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PubMed1992

Characteristics of polymorphism at a VNTR locus 3' to the apolipoprotein B gene in five human populations.

We have analyzed the allele frequency distribution at the hypervariable locus 3' to the apolipoprotein B gene (ApoB 3' VNTR) in five well-defined human populations (Kacharis of northeast India, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, and a relatively homogeneous Caucasian population of northern German extraction) by using the PCR technique. A total of 12 segregating alleles were detected in the pooled sample of 319 individuals. A fairly consistent bimodal pattern of allele frequency distribution, apparent in most of these geographically and genetically diverse populations, suggests that the ApoB 3' VNTR polymorphism predates the geographic dispersal of ancestral human populations. In spite of the observed high degree of polymorphism at this locus (expected heterozygosity levels 55%-78%), the genotype distributions in all populations (irrespective of their tribal or cosmopolitan nature) conform to their respective Hardy-Weinberg predictions. Furthermore, analysis of the congruence between expected heterozygosity and the observed number of alleles reveals that, in general, the allele frequency distributions at this locus are in agreement with the predictions of the classical mutation-drift models. The data also show that alleles that are shared by all populations have the highest average frequency within populations. These findings demonstrate the potential utility of highly informative hypervariable loci such as the ApoB 3' VNTR locus in population genetic research, as well as in forensic medicine and determination of biological relatedness of individuals.

Alleles↗
PubMed2004

Mass spectrometry provides accurate characterization of two genetic marker types in Bacillus anthracis.

Epidemiological and forensic analyses of bioterrorism events involving Bacillus anthracis could be improved if both variable number tandem repeats (VNTRs) and single nucleotide polymorphisms (SNPs) could be combined on a single analysis platform. Here we present the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) to characterize 24 alleles from 6 VNTR loci and 11 alleles from 7 SNP loci in B. anthracis. The results obtained with ESI-FTICR-MS were consistent with independent results obtained from traditional approaches using electrophoretic detection of fluorescent products. However, ESI-FTICR-MS improves on the traditional approaches because it does not require fluorescent labeling of PCR products, minimizes post-PCR processing, obviates electrophoresis, and provides unambiguous base composition of both SNP and VNTR PCR products. In addition, ESI-FTICR-MS allows both marker types to be examined simultaneously and at a rate of approximately 1 sample per min. This technology represents a significant advance in our ability to rapidly characterize B. anthracis isolates using VNTR and SNP loci.

Alleles↗
PubMed2006

Application of HLA-DRB1 genotyping by oligonucleotide micro-array technology in forensic medicine.

UNLABELLED: The human leukocyte antigen (HLA) system is known to be the most complex polymorphic system in the human genome. Among all of the HLA loci, HLA-DRB1 has the second largest number of alleles. The purpose of this study is to develop an oligonucleotide micro-array based HLA-DRB1 typing system for use in forensic identification, anthropology, tissue transplantation, and other genetic research fields. The system was developed by analyzing the HLA-DRB1 (DRB1) genotypes in 1198 unrelated healthy Chinese Han individuals originating from various parts of China and residing in Shanghai, China. METHOD: Polymerase chain reaction (PCR) coupled with the oligonucleotide micro-array technology was used to detect and type HLA-DRB1 alleles of the sample individuals. The reliability, sensitivity, consistency and specificity were evaluated for use in forensic identification. Furthermore, a meta-analysis was carried out by comparing the allele frequencies of the HLA-DRB1 locus with those of other Chinese Han groups, Chinese minorities and other ethnic populations. RESULTS: All the DNA samples yielded a 273 bp amplification product, with no other amplification products in this length range. The minimum quantity of DNA detected by this method is 15 ng in a PCR reaction system of 25 microl. The population studied appeared to be not in Hardy-Weinberg equilibrium. Observed heterozygosity (Ho), expected heterozygosity (He), expected probability of exclusion (PE), polymorphic information content (PIC), and discrimination power (DP) of the HLA-DRB1 locus from the Shanghai Han ethnic group were evaluated to be 0.8022, 0.8870, 0.7741, 0.8771, 0.9750, respectively. A total of 25 HLA-DRB1 alleles were identified. HLA-DRB1*09XX, *04XX, *12XX and *15XX were the most frequent DRB1 alleles, which were observed in 58.76% of the sample. One hundred and sixteen genotypes were found. The five most frequent genotypes were: *04XX/*04XX (0.0626), *09XX/*09XX (0.0593), *04XX/*09XX (0.0551), *09XX/*15XX (0.0384) and *08XX/*12XX (0.0351). The meta-analysis showed that there were uniquely distributed features of DRB1 alleles among various ethnic populations and among the studied population groups from various regions with the same ethnic origin. CONCLUSIONS: An HLA-DRB1 genotyping system has been developed and established based on the oligonucleotide micro-array technology. The HLA-DRB1 typing of the Han population in Shanghai has revealed a relatively high heterogeneity. Information obtained in this study will be useful for medical and forensic applications as well as in anthropology research. Large-scale micro-array detection is highly accurate and reliable for DNA-based HLA-DRB1 genotyping. These results suggest that HLA-DRB1 DNA polymorphisms and the database of the Shanghai Han group have useful applications in processing forensic casework (as personal identification, paternity test), tracing population migration and genetic diagnosis.

Animals↗
PubMed2002

Validation of the STR DXS7424 and the linkage situation on the X-chromosome.

X-linked microsatellite markers have proven to be powerful tools for parentage testing, mainly in deficiency paternity cases when the disputed child is female. However, only a small number of X-linked short tandem repeats (STRs) have been comprehensively described for forensic applications to date. We present sequence and population genetic data of the DXS7424 STR (GDB-G00-577-633) which is a trinucleotide repeat polymorphism representing 12 alleles of 147-180 bp in length. DXS7424 is located at Xq22 and closely linked to DXS101, corresponding to a genetic localisation of 104.9-121 cM from Xp-tel.PCR fragment length measurements and sequencing were carried out using the automatic gene analyser ABI 310 (Applied Biosystems). The population of 764 unrelated Germans checked for this STR exhibited the following features: polymorphism information content (PIC) = 0.780; heterozygosity (Het) = 0.843; mean exclusion chance (MEC = 0.766. Kinship tests revealed a typical X-linked inheritance. In 300 meioses under investigation, mutations were not found. Significant deviations from the Hardy-Weinberg equilibrium (HWE) were not established. Linkage studies confirmed closely linkage to DXS101. Additional we found linkage disequilibrium between DXS7424 and DXS101. This requires to use the established haplotype frequencies in kinship testing.

Alleles↗
PubMed1993

A simplified method for phenotyping alpha-2-HS-glycoprotein.

Alpha-2-HS-glycoprotein is considered a reliable genetic marker for paternity testing and forensic investigation. We describe a simple, semiautomated method for phenotyping this protein in serum samples, bloodstains and dental pulp using isoelectric focusing methods followed by immunofixation techniques. This method produces clear results even with very old biological evidence.

Blood Proteins↗
PubMed2001

[The single nucleotide polymorphisms and its application to forensic medicine].

Single-nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variation. These variable sites are present at high density in the genome, making them powerful tool for the diagnosis of genetic and genetic-related diseases, population genetics research and drug development. They are also found widespread application to the forensic medicine. This report mainly describe the SNPs characteristics and its potential applications to the forensic medicine including the possibility, the problems and high-throughput automation detection methods.

Forensic Medicine↗
PubMed1999

Validation of the HumDXS6807 short tandem repeat polymorphism for forensic application.

This paper presents sequence and population genetic data of the HumDXS6807 short tandem repeat (also known as CHLC.GATA52B03) which is a tetranucleotide repeat polymorphism representing seven alleles of 251-275 bp in length. HumDXS6807 is located at Xpter-Xp22.2, i.e., at a genetic distance of more than 87 and 151 cM from the well-known markers HumARA and HumHPRTB, respectively. Kinship tests in 157 family trios revealed a typical X-linked codominant inheritance; mutations were not found. Population genetic data were obtained by analyzing a Caucasian population sample comprising 308 females and 209 males: polymorphism information content (PIC) = 0.640; Heterozygosity (Het) = 0.668; Mean exclusion chance (MEC) = 0.414. The HumDXS6807 allele distribution met the Hardy-Weinberg expectations.

DNA↗
PubMed2001

Development of the X-linked tetrameric microsatellite marker HumDXS6789 for forensic purposes.

This paper presents sequence and population genetic data of the X-linked DXS6789 short tandem repeat (STR). The tetranucleotide repeat polymorphism DXS6789, also known as CHLC.GATA31F01, is located at the Xq22.3 region. This locus is unlinked with DXS6807 and slightly linked with ARA, DXS9898 and HPRTB. In kinship testing, DXS6789 is suitable for concomitant use with DXS6807. Population genetic data were obtained by analysing 250 unrelated males and 315 females from East Germany. In this population, the STR exhibited 12 clearly distinguishable alleles ranging from 154 to 198bps in length. DXS6789 is characterised by the following data: polymorphic information content (PIC)=0.70; observed heterozygosity (Het)=0.78; mean exclusion chance (MEC)=0.70. A deviation from the Hardy-Weinberg equilibrium could not be detected. The investigations we performed in 243 mother-child and 161 father-child meioses did not reveal any mutations.

DNA Fingerprinting↗
PubMed2003

Development of the X-linked tetrameric microsatellite markers HumDXS6803 and HumDXS9895 for forensic purpose.

This paper presents sequence and population genetic data of the X-linked DXS6803 and DXS9895 short tandem repeat (STR). The tetranucleotide repeat polymorphism DXS6803 (also known as CHLC.GATA45H11) and DXS9895 (also known as CHLC.GATA124B04) are located at the Xq12-Xq21.33 and Xpter-Xp22.2 region, respectively. In kinship testing, DXS6803 and DXS9895 are suitable for concomitant use. Population genetic data were obtained by analyzing 182 unrelated females and 110 males from Chinese Han population. In this population, both DXS6803 and DXS9895 exhibited seven clearly distinguishable alleles ranging from 109bp to 128bp and 139bp to 163bp in length, respectively. Testing for Hardy-Weinberg equilibrium (HWE) showed no significant deviation for these two loci. The polymorphism information content (PIC), observed heterozygosity (H(obs)) and power of exclusion for parentage testing of a girl for trios (PE(trio)) and duos (PE(duo)) were 0.67, 0.687, 0.673 and 0.530 for DXS6803, and 0.69, 0.736, 0.688 and 0.547 for DXS9895, respectively. Seventy-eight families studies of these two loci confirmed X-linked codominant inheritance and mutations were not found.

Alleles↗
PubMed1989

DNA fingerprinting.

Hypervariable tandem-repetitive minisatellite regions of human DNA can be used to generate individual-specific DNA fingerprints. Validation studies have demonstrated the reliability of the analysis, the mode of inheritance of the minisatellites, and the unparalleled degree of individual specificity. The uses of hypervariable probes in forensic biology, paternity testing, and the resolution of a wide range of problems in genetics, molecular biology, population biology, and medicine are illustrated.

Animals↗
PubMed2006

[A minisequencing technique for genotyping 12 Y-SNP and its genetic polymorphisms].

OBJECTIVE: The aim of the present study was to establish a rapid and robust assay used to simultaneously genotype SNPs by the single nucleotide primer extension (minisequencing) with the SNaPshot Kit and obtain the population genetic data in Chinese population in Sichuan. The analysis of single nucleotide polymorphisms (SNPs) is a promising application in forensic casework. METHODS: 12 Y-SNPs, which were SRY2627, SRY1532, M13, M20, SRY8299, Tat, M69, M9, 92R7, M17, M19 and M112, were multiple amplificated and the PCR products were pooled, Purified, and then used as templates for the minisequencing reaction with the commol/Lercially available SNaPshot Kit. Then the products of minisequencing reaction were detected by capillary elcetrophoresis. RESULTS: 78 genomic DNA individual samples from Sichuan, China and 5 semen stain samples from sexal criminal scene were analyzed and two haplotypes could be identified. CONCLUSION: A rapid method has been established to analyze the 12 Y-SNPs by multiplex PCR and minisequencing. It can be applied in forensic casework successfully.

Base Sequence↗
PubMedDate not supplied

Overview of principles and current uses of DNA probes in clinical and laboratory medicine.

Fundamental considerations of deoxyribonucleic acid (DNA) probe hybridization reaction including concept of stringency is reviewed. Restriction fragment length polymorphism (RFLP) and its detection using DNA probes are discussed together with the importance of RFLP in genetic linkage analysis. Methodological considerations, such as limitations in sample preparation and improvements effected in techniques, cloning DNA, and labelling of DNA probes, are addressed. Principles of hybridization technology and blotting techniques are reviewed. Amplification of DNA by the polymerase chain reaction (PCR), labelling with PCR, detection of PCR products and separation procedures prior to use of PCR are discussed. Other amplification methods and in-situ hybridization (ISH) procedures are reviewed. Selected current applications of DNA probes in the area of infectious diseases, genetic diseases, HLA typing, paternity and forensic testing are briefly discussed. Emphasis is placed on the use of DNA probes in the area of oncology. Background on activation of proto oncogene, loss of tumor suppressor genes, chromosomal translocation, and chromosome analysis are provided for understanding DNA probe assays for ph1 positive leukemias and applications of Interphase cytogenetic technique in oncology. Finally, analytical strategies for detection of tumor suppressor genes are addressed.

DNA Probes↗
PubMed2026

Evaluation of bone preparation approaches using length-based analysis and targeted sequencing for forensic human identification of historic skeletal remains.

Advances in DNA technology have significantly enhanced the forensic community's ability to develop genetic profiles from unidentified human skeletal remains. However, sampling requires mechanical grinding of hard tissues before DNA isolation. This processing can compromise genetic profiles, particularly in aged bones. We compared the industry-standard pulverization method with an alternative powder-free preparation involving prolonged demineralization and subsequent slicing of 19th-century cortical bone. Data from DNA quantification, STR genotyping, and targeted SNP sequencing were used to evaluate powdered samples versus demineralized slices from paired human bones. Average human DNA yields for pulverized samples and demineralized slices were 0.032&#x2009;ng and 0.692&#x2009;ng, respectively. Demineralized slices recovered more amplifiable DNA than traditional homogenization methods (p&#x2009;<&#x2009;0.05). No pulverized samples produced STR profiles, whereas demineralized slices from the same bone samples yielded partial profiles. Samples underwent DNA repair, library preparation, and hybridization capture using the FORensic Capture Enrichment (FORCE) panel. Applying low-coverage (1X) analysis of high-throughput sequencing (HTS) data, demineralized slices outperformed those prepared by traditional pulverization methods (p&#x2009;<&#x2009;0.05) and substantially increased the information recovered compared with conventional STR analysis methods. Based on HTS data from pulverized samples, DNA fragment length ranged from 27 to 95&#x2009;bp, and FORCE SNP recovery was 33.23%. In contrast, for demineralized slices, DNA fragment length ranged from 85 to 114&#x2009;bp, and FORCE SNP recovery was 83.24%. The required reagents and equipment are typically available in forensic labs, and the workflow outlined herein significantly increases the success of DNA recovery from challenging skeletal samples.

Humans↗
PubMed2002

Novel perspectives in wood certification and forensics: dry wood as a source of DNA.

The importance of wood for human societies can hardly be understated. If dry wood were amenable to molecular genetic investigations, this could lead to major applications in wood forensics, certification, archaeology and palaeobotany. To evaluate the potential of wood for molecular genetic investigations, we have attempted to isolate and amplify, by PCR, DNA fragments of increasing size corresponding to all three plant genomes from different regions of 10 oak logs. Stringent procedures to avoid contamination with external DNA were used in order to demonstrate the authenticity of the fragments amplified. This authenticity was further confirmed by demonstrating genetic uniformity within each log using both nuclear and chloroplast microsatellites. For most wood samples DNA was degraded, and the sequences that gave the best results were those of small size and present in high copy number (chloroplast, mitochondrial, or repeated nuclear sequences). Both storage conditions and storage duration play a role in DNA conservation. Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.

Base Sequence↗
PubMed1998

[The DNA-chip, a new tool for medical genetics].

The DNA (chip) technology, emerged in the last two years, provides an incredible technical development in rapid and automatised performance of genetic identification. The principle of procedure is, that by series of photolitographic and chemical steps on solid-phase of a small surface relatively dense oligonucleotide arrays can be generated. The oligonucleotides produced by the computer-directed in-situ microfabrication may bind complementary fluorescent-labeled DNA fragments from the unknown sample. After scanning, the registered position of positive signals provide information on the identity of DNA fragments. By this novel approach not only DNA sequencing can be performed, but genetic errors of known genes, presence of infectious organisms and the typing of genetic markers (such as HLA) used for transplantation and forensic medicine can be determined. The DNA-chip technology is a revolutionary new milestone in genetic diagnose.

DNA↗
PubMed2003

[A study on the construction of allelic ladders for 4 short tandem repeat loci (D7S817, D10S1432, D10S1213 and D18S865) and their genetic polymorphism in two Chinese populations].

OBJECTIVE: To produce standard allelic ladders for four STR loci(D7S817, D10S1432, D10S1213 and D18S865) by recombined plasmids and use them in the research of genetic polymorphism. METHODS: After being amplified by PCR, different STR allelic fragments were isolated from the polyacryramide gel. The STR allelic fragments were eluted into distilled water and reamplified by PCR to obtain purified allelic fragments. Next, the purified allelic fragments were subcloned individually into the PUC plasmid vectors, and the size and structure of the inserts were confirmed by the analysis of their DNA sequences. Then we transfected the PUC plasmid vectors into E. coli DH5 alpha cells, worked on selective culture, and finally, mixed the alleles of the four STR loci respectively. RESULTS: The standard allelic ladders for four new loci (D7S817, D10S1432, D10S1213 and D18S865) were obtained, with which the genetic polymorphisms of four new loci in Chinese Hans and Dongxiang ethnic groups were studied. CONCLUSION: The standard STR allelic ladders acquired by this method are of high value in forensic practice, and they are applicable to the analysis of genetic polymorphism.

Alleles↗
PubMed2004

Genetic analysis of a Scytho-Siberian skeleton and its implications for ancient Central Asian migrations.

The excavation of a frozen grave on the Kizil site (dated to be 2500 years old) in the Altai Republic (Central Asia) revealed a skeleton belonging to the Scytho-Siberian population. DNA was extracted from a bone sample and analyzed by autosomal STRs (short tandem repeats) and by sequencing the hypervariable region I (HV1) of the mitochondrial DNA. The resulting STR profile, mitochondrial haplotype, and haplogroup were compared with data from modern Eurasian and northern native American populations and were found only in European populations historically influenced by ancient nomadic tribes of Central Asia.

Asia↗