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PubMed2000

Allelic distribution of nine short tandem repeat (STR), HLA-DQA1, and polymarker loci in an Omani sample population.

Allele frequency distributions of nine short tandem repeat (STR) loci, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D7S820, and D13S317, HLA-DQA1 and polymarker (PM) loci were studied in a sample population from Sultanate of Oman, Middle East. Blood samples were collected from 162 unrelated individuals. For all STR, HLA-DQA1 and PM loci, no deviations from Hardy-Weinberg equilibrium, based on the exact test, were observed. The most discriminating loci were D18S51 (PD=0.966) and FGA (PD=0.964), while the least informative locus is GYPA (PD=0.585). The allele frequency data may be useful in forensic case work.

Alleles↗
PubMed1999

Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome.

Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations-that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.

Africa, Northern↗
PubMed2001

Genomic diversity at thirteen short tandem repeat loci in a substructured caste population, Golla, of southern Andhra Pradesh, India.

Genomic diversity based on 13 short tandem repeat (STR) loci was studied in seven population groups of a substructured Golla caste from Chittoor district in southern Andhra Pradesh, India. These groups are traditionally pastoral, culturally homogeneous, and strictly endogamous. Blood samples were drawn from 317 individuals from 30 Golla villages. The 13 STR loci analyzed in five standard multiplex polymerase chain reactions were: (1) CSF1R, TH01, and PLA2A; (2) F13A1, CYP19, and LPL; (3) D21S1446 and D21S1435; (4) D20S481, D20S473, and D20S604; and (5) D5S1453 and D6S1006. The average heterozygosity was found to be low among the Golla subgroups (0.64-0.70) in comparison to that of groups at the upper levels of the hierarchy. The coefficient of gene differentiation was found to be moderate (average GST = 0.031; range between 0.018 and 0.049 among the loci) when compared to that observed for a similar class of markers among populations with relatively higher levels of hierarchy, for example, among castes. It is, however, much higher when compared to the average observed for Indian caste and tribal populations, based on classical markers. Genetic distance measures revealed clusters of populations that are consistent with the known ethnohistorical and geographical backgrounds of the groups. We claim that these hypervariable markers are quite useful in understanding the process of substructuring within the Indian castes, leading to the formation of smaller breeding isolates, the basic Mendelian units within which microevolutionary forces operate.

Consanguinity↗
PubMed2002

Short tandem repeat polymorphism of the D2S1242 locus in a Japanese population.

Allele frequencies and sequence characteristics of the D2S1242 short tandem repeat (STR) locus were studied in a Japanese population sample. A total of 10 D2S1242 alleles and 34 genotypes were identified in 273 unrelated Japanese individuals. The five most common alleles detected had frequencies of over 10%. No deviations from Hardy-Weinberg equilibrium were found when the expected allele values were compared with the observed values. Sequence analysis of each allele showed a tetranucleotide polymorphism. Alleles 9 to 14 had different sequence structures than alleles 15 to 19. Allele 18 had a different sequence in the Japanese sample compared to an Austrian sample. The power of discrimination was 0.95. The present results demonstrate that the D2S1242 STR locus is a useful genetic marker in the Japanese population.

Alleles↗
PubMed1996

Multiplex sets for the amplification of polymorphic short tandem repeat loci--silver stain and fluorescence detection.

Multiplex PCR amplification systems were developed using well-characterized, polymorphic short tandem repeat (STR) loci. Eight loci utilized in the multiplex amplifications included HUMCSF1PO, HUMTPOX, HUMTH01, HUMVWFA31, HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL. From this list, three or four non-overlapping loci were simultaneously amplified, separated by denaturing polyacrylamide gel electrophoresis and visualized using silver stain or fluorescence detection. The multiplex PCR amplification systems offer a non-isotopic method for rapid, simple and accurate analysis of STR loci. This high-throughput method for DNA identification has immediate and valuable application in forensic analysis, paternity determination, tissue culture strain identification and bone marrow transplantation studies.

DNA↗
PubMed2003

[Application of short tandem repeat DNA in model of human-mouse cord blood transplantation].

OBJECTIVE: To evaluate the significance of applying short tandem repeat DNA in the model of human-mouse cord blood transplantation. METHODS: The techniques of STR-PCR and colony forming cell culture were used to examine the engrafting and influence of hematopoietic growth factor on process in the mice after transplantation of human cord blood (CB). RESULTS: 1. Human DNA expression was detected in the mice that had received tail-vein injection of human CB (1-5 x 10(7) MNC per mouse) but it was not detected in the mice that have received intraperitoneal injection of human CB. 2. Human CB transplanted in SCID mice could reconstitute the hematopoietic function of the mice; the expression level of human cell was not related with the use of hematopoietic growth factor. CONCLUSION: STR-PCR analysis provide a simple and accurate indication of engraftment in the model of human-mouse cord blood transplantation.

Animals↗
PubMed2006

[Fifteen short tandem repeat polymorphisms in Han race of North China].

OBJECTIVE: To research on the genetic polymorphism distributions of 15 short tandem repeat (STR) loci in Han race of North China and the genetic data of population genetics. METHODS: The capillary electrophoresis and five-color fluorescent multi-amplifying were applied to detect the genotypes of 15 STR loci in 597 unrelated Chinese Han individuals. RESULTS: No significant deviation from the Hardy-Weinberg Equilibrium was observed. High polymorphism was detected in the loci. Statistical analysis was carried out to obtain some parameters of forensic medicine. The heterozygosity of 15 loci was above 0.62. The values of discrimination power (DP) at 15 STRs ranged from 0.802 to 0.967. The values of excluding probability of paternity (EP) ranged from 0.320 to 0.697. The values of probability matching (Pm) ranged from 0.033 to 0.198. The fifteen loci showed an accumulated total discrimination power (TDP) more than 0.999999, a cumulative excluding probability of paternity (CEP) as 0.99999571, and total probability matching to be 8.93 x 10(-18). CONCLUSION: The data indicated that detecting combined 15 STRs is sensitive and reliable, and can be used to forensic and individual identification cases in Chinese group.

Asian People↗
PubMed2005

Use of a novel panel of nine short tandem repeats for exact and high-resolution fingerprinting of Aspergillus fumigatus isolates.

Here we describe a new panel of short tandem repeats (STRs) for a novel exact typing assay that can be used to discriminate between Aspergillus fumigatus isolates. A total of nine STR markers were selected from available genomic A. fumigatus sequences and were divided into three multicolor multiplex PCRs. Each multiplex reaction amplified three di-, tri-, or tetranucleotide repeats, respectively. All nine STR markers were used to analyze 100 presumably unrelated A. fumigatus isolates. For each marker, between 11 and 37 alleles were found in this population. One isolate proved to be a mixture of at least two different isolates. With the remaining 99 isolates, 96 different fingerprinting profiles were obtained. The Simpson's diversity index for the individual markers ranged from 0.77 to 0.97. The diversity index for the multiplex combination of di-, tri-, and tetranucleotide repeats ranged from 0.9784 to 0.9968. The combination of all nine markers yielded a Simpson's diversity index of 0.9994, indicative of the high discriminatory power of these new loci. In theory, this panel of markers is able to discriminate between no less than 27 x 10(9) different genotypes. The multicolor multiplex approach allows large numbers of markers to be tested in a short period of time. The exact nature of the assay combines high reproducibility with the easy exchange of results and makes it a very suitable tool for large-scale epidemiological studies.

Aspergillus fumigatus↗
PubMed2026

pSTRminer: integrated bioinformatic software for genome-wide identification and population-scale evaluation of polymorphic short tandem repeats.

Animal forensic genetics plays a critical role in criminal investigations by providing crucial evidence through domestic animal individualization and wildlife species identification. While human forensic genetics benefits from standardized short tandem repeats (STR) genotyping systems, animal forensic applications encounter significant challenges, including the limited availability of validated STR markers, the prevalence of error-prone dinucleotide STRs (di-STRs), and insufficient integration of population data. To address these challenges, we developed pSTRminer, an integrated bioinformatic tool that automates genome-wide STR mining and polymorphism evaluation. By applying pSTRminer to domestic cattle (Bos taurus), we identified 775,444 STRs de novo from the reference genome and genotyped them using whole-genome sequencing data from 60 Chinese and 111 African cattle to evaluate polymorphism across diverse genetic backgrounds. This led to the development of the cattle STR database (CSDB), comprising loci with a genotyping success rate&#x2009;&#x2265;&#x2009;40% and polymorphism information content (PIC)&#x2009;&#x2265;&#x2009;0.5. Experimental validation of 30 randomly selected tetranucleotide STRs (tetra-STRs) and 33 di-STRs via next-generation sequencing in a local Chinese cattle population (n&#x2009;=&#x2009;145) confirmed marker reliability. Although tetra-STRs had lower average polymorphism levels, they exhibited significantly lower stutter ratios (p&#x2009;<&#x2009;0.05), providing a viable path for identifying discriminative markers with fewer artifacts. Systematic screening revealed that certain tetra-STRs could surpass di-STRs in polymorphism. In conclusion, pSTRminer provides a scalable framework for developing standardized STR panels, facilitating the identification of robust and informative markers in forensic applications.

Bioinformatic software↗
PubMed2002

A powerful, novel, multiplex typing system for six short tandem repeat loci and the allele frequency distributions in two Japanese regional populations.

A new multiplex system for six tetranucleotide short tandem repeat (STR) loci was devised based on multicolor dye technology. Six loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, and D17S1290), each with high discriminating power (each unbiased estimates of expected heterozygosity, Exp. Hz, > 0.80 in a preliminary test), were selected from more than 100 tetranucleotide STRs included in a commercially available primer set. These loci were also selected so as not to link with general STRs in commercially released kits including the combined DNA index system (CODIS) 13 core STRs. The primers were newly designed in the present study, in which each amplicon size had a range of less than 200 base pairs (bp), in order to genotype from highly degraded template DNA. Using this system, we genotyped 270 Honshu (mainland)-Japanese and 187 Okinawa-Japanese. From these allele frequencies, we performed three tests, a homozygosity test, a likelihood ratio test and an exact test for Hardy-Weinberg equilibrium (HWE), and no significant deviations (p < 0.05) from HWE were observed. We also compared the allele distributions at six STRs between both populations, and they were significantly different (p < 0.05) at three loci (D6S2439, D9S1118 and D4S2639). Furthermore, the Exp. Hz and the power of discrimination (PD) at all loci in the Honshu-Japanese population were higher than 0.80 and 0.93, respectively. These statistical values for discriminating power in the Honshu-Japanese were almost the same as in the Okinawa-Japanese. This novel, multiplex polymerase chain reaction (PCR) amplification and typing system for six STR loci thus promises to be a convenient and informative new DNA profiling system in the forensic field.

Alleles↗
PubMed1998

A methylation imprint mark in the mouse imprinted gene Grf1/Cdc25Mm locus shares a common feature with the U2afbp-rs gene: an association with a short tandem repeat and a hypermethylated region.

We identified a sperm-specific methylation imprint mark (Site II) associated with a short tandem repeat sequence and a site/region methylated in both gametes (Site I) in the Grf1 locus on mouse chromosome 9, which shared a common feature with the U2afbp-rs gene. Sites or regions of gamete-specific methylation in imprinted genes are strong candidates for carrying information regarding the parental origin of alleles. The gamete-specific methylation pattern of Sites I and II was conserved after fertilization, but attained the somatic cell pattern by the blastocyst stage. In primordial germ cells, Site I was methylated, but Site II was unmethylated in both male and female embryos, suggesting that the sperm-specific methylation imprint mark in Site II was established during spermatogenesis. These common features in methylation imprint regions may be a clue to identifying regions carrying primary information for the imprinting regulation.

Animals↗
PubMed2002

A new pentaplex system to study short tandem repeat markers of forensic interest on X chromosome.

A new method has been optimised to amplify five X chromosome short tandem repeat (STR) markers of interest in forensic medicine: human phosphoribosyl transferase (HPRTB), DXS101, androgen receptor (ARA), DXS7423 and DXS8377. Markers were conveniently amplified in a single PCR reaction with fluorochrome-labelled primers, which allowed the analysis of fragment sizes after injection into a capillary electrophoresis system. The most common alleles of each locus were sequenced and used in a control ladder to type unknown samples.

Adult↗
PubMed2006

Genetic polymorphism at 15 tetrameric short tandem repeat loci in four aboriginal tribal populations of Bengal.

POPULATIONS: This study reports the genetic polymorphism observed at 15 short tandem repeat loci D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, D2S1338, D19S433, and FGA in four aboriginal populations of Bengal. The analysis was performed to decipher the suitability of CODIS as well as six other highly polymorphic and unlinked markers in Forensic Testing. Studied populations include four tribes: Karmali, Kora, Maheli, and Lodha.

DNA Fingerprinting↗
PubMed2001

Pentanucleotide short tandem repeat locus DXYS156 displays different patterns of variations in human populations.

AIM: To establish a database for the pentameric short tandem repeat locus DXYS156 from worldwide populations for routine genotyping in forensic identity testing and evolutionary biology. METHODS: Using polymerase chain reaction with a newly designed primer pair, we analyzed 1,408 male and female samples from 28 populations representing four major geographic groups. RESULTS: We observed 11 different alleles, which we sequenced and used to construct an allelic ladder. CONCLUSION: DXYS156 displays a contrasting pattern of X-linked and Y-linked variation among geographic regions, and between X and Y chromosomes. This complex allele distribution may be forensically useful for the ethnic differentiation of unknown stains.

Alleles↗
PubMed2003

[Polymorphisms of six short tandem repeat loci in Zhejiang She ethnic population and Zhejiang Hans of China].

OBJECTIVE: To investigate genetic polymorphism of six short tandem repeat (STR) loci (D3S1358,D16S539, TH01,TPOX, CSF1PO,D7S820) in Zhejiang She ethnic population and Han population. METHODS: By use of AmpFlSTR Cofiler kit, 6 STR loci in 108 She samples and 102 Han samples were amplified. The PCR products were electrophoresed by ABI Prism 377 sequencer; the data were analyzed by Genescan software. RESULTS: All genotype frequencies of the 6 STR loci in She and Han ethnic groups met Hardy-Weinberg equilibrium. In the She population, the heterozygosities (H) in D3S1358,D16S539,TH01,TPOX, CSF1PO and D7S820 were 0.8028, 0.9148, 0.7522, 0.6728, 0.9123,0.8338, the exclusion of paternity(EP) were 0.4067, 0.6057, 0.4437, 0.3200, 0.5250, 0.5358, discrimination power (DP) were 0.6690, 0.7841, 0.6447, 0.5382, 0.7298, 0.7296.The combined DP, PE and polymorphism information content were 0.9991,0.9805,0.9988 respectively. There were significant differences at D3S1358, D16S539 and TPOX loci, compared with Hans. CONCLUSION: She population has its own STR allele distribution characteristic. The above data obtained from She population can be used not only in genetic researches and population investigation, but also in human identity and paternity testing.

China↗
PubMed2004

[Genetic polymorphisms of six short tandem repeat loci in the Han population of Henan province in China].

OBJECTIVE: To investigate the allele frequencies of six short tandem repeats (STR) loci D12S391, D5S818, D18S51, PAHI3, D8S1179, D3S1358 in the Han population of Henan province and to obtain preliminary data. METHODS: DNA was extracted with phenol-chloroform from 140 EDTA-blood specimens of healthy unrelated individuals in Henan population; multiplex PCR technique and PAGE vertical electrophoresis were used to screen the genotype frequencies of six STR systems in Henan population. RESULTS: The test for Hardy-Weinberg equilibrium revealed that the genotype distribution was correspondent with the expected. The observed heterozygosities of six loci were 0.871, 0.769, 0.871, 0.773, 0.901, 0.722. The calculated discrimination power is 0.9999998, the calculated power of exclusion is 0.99845, the calculated matching probability is 2.39 x 10(-7). CONCLUSION: All of the six loci in this study have high power of discrimination and exclusion; they may be very useful genetic markers for individual identification, paternity test and genetics purposes.

Alleles↗
PubMed2006

[Allele frequencies and species specificity of five short tandem repeat loci of Chinese Han population in Chengdu].

OBJECTIVE: To obtain the data in polymorphism distribution of the five short tandem repeat (STR) loci: D18S979, D11S2014, D18S548, D1S1667 and GATA164F07 of Chinese Han population in Chengdu, and to evaluate their usefulness in the field of species specificity in forensic science. METHODS: PCR, polyacrylamide gel electrophoresis (PAGE) and silver staining techniques were used to analyze the DNA samples from 100 unrelated individuals of Chinese Han ethnic group in Chengdu. Twelve different animals: monkey, pig, dog, bull, goat, chicken, duck, eel, mudfish, rabbit, guinea pig and mouse were selected as controls in this study for evaluating the species specificity of the five STR loci. RESULTS: Six alleles and twelve genotypes were observed in D18S979. Five alleles and eleven genotypes were observed in D11S2014. Five alleles and thirteen genotypes were observed in D18S548. Seven alleles and nineteen genotypes were observed in D1S1667. Six alleles and fourteen genotypes were observed in GATA164F07. The genotype distributions of the five loci were analyzed by some related software and no deviation from the Hardy-Weinberg equilibrium was observed. Evaluated by way of using different animals as controls, monkey had amplification products at the extra-typing field of D18S979, D11S2014 and D1S1667. Bull, dog and eel had amplification product at typing field of D18S979, and pig, duck, mouse and rabbit had weak product. Bull had weak product at the typing field of D18S548. Dog, goat and eel had product at the typing field of D1S1667. Dog had weak product at the typing field of GATA164F07. Mudfish, chicken and guinea pig had no amplification product at the five loci. CONCLUSION: These data indicate that D18S979, D18S548, D1S1667 and GATA164F07 are highly polymorphic and D11S2014, D18S548 and GATA164F07 can play a key role in species identification.

Animals↗