies of 15 autosomal STR loci, including 13 CODIS (D8S1179, D21S11, D7S820, CSF1P0, D3S1358, TH01, D13S317, D16S539, vWA, TPOX, D18S51, D5S818, FGA) and two additional loci (D2S1338 and D19S433) in 200 citizens of Kyiv region using an AmpFlSTR Identifiler Plus Kit. No deviations from the Hardy-Weinberg equilibrium were detected for any loci. The highest observed heterozygosity was detected for D18S51 (0.855) while the lowest was found for TPOX (0.575) loci. The population parameters in the sample from Kyiv are similar to the sample of the entire of Ukraine. Comparison of allele frequencies with the sampled population of Ukraine (excluding Kyiv region) showed a difference in the D21S11 locus.

Genetic Polymorphism of 17 STR Loci in Uygur Population of Akesu in Xinjiang.

To investigate the genetic polymorphisms of 17 STR loci in Uygur population of Akesu in Xinjiang Uygur Autonomous Region. Blood samples from 10 094 unrelated individuals of Uygur population of Akesu in Xinjiang were amplified by using the 17+1 PCR amplification kit, and 17 STR loci typing were detected. Allele distribution and population genetic parameters of each locus were calculated, and compared with those of Chinese Han population, and Uygur population of Yili, Hotan and Turpan regions. In the 10 094 unrelated Uygur individuals, 252 alleles were detected. All loci meet the Hardy-Weinberg equilibrium using a chi-square goodness-of-fit test expectation except vWA loci. Fourteen out of the 17 STR loci, including D13S317, showed high power of discrimination. A significant difference on the allele distribution of all the 17 STR loci was observed between Uygur population of Akesu and Chinese Han population, and the difference of some loci existed between Uygur population of Akesu and the other three Uygur populations. The 17 STR loci are highly polymorphic genetic markers, and the polymorphic information could serve as reference data for forensic individual identification and paternity identification in Akesu.

Genetic variation of 15 STR loci in Lisu ethnic minority in southwestern China.

The Lisu is an ethnic minority living in highlands or mountain valleys in the northern region of the Indo-China Peninsula. The paper presents the frequency distribution of allele and statistical genetic parameters of forensic relevance for 15 autosomal STR loci found in the AmpFℓSTR® Identifiler® PCR Amplification Kit among a population sample constituted by 1854 non-related Lisu minority individuals residing in the southwestern region of China. The genetic relationships between Lisu population and 14 related populations were assessed.

Genetic composition of Teochew population in Chaozhou revealed by 19 STR loci: population polymorphism and interpopulation comparisons

Aim: To investigate the genetic polymorphisms of 19 STR loci in the Teochew population of Chaozhou.Subjects and methods: Nineteen STR loci of 631 unrelated Teochew people in Chaozhou were detected by using the AGCU Expressmarker 20 kit.Results: The allele frequency ranged from 0.0008–0.5577. The combined power of discrimination and combined probability of excluding paternity is over 0.999,999,999,999,999,999,999,999,999,999 and 0.999,999,992,549,546, respectively. The principal component analysis based on the 11 shared STR loci showed the Teochew population was most genetically related to the Fujian Han population.Conclusion: The results demonstrate the set of 19 autosomal STRs could provide robust genetics information for individual identification, paternity testing and human genetics research in the Teochew population.

Genetic diversity and forensic characteristics of 15 autosomal short tandem repeats in Tibet highland and Guangdong lowland Han Chinese populations

Background: Much attention has been paid to the genetic variants of microsatellites in East Asian populations; however, genetic diversity of high-altitude adaptation in Tibet Han remains largely uncharacterised.Aim: To profile DNA samples from 338 high-altitude adaptation Han Chinese individuals and 933 low-altitude living Han Chinese individuals for 15 autosomal STRs which are used for human identification purposes and to estimate the forensic parameters as well as explore the genetic relationships among 38 Chinese populations.Subjects and methods: Fifteen autosomal STR loci and amelogenin genes were amplified in 1271 individuals using the AmpFℓSTR® Sinofiler™ PCR Amplification Kit. Allele frequencies and forensic parameters were calculated. Subsequently, population comparisons among 38 groups were analysed via principal components analysis, Reynolds genetic distance, neighbour-joining tree and multidimensional scaling plots.Results: In this study, no departures from Hardy-Weinberg equilibrium are identified in either Tibet or Guangdong Han populations after Bonferroni correction. The cumulative match probabilities are 3.1108 × 10−19 in Guangdong Han and 6.2102 × 10−19 in Tibet Han, and the combined probabilities of exclusion for trios are 0.99999948 and 0.99999936, respectively. Comprehensive population comparisons based on allele frequency distribution indicate that the Tibet Han population has a genetically close relationship with the surrounding population (Tibet Tibetan) and the Guangdong Han population has genetic affinity with southern Chinese populations.Conclusion: In general, genetic polymorphisms and forensic efficiency indicated that the 15 STRs studied are informative and polymorphic in both lowland and highland Han populations.

Genomic Portrait of Guangdong Liannan Yao Population Based on 15 Autosomal STRs and 19 Y-STRs

Here we studied the genetic polymorphism and evolutionary differentiation of the Guangdong Liannan Yao population based on 15 autosomal STR loci and 19 Y chromosomal STR loci. The blood card DNA of 302 unrelated individuals from the Yao Autonomous County of Liannan was directly amplified using an Expressmarker 16 + 19Y kit and genotyped using a 3500XL Genetic Analyzer. For the autosomal STR loci, the CPD value was over 0.999 999 999 999, while the CPE value was over 0.9999. The population comparison revealed a closer relationship between the Liannan Yao population and the She ethnic population than other reported Chinese populations. For the Y-STRs, a total of 102 unique haplotypes were obtained, 87 of which were observed only once. Both RST pairwise analysis and a multidimensional scaling plot showed that the Liannan Yao population is closely related to the Fujian She ethnic population and is significantly different from other Chinese ethnic populations. The results show that the 15 autosomal STR and 19 Y-STR loci are valuable for forensic applications and human genetic studies in the Liannan Yao population.

Forensic genetic analysis of population of Madhya Pradesh with PowerPlex Fusion 6C\u2122 Multiplex System

Performance of PowerPlex Fusion 6C kit (PP F6C) was assessed in 374 unrelated individuals belonging to Madhya Pradesh, an Indian state. The study evaluated the forensic parameters for the loci included in PP F6C Multiplex System. The combined discrimination power (CPD) and combined exclusion power (CPE) were 1 and 0.999999995, respectively, for all 23 autosomal STR loci. SE33 showed the greatest power of discrimination (0.990) in the studied population, whereas TPOX showed the lowest (0.843). The availability of three Y-STR loci in the Multiplex System is suitable for assessing male contribution and amelogenin deletion in a single Multiplex PCR simultaneously. The study also presents the first global report on polymorphism in the Indian population on SE 33 autosomal STR loci and PP Fusion 6C Multiplex System. The results revealed that the studied STR Multiplex System is highly polymorphic and suitable for forensic purposes.

Characterization of the extra copy of TPOX locus with tri-allelic pattern

BackgroundAn STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet.ResultsIn this study, we investigated the extra copy of type 2 tri-allelic pattern at TPOX in various populations. While allele 10 is the major third allele in Africa, allele 11 appears more frequent in America and overwhelming in Chinese and Korean populations, which might attribute to the population substructures. Results from the investigation of family cases showed that the transmission of the extra allele had a similar genetic pattern of autosomal genes. Furthermore, a whole-genome sequencing followed by bioinformatics analysis revealed that the intact form of chromosomal duplication and rearrangement occurred ~ 407 kb away from the authentic TPOX locus on chromosome 2 in two cases. The breakpoints of the insertion were further validated in most other tri-allelic subjects, which can imply the identical origin from the ancestral extra copy. Nevertheless, de novo chromosomal duplication and rearrangement at thyroid peroxidase gene occur in populations.ConclusionsInstead of the extra allele 10 in African populations, the main third allele at TPOX with tri-allelic pattern is allele 11 in Chinese and Korean populations. The insertion of the extra copy into chromosome 2 occurs in most subjects with tri-allelic pattern at TPOX and demonstrates the transmission of the third allele from parents to offspring. The breakpoints of the ancestral extra copy are defined, which shows evidence of its inheritance from African populations. In addition, the simple validation method would help improve tri-allelic pattern calling, distinguish de novo chromosomal rearrangements, and also count the frequencies among different geographic regions. Therefore, the statistical interpretation of tri-allelic pattern at TPOX could be enhanced during forensic practice.

Polymorphism analyses of 19 STRs in Labrador Retriever population from China and its heterozygosity comparisons with other retriever breeds.

Pure breed dogs of Western origin are increasingly more popular in China as is a need to differentiate breeds and individual dogs for personal and forensic reasons. Research on genetic diversities of the canine population in China is rarely conducted. In this study, genetic distributions and forensic efficiencies of 19 canine STR loci in Labrador Retriever population from China were evaluated by using one available commercial canine kit in China. This panel was used to genetically define 214 Labrador Retrievers in China, as an example of one of the most important Western breeds and to compare them with Labrador Retrievers from America based on three overlapping STR loci. Moreover, genetic relationship analyses between Labrador Retriever population and two reference populations in America were performed. All 19 STR loci were polymorphic and conformed to Hardy-Weinberg equilibrium in the studied population. The STR panel was able to discern individual dogs with a high degree of accuracy. Breed-wide genetic heterozygosity comparisons based on present and published allele frequencies revealed that the studied population had the lower genetic heterozygosity than canine populations in America. Principal component analysis among Labrador Retriever population and other reference populations showed that the studied Labrador Retrievers were genetically close to the retriever breeds in America. Population genetic structure analyses among these canine breeds further revealed genetic differentiations between the studied Labrador Retriever population and other compared breeds. In conclusion, these STR loci had relatively high forensic values in Labrador Retriever population in China, which could be employed for individual identification and kinship testing.

Separation and forensic identification of sperm from cell mixtures using anti-hLCN6 monoclonal antibody coupled magnetic beads

Human lipocalin 6 (hLCN6) is an epididymis-specific secretory protein. It binds to sperm and plays important role in sperm maturation. To explore the feasibility for isolating spermatozoa from mixed cells using anti-hLCN6 monoclonal antibody-conjugated immunomagnetic beads (anti-hLCN6 IMBs) and establish a new method for the separation of sperms from mixed stains, 2 sets of 30 cases of cell mixture suspensions and stains containing different proportions of sperm and epithelial cells were prepared. Biotin-labeled anti-hLCN6 monoclonal antibody (mAb) was incubated with the cell mixtures, and the spermatozoa were then isolated with avidin-coated IMBs. Sperm DNA was extracted and analyzed by PCR-STR typing. Differential lysis was also conducted to compare the effect of the two different isolation methods. The dissociation constant (Kd) of anti-hLCN6 mAb was 3.47×10⁻⁹ mol/L measured by ELISA. Western blotting and immunofluorescence assays showed that hLCN6 was detectable on sperm cells and mainly located on the post-acrosomal region of the sperm head, but not in epithelial cells. Anti-hLCN6 IMBs could capture and separate the sperm cells successfully. Microscopic observation showed that the IMBs could bind to the head of sperm specifically. The success rate of STR typing (more than 13 STR loci, RFU>200) was 90% when the number of sperm cells was 10³/mL and 100% when the sperm cells number was equal to or more than 10⁴/mL. When the number of sperm cells was 10³/mL, 10⁴/mL and 10⁵/mL in mixed stain samples, the success rate of STR typing were 40%, 90% and 100%, respectively. Taken together, the anti-hLCN6 immunomagnetic beads (IMB) method described here could be effective for the isolation of sperm from mixed cells, and the success rate was higher than that of the traditional differential lysis strategy. IMB sorting is a simple and efficient method for the separation of sperms from sperm and epithelial cell mixture, and can be utilized as a supplementary method for forensic mixture samples analysis in sexual assault cases.

Genetic data for PowerPlex 21™ autosomal and PowerPlex 23 Y-STR™ loci from population of the state of Uttar Pradesh, India.

In the present study, the statistical forensic parameters were evaluated for the loci present in PowerPlex 21 autosomal and PowerPlex 23 Y-STR multiplex systems in 168 unrelated individuals living in the state of Uttar Pradesh, India. The combined discrimination power (CPD) and combined exclusion power (CPE) was 1 and 0.999999 respectively for all 20 autosomal STR loci. Penta E showed the greatest (0.980) and CSF1PO showed the lowest (0.855) power of discrimination in the studied population. The haplotype diversity for 23 Y-STR loci was observed to be 0.999. The study also presents the first global report on polymorphism on D1S1656, D6S1043 and D12S391 autosomal STR loci in the Indian population. The resulting data revealed that these STR multiplex systems are highly polymorphic and can be used for forensic purposes.

Forensic characteristics and phylogenetic analysis of 23 Y-STR loci in the Miao population from Guizhou province, southwest China

Background: Investigation of haplotype/allele frequency data of Y-STR loci in ethnically diverse populations is essential for forensic reference database construction and genetic application. However, the population genetic characteristics of the Chinese Miao minority from Guizhou Province remain uncharacterised.Aim: To assess forensic characteristics for 23 Y-Chromosomal STR loci in Guizhou Miao and explore population genetic relationships with geographically neighbouring populations.Subjects and methods: Twenty-three Y-Chromosomal STRs were genotyped using the Powerplex® Y23 system in 103 unrelated Chinese Miao males from Guizhou Province, southwest China. Haplotypes and forensic parameters were obtained. Population relationships of Guizhou Miao with others were revealed using AMOVA and an MDS plot.Results: A total of 96 haplotypes were identified with overall haplotype diversity (HD) and discrimination capacity (DC) of 0.9985 and 0.9320, respectively. Genetic differentiation was observed with most of the comparison populations, prominently for Guizhou Shui.Conclusion: The 23 Y-STR loci were highly polymorphic and discriminating in the Guizhou Miao population and could be used for forensic practice and population genetic studies. Population relationship analysis revealed Guizhou Miao had a close genetic relationship with geographically close Guizhou Gelao, as well as Han majorities derived from different regions.

Human Genetic Identification in Paternity testing by multiplex STR analysis using ABI 3500 xl Genetic Analyzer

The present study explores the use of 15 STR loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA in addition to a gender identification marker, amelogenin in forensic investigation & paternity testing.

ВЛИЯНИЕ МЕТОДОВ СЕЛЕКЦИИ НА МОЛЕКУЛЯРНО-ГЕНЕТИЧЕСКУЮ СТРУКТУРУ ЛОШАДЕЙ БУДЕННОВСКОЙ ПОРОДЫ

Budenny horse breed was obtained as a result of the crossing of Don and local Black Sea mares with Thoroughbred stallions during 1920-1920. To improve the athletic qualities of Budenny horses Thoroughbred stallions are regularly used in breeding, which inevitably affects the breeding qualities of the received offspring. The task of the research was to study the genetic features of the polymorphism of microsatellite loci in Budennny horses, taking into account the origin and Thoroughbred horses’ blood propotion. Tested on 17 loci of microsatellites, horse DNA of the Budenny breed (n = 155) were subdivided into 5 groups, taking into account the type of selection and the proportion of blood. In the 5th experimental group horses with unregistered ancestors in the pedigree from the “Pobeda” farm were included. A comparative genetic-population analysis of different groups of horses was performed on a number of indices, including the level of polymorphism (Ae), the observed (Ho) and the expected (He) heterozygosity, as well as Wright's F-statistics indices using Microsoft Excel 2010. As a result of testing 127 alleles of STR loci were identified in Budenny breed that evidences a sufficient reserve of genetic diversity. The number of alleles in the studied loci varied from 3 to 13, the most polymorphic ones were the ASB17 (13), VHL20 (9) ANT4 (9) and LEX3 (9) loci. Horses of the all 5 groups differed both in the spectrum of alleles and in the degree of heterozygosity. The highest level of the main parameters (MNA, Ae, Ho and He) had horses of a consolidated origin and Thoroughbred blood proportion at the level of 5/8. The practiced crossing with Thoroughbred stallions led to an increase in the proportion of blood and the decrease in Ae polymorphism level from 3.803 to 3.588, the degree of heterozygosity lowed from 0.737 to 0.703. The results of phylogenetic analysis indicate that the four groups of Budenny horses form a common cluster, in the center of which are horses with a consolidated origin. Microsatellite markers used to control the origin of horses can be additionally used for genetic control of breeding processes in populations and breeds of horses.

Molecular-genetic analysis of a rare forensic case of partial deletion of the Y-chromosome

The amelogenin gene encodes dental enamel protein and is present in humans in two forms - AMELX and AMELY, located on the X- and Y-chromosomes, respectively. This rare case depicts a partial deletion of the AMELY gene. In the Into-Stil LLC laboratory, we performed the genetic testing of the DNA samples extracted from buccal epithelial cells of the alleged father and the disputed child (a boy). Genotyping was carried out using COrDIS Plus ('Gordis', Russian Federation) and AmpFLSTR Identifiler Direct PCR Amplification ('Applied Biosystems', USA) Kits. Our findings have demonstrated that both the alleged father and the disputed child lacked the fragments corresponding with the AMELY gene. Using both STR-systems, we detected, in the disputed child's genome, the allele formally identical to the allele in the genome of the alleged father. Further analysis using the COrDYS ('Gordis', Russian Federation) kit allowed us to detect the amplified fragments corresponding with all the STR loci of Y chromosome, except DYS576 and DYS449, which confirmed that both studied individuals belonged to male biological sex.

Forensic and phylogenetic analyses among three Yi populations in Southwest China with 27 Y chromosomal STR loci.

We have analyzed the Y chromosome haplotypes of 510 non-related Yi males grouped in three Chinese provinces (Guizhou, Sichuan, and Yunnan) using the Yfiler® Plus Kit. A total of 484 haplotypes were detected, out of which 460 were unique. The observed haplotype diversity and discrimination capacity were 0.9998 and 0.9490, respectively. To investigate the genetic relationship of the studied population, multidimensional scaling (MDS) plot and neighbor-joining (NJ) tree phylogenetic analyses were constructed which demonstrated that the Y chromosome lineage among the Yi ethnicity was different.

Compound stutter in D2S1338 and D12S391

Compound repeats provide a testing ground for evaluating hypotheses on the causes and consequences of stutter. As compound repeats have two repeating motifs, each motif may produce stutter variants; thus as the repeat within the locus is compound, so is the resultant stutter. Further, the rates of stutter formation between these motifs may not be independent. This lack of independence may complicate modeling strategies, thus contributing to the challenges of mixture interpretation that rely on nucleotide sequence. This study evaluates compound stutter in two STR loci: D2S1338 and D12S391. The effects of flanking variation, as well as possible interactions between the two different uninterrupted stretches (US) and their respective stutter variants are assessed. Multivariate multiple linear regression (MMLR) was used to show that, as with simple repeats, the rate of stutter product formation of a particular repeating motif is not solely a function of the US of that repeat. The nucleotides adjacent to the repeating motif also appear to influence the rate of stutter formation of that motif, with those nucleotides sometimes including the other motif. MMLR was used to estimate the size of these effects and to construct an example of a two-dimensional (thus, a compound) stutter prediction. This example may merit further investigation in the application of massively parallel sequencing data to mixture interpretation and probabilistic genotyping.

Analysis of Genetic Diversity in three Kazakh Sheep using 12 Microsatellites

The genetic structure of three Kazakh sheep breeds was examined by using 12 microsatellite loci. A total of 144 alleles were detected from the 12 STR loci, with a mean value of 12.0. The highest allele diversity was found at the locus CSRD247 (16 alleles). PIC value showed that all studied STR markers are more informative and appropriate for genetic analysis of three Kazakh sheep populations. Beside of INRA006, all markers had high level of genetic variability. As Fixation index shows, the excess of the heterozygosity was observed only in loci MAF065. Obtained number of private alleles in Edilbai, Kazakh Arkhar Merino and Kazakh Fine-wool sheep were 25, 17 and 15 respectively. Genetic diversity was higher in Edilbai population than in other two populations. The genetic variability was lower in Kazakh Arkhar Merino sheep than in the Edilbai and Kazakh Fine-wool sheep breeds. The genetic distance was the largest between Edilbai and Kazakh Arkhar Merinos. Also, the moderate differentiation was observed between Edilbai and Kazakh Arkhar Merinos.  Â