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At least 667 records · Page 37Linked to original sources
PubMed1999

Genetic variation at six STR loci (HUMTH01, HUMTPOX, HUMCSF1PO, HUMF13A01, HUMFES/FPS, HUMVWFA31) in Aragon (north Spain).

The STR loci HUMTH01, HUMPTPOX, HUMCSF1PO, HUMF13A01, HUMFES/FPS and HUMVWFA31 are widely used in forensic casework analyses and population data are necessary to estimate the frequency of a DNA profile. This paper presents the results of a survey aimed to investigate the allele frequency distribution of these loci in an important Spanish population (Aragon, North Spain). Statistical analysis to determine whether allele frequencies were in Hardy-Weinberg Equilibrium was carried out and also to obtain some parameters of medico-legal interest. There was no evidence of association between the alleles of the loci. The Aragonese sample does not differ substantially from other Caucasian populations.

Data Collection↗
PubMed1999

Population data on the D1S1656 and D12S391 STR loci in Andalusia (south Spain) and the maghreb (north Africa).

Allele and genotype frequencies for two tetrameric short tandem repeat (STR) loci were determined in two population samples, from Andalusia (S Spain; n = 127) and the Maghreb (N Africa; n = 40). After denaturing polyacrylamide gel electrophoresis, 14 alleles were identified for D12S391 and 13 alleles for D1S1656. No deviations from the Hardy-Weinberg equilibrium were detected. Some statistical parameters of forensic interest (H, PD, EC) were also calculated, and the data obtained for both populations were compared. Sequencing data of several intermediate D12S391 alleles designated 17.3, 18.3, and 19.3 are also presented.

Africa, Northern↗
PubMed1999

Genetic variation at nine STR loci in populations from the Philippines and Thailand living in Taiwan.

In order to apply a set of nine STR loci and the amelogenin locus in forensic testing, we have performed a population study on individuals from the Philippines and Thailand living in Taiwan (273 Philippine and 146 Thai individuals were typed by commercially available kits and an automated sequencer). A total of 73 alleles for all systems for both populations could be observed in these two populations. No new intermediate fragments were found. Allele frequencies showed no deviation from Hardy-Weinberg equilibrium. The mean exclusion power (MEP) ranged from 0.327 (TPOX) to 0.706 (FGA), the discriminating power (DP) ranged from 0.790 (TPOX) to 0.963 (FGA) for Philippinos, MEP ranged from 0.247 (TPOX) to 0.723 (FGA), DP ranged from 0.761 (TPOX) to 0.968 (FGA) for Thais, the combined MEP is > 0.9988 and the combined DP is > 0.9999999993 for both Philippinos and Thais.

Alleles↗
PubMed1993

Definition and mapping of STSs at STR and RFLP loci in Xp11-Xq22.

New primer pair sequences specific for 25 loci in the Xp11-q22.1 region are described. Eighteen of the pairs span segments containing significant CA dinucleotide repeats, with 9 of these revealing polymorphisms of greater than 50% heterozygosity. Four of the CA-containing segments occur in probes previously reported to detect RFLPs, while the remaining 14 are from newly isolated clones. STSs were also developed for 7 other RFLP-only loci. All of these 25 STSs plus 11 other published STR markers have been fine-mapped with respect to chromosomal breakpoints, defining 15 subintervals in Xp11-Xq22. This map of 36 STSs, nearly all of which are associated with markers that are genetically mapped and/or highly polymorphic, will significantly aid efforts to construct a complete physical map of this region and to correlate it with the high-density genetic map.

Base Sequence↗
PubMed2000

Y-chromosomal STR haplotyping in a Japanese population.

The Y-specific STR systems including DYS19, DYS385, DYS389I, DYS390, DYS391 and DYS393, were investigated in 117 Japanese males. Analysis of the 6 loci permitted classification of the samples into 90 haplotypes, and the haplotypic diversity was estimated to be 0.984. Distribution of the haplotypes in the Japanese population studied was different from that in European populations.

Journal Article↗
PubMed2003

Asian online Y-STR Haplotype Reference Database.

For several years Y-chromosomal microsatellites (short tandem repeats, STRs) have been well established in forensic practice. In this context, the genetic characteristics of the Y chromosome (i.e. its paternal inheritance and lack of recombination) render STRs particularly powerful. However, genetic differences between male populations appear to be larger for Y-STRs than for autosomal STRs, a fact that is most likely due to the higher sensitivity of Y-chromosomal lineages to genetic drift (Forensic Sci Int 118 (2001) 153). The assessment of probabilities for matches between haplotyped male persons or traces/persons requires the typing of a large number of haplotypes in the appropriate reference populations. The haplotype data of a large number of European as well as South and North American populations have been collected and are continuously published online (Y-STR Haplotype Reference Database--YHRD; http://www.ystr.org). The most recent multicentric effort has led to the establishment of an Asian YHRD (http://www.ystr.org/asia) which has been available since January 2002. All databases are maintained and curated at the Institute of Legal Medicine, Humboldt-University, Berlin and will soon be fused to a global repository including populations from all continents.

Asia↗
PubMed2003

Allele frequencies and sequence characteristics of D2S1242 STR locus in Chinese population.

Sequence characteristics and allele frequencies of D2S1242 short tandem repeat (STR) locus were determined in a Chinese population using polymerase chain reaction (PCR) and sequence analysis. In 213 individuals studied, 32 genotypes representing the products of ten D2S1242 alleles were differentiated. The allele frequencies ranged from 0.002 to 0.234, and all the five most common alleles detected had frequencies over 10%. The observed and expected genotype values provided a complete fit to the Hardy-Weinberg equilibrium. The sequence structure of each D2S1242 allele showed a tetranucleotide repeat, and alleles 9-14 had different sequence structures compared to alleles 15-19. The power of discrimination was 0.94, showing a high degree of polymorphism as in other population data.

Asian People↗
PubMed1999

Evaluation of two new STR loci 9q2h2 and wg3f12 in a Japanese population.

Two short tandem repeat (STR) loci (9q2h2 and wg3f12) have been evaluated in a Japanese population. Ten and seven different alleles were observed in 9q2h2 and wg3f12 respectively. 9q2h2 displayed simple polymorphism in tetrameric repeat structure; by contrast, wg3f12 contained variable numbers of tetrameric repeats and a 30-bp deletion/insertion polymorphism. No "interalleles" were found. The expected heterozygosities of 9q2h2 and wg3fl2 were 0.749 and 0.574, respectively. No deviation from Hardy-Weinberg equilibrium was found.

Journal Article↗
PubMed2001

Evidence for population sub-structuring in São Tomé e Príncipe as inferred from Y-chromosome STR analysis.

Seven Y-chromosome STR loci, DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393 have been analysed in population samples of Angolares, Forros and Tongas, three ethnic groups from the African archipelago of São Tomé e Príncipe (Gulf of Guinea). Complete typings were obtained for 103 chromosomes, which belonged to 79 different haplotypes. The mean heterozygosity per locus in the overall São Tomean sample was 0.566, with the highest value found among Forros and the lowest among Angolares. Angolares also showed the lowest level of haplotype diversity. On average, the mean pairwise difference between two random haplotypes from Angolares, Forros and Tongas was 4.69, 6.74 and 6.23 repeats, respectively. The genetic distances were found to be statistically significant between Angolares and Forros or Tongas. In accordance, AMOVA revealed that the percentage of variation attributable to differences among groups was only significant when we distinguished between Angolares and non-Angolares. Globally, these results indicate that, with respect to the pool of male lineages of São Tomé e Príncipe, some genetic sub-structuring does exist, basically determined by the Angolares ethnic group.

Emigration and Immigration↗
PubMed1999

Comparison of biochemical polymorphisms and short tandem repeat (STR) DNA markers for paternity testing in rhesus monkeys (Macaca mulatta).

Genetic markers are indispensable for molecular and statistical genetic research involving nonhuman primates. Genetic markers must be used to ascertain parentage and to confirm the accuracy of pedigrees based solely on housing or demographic records; otherwise, the results of pedigree, linkage, or quantitative genetic analyses may be unreliable. Until recently, most genetic markers used in nonhuman primates were plasma proteins or isozyme polymorphisms, which were required in large numbers, because levels of genetic variation revealed by these markers were rather low. We compared the newer, PCR-amplified short tandem repeat markers (STRs) with a panel of classical biochemical polymorphic markers, for paternity determination among captive-bred rhesus monkeys. The STR markers exhibited an average genetic diversity of 64% and an expected paternity exclusion probability of 0.443. Both of these were greater than the average 54.5% genetic diversity and 0.298 exclusion probability exhibited by the biochemical markers. The STRs were much more efficient than the biochemical markers for parentage determination, since they required only half the amount of genetic typing data to resolve an average paternity case. Thus, the results of applying these two classes of genetic markers in paternity tests were somewhat different than expected on the basis of theoretical exclusion probabilities. These differences were probably due to inbreeding and other genetic differences among breeding colonies. Because they are more informative and provide rapid and efficient genetic data, STRs are now the method of choice for parentage determination and pedigree corroboration among nonhuman primates.

Animals↗
PubMed2000

Genetic structure of north-west Africa revealed by STR analysis.

We have analysed a large set of autosomal short tandem repeat (STR) loci in several Arabic and Berber-speaking groups from north-west Africa (ie Moroccan Arabs, northern-central and southern Moroccan Berbers, Saharawis, and Mozabites). Two levels of analysis have been devised using two sets of 12STR loci, (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820) and 21 (the former set plus D9S926, D11S2010, D13S767, D14S306, D18S848, D2S1328, D4S243, F13A1, and FES/FPS). For each set, data for a number of external reference populations were gathered from the literature. Several methods of analysis based on genetic distances (neighbour-joining trees, principal coordinate analysis, boundary detection), as well as AMOVA, showed that genetic differentiation among NW African populations was very low and devoid of any spatial pattern. When the NW African populations were grouped according to cultural or linguistic differences, the partition was not associated with genetic differentiation. Thus, it is likely that Arabisation was mainly a cultural process. A clear genetic difference was found between NW African populations and Iberians, which underscores the Gilbraltar Straits as a strong barrier to genetic exchange; nonetheless, some degree of gene flow into Southern Iberia may have existed. NW Africans were genetically closer to Iberians and to other Europeans than to African Americans.

Africa, Northern↗
PubMed1999

A second unrelated bone marrow transplant: successful quantitative monitoring of mixed chimerism using a highly discriminative PCR-STR system.

A second bone marrow transplant (BMT) might be considered as an option in patients with leukaemia with graft failure after BMT. We report the successful treatment of a patient with graft failure by a second stem cell transplant from another unrelated donor. We evaluated the usefulness of an unrelated donor as the source of the second BMT in this clinical setting. In addition to this, a penta PCR-STR system was tested and shown to be sensitive for monitoring of marrow engraftment. The conditioning regimen for the first transplantation consisted of busulfan and cyclophosphamide while anti-thymocyte globulin and CY were used for the second BMT. The patient successfully engrafted at day +11 after second BMT.

Adult↗
PubMed2003

Genetic differentiation of the Cabo Verde archipelago population analysed by STR polymorphisms.

Allele frequencies for 17 STR loci were analyzed in a sample of unrelated males from the Cabo Verde Archipelago. The samples were gathered in such a way that the origin of the subjects was perfectly identified, and they could be included in one of the leeward or windward groups of islands. This study reveals that there are significant differences between both groups of islands, and between Cabo Verdeans and other populations from sub-Sahara Africa including the Guineans, the most probable source population for Cabo Verdeans. This study confirms mtDNA data and, together with HLA and Y chromosome data already published, shows that the Cabo Verde population is sub-structured and atypical, diverging substantially from mainland sub-Saharan populations. Overall these differences are most probably due to admixture between sub-Saharan slaves brought into the islands and other settlers of European origin. In the absence of a clear indication of a different ethnic composition of the first sub-Saharan settlers of Cabo Verde, the differentiation exhibited in both groups of islands can be most probably be attributed to genetic drift.

Africa, Western↗
PubMed1991

Comparison of API Rapid Strep, Baxter MicroScan Rapid Pos ID Panel, BBL Minitek Differential Identification System, IDS RapID STR System, and Vitek GPI to conventional biochemical tests for identification of viridans streptococci.

Viridans group streptococci (36 stock strains and 167 single patient blood culture isolates) were assessed using API Rapid Strep, Baxter MicroScan Rapid Pos ID Panel, BBL Minitek Differential Identification System, IDS RapID STR System, and Vitek GPI methods. Identification data obtained with these systems were compared with those indicated by conventional biochemical procedures. API, Baxter MicroScan, BBL, IDS, and Vitek corresponded with conventional biochemical identification in 74%, 66%, 65%, 50%, and 61% of the isolates, respectively; using recommended supplemental tests, agreement was augmented in 9%, 11%, 20%, 11%, and 21% of the isolates, respectively. Disagreement with conventional biochemical methods occurred in 14%, 17%, 14%, 32%, and 10% of the commercial techniques, respectively; no identification was possible in 2%, 5%, fewer than 1%, 6%, and 8% of specimens, respectively. BBL, API, and Baxter MicroScan systems provided the most reliable rapid identification, although supplemental testing often was required. Until a higher percentage of correct identification data can be obtained without supplemental procedures, conventional biochemical techniques will remain the methods of choice for identification of viridans streptococci.

Bacteriological Techniques↗
PubMed2001

Updating the str and srj (stl) families of chemoreceptors in Caenorhabditis nematodes reveals frequent gene movement within and between chromosomes.

The seven transmembrane receptor (str) and srj (renamed from stl) families of chemoreceptors have been updated and the genes formally named following completion of the Caenorhabditis elegans genome sequencing project. Analysis of gene locations revealed that 84% of the 320 genes and pseudogenes in these two families reside on the large chromosome V. Movements to other chromosomes, especially chromosome IV, have nevertheless been relatively common, but only one has led to further gene family diversification. Comparisons with homologs in C. briggsae indicated that 22.5% of these genes have been newly formed by gene duplication since the species split, while also showing that four have been lost by large deletions. These patterns of gene evolution are similar to those revealed by analysis of the equally large srh family of chemoreceptors, and are likely to reflect general features of nematode genome dynamics. Thus large random deletions presumably balance the rapid proliferation of genes and their degeneration into pseudogenes, while gene movement within and between chromosomes keeps these nematode genomes in flux.

Animals↗
PubMed1995

Analysis of short tandem repeat (STR) allele frequency distributions in a Balinese population.

Genotypes for 53 short tandem repeat (STR) markers distributed at an average of 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village of approximately 2200 individuals has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (P < 0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (P < 0.043). Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant allelic associations between physically unlinked loci. In addition to providing information pertinent to the issue of genetic diversity of STRs in the human population, these analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

Alleles↗
PubMed2003

Evaluation of 15 biparental STR loci in human identification and genetic study of the Kannada-speaking groups of India.

Thirteen tetranucleotide and 2 pentanucleotide repeat units were analyzed in 167 unrelated Kannada-speaking individuals belonging to 3 important communities, namely, Kuruva, Bhovi, and Christians, residing in different districts of Karnataka, India. Allele frequency data obtained from the analysis of 15 short tandem report (STR) markers of the subpopulation groups included in the study were observed to be similar, indicating a common ancestry or gene flow among these communities. Departures from Hardy-Weinberg equilibrium were observed in Kuruva population at locus D5S818 and D18S51 and at locus CSF1PO in the Christian community. The data of these communities were analyzed with allele frequency data of 4 other populations from Karnataka, India-Iyengar Brahmin, Gowda, Lingayat, and Muslim-to compute the combined power of discrimination, ranged from 0.962 to 0.974, with negligible difference between populations. The combined power of exclusion, however, remained constant at 0.999 for all populations evaluated in the study. Thus, the 15 markers selected for this study were found to be highly suitable in human identification and for providing information on genetic polymorphism.

Ethnicity↗