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PubMed2002

Allele frequency data for 16 STR loci in the Vietnamese population.

The short tandem repeat systems ACTBP2, D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA were studied in a population sample from Vietnam (178 individuals, mainly from the Hanoi area). The 16 loci met Hardy-Weinberg expectations and possess a combined power of discrimination greater than 0.9999999999999999998 and a combined power of exclusion greater than 0.99999994 in this Vietnamese population.

Alleles↗
PubMed2003

Use of X-linked markers for forensic purposes.

In forensic science, X-chromosomal short tandem repeats (ChrX STRs) bear the potential to efficiently complement the analysis of other genetic markers (autosomal, Y-chromosomal or mitochondrial). We review the population genetic properties and forensic utility of selected ChrX markers, and discuss the problems and limitations arising with their practical use. Formulae required to assess the evidential power of individual markers in different contexts are summarised and applied to ChrX STRs of interest. Since linkage and linkage disequilibrium between markers affect the inferential interpretation of genotype data, practically relevant information regarding the co-localisation and haplotypic association of ChrX STRs is provided. Finally, two examples of complex kinship testing are presented which serve to highlight the particular importance of ChrX STRs for solving deficiency cases and cases involving blood relatives.

Chromosome Mapping↗
PubMed2003

Population genetic comparisons of three X-chromosomal STRs.

The X-chromosomal short tandem repeats (STRs) DXS6800, DXS101 and DXS8377 were analysed in male and female population samples from Germany and Austria using a PCR multiplex approach. We investigated 135 family trios from Innsbruck (Austria) and surrounding areas and 50 families and further male and female samples from Ulm (Germany) and surrounding areas. The comparisons of the allele frequencies gave similar distributions for Innsbruck and Ulm although minor variations were found for some alleles. Additionally, some differences were found when comparing the allele frequencies of the male and female samples independently. The forensic efficiency values demonstrate that especially DXS101 and DXS8377 are highly informative markers for kinship analysis and deficiency cases. Based on the investigated meiotic events no new mutations were detected.

Adolescent↗
PubMed2003

Y-chromosomal STR haplotypes in a population sample from southwest Germany (Freiburg area).

In the present study Y-chromosomal short tandem repeat (Y-STR) haplotypes of 433 unrelated male individuals from southwest Germany (Freiburg area) were analyzed. Population data for the loci DYS19, 389I, 389II, 390, 391, 392, 393, 385 and YCA II are given. Analysis of these loci provides the data that is defined as the "extended haplotype" and is available in the on-line Y-STR haplotpye reference database (YHRD) at http://ystr.org. Special emphasis is placed on the sequence and nomenclature of YCA II.

Base Sequence↗
PubMed2003

Erroneous identification in a mixed population: simulation using Israeli STR data.

Allele distributions of 10 short tandem repeat (STR) polymorphic DNA loci used in forensic and paternity testing were determined for a cohort comprising 163 individuals representing a mixed Jewish Caucasian population. Typing was carried out by the commercial AmpF lSTR SGM Plus kit. The polymorphism and the utility of three of these markers for forensic studies in Israel were established for the first time. Results were compared with data for U.S. Caucasians and African Americans. The probability of identity of two persons of different ethnic origins for identification purposes is discussed. A lemma is presented to show that the chance of erroneous identification of an innocent person who belongs to a population that had not committed a crime will, in most cases, be smaller than for those who belong to a population that had truly committed the crime.

Black or African American↗
PubMed2003

Genetic analysis of human remains found in two eighteenth century Yakut graves at At-Dabaan.

We extracted DNA from three skeletons belonging to the Yakut population, which were excavated from the At-Dabaan site (dating back 300 years) in the Sakha Republic (Russia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these three skeletons were not close relatives but probably linked to the same clan structure. Comparison of their haplotypes with the haplotypes of 8,774 Eurasian individuals suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last 3 centuries.

Anthropology, Physical↗
PubMed2003

Five highly informative X-chromosomal STRs in Koreans.

The five X-chromosomal short tandem repeats (STRs) GATA172D05, HPRTB, DXS8377, DXS101 and HumARA were analyzed in 150 males and 150 females from Korea. Markers were amplified in a quadruplex and a monoplex PCR reaction with fluorescently labeled primers. For accurate and reproducible STR typing, sequenced allelic ladders were constructed and a Genotyper macro was programmed. Some differences were found on comparing the allele frequencies of Koreans with those of other populations in DXS8377, DXS101 and HumARA. The forensic efficiency parameters showed that the five X-linked STRs are highly informative for forensic application in Koreans.

Chromosomes, Human, X↗
PubMed2004

Duplication of DYS19 flanking regions in other parts of the Y chromosome.

During the testing of alternative primers for the Y chromosome short tandem repeat marker DYS19, a duplicated region of the Y chromosome was discovered. The duplicated sequence is contained within GenBank accession AC006335 and has a high degree of homology with the DYS19 flanking region (GenBank accession AC017019) but without the polymorphic TAGA repeat. Bioinformatic approaches have been taken to try and understand the implications of this homolog to enable improved primer design for DYS19. Sequence alignments and careful placement of primers in order to obtain specific amplification of the DYS19 locus are discussed in the context of all previously published primer sets. Since the DYS19 locus is part of the widely used minimal haplotype, its robust amplification is highly desirable particularly in multiplex reactions. The discovery of this duplicated region of the Y chromosome shows the value of newly available human genome sequence information for assay design and the importance of using sequence queries and alignments in the primer design process.

5' Flanking Region↗
PubMed2004

Separate analysis of DYS385a and b versus conventional DYS385 typing: is there forensic relevance?

In order to determine to what extent the separate analysis of both copies of DYS385 improves Y-chromosomal short tandem repeat (Y-STR) haplotyping, we followed a recently published protocol for the separate amplification of DYS385a and DYS385b with modifications and compared the results with those obtained by conventional analysis in a population sample comprising 133 unrelated Caucasian males from Austria. Additionally, we typed all markers of the minimal haplotype (minHT) and a set of Y-chromosomal single nucleotide polymorphisms (Y-SNPs) in order to interpret the STR data depending on the Y-SNP haplogroup structure. The separate amplification of DYS385a and b improved the power of discrimination of this marker when compared to the results obtained with the conventional non-locus-discriminating amplification strategy. However, the degree of this improvement varied greatly between different haplogroups and was found to be highest in clade K. In the forensically relevant context of the minHT, the separate analysis of the DYS385 alleles had no effect on the differentiation of paternal lineages in our study. Furthermore, the amplicon lengths of 700-780 base pairs obtained in the course of the locus-discriminating approach restrict the applicability of this amplification strategy to high quality DNA samples.

Austria↗
PubMed2004

Genetic characteristics and population study of 4 X-chromosomal STRs in Koreans: evidence for a null allele at DXS9898.

The four X-chromosomal short tandem repeats (STRs), DXS9898, DXS6809, DXS7424 and DXS10011 were analyzed by single multiplex PCR in 150 male and 150 female Koreans. The loss of an allele at DXS9898 was observed in 13 out of 450 chromosomes (2.9%) and the PCR analysis showed that the X-chromosome with a null allele at DXS9898 has more than 1 kb deletion at the DXS9898 locus. Statistical analyses for these four X-STRs showed that they are highly informative for forensic application in Koreans. No linkage disequilibrium was observed among these four STRs and the previously reported five polymorphic STRs, HumARA, DXS101, GATA172D05, HPRTB and DXS8377 in Koreans. The test of homogeneity between allele frequencies revealed that there are some discrepancies in allele distributions between Koreans and Germans.

Chromosomes, Human, X↗
PubMed2004

Development of the AmpFISTR SEfiler PCR amplification kit: a new multiplex containing the highly discriminating ACTBP2 (SE33) locus.

The AmpFISTR SEfiler kit co-amplifies 11 short tandem repeat loci including SE33 in a single multiplex. After establishing the optimum in primer titration studies, the primer concentrations of all loci in the multiplex were chosen such that the heterozygote peak height ratios of each of the loci were balanced. The combined primer set was then tested to determine the robustness of the multiplex under various conditions. Different MgCl(2) concentrations were evaluated to establish the optimum concentration for the multiplex. The amplification of the various loci in the multiplex was tested at several annealing temperatures (55-63 degrees C). Additionally, DNA from primates, non-primates and microorganisms were amplified to investigate the specificity of the kit. The stability of the AmpFISTR SEfiler kit was determined by addition of hematin, to simulate inhibition, and the use of degraded DNA. Population studies revealed a probability of identity of 6.47x10(-15) for African Americans and 7.46x10(-14) for US Caucasians. To assess the ability of the multiplex to analyze forensic samples, testing on blood, oral swabs and mixtures was performed. Based on the various studies, it was determined that the AmpFISTR SEfiler PCR amplification kit can be used to successfully analyze a variety of forensic, databasing and paternity samples.

Animals↗
PubMed2005

Wonder or fake - investigations in the case of the stigmatisation of Therese Neumann von Konnersreuth.

We investigated two compresses used by Therese Neumann (T.N.), a woman who lived from 1898 until 1962 in Konnersreuth, Germany. The compresses were soaked with blood during the appearance of stigmata on T.N.'s body on a Friday. T.N. became very popular among the faithful in Germany at this time. The question was whether this blood was from T.N. herself or from a family relative or an animal. The comparison of the HV1 and HV2 mtDNA sequence obtained from the compresses with the sequences from a reference sample from a maternally related niece of T.N. revealed an identity. Furthermore, we obtained a short tandem repeat (STR) profile from the bloodstains that were identical with the STR profile from a gummed envelope. The envelope contained a letter written by T.N. in the 1930s. Therefore, our investigations gave no indication for any manipulation.

Bandages↗
PubMed2005

DXS6797 contains two STRs which can be easily haplotyped in both sexes.

DXS6797 is a complex X-chromosomal locus which contains two variable short tandem repeats (STRs) (motif ATCT) separated by 128 non-polymorphic nucleotides. The two STRs can be cleaved apart by Taq I digestion. Conventionally, DXS6797 is typed by measuring the overall amplicon length, providing only eight alleles [polymorphism information content (PIC) 0.733, mean exclusion chance (MEC) 0.712]. Separate amplification would increase the discrimination but obscure the haplotype constellation in females. Therefore, we proceed by amplifying the whole sequence containing both repeats (DXS6797 I and DXS6797 II) using a Fam-labelled forward primer and a Tamra-labelled reverse primer. We then measure the length of the entire double-labelled amplicon and a Taq-I-digested aliquot to infer, for both males and females, compound haplotypes consisting of DXS6797 I and DXS6797 II repeat length. This procedure has the potential to provide 42 DXS6797 haplotypes. If the crossover rate between both STRs is assumed to be <1.5x10(-6), DXS6797 haplotypes could be used for kinship testing like STR alleles. In our German sample (780 X chromosomes), we determined 27 haplotypes (PIC 0.842, MEC 0,834) and in 220 meioses, we found no new mutations.

Adolescent↗
PubMed2005

Allele frequencies of the six miniSTR loci in a population from Japan.

Allele frequencies and forensic parameters for the six miniSTR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045 were investigated in a sample of 142 unrelated healthy Japanese individuals. The polymerase chain reaction (PCR) products contained within the six loci were less than 119 bp in size. The frequency distributions in the six short tandem repeat (STR) loci showed no deviations from Hardy-Weinberg equilibrium expectations. The accumulated powers of discrimination and power of exclusion for the six loci were 0.999998 and 0.98, respectively. It was thus considered that due to the small PCR products and the moderate degree of polymorphism, analysis with use of the six miniSTR loci was highly beneficial for the forensic analysis of degraded DNA.

Asian People↗
PubMed2006

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis.

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods

Alleles↗
PubMed2005

A new Web site compiling forensic chromosome X research is now online.

We would like to announce the opening of a new Web site ( http://www.chrx-str.org ), which contains a database surveying current research on chromosome X markers used for forensic purposes, evolutionary anthropology and other genetic research. Currently, we summarise short tandem repeat data with regard to the physical and genetic localisation, repeat structure, allele nomenclature, mutation rates and population genetics. In the future, we may include diallelic markers. The results contained in this database come from published journal articles. The authors of published articles are invited to complement their own papers by submitting data obtained from follow-up studies here. Furthermore, population data which are not able to find space in journals may be published at this Web site. The growing field of ChrX haplotyping is producing an extensive amount of data, which requires a place that can complement journal publications.

Chromosomes, Human, X↗
PubMed2005

Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit.

In forensic DNA analysis, improvement of DNA typing technologies has always been an issue. It has been shown that DNA amplification in low volumes is a suitable way to enhance the sensitivity and efficiency of amplification. In this study, DNA amplification was performed on a flat, chemically structured glass slide in 1-microl reaction volumes from cell line DNA contents between 1,000 and 4 pg. On-chip DNA amplification reproducibly yielded full allelic profiles from as little as 32 pg of template DNA. Applicability on the simultaneous amplification of 15 short tandem repeats and of a segment of the Amelogenin gene, which are routinely used in forensic DNA analysis, is shown. The results are compared to conventional in-tube amplification carried out in 25-microl reaction volumes.

Case-Control Studies↗
PubMed2005

Mutations or exclusion: an unusual case in paternity testing.

In an immigration case with the scope of family reunification, the DNA extracted from the saliva samples of the male child, the alleged mother and the putative father was typed with 22 autosomal short tandem repeat (STR) systems. In seven STR systems, the alleged mother could be excluded from maternity, and the case then had to be regarded as a deficiency case. Taking this fact into consideration, only two exclusions were found for the putative father, and the question arose whether there was an exclusion of the putative father or the existence of two mutations. Autosomal STR typing could not clarify the case, but the application of eight Y-chromosomal markers showed that the alleged father could be excluded from paternity.

Child↗