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PubMed1998

Quadruplex fluorescent STR typing system (HUMVWA, HUMTH01, D21S11 and HPRT) with sequence-defined allelic ladders identification of a new allele at D21S11.

A protocol for simultaneous amplification of the tetrameric STR loci HUMVWA, HUMTH01, D21S11 and HPRT has been developed in this study. Fluorescent amplified alleles were detected by laser scanning on the ALF DNA sequencer, and identified with locus specific allelic ladders. A sequencing survey of these STR loci was performed in 40 selected individuals from three major ethnic groups and confirmed the data reported previously. At the D21S11 locus, a new allele of 207 bp, was found in a Belgian Caucasian individual and designated as allele 25.2. Sequence analysis of this allele revealed that it contained a 14 bp deletion of (TCTA)3 TA at the beginning of the constant region. A nonconsensus allele of 245 bp, described and designated as allele 33.2.3(2x) by Brinkmann et al. (1996), was identified in an individual of central African origin. In addition, three new sequence variants of the allele 29, 30 and 32 were observed at D21S11.

Alleles↗

PubMed1998

Tandem repeat structure of the duplicated Y-chromosomal STR locus DYS385 and frequency studies in the German and three Asian populations.

The Y-chromosomal short tandem repeat (STR) locus DYS385 can be typed using PCR amplification and separation of the resulting polymorphic fragments by non-denaturing high resolution polyacrylamide gel electrophoresis followed by silver staining. The PCR primers amplify a duplicated repeat sequence on the Y chromosome revealing a two-band pattern in male individuals. To determine the internal repeat structure as a basis for a consensus nomenclature, DNA sequence analysis was carried out after subcloning of PCR-amplified fragments revealing the uniform 4-bp repeat structure 'GAAA'. The shortest allele observed consisted of 10 repeat units thus providing the basis for the designation 'allele 10'. Except for isolated point mutations, no systematic differences could be observed either in the repeat sequence or in the flanking regions between the two fragments of a given individual. Thus it was not possible to discriminate between the two loci of the DYS385 system. Four population samples of German (n = 146), Chinese (n = 100), Japanese (n = 100), and Thai (n = 95) origin were studied. In the four groups, alleles 10 to 24 could be observed and genotype frequencies differed significantly. In Germans only one common genotype was present (11-14; 33.8% frequency). In the Asian populations, the frequencies were more evenly distributed with the 13-13 genotype (9%) in Chinese, the 13-17 genotype (14%) in Japanese and the 14-18 genotype (7%) in Thai being the most common. Overall, 69 different genotypes were found, of these 36 were observed in Germans, 36 in Chinese, 33 in Japanese and 44 in Thai. No mutations were detected in 62 father-son pairs. Thus DYS385 is a highly polymorphic STR system with population-specific genotype distributions.

Asia, Southeastern↗

PubMed1998

Fluorescent multiplex analysis of nine STR loci: Spanish population data.

A total of 171 Caucasians living in Andalucia (southern Spain) have been typed for nine short tandem repeat (STR) loci by multiplex PCR amplification using a commercially available kit (Profiler Plus; Perkin-Elmer, Norwalk, CT, USA) and semi-automatic electrophoresis (ABI Prism 377 DNA Sequencer, Applied Biosystems, Foster City, CA, USA). The kit enables typing of the STR loci D3S1358, VWA, FGA, D5S818, D13S317, D7S820, D8S1179, D21S11, and D18S51. All loci, except D7S820, meet Hardy-Weinberg equilibrium. Because of the large number of loci that can be analyzed, the power of discrimination (PD) is greater than 0.99999, and the probability of exclusion (PE) reaches 0.99991 in our population sample.

Alleles↗

PubMed1999

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↗

PubMed2000

Report of the European Network of Forensic Science Institutes (ENSFI): formulation and testing of principles to evaluate STR multiplexes.

This paper describes a collaborative exercise organised under the auspices of the European Network of Forensic Science Institutes (ENFSI). The purpose of this EU (European Union) funded group is to carry out research to enable STR loci to be compared between European laboratories, ultimately leading to the formation of a pan-European database. Accordingly, an exercise was designed to evaluate a prototype STR multiplex system manufactured by Applied Biosystems (ABD). Each laboratory was sent 12 samples to analyse along with a multiplex kit. Of specific interest was the definition of parameters to define the efficiency of the system. Stutter, split allelic peaks (differing by one base), pull-up, heterozygous balance and between locus balance were all objectively measured. Once the important parameters are defined it is possible to directly compare performances of different multiplexes and the different laboratories carrying out the tests. Since the multiplex used was a prototype system, this exercise cannot be regarded as a proficiency test.

Alleles↗

PubMed2000

Allelic distribution of nine short tandem repeat (STR), HLA-DQA1, and polymarker loci in an Omani sample population.

Allele frequency distributions of nine short tandem repeat (STR) loci, D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D7S820, and D13S317, HLA-DQA1 and polymarker (PM) loci were studied in a sample population from Sultanate of Oman, Middle East. Blood samples were collected from 162 unrelated individuals. For all STR, HLA-DQA1 and PM loci, no deviations from Hardy-Weinberg equilibrium, based on the exact test, were observed. The most discriminating loci were D18S51 (PD=0.966) and FGA (PD=0.964), while the least informative locus is GYPA (PD=0.585). The allele frequency data may be useful in forensic case work.

Alleles↗

PubMed2006

Fluorescent multiplex amplification of three X-STR loci.

This study was carried out to evaluate the value of three X-STR loci (DXS6803, DXS981and DXS6809) in forensic application and thereby investigate their polymorphism. The primer for each locus was labeled with fluorochrome 6-FAM. A fluorescent multiplex PCR for simultaneously amplifying three X-STR loci was set up. The PCR products that were obtained were analyzed using capillary electrophoresis and ABI PRISM 3100 Genetic Analyzer, with GENESCAN Analysis Software. When 340 male and 195 female individuals of Han population in China were tested, 13, 12, and 11 alleles were observed for DXS6803, DXS981 and DXS6809, respectively. One hundred and eighty three haplotypes were detected in the male individuals. The haplotype diversity reached 0.9926. The results show that the three loci of the multiplex system provide significant information on polymorphism for forensic identification and paternity testing, particularly for complicated paternity deficient cases.

Chromosomes, Human, X↗

PubMed2000

Genetic analysis of the STR system D20S161 in Japanese and Bangladeshi.

The allele distributions of the STR locus D20S161 have been investigated in Japanese and Bangladeshi people. No deviation from the Hardy-Weinberg equilibrium was observed in either population. D20S161 was found to be a polymorphic STR with seven alleles in Japanese and with six alleles in Bangladeshi. The distribution of allele frequencies in Japanese was very similar to that in Bangladeshi. The D20S161 system can be a potential marker for medicolegal individualization and paternity testing.

Journal Article↗

PubMed2002

Analysis of the polymorphic structure of the D7S808-short tandem repeat (STR) locus.

We analyzed the polymorphic structure of the short tandem repeat (STR) (AARG) locus D7S808 by DNA sequencing and examined the D7S808 allele distribution in a Japanese population. The sequence analysis confirmed that this locus consists of repeats of the tetranucleotides cttt and cctt, but that the number of repeats of the cctt motif does not vary with the allele, and that this STR polymorphism is due to variation in the number of cttt repeats alone. Although the results in this study suggest that the numbers of repeats range from 7 (allele 7) to 22 (allele 22), alleles 9, 10, 19, and 21 were not observed in the Japanese samples examined. Analysis of DNA samples from 355 unrelated individuals revealed the occurrence of 286 heterozygotes (observed heterozygosity 80.6%). Alleles 15, 14, 16, and 17 had high frequencies of 0.261, 0.192, 0.166, and 0.120, respectively and, together with allele 7 with a slightly high frequency of 0.059, showed a bimodal distribution. In addition, we prepared primers yielding shorter amplification products (232-292 bp) than those (435-480 bp) obtained with the originally reported primers. The newly designed primers can be used for polymerase chain reaction, making this locus extremely useful in forensic science practice.

Journal Article↗

PubMed1999

Tetrameric short tandem repeat (STR) system D15S233 (wg1d1): sequencing and frequency data in the japanese and Chinese populations.

We evaluated the forensic usefulness of D15S233 (wg1d1), a tetrameric short tandem repeat (STR) locus, in the Japanese and Chinese populations. Typing was performed by denaturing polyacrylamide gel electrophoresis followed by silver staining. Nine different alleles were found in 472 Japanese chromosomes and seven in 186 Chinese chromosomes. 102 alleles sequenced were composed of two kinds of repeats (AGGA and GGGA). All alleles differed in size by one tetranucleotide repeat unit, and no insertion or deletion was found. The expected unbiased heterozygosities in Japanese and Chinese were 0.766 and 0.785, respectively. No significant deviations from the Hardy-Weinberg equilibrium were found in either population. We retyped all samples using an alternative pair of flanking primers in order to detect any spurious appearances of homozygotes due to sequence variation at the primer annealing site. One heterozygous sample had unbalanced density bands when the original primer set was used, but equal density bands when our newly designed primer set was used. Sequencing analysis revealed that the sparser allele had one nucleotide substitution near the 5' end of the annealing site of the original primer region. Thus, all apparently homo/heterozygous samples were thought to be truly homo/heterozygous. We also applied the D15S233 locus to paternity testing and forensic identification. Our results suggest that this locus should be a very useful STR locus for forensic practice in Japanese and Chinese.

Journal Article↗

PubMed2003

Identification of HepG2 variant cell lines by short tandem repeat (STR) analysis.

In the past years, in our laboratory, several cell lines have been generated starting from a human liver (H7). Some of them have been used successfully in studies of the infection with and propagation of Hepatitis B and Hepatitis C viruses. Recently, several lines of evidence indicated that the origin of these cell lines was uncertain. Therefore, we now have determined the genetic characteristics of these cell lines in comparison to HepG2 cells received from ATCC and to HepG2 isolates grown at other laboratories. Quadruplex fluorescent short tandem repeat (STR) typing and karyotyping were performed. In addition, some biochemical characteristics of selected clones were studied. Genetically, all H7-derived cell lines were identical to HepG2 cells. However, some liver-specific functions varied between the different sub-cloned lines. The H7-derived cell lines that were generated proved to be sub-cloned lines of HepG2. The problem of cross-contamination during cloning of cell lines appears to be not uncommon. We found that two out of six HepG2 isolates obtained from other laboratories were not derived from the same individual as the original HepG2 cells. Therefore, STR typing should be applied as a rapid and sensitive technique to determine and monitor the origin of cell lines and to safeguard against contamination.

Albumins↗

PubMedDate not supplied

Reconstruction of a historical genealogy by means of STR analysis and Y-haplotyping of ancient DNA.

Archaeological excavations in St Margaretha's church at Reichersdorf, Germany, in 1993 led to the discovery of eight skeletons, so far assumed to be of the Earls of Königsfeld, who used the church as a family sepulchre over a period of seven generations from 1546 to 1749. DNA-based sex testing and analysis of autosomal short tandem repeat systems (STR) was carried out to confirm the assumption of kinship. Since five of the individuals were determined as males, analysis of Y-specific STRs seemed feasible. A comparison of Y-haplotypes revealed that one individual could not be linked to the Königsfeld patrilineage, an observation supported by autosomal STR evidence. Two individuals typed as females posed an identification problem, since supposedly only male members of the family were buried in St Margaretha's. Nevertheless, these individuals could tentatively be identified as members of the House of Königsfeld through genetic fingerprinting.

Burial↗

PubMed1998

Variation in mutation rate and direction between tetranucleotide STR loci in human colorectal carcinomas.

Replication error (RER) is defined as mutation events in repetitive DNA segments. To investigate further the RER phenomenon and reveal any differences in mutation outcome between different short tandem repeat (STR) loci, we have investigated the somatic mutation rate and the size distribution of new tumour alleles in four tetranucleotide STRs in a large material of unselected colorectal adenocarcinomas. DNA was extracted from the blood and carcinomas of 217 patients. All blood/tumour pairs were analysed using the STRs HUMTHO1, HUMFES/FPS, HUMVWA31/A and HUMF13A1. Mutations are detected at all four loci. There are substantial differences in mutation rate and mutation direction (i.e. expansion versus contraction) between different STR loci. In all four STRs, the majority of events represent gain or loss of a single repeat. Almost all new tumour alleles correspond to known alleles in a population database, indicating that these are also composed of integers of the four base pair repeat. There is no statistically significant size bias in the mutating alleles as compared to the allelic distribution in the population database.

Adenocarcinoma↗

PubMedDate not supplied

Population genetic study of the STR loci (HUMCSF1PO, HUMTPOX, HUMTHO1, HUMLPL, HUMF13A01, HUMF13B, HSFESFPS and HUMVWA) in North Indians.

BACKGROUND: Highly polymorphic genetic markers like short tandem repeats (STRs) have been used successfully in disease analysis and studies of human evolution and population genetic diversity. However, DNA-based population genetic studies of Indian populations are limited. SUBJECTS AND METHODS: To enlarge our understanding of genetic variation in Indian populations, a population genetic study was carried out on Jat Sikh (Punjab, North India) individuals (n = 150) using a battery of the STR loci. The STR loci analysed by means of PCR amplification followed by electrophoresis and silver staining included HUMCSF1PO, HUMTPOX, HUMTHO1, HUMLPL, HUMF13A01, HUMF13B, HUMFESFPS and HUMVWA loci. RESULTS: The overall pattern of allele frequencies was similar to many Caucasian and Indian populations and heterozygosity varied from 65% (HUMLPL) to 85% (HUMVWA). For all eight loci, no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. Significant differences were observed between Jat Sikhs and African, Chinese and Indian tribes. The mean exclusion probability ranged from 35% to 70%, and the power of discrimination from 81% to 93%, indicating the potential of these loci for forensic and paternity investigations. CONCLUSION: The allele frequency spectrum, heterozygosity, probability of exclusion, match probability and discrimination probability estimates show interesting variation and suggest the usefulness of these loci for anthropogenetic, paternity and forensic investigations in Indian populations.

DNA Fingerprinting↗

PubMed2006

Determination of twin zygosity using a commercially available STR analysis of 15 unlinked loci and the gender-determining marker amelogenin--a preliminary report.

BACKGROUND: The aim of this preliminary study was to estimate the accuracy of the zygosity determination in twin pregnancies. METHODS: Seventy-three sets of twin pregnancies were enrolled in this study, including 48 sets of twins resulting from assisted reproductive techniques (ART) and 25 sets of spontaneously conceived twins. Determination of zygosity was made by PCR-amplified short tandem repeat (STR) analysis with a commercially available panel, comprising 15 autosomal, codominant, unlinked loci and the gender-determining marker, amelogenin. Monozygotic (MZ) twins were determined when all these unlinked loci and the gender-determining marker were identical. Chorionicity and placenta were examined after delivery of the newborns to check their relationships to the twin zygosities. RESULTS: Three of 48 (6.25%) sets of twins produced by ART and 18 of 25 (72%) sets of spontaneously conceived twins were MZ. Monozygosity could be evaluated based on 'like sex' in spontaneously conceived twins, because they had a greater incidence of MZs than those produced by artificial reproductive techniques. The MZ prediction rate was 78.6%, and the overestimated rate was 21.4% if the monochorionic like-sexed twins (LST) had a grossly single placenta. The underestimated rate of MZs was 26.7% when the dichorionic LST had apparently separate placentas. CONCLUSION: With the DNA-based 15 STR analysis amplified in a multiplex PCR, the determination of the zygosity in multifetal pregnancies is not only cost and time saving but also yields greater sensitivity and precision than conventional methods.

Adult↗

PubMed1998

Phylogenetic resolution of complex mutational features at Y-STR DYS390 in aboriginal Australians and Papuans.

Y-chromosomal short tandem repeats (STRs) are used for the study of male aspects of human evolution as well as for forensic applications and paternity testing. Both applications require an understanding of the underlying mutational mechanisms that create variability. We describe complex mutations at the substructured DYS390 STR locus in 97 natives of the New Guinea/Australian region. Sequencing of short alleles in these populations indicates multirepeat deletions. All samples are further characterized using the five additional Y-STR loci DYS19, DXYS156-Y, DYS391, DYS392, and DYS393. Phylogenetic analysis of the resulting haplotypes yields ethnically specific clusters predating the settlement of Australia and Papua New Guinea (although archaic Homo sapiens or Homo erectus lineages are absent). The phylogeny confirms that DYS390 violates the stepwise mutation model and demonstrates that the DYS390 locus mutates relatively rapidly and retains its variability after structural change.

Alleles↗

PubMed2006

Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system.

In the past 5 years, there has been a substantial increase in the use of Y-short tandem repeat loci (Y-STRs) in forensic laboratories, especially in cases where typing autosomal STRs has met with limited success. The AmpFlSTR Yfiler PCR amplification kit simultaneously amplifies 17 Y-STR loci including the loci in the "European minimal haplotype" (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393), the Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended Y-STR loci (DYS438 and DYS439), and the highly polymorphic loci DYS437, DYS448, DYS456, DYS458, Y GATA H4, and DYS635 (formerly known as Y GATA C4). The Yfiler kit was validated according to the FBI/National Standards and SWGDAM guidelines. Our results showed that full profiles are attainable with low levels of male DNA (below 125 pg) and that under optimized conditions, no detectable cross-reactive products were obtained on human female DNA, bacteria, and commonly encountered animal species. Additionally, we demonstrated the ability to detect male specific profiles in admixed male and female blood samples at a ratio of 1:1000.

Animals↗

PubMed2000

Cloning and characterization of the str operon and elongation factor Tu expression in Bacillus stearothermophilus.

The complete primary structure of the str operon of Bacillus stearothermophilus was determined. It was established that the operon is a five-gene transcriptional unit: 5'-ybxF (unknown function; homology to eukaryotic ribosomal protein L30)-rpsL (S12)-rpsG (S7)-fus (elongation factor G [EF-G])-tuf (elongation factor Tu [EF-Tu])-3'. The main operon promoter (strp) was mapped upstream of ybxF, and its strength was compared with the strength of the tuf-specific promoter (tufp) located in the fus-tuf intergenic region. The strength of the tufp region to initiate transcription is about 20-fold higher than that of the strp region, as determined in chloramphenicol acetyltransferase assays. Deletion mapping experiments revealed that the different strengths of the promoters are the consequence of a combined effect of oppositely acting cis elements, identified upstream of strp (an inhibitory region) and tufp (a stimulatory A/T-rich block). Our results suggest that the oppositely adjusted core promoters significantly contribute to the differential expression of the str operon genes, as monitored by the expression of EF-Tu and EF-G.

Amino Acid Sequence↗