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At least 199 records · Page 11Linked to original sources
PubMed2000

Haplotype frequencies and population data of nine Y-chromosomal STR polymorphisms in a German and a Chinese population.

Y-chromosomal STR loci are of increasing interest in paternity testing, forensic casework, anthropological and evolutionary studies. We participate in a cooperation to establish an international reference database of at least nine Y-chromosomal STR loci to be used for biostatistic calculations. We present frequency distributions of nine Y-chromosome specific STR polymorphisms and frequencies of compound haplotypes in two populations. We chose the loci DYS393, DYS19, DYS392, DYS385I, DYS385II, DYS390, DYS391 and DYS389I and II. Blood samples were taken from 136 unrelated male individuals from Cologne (Germany) and of 63 unrelated males from Chengdu (Sichuan Province, PR China). DNA was extracted by a salting out procedure or chelex extraction. PCR was carried out in two multiplex reactions. Fragment analysis was conducted on an ALF- or ALF-express sequencer. Frequency profiles of the German men showed no significant differences compared to most European populations. Mean exclusion chances were between 0.44 for DYS393 and 0.94 for DYS385. Haplotype diversity for the complete haplotype was 86.66% in Germans and 98% in Chinese. The Chinese men showed for all analysed loci except for DYS389I and DYS390 remarkably different allele distributions.

Asian People↗
PubMed2001

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

Databases, Factual↗
PubMed2001

DYS STR analysis with epithelial cells in a rape case.

We report here the application of Y-chromosomal DNA analysis in a rape case, which occurred in Stuttgart, Germany. Microscopic examination of the victim's vaginal swabs and her underwear showed no sperm cells. DNA was extracted from vaginal and epithelial cells and analysed with the autosomal systems SE33, THO1 (singleplex) and with the multiplex Profiler Plus (Applied Biosystems, Foster City, USA). The results of these autosomal STR analysis gave no hint at a mixed sample and failed to identify a male profile. DYS STR analysis with the systems DYS391, DYS392, DYS393, DYS19 and DYS389 I/II showed the same characteristic features as the suspect. We used this incomplete haplotype to search in the Y-STR Haplotype Reference Database via Internet. In a Caucasian population sample of 3589 minimal haplotypes we found 71 matches. The suspect confessed the crime and was finally condemned to 4 years imprisonment.

DNA↗
PubMed2001

Routine Y-STR typing in forensic casework.

In the field of molecular diagnosis, forensic casework analysis is one of the most demanding investigations, due to its social impact. Optimization of DNA typing multiplex reactions with identical cycling conditions as those required by autosomal short tandem repeats (STR) multiplex reduces errors, and saves time and reagents. Previously, we validated a five Y-STRs set, all of them generating single band patterns. This work reports the optimization of combined multiplexes, a triplex (DYS19, DYS390 and DYS391) and a duplex (DYS392 and DYS393), that can be amplified in identical cycling conditions as those required by commercially available multiplex autosomal STR kits. In addition both Y chromosome multiplexes can be combined for co-injection on a capillary electrophoresis based automated sequencer. Statistical attributes of the haplotypes of the five Y-STR investigated were evaluated in unrelated males from different metropolitan areas of Argentina. This system was successfully used for investigating more than 350 forensic routine cases in our country.

Argentina↗
PubMed2001

Stability of prostate specific antigen (PSA), and subsequent Y-STR typing, of Lucilia (Phaenicia) sericata (Meigen) (Diptera: Calliphoridae) maggots reared from a simulated postmortem sexual assault.

Rape-homicide represents one of the most heinous crimes, but which are also the hardest to solve due to the high occurrence of stranger-to-stranger interaction. This is the first case of obtaining P30 and Y-STR typing from a simulated postmortem sexual assault. 2, 3.5 and 6 microl of liquid semen was added to a liver substrate and Lucilia (Phaenicia) sericata (Meigen) eggs added. The larvae fed upon the semen coated substrate and were removed for testing after 48 and 145h after initial liquid semen deposition. P30 was recorded from whole postfeeding larvae after 145h, with correct Y-STR profiles obtained from the crop of actively feeding second instar larvae after 48h of initial semen deposition. The ability to obtain P30 and Y-STR profiles from larvae infesting a cadaver, with the suspicion of sexual assault having occurred prior to death, provides a new avenue to aid in the solving of such crimes.

Adult↗
PubMed2001

A STR mutation in a heteropaternal twin case.

A heteropaternal male twin case with two men being alleged fathers was investigated as requested by the Court. Up to 37 PCR-based polymorphic DNA systems were studied in this case which was complicated by a paternal ACTBP2 mutation detected in one twin. This is the first report on a STR mutation in a double paternity case where both biological fathers were indisputably identified. The STR systems enable the resolution of these complex genetic relationships even in a case where a mutation in one STR locus was encountered.

DNA Fingerprinting↗
PubMed2002

Y-STR DNA amplification as biological evidence in sexually assaulted female victims with no cytological detection of spermatozoa.

Identification of spermatozoa is the biological evidence most often sought in specimens from rape victims. Absence of spermatozoa usually terminates biological investigations, and the victim's testimony can be contested. We assessed the utility and reliability of PCR amplification using Y-chromosomal STR polymorphisms in specimens from female victims of sexual assault with negative cytology. One hundred and four swabs without spermatozoa detected by cytology were collected from 79 alleged sexually assaulted female victims and amplification of Y-STR and of amelogenin was performed.Overall, Y-chromosome was detected and evidenced sexual penetration in 28.8% of swabs. In the population of victims examined more than 48 h after the sexual assault, Y-STR were still evidenced in 30% of the cases. These results show that swabs should be taken from victims for Y-chromosome DNA typing even after long delays between sexual assault and medical examination.

Adult↗
PubMed2003

Inferring recent human phylogenies using forensic STR technology.

STR loci are characterized by extremely high mutation rates and thus, high levels of length polymorphism both within and among populations. In addition, much of the observed variation is believed to be nearly selectively neutral. Because of these features, STRs are ideal markers for genetic mapping, intra-species phylogenetic reconstructions and forensic analysis. In the present study, we investigate the application of five STR loci (CS1PO, TH01, TPOX, FGA and vWA) routinely used in forensic analysis for delineating the phylogenetic relationships of 10 human populations representing the three major racial groups (African-Caribbean, Croatian from the island of Hvar, East Asian, Han Chinese, Italian, Japanese, Portuguese, UK Caucasian, US Caucasian and Zimbabwe). The resulting tree topology exhibited strong geographic and racial partitioning consistent with that obtained with mtDNA haplotypes, Y-chromosome markers, SNPs, PAIs (polymorphic Alu insertions) as well as classic genetic polymorphisms. These findings suggest that forensic STR loci may be particularly powerful tools and provide the necessary fine resolution for the reconstruction of recent human evolutionary history.

DNA Fingerprinting↗
PubMed2003

Genetic profiling of a central Venezuelan population using 15 STR markers that may be of forensic importance.

The AmpFlSTR Identifiler kit has recently been accepted for use in DNA databasing of forensic samples in the FBI's National DNA Index System. In the present study, we used this kit to analyze the allele distribution of 15 short tandem repeat markers (STR) in individuals living in Caracas city, Venezuela. The allele frequencies of two of these STR, D2S1338 and D19S433, have not previously been reported for this or any other Latin American population. The results indicate that for the population here studied, the 15 STR tested are useful markers for paternity testing and forensic casework.

Alleles↗
PubMed1997

Multiplex amplification of STR loci with gender alleles using infrared fluorescence detection.

The analysis of short tandem repeat (STR) polymorphisms has proven extremely useful for gene mapping, paternity testing, and forensic analysis. Several commercial products are currently available for performing amplification and analysis of STRs. We have adapted Promega Geneprint Systems for use with a high sensitivity infrared (IR) fluorescent automated DNA sequencer. IR-labeled amplification products are generated by including a small quantity of IR-labeled dATP in the reaction. Several Geneprint STR loci can be multiplexed together with the amelogenin sex identification locus in a single amplification reaction. We have successfully amplified up to five Geneprint STR loci together with the amelogenin locus thus improving the throughput of analysis. Purified genomic DNA as well as simulated forensic samples have been utilized for these multiplex amplifications.

Alleles↗
PubMed1997

Subtyping of D20S85 STR alleles by single-strand conformation polymorphism (SSCP) analysis.

During a population study of STR locus D20S85, we discovered two types of sequence variations by direct sequencing of the alleles: two transitions each of G to A and A to G occur in the 5' flanking region in the individuals possessing allele 6 and some of those possessing allele 7 [1]. Using single-strand conformation polymorphism (SSCP) analysis, we were able to distinguish two subtypes of allele 7 from each other. This analysis method enables rapid screening for STR alleles of the same length with different sequences, and should find application to other complex STR loci because of the practical advantage of simplicity in comparison to sequencing.

Forensic Medicine↗
PubMed1999

Results of collaborative study regarding the standardization of the Y-linked STR system DYS385 by the European DNA Profiling (EDNAP) group.

Y-chromosome linked short tandem repeat (STR) loci are inherited as a closely linked haplotype, which appears to remain stable in a given paternal lineage over many generations. In forensic cases, Y-linked STRs are particularly useful for the identification of human remains as well as in rape cases with mixed male/female stain samples. DYS385 is derived from tandemly duplicated segments of the Y chromosome thus giving rise to two fragments of variable length which do not behave like alleles but genotypes. The European DNA Profiling (EDNAP) group has carried out a collaborative exercise among 14 participating laboratories using DYS385 for typing of five unknown bloodstains and a control sample. Furthermore, population data from eight different European countries with samples sizes between 91 and 150 male individuals were collected. The results confirm previous observations that DYS385 is one of the most informative Y-linked STR loci. It could also be demonstrated that reproducible results can be obtained independently from the electrophoretic separation and detection methods used. Thus DYS385 may serve as a useful complementation to the routinely used autosomal STR systems in special cases.

Blood Protein Electrophoresis↗
PubMed2002

CEPH family 1362 STR database: an online resource for characterization of PCR products using electrospray ionization mass spectrometry.

An online database has been established in order to validate electrospray ionization mass spectrometry (ESI-MS) for genotyping and to publicize the procedures developed in our laboratory for the characterization of PCR products by ESI-MS. Genotypes derived from short tandem repeat (STR) loci that were obtained using ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) have been posted for fifteen members of the CEPH family 1362 pedigree. The website provides specific information such as PCR parameters, PCR product cleanup approaches, and ESI solution compositions to enable other laboratories to reproduce our data. Links are provided to related websites in an effort to integrate information regarding the CEPH family, STR genotyping, and mass spectrometry. The database, currently available at http://www.people.vcu.edu/ -dcmuddim/genotype/ will be routinely updated with genotypes from additional STR loci including PCR parameters as well as PCR cleanup strategies as further developments are completed.

DNA, Complementary↗
PubMed2000

Japanese population data for two STR loci, HumTPO and HumLPL.

The two short tandem repeat (STR) systems, HumTPO and HumLPL, were investigated in blood samples obtained from approximately 800 unrelated Japanese individuals living in seven geographically different areas of Japan. Neither deviation from a Hardy-Weinberg equilibrium nor significant difference between the allele distributions was found among the seven Japanese populations in the two STR systems. These findings indicate that there is a general uniformity for both the STR loci in the Japanese population.

Journal Article↗
PubMed2000

A Catharanthus roseus BPF-1 homologue interacts with an elicitor-responsive region of the secondary metabolite biosynthetic gene Str and is induced by elicitor via a JA-independent signal transduction pathway.

Plants respond to pathogen attack by induction of various defence responses, including the biosynthesis of protective secondary metabolites. In Catharanthus roseus, the elicitor-induced expression of the terpenoid indole alkaloid biosynthetic gene Strictosidine synthase (Str) is mediated via the plant stress hormonejasmonate. In the promoters of several defence-related genes, cis-acting elements have been identified that are important for transcriptional regulation upon stress signals. Here we show that an upstream region in the Str promoter confers responsiveness to partially purified yeast elicitor and jasmonate. Yeast one-hybrid screening with this element as a bait identified a MYB-like protein, which shows high homology to parsley box P-binding factor-1 (PcBPF-1). In vitro analyses showed that the Str promoter fragment contained a novel binding site for BPF-1-like proteins with higher binding affinity than the previously described box P. CrBPF-1 mRNA accumulated rapidly in elicitor-treated C. roseus suspension cells, whereas no induction was observed with jasmonate. Inhibitor studies indicated that CrBPF-1 plays a role in an elicitor-responsive but jasmonate-independent signal transduction pathway, acting downstream of protein phosphorylation and calcium influx.

Amino Acid Sequence↗
PubMedDate not supplied

Short tandem repeat (STR) variation in eight village populations of the island of Korcula (Croatia).

The aim of this study was to analyse short tandem repeat (STR) variation using the data on nine loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in the populations from eight villages on the island of Korcula, Croatia, in order to analyse its genetic and population structure. The analysis of STR data in this study indicated an appreciable degree of genetic homogeneity among the studied village populations on the island, even though a so-called 'east-west dichotomy' and differentiation between the inhabitants of the most recent settlement and the remaining ones was indicated with respect to the loci CSF1PO and TPOX, respectively. The validity of STR markers in assessing genetic structure of small populations and especially in determining the relationships among geographically closely related but reproductively isolated groups remains to be further evaluated, especially in terms of a larger number of studied loci in order to possibly find specific markers useful for resolving genetic patterns of variability at regional levels.

Croatia↗
PubMed1996

A comparative transcription map of the murine bare patches (Bpa) and striated (Str) critical regions and human Xq28.

The X-linked developmental mouse mutations bare patches (Bpa) and striated (Str) may be homologous to human X-linked dominant chondrodysplasia punctata (CDPX2) and incontinentia pigmenti (IP2), respectively, based on their genetic mapping and clinical phenotypes. Bpa and Str have been localized to an overlapping critical region of 600 kb that demonstrates conserved gene order with loci in human Xq28 between DXS1104 and DXS52. As part of efforts to isolate the genes involved in these disorders, we have begun to develop a comparative transcription map spanning this region in both species. Using techniques of cross-species conservation and hybridization, exon trapping, and cDNA selection we have identified four known genes or members of gene families--caltractin, a member of the gamma-aminobutyric acid (GABAA) receptor gene family, a member of the melanoma antigen gene (MAGE) family, and several members of the murine-specific, X-linked lymphocyte regulated gene (Xlr3) family. Trapped exons and, in some cases, longer cDNAs have been isolated for potentially 7-9 additional genes. One cDNA demonstrates highly significant homology with members of the Krüppel family of zinc finger transcription factors. A second novel cDNA demonstrates homology at the 3' end of the predicted amino acid sequence to a LIM domain consensus. Gene order appears conserved among those cDNAs determined to be present in both human and mouse. Three of the murine transcripts appear to be present in multiple copies within the Bpa/Str critical region and could be associated with a predisposition to genomic rearrangements. Reverse transcriptase PCR (RT-PCR) and Northern analysis demonstrate that several of the transcripts are expressed in mid-gestation murine embryos and neonatal skin, making them candidates for the Bpa and Str mutations and their respective homologous human disorders.

Amino Acid Sequence↗
PubMed1994

The STR system in the human phenylalanine hydroxylase gene: true fragment length obtained with fluorescent labelled PCR primers.

We present a simple, fast, non-radioactive method for the analysis of the polymorphic short tandem repeat (STR) system in the human phenylalanine hydroxylase gene. Previously, sizing of the STR marker involved radiolabelling of PCR amplified fragments and resolution on denaturing polyacrylamide gels using M13 sequencing ladder as a standard. However, this method consistently gave sizes 2 bp longer than the known sequence. The fluorescent method presented here employs internal lane standards and enables accurate sizing of the fragments. To avoid confusion, we suggest that the true fragment lengths are used as reference values in the future. The analysis of STR alleles is valuable for population genetic studies and for targeted mutation screening in phenylketonuria (PKU). It can replace RFLP-based haplotype analysis for carrier detection, and we report its use for prenatal diagnosis in a Northern Irish family with PKU. The analysis of 250 Northern Irish chromosomes, including 128 PKU alleles, showed no significant difference between normal and PKU alleles, with fragment lengths of 238 and 242 bp most common in both groups.

Genetic Testing↗