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PubMed2004

Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis.

DNA typing with short tandem repeat (STR) markers is now widely used for a variety of applications including human identification. Capillary electrophoresis (CE) instruments, such as the ABI Prism 310 and ABI 3100 Genetic Analyzers, are the method of choice for many laboratories performing STR analysis. This review discusses issues surrounding sample preparation, injection, separation, detection, and interpretation of STR results using CE systems. Requirements for accurate typing of STR alleles are considered in the context of what future analysis platforms will need to increase sample throughput and ease of use.

Electrophoresis, Capillary↗
PubMed2003

Inferring recent human phylogenies using forensic STR technology.

STR loci are characterized by extremely high mutation rates and thus, high levels of length polymorphism both within and among populations. In addition, much of the observed variation is believed to be nearly selectively neutral. Because of these features, STRs are ideal markers for genetic mapping, intra-species phylogenetic reconstructions and forensic analysis. In the present study, we investigate the application of five STR loci (CS1PO, TH01, TPOX, FGA and vWA) routinely used in forensic analysis for delineating the phylogenetic relationships of 10 human populations representing the three major racial groups (African-Caribbean, Croatian from the island of Hvar, East Asian, Han Chinese, Italian, Japanese, Portuguese, UK Caucasian, US Caucasian and Zimbabwe). The resulting tree topology exhibited strong geographic and racial partitioning consistent with that obtained with mtDNA haplotypes, Y-chromosome markers, SNPs, PAIs (polymorphic Alu insertions) as well as classic genetic polymorphisms. These findings suggest that forensic STR loci may be particularly powerful tools and provide the necessary fine resolution for the reconstruction of recent human evolutionary history.

DNA Fingerprinting↗
PubMed1995

A novel human phosphoglucomutase (PGM5) maps to the centromeric region of chromosome 9.

The phosphoglucomutases (PGM1-3) in humans are encoded by three genes, PGM1, PGM2, and PGM3. These enzymes are central to carbohydrate metabolism. All three isozymes show genetic variation, and PGM1 has achieved prominence as a key marker in genetic linkage mapping and in forensic science. The human PGM genes are assumed to have arisen by gene duplication since their products are broadly similar in structure and function; however, direct proof of their evolutionary relationship is not available because only PGM1 has been cloned. During a search for other members of the PGM family, a novel sequence with homology to PGM1 was identified. Mapping using fluorescence in situ hybridization and somatic cell hybrids locates this gene to the centromeric region of chromosome 9. RT-PCR and Northern analysis indicate that this is an expressed PGM gene with widespread distribution in adult and fetal tissues. We propose that this gene be designated PGM5 and that it represents a novel member of the PGM family.

Adult↗
PubMed2003

A method for genotyping Y chromosome-linked DYS385a and DYS385b loci.

We developed a method for genotyping Y chromosome-linked homologous DYS385 loci individually, combining locus-specific polymerase chain reaction (PCR) amplification and previously reported procedures. Duplicated DYS385a (5'-end) and DYS385b (3'-end) loci were located about 41 kb apart and inverted to each other in the Y chromosome, which data was obtained from the human genome sequence in National Center for Biotechnology Information (NCBI), and sequence differences were found at 424 bp down- and upstream of each locus. The locus-specific amplifications were performed using primers designed for this intergenic region, and fragments about 900 bp in length were produced. Polymorphic tetranucleotide arrays in the PCR products were typed according to procedures reported previously. Twenty male subjects were genotyped using this method. Alleles (GAAA)13-(GAAA)21 were observed at the DYS385a locus, and those at DYS385b included alleles (GAAA)9-(GAAA)15. DYS385a alleles, excluding those of identical arrays, were always larger than DYS385b alleles in the same subjects. These data suggest that the DYS385a and DYS385b loci can be amplified completely for discrimination, and the genotypes of the alleles provide information useful for forensic case work and population genetics.

Alleles↗
PubMed2000

Short tandem repeat methodology for genotypic identification of single-person versus multi-person use of syringes.

OBJECTIVE: To develop laboratory methods to differentiate between single- versus multi-person use of syringes by injection drug users. METHODS: Forensic short tandem repeat (STR) genetic analysis was undertaken to cross-validate a test panel of trace blood contents from syringes representing single- versus multi-person syringe use. Laboratory-simulated scenarios of needle sharing generated 34 syringe washes that were blinded for evaluation. Polymerase chain reaction was used to amplify the polymorphic STR locus D6S502 from blood trace contents in used syringes. Alleles were sized and quantified using a commercial gene sequencer. A statistical algorithm was developed to determine the number of alleles present in the amplified DNA fragments. Syringes with more than two expected alleles were considered to represent multi-person syringe use. Sensitivity, specificity and the kappa coefficient were calculated. RESULTS: Allelic matrix-based analysis of alleles from the single STR successfully characterized single-use (n = 12) and multiple-use (n = 22) syringes with 68% sensitivity and 100% specificity upon re-analysis. The extent of agreement over and above chance (kappa = 0.6; P < 0.0001) indicated good agreement for differentiating single- versus multi-person syringe use. CONCLUSIONS: These findings suggest that improved genotypic STR analysis of syringe material could be an adjunct to methods for validating self-reported needle sharing, conducting behavioral surveillance of needle-sharing behaviors, and evaluating interventions such as needle-exchange programs. Assays based on multiple STR loci will undoubtedly improve upon the promising results obtained from laboratory simulations of needle sharing.

Alleles↗
PubMed1997

Multiplex systems for the amplification of short tandem repeat loci: evaluation of laser fluorescence detection.

Short tandem repeat (STR) loci are ideal markers for personal identification and for genomic mapping. Two fluorescent multiplex systems, each designed for simultaneous PCR amplification of four polymorphic STR loci (HUMCSF1PO, HUMTPOX, HUMTH01 and HUMVWFA31, and HUMF13A01, HUMFESFPS, HUMBFXIII and HUMLIPOL), were evaluated on three laser fluorescence detection instruments. Concordant DNA typing results were obtained with all three detection methods. These fluorescent multiplex STR systems offer an accurate, reproducible and versatile method of DNA profiling that is well-suited for forensic identity testing and other genetic analyses.

Alleles↗
PubMed2005

Y chromosome SNP analysis using the single-base extension: a hierarchical multiplex design.

Single nucleotide polymorphisms (SNPs) are the most frequent polymorphisms described in the human genome, and their analysis is becoming an extensive routine in molecular biology, not only in the forensic field, but also in population and clinical genetics. In particular, SNPs located on the Y chromosome have a specific utility as forensic tools, and based on this fact, we have designed a strategy that allows us to identify the most frequent haplogroups in European populations. We selected 29 markers among the 245 binary polymorphisms described in the Y-Chromosome Consortium tree. The whole set was grouped into four multiplexes in a hierarchical way, allowing us to determine the final haplogroup using only one or two multiplexes. In this way, we only type in the best-case nine SNPs, and in the worst possible combination 17 SNPs, to define the haplogroup. The selected strategy to type the SNPs was a single-base extension method using the SNaPshot multiplex kit from Applied Biosystems, and detailed practical procedures are described here. With this hierarchical strategy adapted for European populations the massive typing of SNPs was avoided, and therefore the time and money involved in the study was also reduced.

Base Sequence↗
PubMed1990

Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay.

DNA diagnostics, the detection of specific DNA sequences, will play an increasingly important role in medicine as the molecular basis of human disease is defined. Here, we demonstrate an automated, nonisotopic strategy for DNA diagnostics using amplification of target DNA segments by the polymerase chain reaction (PCR) and the discrimination of allelic sequence variants by a colorimetric oligonucleotide ligation assay (OLA). We have applied the automated PCR/OLA procedure to diagnosis of common genetic diseases, such as sickle cell anemia and cystic fibrosis (delta F508 mutation), and to genetic linkage mapping of gene segments in the human T-cell receptor beta-chain locus. The automated PCR/OLA strategy provides a rapid system for diagnosis of genetic, malignant, and infectious diseases as well as a powerful approach to genetic linkage mapping of chromosomes and forensic DNA typing.

Base Sequence↗
PubMed1997

Lewis genotyping by the PCR-RFLP method in a Japanese population and its evaluation in forensic analysis.

Lewis phenotyping of red blood cells has many problems such as the influence of many biological conditions, the change during the period from newborn to early childhood and mistyping by non-specific anti-Lewis antibodies. Therefore, it would be useful to determine the Lewis genotype. Recently a method of Le-genotyping by PCR-RFLP was established. We determined the frequencies of Lewis genotypes in a Japanese population and discuss the applicability to paternity tests and other forensic applications. The gene frequencies of Le, le1 and le2 in the Japanese population studied were 0.7032, 0.2358 and 0.0610 respectively. Out of 12 paternity cases where paternity was excluded by other markers, 3 alleged fathers could also be excluded by Lewis genotyping. The genotype from organs of a fetus from a 3-month pregnancy was Le/Le. The determination of Lewis genotypes could play a useful role as a genetic marker in paternity tests and forensic analyses.

Asian People↗
PubMed2001

[Study on the construction of standard D1S549 allelic ladder via molecular cloning and its genetic polymorphism in Chinese three populations].

OBJECTIVE: To resolve the problem of the accuracy and standardization of STR-PCR typing in forensic practice, we have designed a new method to produce standard D1S549 allelic ladder. METHODS: Eight different PCR amplified D1S549 allelic fragments were isolated from the gel, eluted into the distilled water and re-amplified by PCR. The purified allelic fragments were then blunt-end subcloned individually into the pUC plasmid vectors and transfected into competent E. coli DH5 alpha cells. RESULTS: The sequencing results confirmed that the size and the construe of the inserts were correct. The recombinant plasmids DNA with 8 inserts were then used as templates for re-amplification to generate D1S549 standard ladder, with which the genetic polymorphisms of D1S549 locus in Chinese Han population in chengdu, Hui population in Gansu and Wei population in Xinjiang were studied. CONCLUSION: The results showed that the standard ladder made via this method is excellent, and D1S549 locus is robust for genetic research and forensic application.

Alleles↗
PubMed2006

[Genetic polymorphism of penta e locus in four Chinese nationalities].

To study the genetic polymorphism of Penta E locus in four Chinese nationalities using home made reagent kits, DNA samples were obtained from about 400 unrelated peoples of four different Chinese nationalities. As a result, we found 20 alleles in the four nationalities with frequencies ranging from 0.0048 to 0.2396. The genotype frequencies of Penta E locus met Hardy-Weinberg equilibrium. It proved that Penta E locus was a high polymorphic STR genetic marker and was valuable for forensic science.

Asian People↗
PubMed2005

[The joint applications of DNA chips and single nucleotide polymorphisms in forensic science].

DNA chip technology, being a new high-technology, shows its vigorous life and rapid growth. Single Nucleotide Polymorphisms (SNPs) is the most common diversity in the human genome. It provides suitable genetic markers which play a key role in disease linkage study, pharmacogenomics, forensic medicine, population evolution and immigration study. Their advantage such as being analyzed with DNA chips technology, is predicted to play an important role in the field of forensic medicine, especially in paternity test and individual identification. This report mainly reviews the characteristics of DNA chip and SNPs, and their joint applications in the practice of forensic medicine.

Forensic Medicine↗
PubMed2006

What do the X and Y chromosomes tell us about sex and gender in forensic case analysis?

Sex determination can be particularly crucial in forensic casework such as rape cases or cases of missing persons. Biological traces have to be genetically typed and the classification of the sex is of great importance for further investigations. Lately, several papers were published on reliability of sex determination by genetic typing of amelogenin gene-specific fragments. Problems may arise not only from false detection (or non-detection) of amelogenin-specific fragments, but also in cases of chimerism (bone marrow transplants) or micro chimerism (pregnant women carrying male fetuses), and from the possible discrepancies between the biological gender and the (forensic relevant) legal gender in the personal identity documents. The phenotype based classification of the legal gender may contradict the genetic sex under several conditions as there are genetic diversity, intersex conditions and transsexualism. The forensic relevance of the possible misinterpretation (sex is not necessarily legal gender) should not be underestimated.

Amelogenin↗
PubMed1999

[Analysis of DNA polymorphism in populations of the Volga-Ural region using genome fingerprinting with phage M13 DNA].

The hyperpolymorphism of minisatellite DNA hybridizing with DNA of bacteriophage M13 was analyzed in seven Turkic and Finno-Ugric populations from the Volga-Urals region. In total, hybridization revealed 80 BspRI genomic DNA fragments ranging in size from 1.7 to 10 kb; the average frequency of an individual fragment was 0.299 +/- 0.020. The average number of hybridization fragments per pattern (varying from 14 to 20 in different populations) and frequencies of individual fragments showed significant interpopulation differences. Parameters of this polymorphic system were assumed to reflect phenotypic diversity of populations. Genome fingerprinting with the use of phage M13 can be employed in the studies of population genetic structure and differentiation and in forensic medicine, for more accurate personal identification.

Bacteriophage M13↗
PubMed2000

Mitochondrial DNA in the Central European population. Human identification with the help of the forensic mt-DNA D-loop-base database.

Sequencing of mtDNA is an advanced method for the individualisation of traces. Disadvantages of this method are expensive and time-consuming analysis and evaluation procedures as well as the necessary stock of population-genetic data which is still insufficient. Central European institutes of forensic medicine from Germany, Austria, and Switzerland have been working together since the beginning of 1998 to establish a mtDNA database. The aim is to build up a large stock of forensically established data and provide population-genetic data for frequency investigations, which will serve as a basis for expert opinions and scientific research. Good data quality is ensured by using original sequences only. Ring tests, which have been conducted to enhance analytical reliability, revealed a high correspondence rate of the analytical results obtained by the individual member institutes. Today 1410 sequences are available for comparison, of which 1285 sequences in the HV1 and HV2 regions cover the full ranges from 16051 to 16365 and from 73 to 340 (according to Anderson). The major part is formed by Central European sequences comprising 1256 data sets from Germany, Austria, and Switzerland. Today the database contains sequences from a total of 12 European, six African and three Asian countries including 100 sequences from Japan. This paper is aimed at discussing the individualisation potentials of mtDNA as well as the possibilities and limits of ethnic differentiation by means of pairwise sequence differences on the basis of the data stock available.

Austria↗