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PubMed2005

Which short tandem repeat polymorphisms are required for identification? Lessons from complicated kinship cases.

This paper presents 5 examples of complicated deficient parentage cases, which were sufficiently resolved by extensive DNA typing using short tandem repeat (STR) and restriction fragment length polymorphisms (RFLPs). The latter have greatly contributed to the solution of deficiency cases, although their application is only feasible, if high molecular weight DNA and time are in abundance. This apart, RFLP technique is available in a few laboratories only, and its extinction can be expected in medium term. This development will pose a problem unless more highly polymorphic STR systems are at the service of forensic genetic laboratories. The required "new" additional STR polymorphisms must be able to fully replace RFLPs in terms of their respective information content. STR loci of this quality are e.g. ACTBP2 (SE33), D5S2360, and gonosomal loci. Moreover, the newly introduced STR kit "Humantype Chimera" is considered valuable from this point of view.

Family↗
PubMed1997

Genetic diversity at six short tandem repeat loci within the state of Victoria, Australia.

A new multiplex PCR system, developed by the Forensic Science Service (FSS) in the United Kingdom, permits the coamplification and typing of six short tandem repeat (STR) loci: HUMFGA, D8S1179, HUMTHO1, HUMvWA, D18S51, D21S11 and the sex determining marker Amelogenin. Data are presented on these six STRs for two populations in the state of Victoria, Australia: Caucasian and Asian. Whilst several worldwide databases are already available for the STR loci HUMTHO1 and HUMvWA, only relatively few databases exist for D8S1179, D18S51, D21S11 and HUMFGA. Allele frequencies at each locus displayed some fluctuations between the two populations. This is particularly so for HUMTHO1. Generally, however, the most common allele at each locus was the same in all populations, at all loci. A novel D8S1179 allele was found in Asians, provisionally identified as allele 19. Results for the six loci were compared with similar data from three UK resident populations: Caucasian, Afro-Caribbean and Asian (Indian/Pakistani) populations. These indicated that ethnically similar populations display similar allele frequencies, while the Australian Asian and UK Afro-Caribbean were found to be distinct.

Alleles↗
PubMed1998

Analysis of two multiplexed short tandem repeat systems using capillary electrophoresis with multiwavelength fluorescence detection.

A series of experiments was performed to analyze the utility of capillary electrophoresis (CE) with multiwavelength detection capabilities for multiplex typing of short tandem repeat loci. Characteristics of the sieving polymer, hydroxyethylcellulose, which affect resolution of single strand (ss) DNA fragments were examined. Additionally, the effects of denaturant in the polymer system, separation voltage, and analysis temperature were studied to ascertain their effects on DNA separations and capillary lifetime. The use of elevated run temperature (60 degrees C) was found to improve sizing precision, to increase the lifetime of capillaries (100 runs or more per capillary), and to provide runtimes of under 20 min. Finally, 100 individual human DNA samples were typed successfully using CE. The average resolution obtained was 1.4 bases for a 200 base fragment with a standard deviation of sizing of 0.2 bases, allowing all alleles examined to be distinguished clearly.

DNA, Single-Stranded↗
PubMed2005

Cancer cell line identification by short tandem repeat profiling: power and limitations.

Cancer cell lines are used worldwide in biological research, and data interpretation depends on unambiguous attribution of the respective cell line to its original source. Short-tandem-repeat (STR) profiling (DNA fingerprinting) is the method of choice for this purpose; however, the genetic stability of cell lines under various experimental conditions is not well defined. We tested the effect of long-term culture, subcloning, and generation of drug-resistant subclones on fingerprinting profiles in four widely used leukemia cell lines. The DNA fingerprinting profile remained unaltered in two of them (U937 and K562) throughout 12 months in culture, and the vast majority of subclones derived therefrom by limiting dilution after long-term culture revealed the same profile, indicating a high degree of stability and clonotypic homogeneity. In contrast, two other cell lines (CCRF-CEM and Jurkat) showed marked alterations in DNA fingerprinting profiles during long-term culture. Limiting dilution subcloning revealed extensive clonotypic heterogeneity with subclones differing in up to eight STR loci from the parental culture. Similar heterogeneity was observed in subclones generated by selection culture for drug resistance where DNA fingerprinting proved useful in identifying possible resistance mechanisms. Thus, common tissue culture procedures may dramatically affect the fingerprinting profile of certain cell lines and thus render definition of their origin difficult.

Apoptosis↗
PubMed1996

Amplification of human short tandem repeats from medieval teeth and bone samples.

The suitability of typing hypervariable DNA loci for the genetic analysis of prehistoric populations is demonstrated for the first time. Alleles of the human short tandem repeat locus VWA31/A have been amplified from ancient teeth and bone samples derived from an early medieval burial site at Weingarten, Germany, using the polymerase chain reaction. The DNA results for 76 individuals reveal remarkable similarity of the allelic frequencies between the past and modern populations. A surplus of apparent homozygotes in the ancient population is most likely due to a stochastic problem of amplification of degraded DNA. Therefore technical obstacles for the application to ancient DNA were evaluated. The substantial perspectives of using microsatellite typing for the analysis of heritable diseases, determination of relatedness, and establishment of genealogies in prehistoric populations are outlined.

Alleles↗
PubMed1994

Fluorescent-based typing of the two short tandem repeat loci HUMTH01 and HUMACTBP2: reproducibility of size measurements and genetic variation in the Swedish population.

The aim of this study was to investigate the reproducibility of genetic typing of two tetrameric short tandem repeat (STR) loci and the extent of genetic variation in the Swedish population. An automated, fluorescent-based Applied Biosystems 373A sequencer was used for typing of the HUMTH01 and HUMACTBP2 loci (also named SE33). The former locus has seven alleles in the size range of 154-174 bp, while the latter is a complex locus with more than 32 alleles in the range of 227-316 bp. Using different fluorescent dyes, polymerase chain reaction (PCR) products from the two STR loci were sized in one lane using an internal size standard. In order to compare within- and between-gel reproducibility of fragment size estimates, a control sample was typed three times on each of 20 gels. Within the gel, the standard deviation (SD) of fragment size variability was less than 0.1 bp for four fragment sizes between 158-291 bp. Standard deviations between gels were slightly higher for the two shorter fragment sizes (HUMTH01), while the larger fragments varied between 0.3 and 0.4 bp (HUMACTBP2). The amount of genetic variation was investigated in samples from three Swedish cities (n = 301). Seven alleles were found at HUMTH01 and the observed heterozygosity was 0.77. At the HUMACTBP2 locus more than thirty alleles were found and the observed heterozygosity was 0.96. The observed genotype frequencies at HUMTH01 and HUMACTBP2 did not deviate significantly from Hardy-Weinberg expectations. No indication of a significant excess of homozygotes was found at any of the loci. We conclude that both HUMTH01 and HUMACTBP2 can be reliably typed using the method described. However, the latter locus requires an allelic ladder to be run on each gel.

Alleles↗
PubMed1998

Population study of the short tandem repeat polymorphisms HumTH01, HumvWA31, HumFESFPS and HumF13A01 in Sicily (Southern Italy).

Population genetic studies were carried out on randomly selected and unrelated healthy individuals from Sicily (n = 140-150 individuals) using the short tandem repeat (STR) systems HumTH01, HumvWA31, HumFESFPS and HumF13A01. After vertical electrophoresis on polyacrylamide denaturing gels 6 alleles could be identified for TH01, 9 for vWA31, 7 for FESFPS and 11 for F13A01. No significant deviations from Hardy-Weinberg were observed.

Alleles↗
PubMed2001

Analysis of 168 short tandem repeat loci in the Japanese population, using a screening set for human genetic mapping.

We devised a multiplex polymerase chain reaction (PCR) amplification and loading system for the convenient typing of 168 short tandem repeat (STR) polymorphic markers in a commercially available screening primer set for human linkage analysis. We genotyped all these 168 STR loci with 32 healthy unrelated Japanese, calculated allele frequencies at each STR locus, and performed three kinds of tests for Hardy-Weinberg equilibrium (HWE). Significant deviations from HWE in all three tests were observed at only three loci, and the average heterozygosity in the Japanese (0.733) was slightly lower than that in Caucasians (0.773). We also examined 32 Caucasians at some selected loci, to be compared with Japanese. Some markers showed greatly different heterozygosities or allelic distributions in Japanese and Caucasian populations. In two groups of STRs, those with and without irregular alleles (or interalleles), the former had a higher proportion of bimodal allelic distribution and possessed more alleles per locus than the latter. However, no significant differences in the observed and expected heterozygosities, or in the powers of discrimination, were found between the two groups. The present basic study of allele frequency databases of these STRs will contribute to further applications in forensic science and human genetics.

Gene Frequency↗
PubMed2000

Y chromosomal short tandem repeat (STR) loci in a representative group of males living in South Württemberg: a database for application in forensic medicine.

In this study, we resolved the allelic distribution of three Y chromosomal short tandem repeats (STRs), DYS19 (n=218), DYS390 (n=257) and DYS393 (n=215), in a population study of 257 unrelated men living in the area of South Wüerttemberg/Hohenzollern. In DYS19 and in DYS393, five different alleles were discovered, and in DYS390, six different alleles. Forty-nine different haplotypes were found in 202 unrelated male individuals. By investigating each of the three STR systems separately, the most powerful results were found in DYS390, with a PE (power of exclusion) of 0.74, followed by DYS19 (PE: 0.65) and DYS393 (PE: 0.47). Using a combination of two systems (n=202), the PEs ranged from 0.79 (DYS19 and DYS393) to 0.89 (DYS19 and DYS390). The combination of all three STR systems revealed a PE of 0.93.

DNA Fingerprinting↗
PubMedDate not supplied

Genetic variation observed at two tetrameric short tandem repeat loci on chromosome 12 (D12S66 and D12S67) among five distinct ethnic groups of India: detection of two new alleles.

OBJECTIVE: The present investigation reports the genetic variation observed at two tetrameric short tandem repeat (STR) loci on chromosome 12 (D12S66 and D12S67) among five anthropologically distinct population groups of India. SUBJECTS AND METHODS: A total of 277 random, normal and healthy volunteers were investigated for the D12S66 locus, and 236 for the locus D12S67, from five ethnic groups of India. Two of these belong to the state of Maharashtra in western India (Konkanastha Brahmins and Marathas) and three from the state of Kerala in South India (Nairs, Ezhavas and Muslims). DNA was extracted from peripheral blood samples, amplified by duplex polymerase chain reaction (PCR) and electrophoresed on 6% denaturing urea (7 M) gel electrophoresis. The analysis was performed on ALF Express DNA sequencer (Amersham Pharmacia Biotech) using Fragment Manager software. Statistical analysis was done by using Arlequin ver. 1.1. RESULTS: At D12S66 locus, a total of nine alleles (8-17 repeats) and 27 genotypes were detected with an observed heterozygosity ranging from 0.55 to 0.91. At the D12S67 locus, nine alleles (36-44 repeats) and 33 genotypes were observed with a heterozygosity ranging from 0.74 to 0.89. Both the loci displayed high Power of Discrimination (PD) which ranged from 0.81 to 0.91 and Polymorphic Information Content (PIC) ranging from 0.68 to 0.84. At D12S66, two alleles were detected for the first time in these population groups which were not reported earlier. The level of gene differentiation (G(ST) value, 0.02) was moderate at these two loci, indicating a close relationship among the population groups. CONCLUSIONS: From this investigation, it is concluded that both the tetrameric loci are highly polymorphic and informative, and can be used for the characterization of the Indian population groups in addition to other well-studied STR loci.

Alleles↗
PubMed2001

Diagnosis of trisomy 21 in fetal nucleated erythrocytes from maternal blood by use of short tandem repeat sequences.

BACKGROUND: The purpose of this study was to determine whether aneuploid fetal nucleated erythrocytes (NRBCs) could be detected in maternal blood through the use of fluorescent PCR amplification with polymorphic short tandem repeat (STR) markers as an alternative or complementary method to analysis by fluorescent in situ hybridization (FISH). METHODS: Peripheral blood samples were obtained from women who had just undergone termination of pregnancy because of fetal trisomy 21 (three cases, 47,XY,+21; four cases, 47,XX,+21). Candidate fetal cells were isolated by flow-sorting by antibodies to the gamma chain of fetal hemoglobin and Hoechst 33342. FISH analysis was performed by the use of chromosome-specific probes for X, Y, and 21. Fetal NRBCs, as defined by the presence of gamma staining, characteristic morphology, and three chromosome 21 signals, along with maternal leukocytes, defined as gamma negative and two chromosome 21 signals, were micromanipulated separately and subjected to fluorescent PCR amplification of chromosome 21 STR markers (D21S11, D21S1411, and/or D21S1412). RESULTS: In five of seven cases analyzed, fetal NRBCs were aneuploid, as determined by the presence of triallelic or diallelic peaks of chromosome 21 sequences when compared with sequences from the maternal leukocytes. CONCLUSIONS: Fluorescent PCR amplification of STRs can detect fetal aneuploidy and may be useful in the setting of poor hybridization efficiency with FISH analysis. These results suggest that combined fetal aneuploidy and single-gene diagnoses by the use of DNA microarrays may be feasible in the near future.

Aneuploidy↗
PubMed2004

Rapid and accurate characterisation of short tandem repeats by MALDI-TOF analysis of endonuclease cleaved RNA transcripts.

We describe the application of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for the characterisation of short tandem repeat (STR) sequences by the analysis of endonuclease cleaved RNA transcripts. Several simple bovine STR loci as well as interrupted and compound microsatellites were chosen as model loci to evaluate the capabilities of MALDI-TOF MS for STR analysis. In short, the described approach consists of a PCR amplification of the investigated STR sequence, which then is transcribed into RNA and cleaved by G-specific RNase T1. Base-specific cleavage of the transcript results in high informative fragment patterns from both the repetitive core sequence and the flanking region. Since sequence specificity from endonuclease cleavage is combined with the accuracy of MALDI-TOF measurements, this technique allows for fast and reliable determination of simple repeat lengths as well as for further characterisation of STR allele sequences, which is of high interest especially in more complex STR loci.

Dinucleotide Repeats↗
PubMed2001

Genotyping of simple and compound short tandem repeat loci using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

The utility of electrospray ionization Fourier transform ion cyclotron resonance (ESI-FIICR) mass spectrometry as a new approach for genotyping short tandem repeats (STRs) is demonstrated. STRs are currently valued as a powerful source of genetic information with repeats that range in structure from simple to hypervariable. Two tetranucleotide STR loci were chosen to evaluate ESI-FTICR mass spectrometry as a tool for genotyping: HUM-TH01, a simple STR with nonconsensus alleles, and vWA, a compound STR with nonconsensus alleles. For HUM-TH01, the genotype (i.e., repeat number of each allele) was determined for each of 30 individuals using mass measurements of double-stranded amplicons. Low-intensity peaks observed in the spectra of amplicons derived from heterozygous individuals were identified by mass as heteroduplexes that had formed between nonhomologous strands. Mass measurement of the double-stranded vWA amplicon was not sufficient for determining whether the individual was homozygous for allele subtype 18 or 18' since the amplicons differ by only 0.99 Da. Therefore, single-stranded amplicons were generated by incorporating a phosphorylated primer, prepared using T4 polynucleotide kinase, into the PCR phase and subsequently digesting the bottom strand using lambda-exonuclease. Accurate mass measurements were obtained for the single-stranded amplicons using internal calibration and the addition of a correction factor to adjust for the natural variation of isotopic abundances, confirming that the individual is homozygous for allele 18. Our results clearly demonstrate that ESI-FTICR mass spectrometry is a powerful approach to characterize both simple and compound STRs beyond the capabilities of electrophoretic technologies.

Cyclotrons↗
PubMed1995

Short tandem repeat polymorphism linkage studies in a new family with X-linked mental retardation (MRX20).

A family with X-linked recessive mental retardation (XLMR) without other obvious manifestations (MRX20) was studied with 14 short tandem repeat polymorphism (STRP) markers. Two-point lod scores above 3 were obtained with DXS1003, DXYS1, DXS3, and DXS458. A multipoint lod score of 4.25 was obtained with peak at DXS1003. Recombination events identify a 55.6 cM interval between DXS1068 and DXS454, while a one unit support interval identifies 40 cM between MAOA and DXS458.

Genetic Linkage↗
PubMed2004

Evaluation and validation of the ABI 3700, ABI 3100, and the MegaBACE 1000 capillary array electrophoresis instruments for use with short tandem repeat microsatellite typing in a forensic environment.

The demand for high-throughput DNA profiling has increased with the introduction of national DNA databases and has led to the development of automated methods of short tandem repeat (STR) profile production; however, a potential bottleneck still exists at the gel electrophoresis stage. Capillary electrophoresis sequencers capable of processing 96 samples with considerably reduced manual intervention are now available. In this paper, we compare the ABI Prism 377 slab-gel sequencer currently used by the Forensic Science Service with three leading capillary array electrophoresis instruments: the ABI Prism 3700, the Amersham MegaBACE 1000 and the 16-capillary ABI Prism 3100. We describe the experiments used to evaluate and validate these platforms for forensic use with the STR multiplex Ampf/STR SGMplus [1, 2], along with comparative data from the ABI Prism 377 sequencer.

Databases, Nucleic Acid↗
PubMed2003

Short tandem repeat data analysis in a Mongolian population.

Fifteen somatic (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) and five Y-chromosome (DYS19, DYS390, DYS391, DYS392, DYS393) short tandem repeat (STR) system analyses were carried out in a Mongolian population in order to define the possible relationship between Mongolians and old Hungarian population. For STR data analysis the Microsoft Excel-PowerStats program was used. Inter-population data analysis was performed with Arlequin Software ver. 2.000. The somatic markers showed meaningful difference between Mongolians and old Hungarians but the distribution of the Y-chromosome STR systems refers to a closer relationship between the old Hungarian and oriental populations.

Chromosomes, Human, Y↗
PubMed2001

Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates.

BACKGROUND: Genetic analysis of microsatellite DNA is a powerful tool used in linkage analysis, gene mapping, and clinical diagnosis. To address the expanding needs of studies of short tandem repeats (STRs), we demonstrated high-performance STR analysis on a high-throughput microchannel plate-based platform. METHODS: Energy-transfer-cassette-labeled STR amplicons were separated and typed on a microfabricated 96-channel radial capillary array electrophoresis (CAE) microchannel plate system. Four-color detection was accomplished with a laser-excited confocal fluorescence rotary scanner. RESULTS: Multiplex STR analysis with single base-pair resolution was demonstrated on denaturing polyacrylamide gel media. The high-throughput multiplex capabilities of this genetic analysis platform were demonstrated by the simultaneous separation of STR amplicons representing 122 samples in ninety-six 5.5-cm-long channels in <8 min. Sizing values obtained for these amplicons on the CAE microchannel plate were comparable to those measured on a conventional commercial CAE instrument and exhibit <1% sizing variance. CONCLUSIONS: Energy-transfer-cassette labeling and microfabricated CAE microchannel plates allow high-performance multiplex STR analyses.

Cell Line↗
PubMed1999

[Polymorphisms of five short tandem repeat systems in Chinese Han population in Chengdu].

OBJECTIVE: To get preliminary genotype and allele frequency distributions of D6S366, D6S477, D12S375, D12S391 and PLA2A loci in Chinese Han population in Chengdu area and to validate more short Tandem repeat (STR) systems for forensic application. METHODS: The polymerase chain reaction (PCR) was used. Five STR systems (D6S366, D6S477, D12S375, D12S391 and PLA2A) were amplified on DNA samples, which were extracted from 108 unrelated individuals EDTA-blood by Phenol/Chloroform method. The PCR products were analyzed by PAG vertical electrophoresis. RESULTS: Seven alleles were found at D6S366 locus, nine alleles at D6S477 locus, five alleles at D12S375 locus, nine alleles at D12S391 locus and seven alleles at PLA2A locus. No deviations from Hardy-Weinberg equilibrium were observed. The heterozygosities observed were 0.69, 0.78, 0.81, 0.68 and 0.79 for D6S366, D6S477, D12S375, D12S391 and PLA2A respectively. The chances of exclusion were 0.3621, 0.6004, 0.4581, 0.7014 and 0.5589 and the discriminating powers were 0.79, 0.93, 0.86, 0.96 and 0.91. CONCLUSION: All of the five loci in this study were useful markers for individual identification and paternity test and for genetics purposes.

Alleles↗