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PubMed2000

Population genetics of the STR loci HUMCSF1PO, HUMF13A01, HUMFES/FPS and D12S391 in Asturias (northern Spain).

In order to use genetic loci in forensic identity testing, some population data are needed. This paper presents a report of allele frequency data for the loci HUMCSF1PO, HUMF13A01, HUMFES/FPS and D12S391 in a population sample from Asturias (northern Spain). No deviation from the Hardy-Weinberg equilibrium was detected in any of the four markers investigated and there was no evidence of association between the alleles of these loci. Statistical analysis was also carried out to obtain some parameters of medico-legal interest and comparative studies were carried out with other populations studied to date for these loci. The Asturian sample does not differ substantially from other Caucasian and Spanish populations.

DNA Fingerprinting↗

PubMed1994

[Application of ORM1 phenotyping in forensic science].

ORM1 is an important genetic marker for both parentage testing and personal identification in forensic science. We have examined the ORM1 phenotypes in the human serum and dried bloodstains using the ULPAGIF method. ORM1 phenotypes were successfully demonstrated from dried bloodstains stored at 4 degrees C and room temperature for up to twenty-four weeks. In bloodstains stored at 37 degrees C, the 100% of ORM1 phenotyping was no longer possible after 12 weeks. We examined 9 bloodstains stored at room temperature for one, two and three years, respectively. For the one-year-old bloodstains, all of the samples could be phenotyped correctly, for the two-year-old bloodstains 8 out of the 9 and for the three-year-old bloodstains 7 out of the 9 samples could be phenotyped correctly. The results have indicated that ORM1 is relatively stable, for it is tolerable toward high temperature and long duration. It was suggested that the bloodstains should be ultrasonicated before ULPAGIF, because the ultrasonication could elevate the detectable rate of ORM1 phenotypes from bloodstains. ORM1 phenotypes was performed in five disputed parentage cases. One of the alleged fathers was excluded.

Blood Stains↗

PubMed2001

Variations in primer sequences are the origin of allele drop-out at loci D13S317 and CD4.

STRs have become almost the exclusive tool of genetic scientists in forensic typing work. Consequently, large numbers of samples are genotyped and the detection of rare abnormalities is to be expected. We found rare losses of alleles, also known as drop-out, at the two STR loci D13S317 and CD4. Drop-out at D13S317 was accidentally found in typing of suspects in a murder case and three other examples of drop-out were found at locus CD4 during paternity testing. The lost alleles reappeared when alternative PCR primer pairs were used. Sequences of lost alleles were characterised at the molecular level after cloning. Variations were found in the primer sequences and these are believed to prevent amplification or to reduce amplification yield and to be the origin of the allele drop-out.

Alleles↗

PubMed2002

Validity of PCR with emphasis on variable number of tandem repeat analysis.

OBJECTIVES: Variable number of tandem repeat polymorphisms (VNTR) are frequently analyzed by PCR in genetic, epidemiologic and forensic studies. We wanted to explore the validity of these PCR analyses. DESIGN AND METHODS: The amplification of the different alleles of the 17- and the 44-bp VNTR of the serotonin transporter gene and the 39-bp VNTR of the glycoprotein Ibalpha gene was analyzed. We studied the effects of the parameters magnesium, dimethylsulfoxide, 7-deaza-dGTP, formamide, betaine, PCR temperatures and different types of polymerases. RESULTS: In all three VNTR polymorphisms selective amplification of one of the alleles of heterozygous individuals could be obtained by change of the magnesium concentration. This problem could be minimized by a combination of Taq- and Pwo-polymerases and by use of 7-deaza-dGTP. CONCLUSION: PCR analysis of all of these VNTRs may give reproducibly wrong results in truly heterozygous subjects due to selective amplification of only one of the alleles.

Betaine↗

PubMed2001

Rapid sizing of microsatellite alleles by gel electrophoresis on microfabricated channels: application to the D19S394 tetranucleotide repeat for cosegregation study of familial hypercholesterolemia.

This study evaluated the applicability of microchip electrophoresis to the sizing of microsatellites suitable to genetic, clinical and forensic applications. The evaluation was performed with the D19S394 tetranucleotide (AAAG) repeat characterized by a wide variation in the repeat number (1-17) and a short recombination distance from the low-density lipoprotein (LDL)-receptor gene that makes it suitable to cosegregation analysis of familial hypercholesterolemia (FH). The study was performed with 70 carriers of two LDL-receptor mutations common in northern Italy (i.e., the 4 bp insertion in exon 10 known as FH-Savona and the D200G missense mutation in the exon 4, known as FH-Padova 1) and 100 healthy controls. The polymerase chain reaction (PCR) amplification products prepared with a cosolvent PCR protocol and an antibody-protected polymerase were directly analyzed with an apparatus for high-voltage capillary electrophoresis on microchips and laser-induced fluorescence detection equipped with chips for the analysis of 25-500 bp dsDNA fragments. The test could not be extended to dinucleotide repeats due to the resolution characteristics of the available microchip. This novel approach was able to distinguish 17 microsatellite alleles varying from 0 to 17 repeats. Many of these alleles were quite rare, but the seven more abundant accounted for over the 70% of allele distribution in control population. The standard deviation in the sizing of the most abundant alleles ranged from +0.60 to +/- 0.75 bp. This indicated that the size attribution to a conventional allele using the +/- 1 bp range around it allowed a confidence limit above the 80 %. The sizing of D19S394 obtained this way allowed the cosegregation analysis with both the FH mutations tested. Therefore, this innovative approach to microsatellite sizing was much simpler, but equally effective as traditional capillary electrophoresis, at least with tetranucleotide repeats.

Alleles↗

PubMed2004

Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci.

Precise estimates of mutation rates at Y-chromosomal microsatellite STR (short tandem repeat) loci make an important basis for paternity diagnostics and dating of Y chromosome lineage origins. There are indications of considerable locus mutation rate variability between (inter-) and within (intra-) loci. We have studied nine Y-STR loci-DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385, and DYS388-in 1,766 father-son pairs of confirmed paternity (a total of 15,894 meioses). Five biallelic markers were also analyzed in the fathers-Tat, YAP, 12f2, SRY1532, and 92R7-defining haplogroups 1, 2, 3, 4, 9, and 16, respectively. A total of 36 fragment length mutations were observed: 24 gains (22 single-step, two double-step) and 12 single-step losses. Thus, there was a significant surplus of gains (p=0.045). Overall, the mutation rate was positively correlated to STR repeat length and there was a significant relative excess of losses in long alleles and gains in short alleles (p=0.043). In contrast to the situation in autosomal STR loci and in MSY-1, no noteworthy correlation between mutation rate and the father's age at the child's birth was observed. We observed significant interlocus differences in Y-STR mutation rates (p<0.01). The number of observed mutations ranged from zero in DYS392 to eight in DYS391 and DYS390. We have also demonstrated obvious differences in mutation rates between the haplogroups studied (p=0.024), a phenomenon that is a reflection of the dependence of mutation rate on allele size. Our study has thus demonstrated the necessity of not only locus-specific, but even allele-specific, mutation rate estimates for forensic and population genetic purposes, and provides a considerable basis for such estimates.

Adolescent↗

PubMed1993

On the essence of "meaningless" simple repetitive DNA in eukaryote genomes.

Various kinds of simple tandemly repetitive DNA sequences are abundantly interspersed in the genomes of practically all eukaryotic species studied. The comparatively elevated mutation rates of simple repeat blocks result in highly polymorphic and therefore extremely informative investigation systems for studies on forensic, ecological and genetic relationship questions. Recently the techniques for analyzing simple repeats have achieved great effectivity and simplicity. Beyond their utility as tools for differentiation and individualization, certain of these repeated elements harbor quite unexpected qualities which may be discussed in the context of their biological meaning. i) A specific subset of simple (cac)n or (gtg)n repeats is expressed in mature mRNA and total cellular RNA. ii) Despite the apparently high mutation rate certain (gt)n or mixed (gt)n/(ga)m stretches of intronic simple repeats are preserved in immunologically relevant genes for at least 70 x 10(6) years and they bind nuclear protein molecules with high affinities. Consequently in addition to their tool character, the biological aspects of simple repeated DNA should be taken into consideration.

Animals↗

PubMed1989

Hypervariable polymorphism of autosomal origin detected by the Y-chromosome derived probe, pHY10.

A recombinant DNA probe (pHY10) hybridizing specifically to human DNA family DYZ1, 3,000 copies of which are present on the long arm of the Y chromosome, was used for probing human genome DNA digested with various restriction enzymes. To our surprise, the probe detected a hypervariable polymorphism of autosomal origin in human DNA when digested with TaqI. None of other 12 restriction enzymes revealed polymorphic patterns. Codominant segregation of the polymorphism was established in family studies. This probe has been widely used in the detection of the Y chromosome. Its ease of availability as well as highly discriminating polymorphic pattern makes it potentially very useful for forensic and human genetic purposes.

DNA Probes↗

PubMed2005

Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia.

We have analyzed 11 Y-STR loci (DYS19, the two DYS385 loci, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DXYS156Y) in 700 males from ten ethnic groups in east Asia in order to evaluate their usefulness for forensic and population genetic studies. A total of 644 different haplotypes were identified, among which 603 (86.14%) were individual-specific. The haplotype diversity averaged over all populations was 0.9997; using only the nine Y-STRs comprising the "minimal haplotype" (excluding DYS388 and DXYS156Y) it was 0.9996, a value similar to that found in 1924 samples from other Asian populations (0.9996; Lessig et al. Legal Medicine 5(2003) 160-163), and slightly higher than in European populations (0.9976; n=11,610; Roewer et al. For Sci International (2001) 118:103-111). All of the individual east Asian populations examined here had high haplotype diversity (> or =0.997), except for the Mongolians (0.992) and Manchurians (0.960). The most frequent haplotype identified by the nine markers was present at only 1% (7/700). Population comparisons based on Phi(ST) or rho genetic distance measures revealed clustering according to the traditional northeast-southeast distinction, but with exceptions. For example, the Yunnan population from southern China lay among the northern populations, possibly reflecting recent migration, while the Korean population, traditionally considered northern, lay at the boundary between northern and southern populations. An admixture estimate suggested 55(51-59)% northern, 45(41-49)% southern contribution to the Koreans, illustrating the complexity of the genetic history of this region.

Asia, Southeastern↗

PubMed2001

VWA STR genotyping: further inconsistencies between Perkin-Elmer and Promega kits.

We report a simultaneous study of the VWA STR locus by the Perkin-Elmer Profiler Plus kit and the Promega GenePrint CTTv kit in a population sample from North Portugal and in 418 meiosis from family material and paternity cases. PCR amplification and genotyping were performed according to the manufacturer's instructions using ABI 377 or ABI 310 automatic sequencers. Biological kinship in family material and paternity cases was validated by the use of the STR loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA, CSF1PO, TH01 and TPOX. Out of 434 unrelated individuals we found 4 inconsistencies between the genotypes obtained using each kit. No exclusions were found in the meiotic analyses. In all cases, these inconsistencies were due to an annealing failure of the Perkin-Elmer forward primer resulting in false homozygotes. Sequencing analysis revealed an A-to-T substitution at position 1631 (GenBank sequence M25858), 52 bases upstream of the first TCTA motif of the repeat region. An estimate of the null allele frequency (s) in this study is thus obtainable from the expression s = 4/(2 x 434) = 0.46%. The relatively high frequency of these discrepancies in our population demonstrates the need for caution when comparing genotype or gene frequency estimates made from amplicons produced by different primers, when evaluating apparent exclusions in paternity testing and when searching for a match between individual genetic profiles in forensic databases. Our findings are also compared with those previously reported.

Alleles↗

PubMed1999

Simultaneous typing of the STR loci, vWF and HumTPO, using discontinuous polyacrylamide gel electrophoresis.

Analyses of short tandem repeat (STR) loci are very useful for improving the accuracy of paternity determination. Combined use of several STRs makes this test even more accurate. We have devised a simple but effective method which consists of the co-amplification of two STR loci (vWF and HumTPO) in a single test tube, separation of the PCR products using discontinuous polyacrylamide gel electrophoresis, and detection using sensitive silver staining. An appropriate combination of PCR primer pairs gave a high resolution and good separation of the two STR bands in the same lane on the same gel. Many combinations of STR loci have potential usefulness in paternity and individualization testing or population genetic studies in forensic practice.

Journal Article↗

PubMedDate not supplied

[Cerebral palsy (II)--clinical symptoms and etiopathogenesis].

In our first report we analysed the criteria for defining the term 'cerebral palsy'. In this paper we deal with the problems arising from this terminology and exemplify this by presenting some case reports. It will be shown that the usage of the term 'CP'--misunderstood as a diagnosis--often hinders the correct analysis of the underlying pathogenesis and aetiology. Thus genetic, therapeutic and forensic implications of the underlying disease or lesion are easily over-looked.

Adolescent↗

PubMed1995

Clearance of HIV infection in a perinatally infected infant.

BACKGROUND: We describe a child who was identified shortly after birth as infected with the human immunodeficiency virus type 1 (HIV-1), but whose infection appears to have completely cleared. Asymptomatic HIV-1 infection was diagnosed in the mother during the fourth month of pregnancy. The infant was delivered vaginally at 36 weeks, received no blood products, and was not breast-fed. METHODS AND RESULTS: HIV-1 was detected by culture of the infant's peripheral-blood mononuclear cells at 19 and 51 days of age. Plasma from the infant was also culture-positive for HIV-1 at 51 days of age by DNA polymerase chain reaction (PCR). Nucleotide-sequence analysis of HIV-1 DNA showed extremely close homology of the cultures obtained 32 days apart, and forensic markers of genetic identity for the two cultures were identical. Hence, inadvertent viral contamination or error in the collection of specimens was highly unlikely. At 12 months of age the infant was seronegative for HIV-1, and numerous subsequent cultures and tests by PCR have also been negative for HIV-1. The child is five years of age at this writing, is HIV-seronegative, and remains well, with normal growth and development and no laboratory or clinical evidence of HIV-1 infection. CONCLUSIONS: The infant we describe was infected perinatally with HIV-1, but the infection subsequently cleared and the infant remained without detectable HIV-1 infection five years later.

Adult↗

PubMed2003

Comparison of minisatellites.

In the class of repeated sequences that occur in DNA, minisatellites have been found polymorphic and became useful tools in genetic mapping and forensic studies. They consist of a heterogeneous tandem array of a short repeat unit. The slightly different units along the array are called variants. Minisatellites evolve mainly through tandem duplications and tandem deletions of variants. Jeffreys et al. (1997) devised a method to obtain the sequence of variants along the array in a digital code and called such sequences maps. Minisatellite maps give access to the detail of mutation processes at work on such loci. In this paper, we design an algorithm to compare two maps under an evolutionary model that includes deletion, insertion, mutation, tandem duplication, and tandem deletion of a variant. Our method computes an optimal alignment in reasonable time; and the alignment score, i.e., the weighted sum of its elementary operations, is a distance metric between maps. The main difficulty is that the optimal sequence of operations depends on the order in which they are applied to the map. Taking the maps of the minisatellite MSY1 of 609 men, we computed all pairwise distances and reconstructed an evolutionary tree of these individuals. MSY1 (DYF155S1) is a hypervariable locus on the Y chromosome. In our tree, the populations of some haplogroups are monophyletic, showing that one can decipher a microevolutionary signal using minisatellite maps comparison.

Algorithms↗

PubMed1991

Isolation and characterization of DNA from archaeological bone.

DNA was extracted from human and animal bones recovered from archaeological sites and mitochondrial DNA sequences were amplified from the extracts using the polymerase chain reaction. Evidence is presented that the amplified sequences are authentic and do not represent contamination by extraneous DNA. The results show that significant amounts of genetic information can survive for long periods in bone, and have important implications for evolutionary genetics, anthropology and forensic science.

Animals↗

PubMed1993

Synthesis and characterization of 5'-fluorescent-dye-labeled oligonucleotides.

Fluorescent-dye-labeled oligonucleotides are used in many procedures, including DNA sequencing, PCR, restriction mapping, the study of genetic disease, and forensics identification. In this paper, we describe detailed methods for the synthesis, purification, and quantification of 5'-fluorescent-dye-labeled oligonucleotides. The relationship of specific and nonspecific dye attachment to synthetic oligonucleotides is discussed, and the importance of primer design is considered as a way to prevent chemical problems from interfering with biological reactions.

Chromatography, High Pressure Liquid↗

PubMed2006

The dbMHC microsatellite portal: a public resource for the storage and display of MHC microsatellite information.

Major histocompatibility complex (MHC) region Microsatellites (Msat) have been extensively used in various applications, such as disease mapping, forensics, and population genetics. A comprehensive review of HLA Msat primers has been previously published based on literature and sequence analysis, but electronic tools are lacking to make it easily accessible and actually used by the community. We have integrated data from this review, with an overlapping set of 31 Msat markers used in the 13th International Histocompatibility and Immunogenetics Workshop (IHIWS) to create a public archive that will synchronize published descriptions to a common framework. http://www.ncbi.nlm.nih.gov/projects/mhc. Currently, the dbMHC contains 389 primer pairs across the extended MHC targeting 281 distinct repeat regions (approximately 1/45 kb). Literature review and analysis of the primers reveal that over 200 synonymous names have been published for these markers. Users may view or download specific Msat data sets using the portal. Query options include name or partial name, primer sequence, neighboring genes, and/or position. Query results include locus name(s), a graphic showing of the relative location of the marker in relation to the classical HLA genes, a listing of the constituent primer pairs and name, a link to UniSTS, aliases, allele range (bp), overlapping single nucleotide polymorphisms, a link to e-polymerase chain reaction, and physical mapping information. To increase the utility of this resource, researchers using Msat markers in the HLA region are encouraged by the authors to submit new primers to the dbMHC. The minimal Msat submission consists of primers sequences, a submitter's name and contact information. Additional information recommended but not required is the laboratory protocol(s), known allele size range (bp), known aliases, and an exemplar sequence. Assigned UniSTS numbers can be used for primer pair standard identification.

Animals↗

PubMed1986

The use of DNA polymorphisms demonstrated by means of the HLA system.

The advances reached by using DNA polymorphisms (restriction fragment length polymorphisms) in blood group serology are demonstrated by means of the HLA system. The potentialities for various applications (e.g. better definition of alloantigens, association with diseases, paternity testing, forensic medicine or genetic counselling) are mentioned.

DNA↗