Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “STR”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
PubMed2000

Analysis of eight STR loci in two Hungarian populations.

A collection of eight STR loci (D3S1358, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) was used to generate allele frequency databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. During the analysis two intermediate sized alleles and a sequence variant allele were observed at the D7S820 locus. All three types of allelic variants were found to have modification (deletion, insertion, transversion) in the same block of a (T)(9) stretch located within the 3' flanking region of each allele, which may indicate a possible higher mutation rate of this (T)(9) block. For the loci D3S1358 and D7S820 the Romany population database showed departures from Hardy-Weinberg equilibrium. The forensic efficiency values for the Romany population were slightly different from those found in the Hungarian Caucasian population. Comparing the allele frequency values by G-statistic, calculating the F(st) indices and with the pairwise comparisons of inter-population variance, the two Hungarian populations could be distinguished using data of the eight STR loci.

Consanguinity↗
PubMed2000

Y chromosomal short tandem repeat (STR) loci in a representative group of males living in South Württemberg: a database for application in forensic medicine.

In this study, we resolved the allelic distribution of three Y chromosomal short tandem repeats (STRs), DYS19 (n=218), DYS390 (n=257) and DYS393 (n=215), in a population study of 257 unrelated men living in the area of South Wüerttemberg/Hohenzollern. In DYS19 and in DYS393, five different alleles were discovered, and in DYS390, six different alleles. Forty-nine different haplotypes were found in 202 unrelated male individuals. By investigating each of the three STR systems separately, the most powerful results were found in DYS390, with a PE (power of exclusion) of 0.74, followed by DYS19 (PE: 0.65) and DYS393 (PE: 0.47). Using a combination of two systems (n=202), the PEs ranged from 0.79 (DYS19 and DYS393) to 0.89 (DYS19 and DYS390). The combination of all three STR systems revealed a PE of 0.93.

DNA Fingerprinting↗
PubMed2000

A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males.

A 9-locus microsatellite framework (minimal haplotype), previously developed for forensic purposes so as to facilitate stain analysis, personal identification and kinship testing, has been adopted for the establishment of a large reference database of male European Y-chromosomal haplotypes. The extent of population stratification pertaining to this database, an issue crucial for its practical forensic application, was assessed through analysis of molecular variance (AMOVA) of the 20 regional samples included. Despite the notion of some significant haplotype frequency differences, which were found to correlate with known demographic and historic features of Europeans, AMOVA generally revealed a high level of genetic homogeneity among the populations analyzed. Owing to their high diversity, however, accurate frequency estimation is difficult for Y-STR haplotypes when realistic (i.e. moderately sized) datasets are being used. As expected, strong pair-wise and higher order allelic associations were found to exist between all markers studied, implying that haplotype frequencies cannot be estimated as products of allele frequencies. A new extrapolation method was therefore developed which treats haplotype frequencies as random variables and generates estimates of the underlying distribution functions on the basis of closely related haplotypes. This approach, termed frequency 'surveying', is based upon standard population genetics theory and can in principle be applied to any combination of markers located on the Y-chromosome or in the mitochondrial genome. Application of the method to the quality assured reference Y-STR haplotype database described herein will prove very useful for the evaluation of positive trace-donor matches in forensic casework.

Alleles↗
PubMed2001

Sequenced allelic ladders and population genetics of a new STR multiplex system.

The advent of PCR technology and use of short tandem repeat (STR) loci improves throughput and reduces costs whilst a high level of discrimination can be achieved. A new system, comprising seven STRs, was developed to compliment the existing systems. This paper describes the preparation of allelic ladders of the most commonly observed alleles of a new STR multiplex system (third generation; TGM multiplex); all alleles have been sequenced. Meioses studies estimated a mutation rate of 0-0.4% across loci. Statistical independence was investigated by employing exact tests; chi(2)-tests and excess homozygosity tests. The results demonstrated that the allele proportions do not differ from those expected and that there was no consequential dependence between loci. The discriminating power of the system was examined using 295 Caucasian, 140 Afro-Caribbean and 212 Asian unrelated samples, and was found to be approximately 1 in 50 million, 1 in 85 million and 1 in 20 million for each of these groups, respectively.

Alleles↗
PubMed2001

Application of a Y-STR-pentaplex PCR (DYS19, DYS389I and II, DYS390 and DYS393) to sexual assault cases.

A survey of 89 random rape cases including 166 semen traces, according to the prostate-specific-antigen test, showed the need for a more efficient method of DNA-profiling. No male autosomal STR-profile could be detected, after differential lysis, in 35% of the 84 samples usually containing high amounts of the victim's cells, i.e. vaginal/anal washings and knickers. A Y-STR-pentaplex was applied to the stored sperm fraction of 50 unsolved semen traces, with success in 48% of them. The chance of success depends of the amount of total DNA available and of the quality of the extracted DNA.

Belgium↗
PubMed2001

Further characterization and population data for the pentanucleotide STR polymorphism D10S2325.

Pentanucleotide tandem repeat markers are interesting for forensic sciences, because they may present less stutter on the electrophoretic pattern. We focused on the analysis of the DNA sequence for each allele at the pentanucleotide STR locus D10S2325 in order to understand their structures in the human genome and to construct human allelic ladder, which is necessary for forensic DNA typing. In order to evaluate the forensic applicability of D10S2325 and to construct a preliminary database, the genotype distributions and allele frequencies in three major ethnic groups were investigated. The population samples included Caucasians (Germans), Africans (African Americans), and Asians (Chinese). A total of 520 samples from unrelated individuals was analyzed by Amp-FLP. An example of each allele and new alleles were sequenced. Allele determination was carried out by comparison with a sequenced human allelic ladder made in-house. This pentanucleotide STR provided easily interpretable results. A total of 15 alleles was found in our population samples. Three new alleles were observed and named as alleles 19 and 21 based on the number of repeat motifs, while allele 19 can be divided further into two alleles, 19a and 19 according to analysis of the sequence. No evidence of deviation from Hardy-Weinberg equilibrium was observed. In 64 confirmed father/mother/child triplets no mutation event was observed. Using a maximum likelihood method, the mutation rate was indirectly estimated as 2.5 x 10(-5). These results suggest that D10S2325 is a useful marker for forensic casework and paternity analysis.

Black or African American↗
PubMed2002

Validation of the STR DXS7424 and the linkage situation on the X-chromosome.

X-linked microsatellite markers have proven to be powerful tools for parentage testing, mainly in deficiency paternity cases when the disputed child is female. However, only a small number of X-linked short tandem repeats (STRs) have been comprehensively described for forensic applications to date. We present sequence and population genetic data of the DXS7424 STR (GDB-G00-577-633) which is a trinucleotide repeat polymorphism representing 12 alleles of 147-180 bp in length. DXS7424 is located at Xq22 and closely linked to DXS101, corresponding to a genetic localisation of 104.9-121 cM from Xp-tel.PCR fragment length measurements and sequencing were carried out using the automatic gene analyser ABI 310 (Applied Biosystems). The population of 764 unrelated Germans checked for this STR exhibited the following features: polymorphism information content (PIC) = 0.780; heterozygosity (Het) = 0.843; mean exclusion chance (MEC = 0.766. Kinship tests revealed a typical X-linked inheritance. In 300 meioses under investigation, mutations were not found. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were not established. Linkage studies confirmed closely linkage to DXS101. Additional we found linkage disequilibrium between DXS7424 and DXS101. This requires to use the established haplotype frequencies in kinship testing.

Alleles↗
PubMed2002

Distribution of alleles of 15 STR loci of the Powerplex 16 Multiplex system in four predominant population groups of South India.

Allele distribution of the 15 STR loci of Powerplex 16 Multiplex System were studied in four predominant population groups of South India for evaluating their significance in human identification and population study: Iyengar Brahmin (65), Gowda (59), Lingayat (98) and Muslim (45) from the state of Karnataka. The loci analyzed are--D3S1358, THOI, D2ISI I, D18S51, D5S818, Penta E, D13S317, D7S820, D16S539, CSFIPO, Penta D, vWA, D8S179, TPOX and FGA. Out of 15 STR loci Penta D and D18S51 were found highly polymorphic in the studied populations.

Alleles↗
PubMed2002

Archived or directly swabbed latent fingerprints as a DNA source for STR typing.

Former studies [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501, J. Forensic Sci. 45 (3) (2000) 687] have shown that even a single skin contact, documented by a latent fingerprint, can transfer enough DNA for a genetic analysis. It was proven in these studies that it is possible to swab fingerprints from surfaces [Nature (1997) 387, Electrophoresis 20 (1999) 2870, P. Van Renterghem, D. Leonard, C. De Greef, Progress in Forensic Genetics, Vol. 8, 2000, p. 501] and use them as a DNA source. Usually, however, discovered fingerprints are removed with scotch tape and placed on evidence cards for further investigation.In this study, we tried to assess the potential use of latent fingerprints as a DNA source for STR typing. The materials (magnetic powder, soot powder and scotch tape) used for visualization and archiving fingerprints in Germany were tested for their PCR inhibitory characteristics. Then, fingerprints were placed on clean glass surfaces, visualized and tested for their usefulness as a DNA source. Obtained DNA was quantified and tested in an STR system. Partly it proved possible to type fingerprints taken directly from the surface as well as fingerprints removed from the surface with scotch tape.

DNA Fingerprinting↗
PubMed2002

A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers.

A multiplex polymerase chain reaction (PCR) assay capable of simultaneously amplifying 20 Y chromosome short tandem repeat (STR) markers has been developed to aid human identity testing and male population studies. These markers include all of the Y STRs that make up the "extended haplotype" used in Europe (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAII) plus additional polymorphic Y STRs (DYS437, DYS438, DYS439, DYS447, DYS448, DYS388, DYS426, GATA A7.1, and GATA H4). Primers for the markers DYS385, DYS389, and YCAII target duplicated regions of the Y chromosome and thus can provide two polymorphic peaks for each respective primer set. This Y STR 20plex, which utilizes 34 different PCR primers, is the first to include a simultaneous amplification of all the markers within the European "minimal" and "extended" haplotypes. Relative primer positions are compared between the newly developed primers described here and previously published ones. Efforts were made to avoid X chromosome homology in the primer design as well as close packing of PCR product size ranges in order to keep all alleles less than 350 bp through careful examination of known allele ranges. Haplotype comparisons between the 20plex and a commercially available kit found excellent agreement across the 76 samples in the Y chromosome consortium panel.

Alleles↗
PubMed2002

Population studies on three Native Alaska population groups using STR loci.

Allele distributions for 13 short tandem repeat (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, CSF1PO and D16S539 were determined for three Native Alaskan population groups-Athabaskans, Inupiats, and Yupiks. Although genetic diversity is lower in the Native Alaskan populations compared with Caucasians and Africans, almost all loci are highly polymorphic in all three Native Alaskan groups. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Only two examples of detectable departures from HWE out of 39 locus-population tests performed were observed based on the exact test (Yupik, D8S1179, P=0.030; Yupik, D5S818, P=0.016). The F(ST) estimate overall 13 STR loci is 0.0309 for the Native Alaskan populations. Based on a genetic distance measure, Athabaskans are more closely related to Apaches and Navajos (all of the same linguistic group) than the other Native Alaskan groups. The F(ST) estimate for Athabaskans, Apaches and Navajos is 0.0180 and for Inupiats and Yupiks is 0.0167. The allele frequency data can be used for estimating DNA profile frequencies for Native Americans residing in Alaska.

Alaska↗
PubMed2002

Genetic polymorphism at 15 STR loci among three important subpopulation of Bihar, India.

Genotype polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in three genetically important minor caste groups (Yadav, Kurmi and Baniya) of Bihar, a eastern state of India to evaluate their significance in human identification and population genetics study. The selected communities practice endogamy. Despite of same geographical area, the physical features of Yadavs and Baniyas resemble North Indian Indo-Caucasoids whereas Kurmis resemble more to Indo-Austroloids. Among the chosen 15 loci, two are penta-nucleotide repeat: Penta-D and Penta-E, and 13 are tetra-nucleotide repeat: vWA D8S1179, TPOX, FGA, D5S818, D13S317, D7S820, D16S539, D3S1358, THO1, CSF1PO, D21S11, D18S51 and are validated for other population of India and world for forensic testing and human population study. Thirteen of these STR loci are present in the combined DNA index system (CODIS) [J. Forensic Sci. 44 (1999) 1277] and world-wide data is available.

Humans↗
PubMed2002

Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches--the European picture.

We suggest the use of the mismatch distribution methodology as an easy way to estimate the distance between all pairs of haplotypes present in a sample. This approach allows the evaluation of the proportion of pairs of Y-STR haplotypes that are prone to become identical by state (IBS), in one generation, by recurrent mutation, a statistic of major importance in the forensic field. The mismatch approach presents some advantages alternatively to the empirical one, since it is not necessary to have simultaneous information on STRs and SNPs, and it allows the evaluation of IBS also within-haplogroups. The estimation of IBS at an European scale showed that there is a high population substructuring for this parameter, increasing from southern-central European countries towards west and north, in accordance to what was found for Y-biallelic markers. This result seems to imply a more careful use of large databases for matching evaluation, even in the absence of population structure for general Y-STR diversity. Furthermore, mismatch distribution can be used to measure the distance between a particular haplotype and all the haplotypes in a sample. When applied to the most frequent haplotypes in Europe it revealed that the opportunity for IBS is not directly related to the frequency of a haplotype, but highly dependent on the proportion of neighbouring haplotypes--so, that reporting on the haplotype frequency for evaluating the significance of a match can be misleading.

Chromosomes, Human, Y↗
PubMed2003

A highly polymorphic STR locus in Cannabis sativa.

We report on the first short tandem repeat (STR) locus to be isolated from the plant Cannabis sativa. The STR locus, isolated by a hybrid-capture enrichment procedure, was found to contain a simple sequence repeat motif of 6 bp. This 6 bp repeat motif showed no variation in repeat length but with minor variations in repeat unit sequences. The data show the locus to be highly polymorphic with the number of repeat units ranging from 3 to 40 in 108 screened samples. The observed heterozygosity was approximately 87.04%. The forward and reverse primers (CS1F and CS1R) produced no PCR products in cross-reaction study from 20 species of plants, including highly related species such as Humulus japonicus and Nicotiana tabacum. This hexanucleotide repeat DNA locus could be used to identify cannabis samples and predict their genetic relationship as the test is specific to C. sativa and is highly reproducible.

Alleles↗
PubMed2003

Analysis of STR polymorphisms in the northeast Chinese population.

The distribution of allele frequencies for 12 short tandem repeats (STR) loci were determined in 300 unrelated healthy Chinese individuals living in northeast of China, using AmpFlSTR Profiler Plus kit and AmpFlSTR Green I kit (PE, Applied Biosystems). In these samples, 123 alleles and 399 genotypes were observed for 12 STR loci. The distribution of these observed genotypes were not significantly different from the expected distribution according to Hardy-Weinberg equilibrium.

Alleles↗
PubMed2003

Genetic diversity in four tribal groups of western India: a survey of polymorphism in 15 STR loci and their application in human identification.

Genetic diversity at 15 STR loci: 2 pentanucleotide and 13 tetranucleotide STR loci was determined in four highly endogamous tribal groups, viz. Madia-Gond, Mahadeo-Koli, Katkari and Pawara of western India. The distribution of genotypes at studied 15 loci was found in agreement with expected values according to Hardy-Weinberg equilibrium. The combined power of discrimination of 15 loci was calculated as 0.80 while combined power of exclusion was observed as 0.53 among the studied four tribal groups. The study demonstrate very low heterozygosity and low power of exclusion of the loci of Powerplex 16 among the selected groups indicating less informativeness of the studied markers in human identification testing.

DNA Fingerprinting↗
PubMed2003

Population data of nine STR loci, D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, in Bangladeshis and Indonesians.

Allele frequencies of nine short tandem repeat (STR) loci, D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, were determined for 127 unrelated Bangladeshi individuals and 105 unrelated Indonesian individuals using the AmpFLSTR Profiler Kit. The genotype frequency distributions of the nine STR loci were in the Hardy-Weinberg equilibrium for both populations.

Alleles↗