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[Population genetics of short tandem repeat locus HUMTH01].

The distributions of genotypes and allele frequencies for the short tandem repeat locus HUMTH01 in Chinese and German populations were studied by amplified fragment length polymorphism analysis. The PCR amplification products with different primers were compared by coelectrophoresis and the population data from different laboratories were evaluated. Based on the allele frequencies of HUMTH01, the genetic distances among 25 populations were computed and a phylogenetic tree was constructed accordingly. Some new implications for population genetics were obtained from this phylogenetic tree.

Chromosome Mapping↗

Detection of maternal deoxyribonucleic acid in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of short tandem repeat sequences.

OBJECTIVE: Umbilical cord blood is a source of hematopoietic stem cells for transplantation. Although the first clinical applications have been encouraging, concern has been raised about contamination of umbilical blood by maternal cells, which might constitute a theoretical risk of graft-versus-host disease. The aim of this study was to assess the frequency of maternal deoxyribonucleic acid (DNA) contamination in umbilical cord plasma by using fluorescent polymerase chain reaction amplification of highly polymorphic short tandem repeat DNA markers. STUDY DESIGN: Fifty-seven mother/child pairs were tested for the presence of maternal DNA sequences in cord plasma. After delivery, cord blood samples were collected via gravity. Maternal specific alleles were detected by using polymerase chain reaction amplification of 9 highly polymorphic short tandem repeat markers (D21S11, D21S1411, D21S1412, D18S386, D18S535, MBP-A, MBP-B, D13S631, and D13S634). RESULTS: All 57 mother-child pairs were informative for the identification of uniquely maternal alleles in at least 2 of 9 different short tandem repeat markers used per case. Uniquely maternal DNA sequences were found in 43 of 57 (75%) cord plasma samples. CONCLUSION: The results of our study demonstrate that maternal DNA is present in the majority of umbilical cord blood plasma samples. The technique described herein might have application in the screening of umbilical cord blood samples for the presence of contaminating maternal genetic material.

Alleles↗

A continuous linkage map of 22 short tandem repeat polymorphisms on human chromosome 12.

A continuous linkage map consisting of 22 short tandem repeat polymorphisms has been constructed for human chromosome 12 using 23 non-CEPH pedigrees. The markers were distributed at an average distance of 9.35 cM (3.1-33.9 cM). Eighteen of the markers could be positioned uniquely with a likelihood of > 1000:1. The physical locations of some of the markers suggest that the map covers 85-95% of the chromosome. This framework map of 18 markers has a female length of 213 cM and a male length of 131 cM. Female recombination frequencies were greater than male recombination frequencies except in the distal portion of the short arm. The map provides confirmatory evidence for orders established previously on CEPH pedigrees and uniquely positions 4 additional markers (CD4, ATPSB, D12S56, PLA2).

Chromosome Mapping↗

Population genetic study of four short tandem repeat loci in the Belgian population, using capillary electrophoresis.

Allele frequencies of four short tandem repeat loci (HumCD4, HumTH01, HumD21S11 and HumSE33) were investigated in a sample of 395 unrelated Belgian individuals using multiplex polymerase chain reaction and capillary electrophoresis. Automated laser fluorescence was used to detect four fluorescent dyes, enabling the use of an internal standard within each lane. With this method rapid typing with high resolution was obtained and the different alleles were grouped on a statistical base. All loci meet Hardy-Weinberg expectations. The allelic frequency data, together with the constructed allelic ladder, can be used in paternity testing and personal identification in the medical and forensic sciences.

Belgium↗

Analysis of nine short tandem repeat (STR) loci in the Slovenian population.

A polymerase chain reaction (PCR)-based short tandem repeat (STR) system consisting of nine loci has recently been introduced in Slovenia for use in routine forensic identity testing. Fluorescently labelled PCR products were analysed using an ABI PRISM 310 Genetic Analyzer. The STR loci analysed exhibit between 6 and 14 observed alleles per locus and have a combined matching probability of 2.3 x 10(-10).

Alleles↗

Allele frequencies of 13 short tandem repeats in population samples from the Iberian Peninsula and northern Africa.

The 13 short tandem repeat (STR) loci D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 as well as the amelogenin locus, contained in AmpFlSTR Profiler Plus and/or AmpFlSTR Cofiler and/or AmpFlSTR Green I PCR amplification kits, were studied in four populations from the Iberian Peninsula, Basques, Catalans, Andalusians and Portuguese and two North African populations (Moroccan Arabs and Berbers). The aim of the study was to obtain accurate allele frequency data and other genetic parameters of forensic interest on the main representative human groups living in Iberia and Morocco using an automated method and commercial amplification kits.

Africa, Northern↗

Typing of eight short tandem repeat (STR) loci in a Saudi Arabian population.

Allele frequency data for eight short tandem repeat (STR) loci, HUMF13A01, HUMFESFPS, HUMF13B, HUMLPL, HUMCSF1PO, HUMTPOX, HUMTHO1 and HUMvWA, were obtained for unrelated individuals in a Saudi Arabian population. All loci, except F13B (P = 0.037) and LPL (P = 0.035), meet Hardy-Weinberg expectations, based on the exact test. The most informative locus is HUMvWA (PD = 0.936) and the least discriminating is the HUMTPOX locus (PD = 0.820). There was only one observation of a departure from expectation from pairwise locus comparisons. These data can be used for estimating the frequency of STR profiles in a Saudi Arabian population.

Alleles↗

Genetic variation at nine short tandem repeat loci in Chamorros and Filipinos from Guam.

Allele distributions for nine tetrameric short tandem repeat (STR) loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA and vWA were determined in Chamorros and Filipinos residing in Guam. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the only locus that departs significantly from HWE is D8S1179 (p=0.005, Chamorros; p=0.030, Filipinos). There is little evidence for association of alleles between the loci in these databases. The number of pairwise locus departures from expectations is no more than would be expected by chance. The allelic frequency data are similar to comparable published data within the same population group (e.g., a comparison of Filipinos with Filipinos) and significantly different compared with other major population groups, such as African Americans, Caucasians, and Hispanics. The F(ST) estimate over all nine STR loci is 0.0090.

Journal Article↗

Analysis of 15 short tandem repeats reveals significant differences between the Arabian populations from Morocco and Syria.

The short tandem repeat (STR) systems D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA were studied in Arabian population samples from Morocco and Syria. No significant deviation from Hardy-Weinberg equilibrium could be observed in either preparation. Comparing the Moroccan and Syrian populations using the program RxC, no similarity could be observed at all 15 loci. In the Moroccan and Syrian populations the matching probability is 1 in 1.4 x 10(17) and 1 in 2.6 x 10(17), respectively. Thus, the combination of these 15 STR loci is powerful tool for forensic identification in Arabian populations.

DNA Fingerprinting↗

Data on six short-tandem repeat polymorphisms in an autochthonous Basque population.

Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, HUMFES/FPS, and HUMvWF) were carried out on a sample of 326 autochthonous Basques. Comparing with other European samples, we found the highest frequencies known so far for allele 11 of the HUMCSF1P0 locus (0.380), allele 10 of the HUMFES/FPS locus (0.384), and allele 17 of the HUMvWF locus (0.329). On the other hand, we found the lowest frequencies recorded in Europe for allele 12 of the HUMCSF1P0 locus (0.291), allele 7 of the HUMTH01 locus (0.128), and allele 11 of the HUMFES/FPS system (0.317). These results support the hypothesis that the Basque population is a remnant of early European settlers.

Ethnicity↗

Tibetan population data on the multiplex short tandem repeat loci--D16S539, D7S820, and D13S317.

The multiplex amplification system of three tetrameric short tandem repeats loci (D16S539, D7S820, and D13S317) have been analysed extensively in various populations for forensic application. Population genetic studies were carried out for these three loci in a population sample of 129 unrelated Tibetan individuals by using a multiplex polymerase chain reaction (PCR) followed by 4% polyacrylamide gel electrophoresis (PAGE) and silver staining. All loci were in accordance with the Hardy-Weinberg expectations. The observed heterozygosities of three loci-D16S539, D7S820, and D13S317 were 73.3%, 81.4% and 80.6%, respectively. The polymorphism information contents (PIC) were 0.84, 0.80 and 0.83, respectively. Comparing with Han population, there was no statistically significant difference except for D16S539 locus.

Chromosome Mapping↗

[Study on the mutation of human short tandem repeats at three loci].

OBJECTIVE: To understand the mutational patterns and mechanism of short tandem repeats(STRs). METHODS: The DNA samples of 19 parent-child pairs with mutations in three loci (FGA, D12S391, and D11S554) were genotyped by silver staining on STR. Alleles to be sequenced were excised from gels, reamplified by PCR, and purified. Sequencing was performed by use of cycle sequencing. RESULTS: There were 18 out of 19 pedigrees in which the 'new' alleles gained or lost a single repeat (8 gains, 7 losses, and 3 being indistinguishable). Only one pedigree lost two repeats. In the 19 pedigrees, there were 13 pedigrees whose 'new' alleles came from fathers, 3 from mothers, 3 from either father or mother. The ratio was 4 1 between fathers and mothers. The mutation of three STR loci occurred in the long, uninterrupted tetranucleotide repeat regions ('CTTT' in FGA, 'AGAT' in D12S391, and 'AAAG' in D11S554). CONCLUSION: Single- step mutations accounted for 95% of STR mutation events in these three loci: FGA, D12S391, and D11S554. The rest were double step mutations. There was no insertion or deletion of an incomplete repeat in any of the pedigrees. The mutation was mainly caused by fathers. The long, uninterrupted tetranucleotide repeats in these three loci might be susceptible to mutation.

Alleles↗

[Forensic application of two short tandem repeat (STR) polymorphic markers, FES and HUMTH01].

This paper reports polymorphisms of two short tandem repeats (STR) in the human c-fes/proto-oncogene (FES) and the human tyrosine hydroxylase gene (HUMTH01), and their application to paternity cases. Genomic DNA samples from 213 unrelated Japanese individuals and from 30 paternity cases were subjected to the polymerase chain reaction (PCR) and then the amplified products were electrophoresed in denaturing polyacrylamide sequencing gels. Allelic bands were detected with autoradiography. Seven alleles differing in the numbers of the repeat units were observed at both loci. Heterozygosity (%) and polymorphism information context were calculated, being 69% and 0.641 FES, and 70% and 0.647 for HUMTH01. The allele frequencies of the two STRs in this study were found to be similar to those previously reported on Asians but different from those in Caucasians and Blacks. When the STRs were applied to 30 paternity cases that had been already tested by using conventional markers, there were no discrepancies between the results of the STRs and of conventional markers. Furthermore, the two STRs could be successfully coamplified in multiplex PCR. These results suggest that the two STRs are useful in forensic work in Japan.

Alleles↗

Italian population data on the polymarker system and on the five short tandem repeat loci CSF1PO, TPOX, TH01, F13B, and vWA.

A population study on five short tandem repeat (STR) loci and five sequence specific polymorphism loci was performed on unrelated Italian Caucasians. Separation and detection of the amplified STR fragments were carried out by high resolution vertical denaturing polyacrylamide gel electrophoresis (PAGE) and silver staining, respectively. The sequence specific loci were analyzed using the AmpliType PM Typing Kit (Perkin Elmer, Foster City, CA). All loci, except Gc (p = 0.031), meet Hardy-Wienberg expectations. In addition, there is no evidence for association of alleles between pairs of loci. The combined power of discrimination for the five STR loci is 0.9999862 and for the PM loci is 0.99503. The results suggest that these loci may be useful for human identification cases in Italy.

Alleles↗

Genetic variation at the short tandem repeat loci HumvWA, HumFXIIIB, and HumFES/FPS in the Egyptian and Yemenian populations.

The short tandem repeat systems (STRs) HumvWA, HumFXIIIB, and HumFES/FPS were amplified in a triplex polymerase chain reaction (PCR) on blood samples from 100 unrelated Yemenians and 100 unrelated Egyptians. The samples were analyzed by native horizontal discontinual electrophoresis. No deviations from Hardy-Weinberg equilibrium were detected. The mean exclusion chances for Egyptians and Yemenians were 0.634 and 0.591 (vWA), 0.530 and 0.531 (FXIIIB), and 0.573 and 0.583 (FES); the discriminating powers were 0.937 and 0.924 (vWA), 0.900 and 0.899 (FXIIIB), and 0.918 and 0.921 (FES); and the observed heterozygosity rates were 0.84 and 0.72 (vWA), 0.73 and 0.83 (FXIIIB), and 0.81 and 0.80 (FES). No significant differences were found between the two Arab populations, but the differences between both Arab populations and a European population for HumFES and FXIIIB and between the Yemenian sample and a European sample for vWA were significant. No evidence of linkage disequilibrium between any of the three STRs tested was found.

Alleles↗

Use of short tandem repeats for DNA fingerprinting to rapidly diagnose graft-versus-host disease in solid organ transplant patients.

BACKGROUND: Graft-versus-host disease (GVHD) is a rare complication following liver transplantation and carries a poor prognosis with mortality approaching 90-95%. Diagnosis of GVHD is often delayed due to early symptoms mimicking more common, entities such as drug reactions and viral syndromes. To date, definitive diagnosis has been difficult and has relied on a constellation of clinical and histopathologic variables. We present the use of short tandem repeat DNA "fingerprinting" technology as a method of early, definitive diagnosis of GVHD in patients after liver transplantation. METHODS: A patient status-postorthotopic cadaveric-liver transplant, with an uncomplicated immediate posttransplant course, presented 4 weeks after transplant with fever, diarrhea, and maculopapular rash on her palms, soles, and back. The patient's condition worsened despite empiric treatment for an infectious etiology. Skin and rectal biopsies were suspicious for GVHD. RESULTS: DNA was isolated from the skin and rectal biopsies as well as from a donor lymph node. PCR amplification was done for nine highly polymorphic short tandem repeats for each specimen and a unique DNA "fingerprint" was obtained from each. DNA from skin and rectum demonstrated mixed chimerism with both donor and recipient alleles detected. Thorough analysis confirmed GVHD. CONCLUSION: Short tandem repeats for DNA fingerprinting represents an efficient and reproducible method for the definitive diagnosis of GVHD after liver transplantation. Rapid detection of GVHD using this technology, coupled with early initiation of therapy, may lead to improved survival for patients with GVHD after solid organ transplant.

DNA Fingerprinting↗

[Comparative analysis of allele polymorphism of three short tandem repeats in the Russian, Uzbek and Georgian populations].

The allele polymorphism of the AGC short tandem repeat (STR) of exon 1 of the androgen receptor (AR) gene located in Xq11-12, ATCT STR of intron 40 of the von Willebrand factor (vWF) gene located in chromosome 12p12, and AGAT STR of an anonymous DNA sequence (STRX1) from the short arm of the X chromosome was analyzed in the Georgian, Uzbek, and Russian populations. Polymerase chain reaction (PCR) with DNA of unrelated persons revealed 14 AR, 7 vWF, and 7 STRX1 alleles in Georgians; 14, 8, and 6 alleles, respectively, in Uzbeks; and 16, 8, and 9 alleles, respectively, in Russians. The heterozygosity at these STR was 0.61, 0.78, and 0.46 in Georgians; 0.60, 0.83, and 0.44 in Uzbeks; and 0.80, 0.70, and 0.58 in Russians. The correspondence of genotype frequencies to the Hardy-Weinberg equilibrium was observed with AR STR in Russians and Uzbeks, STRX1 STR in Georgians, and vWF in all three populations. A significant deviation from the equilibrium was found for STRX1 in Russians and Uzbeks and AR in Georgians. The potential of individualization was 0.05 for AR, 0.13 for vWF, and 0.18 for STRX1 in Georgians; 0.04, 0.09, and 0.13, respectively in Uzbeks; and 0.05, 0.14, and 0.07, respectively, in Russians. The allele and genotype frequency distributions of each STR were analyzed in all three populations. Allele frequencies in the populations were compared by the Kolmogorov-Smirnov test. The Russian population significantly differed in allele frequencies of the three STR from Uzbeks and in those of STRX1 and AR from Georgians. Georgians and Uzbeks significantly differed in vWF and STRX1 frequencies. The possibility of using the three STR in molecular diagnosis of the corresponding monogenic diseases, population genetic studies, and personal identification is discussed.

Alleles↗

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗