Spanish population data on 7 tetrameric short tandem repeat loci

Allele and genotype frequencies for 7 tetramerie short tandem repeat loci were determined in a Spanish population sample (N = 186–244) using PCR and subsequent analysis of the PCR products by denaturing polyacrylamide gel electrophoresis followed by silver staining. The loci were HUMFES/FPS, HUMVWA, HUMTHOI, HUMF13B, HUMCSFIPO, HUMF13A1 and HUMTPOX and all loci met Hardy-Weinberg expectations. In addition, little evidence was found for association of alleles among the 7 loci. Thus the allele frequency data can be used in identity testing to estimate the frequency of a multiple PCR-based DNA profile in the Spanish population.     

A Dutch population study of the STR loci HUMTHO1, HUMFES/FPS,HUMVWA31/1 and HUMF13A1, conducted for forensic purposes

We report on a Dutch population study of the STR loci HUMTHOI, HUMFES/FPS, HUMVWA31/1, and HUMF13A1, in which we used multiplex amplification and automated fragment detection. Genotype and allele frequencies showed no deviation from Hardy-Weinberg and linkage equilibrium. The improved Bonferroni procedure was used to combine the results of several tests. The power of discrimination of a complete profile exceeded 0.9998. We compared the allele frequencies in the Dutch sample to the frequencies in other populations using a biplot to visualize alleles and populations simultaneously. The Dutch sample was similar to most other Caucasian samples. The data demonstrate that the genetic systems in this report are a valuable tool for forensic identity testing in The Netherlands.     

Systematische Untersuchungen zur Quantifizierung von genomischer DNA aus Hautproben

In this study we investigated if skin samples are suitable DNA sources for molecular biological examinations. For this purpose appropriate extraction, detection and quantification methods are required. These demands are met by phenol extraction and by the QuantiBlot Human DNA Quantitation Kit. Skin samples were taken from different regions from corpses of both sexes (face, elbow, knee, sole of the foot, neck and back). The parallel use of two extraction methods and subsequent quantification indicated higher yields of genomic DNA with the phenol-extraction than with Chelex-extraction. The average DNA content from skin traces from the neck, back, sole of the foot and elbow was 690.95 ng/mg dried skin. Paraffin-embedded skin samples (average DNA content of ten 5 μm-thick paraffin sections ranged from 2.5 to 25 ng) are are also useful for molecular investigations. All skin samples could be typed with four STR systems (HUMFES/FPS, HUMTH01, HUMF13A01 and HUMVWA31) and Amelogenin. A hit-and-run offence described in this report could be clarified by means of DNA typing of a skin abrasion from the victim on the vehicle.     

Population study of the STRs HUMCD4 and HUMF13A1 in Catalonia (Northeast Spain)

Allele and genotype frequencies were determined in a population sample from Catalonia (Northeast Spain) for two short tandem repeat loci (HUMCD4 and HUMF13A1), using the polymerase chain reaction (PCR). After denaturing PAG electrophoresis, 6 alleles were identified for HUMCD4 in a sample of 157 unrelated individuals, and 11 alleles for HUMF13A1 in a sample of 141 individuals. No deviation from Hardy-Weinberg equilibrium was found. The HUMCD4 and HUMF13A1 loci demonstrated a heterozygosity of 0.6815 and 0.7305 respectively. Received: 24 June 1996 / Received in revised form: 6 November 1996     

Population data on 6 short tandem repeat loci in a sample of Caucasian-Mestizos from Colombia

Blood samples from 409–452 unrelated Colombian Caucasian-Mestizo individuals were amplified and typed for six short tandem repeat (STR) markers (HUMF13A01, HUMFES/FPS, HUMVWA, HUMCSF1PO, HUMTPOX, HUMTH01). The allele frequencies, genotype frequencies, heterozygocity, mean paternity exclusion chance, polymorphism information content, discrimination power, assumption of independence within and between loci and Hardy Weinberg equilibrium were determined. The results demonstrate that all markers conform to Hardy-Weinberg equilibrium expectations. In addition, the results demonstrate the assumption of independence within and between the loci analysed. The mean exclusion chance (MEC) was 0.9851 for all six STR loci analysed and the discrimination power (DP) was 0.9999973. Therefore, this Colombian population database can be used in identity testing to estimate the frequency of a multiple PCR-based locus DNA profile in forensic cases as well as in paternity testing. Received: 24 September 1998 / Received in revised form: 22 December 1998 / Accepted: 11 January 1999     

Allele frequency distributions of the polymorphic STR loci HUMVWA, HUMFES, HUMF13A01 and the VNTR D1S80 in a Filipino population from Metro Manila

Allele frequency distributions at the short tandem repeat (STR) loci HUMVWA, HUMFES, HUMF13A01 and of the variable number of tandem repeat (VNTR) locus D1S80 were determined in a Filipino population from Metro Manila (103 individuals) by use of the polymerase chain reaction (PCR) followed by polyacrylamide gel electrophoresis (PAGE). The exact test demonstrated that all four loci had no deviations from Hardy-Weinberg equilibrium (HWE) with the only reservation that the exact test p-value for F13A01 is weak. The discriminating power is 0.82 for D1S80, and the expected exclusion chance is 0.85 for F13A01, 0.83 for FES, and 0.93 for VWA. The observed heterozygosity rates are 0.63 for D1S80, 0.66 for F13A01, 0.67 for FES, and 0.80 for VWA. The exact test for independance between all loci gave a p-value of 0.0195. This is the first time that Filipino population data of DNA loci of forensic importance are reported. Received: 7 July 1997 / Received in revised form: 18 September 1997     

Hungarian population data on six STR loci — HUMVWFA31, HUMTH01, HUMCSF1PO,HUMFES/FPS,HUMTPOX, and HUMHPRTB —derived using multiplex PCR amplification and manual typing

We present a Hungarian population study for six tetrameric short tandem repeat (STR) loci employing multiplex PCR amplification, electrophoresis of the PCR products in DNA sequencing gels and subsequent detection of allelic fragments by silver staining. The loci were HUMVWFA31, HUMTH01, HUMCSF1PO, HUMFES/FPS, HUMTPOX, and HUMHPRTB. All loci met Hardy-Weinberg expectations in the examined Hungarian Caucasian population sample (N = 223 individuals). In addition, there was no evidence for association of alleles among the five autosomal loci HUMVWFA31, HUMTH01, HUMCSFIPO, HUMFES/FPS, and HUMTPOX.     

A population study of the STR loci HUMLPL, HUMF13B, and HUMF13A01 in Hungary

Allele frequencies of the three STR systems HUMLPL, HUMF13B, and HUMF13A01 were determined in a Hungarian population sample of 223 unrelated Caucasian individuals. All loci met Hardy-Weinberg expectations and there was no evidence for association of alleles among the three STR loci. In addition, little evidence was found for departures from expectations of independence between any of the three STR and other previously investigated microsatellite polymorphisms. Received: 19 October 1996 / Received in revised form: 6 January 1997     

The validation of short tandem repeat (STR) loci for use in forensic casework

A quadruplex reaction has been developed which amplifies the short tandem repeat (STR) loci HUMVWA31/A, HUMTHO1, HUMF13A1 and HUMFES/FPS. Detection of the PCR products employs denaturing poly-acrylamide gels coupled with fluorescent-based technology. This system has been evaluated for use in routine forensic casework and has been shown to be both robust and reproducible. The quadruplex reaction is as sensitive as the commercially available HLA DQ Amplitype typing system and can be used on both degraded and aged material. The problems of environmental contamination have been shown to be limited provided strict procedural practices are followed — i.e. physical separation of sample extraction and amplified products; the use of dedicated equipment such as pipettes; the separation of amplification preparation area. The ability of the system to detect mixtures and the successful analysis of case stains has shown that this system is well suited as a tool for forensic investigation.     

Population study of 3 STR loci in the Basque Country (northern Spain)

The tetrameric STRs, HUMTH01, HUMVWA31A and HUMFES/FPS, were studied in a population from the Basque Country (northern Spain) for their frequency distribution and applicability to identity and paternity testing. All systems conformed to Hardy-Weinberg equilibrium; pairwise comparisons demonstrated the allelic independence between loci, and furthermore, all systems seemed to be in agreement with expectations from the Stepwise Mutation Model (SMM) of the mutation-drift theory, which indicates the homogeneity of the population and suggests a replication slippage mechanism as a possible model for generating alleles. A comparison with other population groups appeared to indicate that frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters a priori probability of exclusion (PEX) and index of discrimination (ID), show the informativeness of these loci for the determination of identity and relatedness of individuals.     

HumFES/FPS and HumF13B: Turkish and German population data

The allele distribution of two STRs has been investigated in two populations, i. e. Turks (n = 203/200) and Germans (n = 414/402). The Turkish population showed 11 alleles in HumFES/FPS and 6 alleles in HumF13B while the German population had 9 (FES) and 8 (F13B) alleles respectively. Although the frequency profiles looked quite similiar in both populations, there exist significant differences mainly due to alleles 8 and 10 (F13B) and allele 12 (FES). Four variant alleles have been sequenced and are described. Investigation of 368 (FES)/372 (F13B) meioses revealed no new mutations.     

Frequencies for five short tandem repeat (STR) systems in a population from North Poland

A population study of unrelated individuals from North Poland (Gdansk area) was carried out to investigate the allele distributions of the five STR systems HUMCD4, HUMFES/FPS, HUMVWA31, HUMTH01 and ACTBP2. PCR products were separated on horizontal non-denaturing polyacrylamide gels followed by silver staining. For all STR systems analysed the distribution of observed phenotypes did not deviate from Hardy-Weinberg equlibrium. A comparison of allele distributions between Polish and other European Caucasian population samples is presented. Received: 15 August 1996 / Received in revised form: 8 October 1996     

Different types of structural variation in STRs: HumFES/FPS,HumVWA and HumD21S11

Summary Alleles of the STR systems HumFES/FPS, HumVWA and HumD21S11 were sequenced and analyzed. Sequence data revealed 3 different systems concerning the complexity of their sequence structure. HumFES/FPS belongs to the STR polymorphism with a simple repeat structure. Only 2 subtypes were found with a base substitution in the 5-flanking region and no variation in the repeat region. In the STR system HumVWA the sequence structure of the repeat region is more complex, because 2 tetranucleotide units TCTA and TCTG were present. Additionally allele 14 revealed a completely different sequence structure leading to a different electrophoretic mobility. The repeat region of HumD21S11 is compound in structure. The possibility of variation at 3 positions leads to the occurrence of microheterogeneities in fragments of apparent length. In the upper allele range alleles arise with an additional incomplete TA-repeat.     

Evaluation of an automated DNA profiling system employing multiplex amplification of four tetrameric STR loci

Summary We have examined the performance and reproducibility of an automated DNA profiling system which is based on the multiplex amplification of 4 tetrameric STR loci — HUMVWFA31/A, HUMTH01, HUMF13A1 and HUMFES/FPS. The system was able to type 100 pg of purified, undegraded, genomic DNA. At lower concentrations of DNA (below 100 pg), allelec drop-out occurred due to stochastic differences in allele copy number. Minor variation of individual PCR reagent concentrations or cycling temperatures did not result in a significant effect on the efficiency of amplification of any of the 4 loci in the quadruplex system. More substantial variation of reagent concentrations or cycling temperatures outside the optimum range of the system resulted in a reduction or complete loss of signal for one or more loci. This was also observed at high ionic strength or extreme pH. However, under all reagent concentrations and conditions studied, no artefact bands that could potentially result in the mistyping of a sample were apparent within the read region (130–240 bases) of the gel. Evaluation of both native and denaturing polyacrylamide gels revealed that, although native gels displayed faster run times, the sizing precision of such gels for certain STR loci was lower than that of denaturing gels. Also, artefact bands may be present within the read region of native gels. In conclusion the quadruplex amplification system decribed, coupled with automated fluorescence-based detection on denaturing polyacrylamide gels, appeared to be a robust and reliable system for individual identification.     

Tibetan population data on the PCR-typed loci D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO

Frequency data for nine tetrameric short tandem repeat loci (D16S539, D7S820, D13S317, HUMF13A01, FESFPS, vWA, HUMTH01, TPOX and CSF1PO) were investigated in a population sample of 107 unrelated Tibetan individuals by using a multiplex polymerase chain reaction (PCR), followed by 4% polyacrylamide gel electrophoresis (PAGE) and silver staining. All loci met the Hardy-Weinberg expectations. The forensically relevant parameters were calculated. This is the first time that Chinese Tibetan population data on DNA loci have been reported that are of forensic importance. Received: 8 February 2000 / Accepted: 7 November 2000     

Validation of the STR system FES/FPS for forensic purposes in an Austrian population sample

The short tandem repeat system FES/FPS was amplified by the polymerase chain reaction (PCR) in 211 unrelated Austrians and analysed by horizontal, non-denaturing electrophoresis. The allele distribution was in Hardy-Weinberg equilibrium. No mutations were found in 25 families (50 meioses). The mean exclusion chance was 0.49, the discriminating power 0.86 and the heterozygosity rate 74.4%. Amplification could be achieved with as little as 100 pg of high molecular weight DNA, which could be reduced to 75 pg by using 32 instead of 30 cycles. By reamplifying 1 l for another 15 cycles, the threshold could be reduced to less than 20 pg. In a degradation experiment DNA extracted from bloodstains stored for up to 24 days in a moist chamber and DNA boiled for up to 18 min could be amplified.     

Effect of environmental factors on PCR-DNA analysis from dental pulp

This study was designed to observe the results of DNA typing on teeth subjected to aging, different temperatures and various environmental factors. A total of 570 teeth were studied. The study included the analysis of the PCR-based polymorphisms HLA DQA1, D1S80, HUMTH01, HUMFES/FPS and the XY homologous gene amelogenin. In general the best results were obtained with the XY homologous gene amelogenin, followed by the two STRs studied (HUMTH01 and HUMFES/FPS). The small fragment sizes and the method of detection used after PCR amplification are the main factors explaining this fact. In general, teeth submerged in water gave the poorest results. Teeth exposed to outdoor conditions provided better results than teeth buried in sand or soil, but even in these cases good results were obtained. Up to 4°C, temperature had only a slight influence on the results. Positive results were obtained in most cases at high temperatures (400°C for 2 min) which are rarely reached in practical casework. Positive typing results for the XY homologous gene amelogenin and the STRs were obtained from teeth 10–30 years old. The usefulness of dental pulp for identification purposes is exemplified in some actual cases.     

Die Optimierung der Amplifikations- und Detektionsbedingungen der Allele des HumF13B-Systems. Eine Populationsanalyse

A population study of HUMF13B locus in a population sample of 426 unrelated individuals was carried out to investigate the allele distribution in north Poland. HUMF13B alleles were identified using a precisely optimised PCR method. Amplification products were separated on horizontal non-denaturing polyacrylamide gels followed by silver staining. The most frequent alleles were 10 (42,6%), 9 (23,9%) and 8 (21,4%) and one rare variant (allele 12) was observed with a frequency of 0,23%. Relatively high indices of discrimination power (0.866), polymorphic information content (0.661) and heterozygosity (0.704) confirm the usefulness of HUMF13B locus for forensic identification purposes.     

French Caucasian population data obtained from fluorescently detected HumvWFA31/A and HumF13A01 short tandem repeat loci

Allele and phenotype frequencies for two tetranucleotide STR (short tandem repeat or microsatellite) systems, HUMvWFA31/A and HUMF13A01, were obtained from a sample of approximately 240 unrelated individuals randomly selected from the French Caucasian population. PCR (polymerase chain reaction) products were analysed on 6% polyacrylamide denaturing gels and visualized using fluorescently labelled primers on the automated 373A ABI DNA sequencer (Applied Biosystems Inc.). French Caucasian allele frequencies were compared to other published Caucasian data. Conditions were optimised for the quadruplex PCR amplification of these two STR loci together with the HUMFESFPS and HUMTHOI loci and the quadruplex PCR was also performed on various forensic DNA samples.     

Analysis of the STR loci HUMF13A01, HUMFXIIIB,HUMLIPOL, HUMTH01, HUMTPOX and HUMVWFA31 in a Japanese population

Population studies on six short tandem repeat loci, HUMF13A01, HUMFXIIIB, HUMLIPOL, HUMTH01, HUMTPOX and HUMVWFA31 were carried out in a sample of unrelated Japanese individuals (n = 337–545) living in Gifu Prefecture (central region of Japan). Five alleles could be identified for HUMFXIIIB, six for HUMF13A01, HUMLIPOL, HUMTH01 and HUMTPOX, and eight for HUMVWFA31. For all/six loci no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. The mean exclusion chance ranged from 0.22 to 0.60, the power of discrimination from 0.63 to 0.93, and the expected heterozygosity from 0.43 to 0.80. Allele frequency distributions for the loci in the Japanese sample were not similar to those in samples from other racial or ethnic groups except for the Chinese (for HUMTPOX). The results demonstrate that HUMTH01, HUMTPOX and HUMVWFA31 are more useful for forensic investigations in the Japanese population than the other three loci.