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PubMed1986

Accuracy and reproducibility of the IDS rapID STR system for species identification of streptococci.

The RapID STR system (Innovative Diagnostic Systems, Inc., Atlanta, Ga.) was evaluated in the identification of 266 streptococci. Organisms included 60 beta-hemolytic streptococci, 71 group D strains (48 enterococci and 23 nonenterococci), 26 Streptococcus pneumoniae, and 109 viridans group strains. With concomitant optochin testing, as is currently recommended by the manufacturer for all alpha-hemolytic strains, the RapID STR system correctly identified 100% of beta-hemolytic strains, 87.3% of group D strains (93.7% of enterococci, 73.9% of nonenterococci), 88.5% of S. pneumoniae, and 72.5% of viridans strains. Without the use of optochin, the correct identification of S. pneumoniae and the viridans group was 26.9 and 52.3%, respectively. The RapID STR system incorrectly identified 3.0% of strains, including four group D streptococci, three pneumococci, and one viridans isolate. Reproducibility was excellent, with 95% of strains tested in triplicate yielding identical results on each of the three occasions. The RapID STR system represents a worthwhile advance in streptococcal species identification, especially for group D and viridans strains.

Reagent Kits, Diagnostic↗
PubMed2004

Comparative study of genetic variation at 15 STR loci in three isolated populations of the Bosnian mountain area.

Fifteen autosomal STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX, and FGA) were studied in three geographically close but isolated populations from the Bosnian mountain area. The three villages are Bobovica, Dejcici, and Lukomir. DNA was obtained from 83 individuals, and the allele frequencies and genetic diversity among the three sample groups were compared. In addition, seven of the STR loci (CSF1PO, D13S317, D3S1358, D5S818, D7S820, FGA, TH01) were used in a comparative population analysis of the Bjelasnica-Treskavica region and the Adriatic islands of Brac, Hvar, and Korcula. Although the sample sizes are relatively small, the observed variation within any of the small isolated populations is high and comparable to less isolated groups. In addition, even though the populations are geographically isolated, the STR data are similar among the populations. The most significant frequency differences were observed at the TH01 locus. Although the specific allele distributions in any untyped population cannot be determined a priori, we find support for a high degree of diversity for the STR loci in most populations. In addition, the multiple locus profile is highly informative not only for various population studies but also for forensic studies, even when specific population data are not available.

Bosnia and Herzegovina↗
PubMed2006

[Genetic polymorphism of 15 STR loci in a Lhasa Tibetan population].

The polymorphism distributions of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA) were investigated in a Lhasa Tibetan population by multiplex PCR amplification using five fluorochromes (6FAM, VIC, NED, PET, LIZ). Gene frequency, discrimination power (DP), heterozygosity (H), polymorphism information content (PIC) and probability of paternity exclusion (EPP) were calculated, and all loci were tested for Hardy-Weinberg equilibrium. Results indicate that the gene frequency of these 15 STR loci is in Hardy-Weinberg equilibrium. The DP is at 0.7515 - 0.9599, H is at 0.5576 - 0.8538, PIC is at 0.5455 - 0.8458, and EPP is at 0.37550.8520. Cumulative DP of the 15 STR is 0.99999999, and cumulative EPP is 0.999999997. Therefore, these 15 STR loci can be used as genetic markers of in Lhasa Tibetan populations in anthropological studies, linkage analysis of genetic diseases, individual identification and paternity testing in forensic medicine.

Ethnicity↗
PubMed2005

Constructing STR multiplex assays.

Multiplex polymerase chain reaction (PCR) refers to the simultaneous amplification of multiple regions of deoxyribonucleic acid (DNA) using PCR. Commercial short tandem repeat (STR) assays that can coamplify as many as 16 different loci have become widely used in forensic DNA typing. This chapter will focus on some of the aspects of constructing robust STR multiplex assays, including careful design and quality control of PCR primers. Examples from the development of a cat STR 12plex and a human Y chromosome STR 20plex are used to illustrate the importance of various parts of the protocol. Primer design parameters and Internet-accessible resources are discussed, as are solutions to problems with residual dye artifacts that result from impure primers.

Chromosomes, Human, Y↗
PubMed2000

The Str mouse as a model for incontinentia pigmenti.

Striated mouse has been proposed as a model for incontinentia pigmenti (IP) based on the similarities in genetic predisposition and syntenic gene localisation in mouse. IP is considered an ectodermal dysplasia with all four characteristic structures involved: sweat glands, hair, teeth and nails. Recently mutations have been found in the Nsdhl, encoding an NAD(P)H steroid dehydrogenase-like protein in Str and Bpa mice. We analysed the phenotype of the Str mouse to evaluate the involvement of ectodermally derived tissues. Our results demonstrated that in Str mouse in addition to abnormal coat texture, sweat glands were severely dystrophic or missing. Retinal degeneration and skeletal abnormalities were also found. We conclude that Str mouse is a good model to get new insights in the pathogenesis of ectodermal dysplasias and X linked male lethality in humans.

Animals↗
PubMed2000

[Genetic polymorphism of 10 STR loci on chromosome 9 and its forensic application in Chinese population].

OBJECTIVE: To have a thorough knowledge of the genetic polymorphism of 10 short tandem repeats loci of chromosome 9 in Chinese population and its application in forensic science. METHODS: The 9 STR tetrameric loci and one trimeric tandem repeat locus were chosen from Genome Databank. Eighty-three EDTA-blood samples were collected from the unrelated family in Baiyin city, Gansu province. DNA was extracted by Chelex method and amplified by the polymerase chain reaction(PCR). The PCR products were analyzed by PAGE electrophoresis. RESULTS: The polymorphisms of all 10 STR loci have been obtained in Chinese Han population. The 10 STR loci follow the Mendel ns law. CONCLUSION: The data of all 10 STR loci is beneficial to understanding the population genetics of them in Chinese Han population.

Chromosomes, Human, Pair 9↗
PubMed2001

Validation of short tandem repeats (STRs) for forensic usage: performance testing of fluorescent multiplex STR systems and analysis of authentic and simulated forensic samples.

The amplification and typing conditions for the 13 core CODIS loci and their forensic applicability were evaluated. These loci are CSF1PO, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11. Results were obtained using the multiplex STR systems AmpFlSTR Profiler Plus and AmpFlSTR COfiler (Applied Biosystems, Foster City, CA), GenePrint PowerPlex (Promega Corporation, Madison, WI), and subsets of these kits. For detection of fluorescently labeled amplified products, the ABI Prism 310 Genetic Analyzer, the ABI Prism 377 DNA Sequencer, the FMBIO II Fluorescent Imaging Device, and the Fluorlmager were utilized. The following studies were conducted: (a) evaluation of PCR parameter ranges required for adequate performance in multiplex amplification of STR loci, (b) determination of the sensitivity of detection of the systems, (c) characterization of non-allelic PCR products, (d) evaluation of heterozygous peak intensities, (e) determination of the relative level of stutter per locus, (f) determination of stochastic PCR thresholds, (g) analysis of previously typed case samples, environmentally insulted samples, and body fluid samples deposited on various substrates, and (h) detection of components of mixed DNA samples. The data demonstrate that the commercially available multiplex kits can be used to amplify and type STR loci successfully from DNA derived from human biological specimens. There was no evidence of false positive or false negative results and no substantial evidence of preferential amplification within a locus. Although at times general balance among loci labeled with the same fluorophore was not observed, the results obtained were still valid and robust. Suggested criteria are provided for determining whether a sample is derived from a single source or from more than one contributor. These criteria entail the following: (a) the number of peaks at a locus, (b) the relative height of stutter products, and (c) peak height ratios. Stochastic threshold levels and the efficiency of non-templated nucleotide addition should be considered when evaluating the presence of mixtures or low quantity DNA samples. Guidelines, not standards, for interpretation should be developed to interpret STR profiles in cases, because there will be instances in which the standards may not apply. These instances include (a) a primer binding site variant for one allele at a given locus, (b) unusually high stutter product, (c) gene duplication, and (d) translocation.

DNA Fingerprinting↗
PubMed2001

Validation of STR typing by capillary electrophoresis.

With the use of capillary electrophoresis (CE), high-resolution electrophoretic separation of short tandem repeat (STR) loci can be achieved in a semiautomated fashion. Laser-induced detection of fluorescently labeled PCR products and multicolor analysis enable the rapid generation of multilocus DNA profiles. In this study, conditions for typing PCR-amplified STR loci by capillary electrophoresis were investigated using the ABI Prism 310 Genetic Analyzer (Applied Biosystems). An internal size standard was used with each run to effectively normalize mobility differences among injections. Alleles were designated by comparison to allelic ladders that were run with each sample set. Multiple runs of allelic ladders and of amplified samples demonstrate that allele sizes were reproducible, with standard deviations typically less than 0.12 bases for fragments up to 317 bases in length (largest allele analyzed) separated in a 47 cm capillary. Therefore, 99.7% of all alleles that are the same length should fall within the measurement error window of +/- 0.36 bases. Microvariants of the tetranucleotide repeats were also accurately typed by the analytical software. Alleles differing in size by one base could be resolved in two-donor DNA mixtures in which the minor component comprised > or = 5% of the total DNA. Furthermore, the quantitative data format (i.e., peak amplitude) can in some instances assist in determining individual STR profiles in mixed samples. DNA samples from previously typed cases (typed for RFLP, AmpliType PM+DQA1, and/or D1S80) were amplified using AmpFlSTR Profiler Plus and COfiler and were evaluated using the ABI Prism 310. Most samples yielded typable results. Compared with previously determined results for other loci, there were no discrepancies as to the inclusion or exclusion of suspects or victims. CE thus provides efficient separation, resolution, sensitivity and precision, and the analytical software provides reliable genotyping of STR loci. The analytical conditions described are suitable for typing samples such as reference and evidentiary samples from forensic casework.

DNA Fingerprinting↗
PubMed2001

DNA typing from skeletal remains: evaluation of multiplex and megaplex STR systems on DNA isolated from bone and teeth samples.

AIM: To evaluate the performance of three multiplex short tandem repeat (STR) systems (AmpflSTR Profiler, AmpflSTR Profiler Plus, and AmpflSTR COfiler), and a megaplex STR system (PowerPlex 16) on DNA extracted from the skeletal remains. By performing a microbial DNA challenge study, we also evaluated the influence of microbial DNA on human DNA typing. METHODS: A subset of 86 DNA extracts isolated from 8-50 years old bone and teeth samples, corresponding to 20 identification cases from mass graves in Croatia and Bosnia and Herzegovina, and to 4 paternity cases involving deceased parents in Spain, were analyzed by the above systems. RESULTS: Bone samples with no detectable human DNA (tested with Quantiblot), as well as teeth samples with detectable human DNA, were successfully amplified. Surprisingly, even in highly degraded samples, PowerPlex 16 offered very robust amplification for the both Penta E and Penta D markers. We observed a few non-specific extra peaks of 202 and 308 base pairs, which appeared to match 16S rRNA of the Pseudomonas halodenitrificans. CONCLUSION: AmpflSTR Profiler Kit, AmpflSTR Profiler Plus Kit, the AmpflSTR COfiler Kit, and the PowerPlex 16 system are very sensitive multiplex STR amplification systems, which can be successfully used to obtain a multilocus STR profile from old teeth and bone samples with minimal amounts (pg) of human DNA or even with no detectable human DNA.

Bone and Bones↗
PubMed2001

Application of Y-chromosomal STR haplotypes to forensic genetics.

This paper delivers population genetic data on Y-chromosomal short tandem repeat (STR) polymorphisms along with reports of unusual observations and casework. Population studies were carried out on the Y-specific STR polymorphisms DYS19, DYS385 I+II, DYS389 I+II, DYS390, DYS391, DYS392, and DYS393 in population samples from North India, Turkey, and Germany. In all three populations the vast majority of haplotypes was observed only once, especially in the Turkish group. Highly unusual cases are reported. In a German individual, we observed the variant allele DYS392*11.1, whereas a Turkish haplotype revealed a duplication at locus DYS19. Application of Y-chromosomal STR markers to forensic genetics was demonstrated in two cases: 1) a deficient paternity case, and 2) a father/son pair, where the Amelogenin primers failed to amplify the Y-homolog. In forensic genetics, Y-chromosomal STR polymorphisms are highly welcomed as an additional tool.

Female↗
PubMed2002

[Genetic map of 10 STR loci on chromosome 9].

To understand the genetic polymorphism of 10 STR loci on chromosome 9 and reveal the difference on the linkage maps of different populations, the author used a set of nine tetranucleotide- and one tritranucleotide-repeat STR markers on chromosome 9 chosen from Genome Data Bank. EDTA-blood was collected from unrelated family in Baiyin City, Gansu province. DNA was extracted by Chelex-100 method and amplified by the polymerase chain reaction (PCR). The PCR products were analyzed using PAGE electrophoresis. We calculated the allele frequencies and heterozygosity and PIC of every ten STR loci. Using the data of Chinese Han pedigree, we constructed a genetic map of chromosome 9 making up with 10 STR loci. Then we compared our map with the map in GDB. Our results indicate that there are some differences on the genetic map between Chinese and GDB. That means, it is essential to do some population genetic evaluations before using the data of GDB into Chinese population.

China↗
PubMed2003

A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population.

We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field.

DNA Fingerprinting↗
PubMed2002

[Studies of STR polymorphisms in Pumi and Lisu minorities in China].

In this study, we investigated the polymorphisms of STR of Pumi and Lisu minorities with STR genescan marked by fluorescence. Eighty-five alleles of 9 STR in Pumi were detected with the frequency 0.0050-0.5250 and 194 genotypes were found with frequency of 0.0098-0.3235. Sixty three alleles with their frequency of 0.0050-0.4802 and 145 genotypes were found out with frequency of 0.0099-0.3664 in Lisu population. Hi-Square test indicated the distribution of genotypes agreed with Hardy-Weinberg equilibrium (P > 0.05). Statistical analysis showed the followings: H > 0.6 in each locus, the average PIC > 0.7, mean DP > 0.8, EPP > 0.5, indicating the STR markers used in the study were of great value in the researches on minority genetics.

Alleles↗
PubMed2003

Systematic study on STR profiling on blood and saliva traces after visualization of fingerprint marks.

This paper describes a systematic study of the influence of optical, physical, and chemical methods used for fingerprint enhancement on subsequent DNA analysis of biological stains. Latent fingerprints as well as fingerprints in contact with blood and saliva on different surfaces were treated with dactyloscopic methods. As a general finding, subsequent STR profiling of the blood/saliva traces led to good results after all the enhancement methods included in this study. Concerning blood enhancement procedures, the airbrush technique showed deleterious effects on subsequent STR analysis in some cases. We therefore recommend the implementation of the layer technique, as it brings advantages for fingerprint enhancement as well. It could also be shown that, as can be necessary in practical casework, two enhancement methods can be performed on a single stain without having influence on STR profiling. In terms of methodological variety, this paper reflects a comprehensive study performed on STR profiling after fingerprint enhancement methods, including rare methods and variations of techniques, which can be a useful alternative in certain case scenarios.

Blood Stains↗
PubMed2004

STR typing of human DNA from fly larvae fed on decomposing bodies.

In homicides with entomological evidence, it may be important to prove the presumed association of fly larvae to a corpse, especially if it is in doubt whether all maggots used for entomological expertise developed and fed on it. The present study demonstrates for the first time the possibility of analyzing human microsatellite DNA present in the digestive tract of necrophagous larvae that fed on decomposed bodies with a postmortem interval up to four months. The obtained human STR profiles support the association of a maggot to a specific corpse. In addition, the identification of the host species (e.g., animal source like pig) can be achieved by analysis of the cytochrome b gene. Maggots were collected from 13 corpses after various postmortem intervals and STR typing and HVR amplifications were performed using their crop contents. In seven cases, a complete STR profile was established, in two cases, an incomplete set of alleles was obtained, and in four cases, STR typing was not successful. HVR analysis was successful in all cases except one. The time of storage of the maggots and the length of the postmortem interval up to 16 weeks appeared to have no particular influence on the quality of the results.

Animals↗
PubMed2004

[Detection of minimal residual disease of chronic myeloid leukemia patients after allogeneic stem cell transplantation by combination of STR-PCR with RT-PCR].

In order to evaluate relapse predication ability of STR-PCR combining with qualitative RT-PCR for the bar/abl transcripts to the patient with chronic myeloid leukemia (CML) fulfilled allogeneic stem cell transplantation (allo-HSCT), 24 patients with CML after allo-HSCT were dynamically investigated for MRD, quantitative analysis of donor chimerism was performed by multiplex PCR amplification of STR markers and capillary electrophoresis with fluorescence detection, qualitative detection of bcr/abl transcripts was detected by nested RT-PCR. The results showed that persistent full donor chimerism (DC >/= 95%) was associated with an absence of MRD. All patients with stable MC (90% </= DC < 95%) and bcr/abl negative had a probability of long-term survival with molecular remission, however the result of bcr/abl positivity was not always associated with leukemia relapse, only the patient with decreasing values of donor chimerism as well as bcr/abl positive proved to be in a higher risk of relapse or graft failure. Decrease of donor chimerism in correlation with MRD positive was detected in 5 patients. Three out of five patients had been proved to have a molecular relapse, one out of five patients had developed to cytogenetic relapse and another patient experienced graft failure. It is concluded that the results of STR-PCR in the range of its sensitivity fully correspond with bcr/abl tests in patients. The combination of STR-PCR with RT-PCR will provide a highly sensitive and valuable tool for MRD detection in CML and can identify these high risk patients with molecular or cytogenetic relapse after allo-HSCT.

Genes, abl↗
PubMed2004

Developmental validation of a single-tube amplification of the 13 CODIS STR loci, D2S1338, D19S433, and amelogenin: the AmpFlSTR Identifiler PCR Amplification Kit.

Analysis of length polymorphism at short tandem repeat (STR) loci utilizing the polymerase chain reaction (PCR) process has proven to be an ideal assay for human identification purposes. The short length of STR loci coupled with the amplification of target sequence through PCR allows for a robust, sensitive, and specific assay for highly polymorphic markers. A multiplex containing fifteen STR loci plus the gender-determining locus Amelogenin was developed to provide a single amplification/detection of all CODIS (Combined DNA Index System) STR loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, and vWA) as well as two internationally-accepted STRs (D2S1338 and D19S433). By incorporating five-dye fragment analysis technology and non-nucleotide linkers, previously optimized AmpFlSTR kit primer sequences have been maintained. This kit has been developed in accordance with the standards of the forensic community as defined by the DNA Advisory Board. Validation studies were performed to include developmental validation, and the results support the use of the AmpFlSTR Identifiler PCR Amplification Kit for human identity and parentage testing.

Animals↗
PubMed2005

[Primary study on the influence of blood transfusion on the STR genotypes of recipient's blood].

OBJECTIVE: To investigate whether any change occurred in recipients' blood collected at different times after transfusion with different quantity of blood. METHODS: Three patients were transfused with 400 ml, 800 ml and 1200 ml blood separately. The blood samples were collected from the recipients before transfusion and at 4 h, 8 h, 12 h after transfusion, and from the donors. DNA were extracted by Chelex-100 method and were amplified by the polymerase chain reaction (PCR). Six loci of D1S549, D18S865, D3S1754, D12S391, D12S375, D6S477 were selected. The PCR products were analyzed by polyacrylamide gel (PAG) vertical electrophoresis and silver staining. RESULTS: The investigations on the six STR loci revealed that the patients' STR genotypes remained unchanged within 12 h after blood transfusion. CONCLUSION: The STR genotypes of the donors would have no influence on the STR genotypes of the patients within 12 h after transfusion providing the volume of blood transfused is less than 1200 ml.

Asian People↗