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PubMed1999

Genetic variation at six STR loci (HUMTH01, HUMTPOX, HUMCSF1PO, HUMF13A01, HUMFES/FPS, HUMVWFA31) in Aragon (north Spain).

The STR loci HUMTH01, HUMPTPOX, HUMCSF1PO, HUMF13A01, HUMFES/FPS and HUMVWFA31 are widely used in forensic casework analyses and population data are necessary to estimate the frequency of a DNA profile. This paper presents the results of a survey aimed to investigate the allele frequency distribution of these loci in an important Spanish population (Aragon, North Spain). Statistical analysis to determine whether allele frequencies were in Hardy-Weinberg Equilibrium was carried out and also to obtain some parameters of medico-legal interest. There was no evidence of association between the alleles of the loci. The Aragonese sample does not differ substantially from other Caucasian populations.

Data Collection↗
PubMed2006

Optimization and evaluation of single-cell whole-genome multiple displacement amplification.

The scarcity of genomic DNA can be a limiting factor in some fields of genetic research. One of the methods developed to overcome this difficulty is whole genome amplification (WGA). Recently, multiple displacement amplification (MDA) has proved very efficient in the WGA of small DNA samples and pools of cells, the reaction being catalyzed by the phi29 or the Bst DNA polymerases. The aim of the present study was to develop a reliable, efficient, and fast protocol for MDA at the single-cell level. We first compared the efficiency of phi29 and Bst polymerases on DNA samples and single cells. The phi29 polymerase generated accurately, in a short time and from a single cell, sufficient DNA for a large set of tests, whereas the Bst enzyme showed a low efficiency and a high error rate. A single-cell protocol was optimized using the phi29 polymerase and was evaluated on 60 single cells; the DNA obtained DNA was assessed by 22 locus-specific PCRs. This new protocol can be useful for many applications involving minute quantities of starting material, such as forensic DNA analysis, prenatal and preimplantation genetic diagnosis, or cancer research.

Buffers↗
PubMed1997

[Use of polymerase chain reaction DNA studies in Hungarian legal practice].

The authors survey the application of polymerase chain reaction (PCR)-based DNA polymorphisms in the Hungarian forensic practice. The combined application of the presented 17 PCR-based sequence- or length-polymorphic DNA systems to criminal cases gives the power of individualization to the hand of the forensic scientist. The joint application of these genetic markers to disputed paternity cases enables the verification of paternity for an unexcluded man with the highest legal category, namely "paternity practically proved". The investigation of sex-chromosome linked STRs and/or the analysis of mitochondrial DNA (mtDNA) D-loop region is useful in solving most of the problematic cases. The highlighted advantages of PCR over restriction fragment length polymorphism (RFLP)-based forensic DNA analyses clearly explain the overwhelming spread of PCR-based methods in the Hungarian forensic practice.

DNA↗
PubMed1993

A computer simulation study of VNTR population genetics: constrained recombination rules out the infinite alleles model.

Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. We show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. We use sampling theory to confirm the intrinsically poor fit to the infinite alleles model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations.

Alleles↗
PubMed2006

Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry.

The identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral genetic diversity among human populations implies that, in practice, a large number of neutral markers will be required to identify the genetic ancestry of one individual. We showed that it is possible to reduce the amount of markers required for detecting continental population structure to only 10 single-nucleotide polymorphisms (SNPs), by applying a newly developed ascertainment algorithm to Affymetrix GeneChip Mapping 10K SNP array data that we obtained from samples of globally dispersed human individuals (the Y Chromosome Consortium panel). Furthermore, this set of SNPs was able to recover the genetic ancestry of individuals from all four continents represented in the original data set when applied to an independent, much larger, worldwide population data set (Centre d'Etude du Polymorphisme Humain-Human Genome Diversity Project Cell Line Panel). Finally, we provide evidence that the unusual patterns of genetic variation we observed at the respective genomic regions surrounding the five most informative SNPs is in agreement with local positive selection being the explanation for the striking SNP allele-frequency differences we found between continental groups of human populations.

Algorithms↗
PubMed2002

Social benefits of non-criminal genetic databases: missing persons and human remains identification.

A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.

Cadaver↗
PubMed1991

Oligonucleotide fingerprinting using simple repeat motifs: a convenient, ubiquitously applicable method to detect hypervariability for multiple purposes.

A panel of simple repetitive oligonucleotide probes has been designed and tested for multilocus DNA fingerprinting in some 200 fungal, plant and animal species as well as man. To date at least one of the probes has been found to be informative in each species. The human genome, however, has been the major target of many fingerprinting studies. Using the probe (CAC)5 or (GTG)5, individualization of all humans is possible except for monozygotic twins. Paternity analyses are now performed on a routine basis by the use of multilocus fingerprints, including also cases of deficiency, i.e. where one of the parents is not available for analysis. In forensic science stain analysis is feasible in all tissue remains containing nucleated cells. Depending on the degree of DNA degradation a variety of oligonucleotides are informative, and they have been proven useful in actual case work. Advantages in comparison to other methods including enzymatic DNA amplification techniques (PCR) are evident. Fingerprint patterns of tumors may be changed due to the gain or loss of chromosomes and/or intrachromosomal deletion and amplification events. Locus-specific probes were isolated from the human (CAC)5/(GTG)5 fingerprint with a varying degree of informativeness (monomorphic versus truly hypervariable markers). The feasibility of three different approaches for the isolation of hypervariable mono-locus probes was evaluated. Finally, one particular mixed simple (gt)n(ga)m repeat locus in the second intron of the HLA-DRB genes has been scrutinized to allow comparison of the extent of exon-encoded (protein-) polymorphisms versus intronic hypervariability of simple repeats: adjacent to a single gene sequence (e.g. HLA-DRB1*0401) many different length alleles were found. Group-specific structures of basic repeats were identified within the evolutionarily related DRB alleles. As a further application it is suggested here that due to the ubiquitous interspersion of their targets, short probes for simple repeat sequences are especially useful tools for ordering genomic cosmid, yeast artificial chromosome and phage banks.

Animals↗
PubMed1980

A new procedure for the determination of transferrin C (Tf C) subtypes by isoelectric focusing. Existence of two additional alleles, Tf C4 and Tf C5.

Isoelectric focusing (IEF) is widely used for the determination of serum protein polymorphisms in forensic investigations. Because of non-genetic heterogeneity of some proteins and of protein-ligand dissociation observed after IEF standardization of procedures is necessary. In this article the authors point out the main difficulties encountered in studying the transferrin subtype polymorphism and describe a new and sensitive method. Two new Tf C subtypes were observed: Tf C4 in North American, Bolivian and Brazilian Indians, Tf C5 in Black Americans, both with polymorphic allele frequencies. In a Pyrenean population the allele frequencies for Tf C1, Tf C2 and Tf C3 were quite similar to those observed in a German population sample.

Alleles↗
PubMed1991

Identification of anti-HIV-1 antibodies in bloodstains of various ages.

The persistence of anti-HIV-1 antibodies in bloodstains has been studied by ELISA and Western Blot (WB) analysis. The immunoblot technique was found to be specific and more sensitive and the antibodies could be detected in 0.7 mg of bloodstains for up to 6 months. The authors emphasize the importance of such an investigation on non-genetic markers in individual diagnosis for forensic purposes.

Blood Stains↗
PubMed2001

Forensic investigations in Kosovo: experiences of the European Union Forensic Expert Team.

The international community has intervened ethnic hostilities in Kosovo, the Federal Republic of Yugoslavia. A team of Finnish forensic experts worked in December 1998 and January 1999 in Kosovo under the mandate of the European Union. The team investigated human remains from three locations of alleged ethnic violence. Concerning the events in Klecka, Volujak and Racak, the International Criminal Tribunal for the former Yugoslavia received documents of great gravity. The standard methods of forensic pathology were complemented with radiological, forensic odontological, physical anthropological and molecular genetic investigations.

Journal Article↗
PubMed2005

Individual identification by DNA polymorphism using formalin-fixed placenta with whole genome amplification.

Polymerase chain reaction (PCR) amplification using formalin-fixed material is very limited. In the present study the use of 6 week formalin-fixed placenta for individual identification was examined based on DNA analyses. The objective of the examination was to prove whether the placenta was from a woman who had just given birth. DNA extraction was carried out from the maternal blood sample and from the formalin-fixed placental samples composed of three parts: maternal side, infant side and umbilical cord. One minisatellite (D1S80), 12 short tandem repeat (STR) polymorphisms and amelogenin X, Y were investigated. All the polymorphic systems were detected in the maternal blood sample. The majority of the DNA isolated from the placental tissues had molecular weights of approximately 500 bp, and only two to four STR loci were amplified using the DNA. In order to amplify more DNA polymorphic markers from the formalin-fixed tissues, whole genome amplification was performed. After amplification by degenerate oligonucleotide-primed PCR (DOP-PCR), the products contained DNA with increased molecular weight up to >10 kbp. More DNA loci were typed using the DOP-PCR products. Furthermore, large molecular size fragments were purified from the DOP-PCR products by agarose electrophoresis, and then the D1S80 locus and 12 STR loci were successfully amplified using these fragments.

Adult↗
PubMed2006

Detection and quantification of the age-related point mutation A189G in the human mitochondrial DNA.

Mutation analysis in the mitochondrial DNA (mtDNA) control region is widely used in population genetic studies as well as in forensic medicine. Among the difficulties linked to the mtDNA analysis, one can find the detection of heteroplasmy, which can be inherited or somatic. Recently, age-related point mutation A189G was described in mtDNA and shown to accumulate with age in muscles. We carried out the detection of this 189 heteroplasmic point mutation using three technologies: automated DNA sequencing, Southern blot hybridization using a digoxigenin-labeled oligonucleotide probe, and peptide nucleic acid (PNA)/real-time PCR combined method on different biological samples. Our results give additional information on the increase in mutation frequency with age in muscle tissue and revealed that the PNA/real-time PCR is a largely more sensitive method than DNA sequencing for heteroplasmy detection. These investigations could be of interest in the detection and interpretation of mtDNA heteroplasmy in anthropological and forensic studies.

Adolescent↗
PubMed2005

Methods for the study of ancient DNA.

Whereas the analysis of ancient DNA (aDNA) has become an increasingly popular mode of investigation in both archaeological and evolutionary studies, this approach is complicated by the degraded nature of ancient nucleic acids, the presence of enzymatic inhibitors in aDNA extracts, as well as the risk of contamination during either excavation or manipulation of samples. Despite these difficulties, numerous methods have been developed to optimize the recovery, study, and authentication of aDNA. In this article, we describe the procedures used in our laboratory to extract and amplify informative DNA segments from prehistoric or protohistoric human samples, as well as the precautions and strategies implemented to avoid or at least detect contaminations.

Archaeology↗
PubMed2003

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices.

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identify various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

DNA↗
PubMedDate not supplied

What is important on the red blood cell surface.

Blood group antigens have provided tools for investigation of the red cell surface and been very useful as genetic markers in family, population and forensic studies. Precise definition of phenotypes is very important. Application of MAIEA (monoclonal antibody-specific immobilisation of erythrocyte antigen), a recently reported technique, to identify antigens and to assign red cell antigens to a particular membrane component is described: location of Knops system antigens on CR1 is confirmed and provisional assignment of Cromer system antigens to the different short consensus regions of decay accelerating factor (DAF) is described. Variability of red cell antigen expression is considered. The possibility is discussed that factors other than alterations in Rh genes may be responsible for some Rh variant phenotypes. Some C variants, two of which are associated with low incidence antigens, are described. The relationship of Xga with the quantitative polymorphism of 12E7 antigen is reconsidered in light of some recent immunochemical studies.

12E7 Antigen↗