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PubMedDate not supplied

An investigation of sequence deletions of amelogenin (AMELY), a Y-chromosome locus commonly used for gender determination.

BACKGROUND: Accurate gender determination is crucial in many scientific disciplines, but especially so in prenatal diagnosis of X-linked diseases and forensic investigations. Today, molecular techniques, especially typing for a length variation in the X-Y homologous amelogenin gene (AMELX and AMELY), are used for gender assignation. This amelogenin test is an integral part of most PCR multiplex kits that are used for DNA profiling, but in 1998 there was a report of two normal males being typed as female with this test. Subsequently, a small number of amelogenin negative (or AMELY null) males have been reported in various populations but little data are available characterising these deletions. AIMS: The study aims to determine the size of the deletion in five AMELY null males by typing DNA samples for markers surrounding this gender-determining locus. The possible relationships among the AMELY null samples are examined through analysis of their deletion size and associated Y-chromosome microsatellite haplotypes. We also attempt to determine the frequency of AMELY negative males in Australia. SUBJECTS AND METHODS: DNA samples from five AMELY null males, from different geographical regions, were made available for this study. The samples were typed for eight sites, all located on the short arm of the Y chromosome, using PCR and gel electrophoresis. Eleven Y-chromosome specific microsatellites were also typed on each sample in order to generate haplotypes for phylogenetic analysis. A questionnaire was sent to all Australian forensic centres requesting information on the frequency of AMELY negative males observed in their laboratories. RESULTS: Two different sized deletions were seen in the five AMELY null samples. One deletion (in two samples) has a size of between 304 and 731 kbp, whereas the other (in three samples) ranges between 712 and 1001 kbp. Y-microsatellite haplotypes indicate that the smaller deletion is probably identical in the two samples, but this is not the case with the larger deletion. The frequency of AMELY negative is rare in Australia, with an overall frequency of 0.02%. CONCLUSION: Comparisons of both deletion size and haplotypes with published data suggest that most AMELY nulls are the result of independent evolutionary events, even in those populations where the frequency is relatively high. Although AMELY null males are extremely rare in most populations, typing an additional gender-determining locus should be considered in forensic investigations where the reference sample is of unknown gender.

Amelogenin↗
PubMed2003

Molecular identification of some forensically important blowflies of southern Africa and Australia.

One major aspect of research in forensic entomology is the investigation of molecular techniques for the accurate identification of insects. Studies to date have addressed the corpse fauna of many geographical regions, but generally neglected the southern African calliphorid species. In this study, forensically significant calliphorids from South Africa, Swaziland, Botswana and Zimbabwe and Australia were sequenced over an 1167 base pair region of the COI gene. Phylogenetic analysis was performed to examine the ability of the region to resolve species identities and taxonomic relationships between species. Analyses by neighbour-joining, maximum parsimony and maximum likelihood methods all showed the potential of this region to provide the necessary species-level identifications for application to post-mortem interval (PMI) estimation; however, higher level taxonomic relationships did vary according to method of analysis. Intraspecific variation was also considered in relation to determining suitable maximum levels of variation to be expected during analysis. Individuals of some species in the study represented populations from both South Africa and the east coast of Australia, yet maximum intraspecific variation over this gene region was calculated at 0.8%, with minimum interspecific variation at 3%, indicating distinct ranges of variation to be expected at intra- and interspecific levels. This region therefore appears to provide southern African forensic entomologists with a new technique for providing accurate identification for application to estimation of PMI.

Animals↗
PubMed1991

Recent advances in the polymerase chain reaction.

The polymerase chain reaction (PCR) has dramatically altered how molecular studies are conducted as well as what questions can be asked. In addition to simplifying molecular tasks typically carried out with the use of recombinant DNA technology, PCR has allowed a spectrum of advances ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences. PCR can provide insights into the intricacies of single cells as well as the evolution of species. Some recent developments in instrumentation, methodology, and applications of the PCR are presented in this review.

Binding Sites↗
PubMed2003

Analysis of short tandem repeat (STR) polymorphisms by the powerplex 16 system and capillary electrophoresis: application to forensic practice.

Allele and genotype frequencies for 15 short tandem repeat (STR) polymorphisms--D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA--in a Japanese population were estimated. No deviations of the observed allele frequency from Hardy-Weinberg equilibrium expectations were found for any of the systems studied. Between 2 new pentanucleotide STR loci, Penta E and Penta D, for which there is only limited data regarding the allelic distribution in Japanese, the Penta E locus was found to be highly polymorphic and exhibited a tri- or tetra-modal distribution pattern having allelic peaks with 5, 11, 15 and 20 repeats. The distribution was significantly different from that of the other ethnic groups. Statistical parameters of forensic importance, the power of discrimination (PD), observed and expected heterozygosity values (H), polymorphism information content (PIC), power of discrimination (PD), matching probability (pM), power of exclusion (PE), and typical paternity index (PI), were calculated for the loci. These parameters indicated the usefulness of the loci in forensic personal identification and paternity testing among Japanese. The systems Penta E, FGA, D18S51 and D8S1179 were the most informative. This method was successfully applied to forensic personal identification and paternity testing among Japanese, thereby confirming its efficacy for forensic practice.

Adult↗
PubMed2005

Comparing bacterial DNA microarray fingerprints.

Epidemiologic and forensic investigations often require assays to detect subtle genetic differences between closely related microorganisms. Typically, gel electrophoresis is used to compare randomly amplified DNA fragments between microbial samples, where the patterns of DNA fragment sizes are viewed as genotype 'fingerprints'. The limited genomic sample captured on a gel, however, is not always sufficient to discriminate closely related strains. This paper examines the application of microarray technology to DNA fingerprinting as a high-resolution alternative to gel-based methods. The so-called universal microarray, which uses short oligonucleotide probes that do not target specific genes or species, is intended to be applicable to all microorganisms because it does not require prior knowledge of genomic sequence. In principle, closely related strains can be distinguished if enough independent oligonucleotide probes are used on the microarray, i.e., if the genome is sufficiently sampled. In practice, we confront noisy data, imperfectly matched hybridizations, and a high-dimensional inference problem. We describe the statistical problems of microarray fingerprinting, outline similarities with and differences from more conventional microarray applications, and illustrate a statistical measurement error model to fingerprint 10 closely related strains from three Bacillus species, and 3 strains from non-Bacillus species.

Journal Article↗
PubMed1999

Frequencies of D8S384 alleles and genotypes in European, African-American, Chinese, and Japanese populations.

D8S384 is a tetranucleotide tandem repeat locus. In order to evaluate the forensic validation of D8S384, the genotype distributions and allele frequencies in ten populations from three main ethnic groups were investigated, including Germans, Slovakians, African Americans, Japanese, and Chinese (Jilin, Guangzhou, Nanning, Hailaer, Dali, and Chengdu). A total of 1011 unrelated individuals, 41 pedigrees, 30 disputed paternity trios and three personal identification cases were analyzed for D8S384 by Amp-FLP technique. Many kinds of tissues, body fluids, secreta and stains have been tested. The alleles were determined by comparison with a human allele ladder. The results showed that D8S384 typing was both precise and reliable. There were eight alleles in these populations. The genotype distributions conformed to Hardy-Weinberg equilibrium predictions. No mutation events were observed. With a maximum likelihood method, the mutation rate was indirectly estimated as 2.14 x 10(-5). The heterozygosity was 0.704 +/- 0.014 at D8S384 locus. All these results suggest that D8S384 locus is a useful marker for forensic identification and paternity analysis.

Adult↗
PubMed1999

Distribution of D1S80 alleles in the Bahrainian population.

This study demonstrates that the locus D1S80 is highly polymorphic in the Bahrainian population. There were 24 different D1S80 alleles and 51 distinct genotypes observed in 198 Bahrainians. There was one allele observed that was smaller than the 14 repeat allele. This data set meets the Hardy-Weinberg expectations (HWE) and could be a useful marker for parentage testing and forensic applications.

Alleles↗
PubMed2000

Population frequency for the short tandem repeat loci D18S849, D3S1744, and D12S1090 in Caucasian-Mestizo and African descent populations of Colombia.

Blood samples from 489 unrelated Caucasian Mestizo and 252 individuals of African descent in Colombia were amplified and typed for three short tandem repeat (STR) markers (D12S1090, D3S1744, and D18S849). All markers conformed to Hardy-Weinberg equilibrium expectations in both populations studied. In addition, heterozygosity, mean exclusion chance, polymorphism information content, discrimination power, and the assumption of independence within and between loci were determined. The mean exclusion chance for all three STR markers is 0.9750 in the Caucasian Mestizo population and 0.9731 in the African Colombian Population. The discrimination power is 0.999925 and 0.999911 in the Caucasian Mestizo and African Colombian respectively.

Black People↗
PubMed2000

STR allelic frequencies in a German skeleton collection.

Chromosomal DNA was isolated from bones from a German skeleton collection (Goslar, 18th century) and detected by PCR. Nine microsatellite regions were amplified by multiplex reactions using the AmpFlSTR Profiler Plus kit and analysed to obtain their allelic distribution. A statistical evaluation of the results revealed no allelic differentiation between the historic sample and a modern German one at each locus.

Alleles↗
PubMed2000

Population frequency distribution of HumF13A01, HumFXIIIB, and HumLIPOL loci in the Basque Country (Northern Spain).

A population study of unrelated individuals from the Basque Country (Northern Spain) was carried out using the GenePrint STR System. The PCR products were separated on denaturing polyacrylamide gels and visualized by silver staining. Three tetrameric loci were evaluated: HumF13A01, HumFXIIIB, and HumLIPOL. All loci fit Hardy-Weinberg expectations, and independence of alleles was found between these STR loci. A comparison with other population groups indicated allele frequencies are well conserved in Caucasians, but differ from other racial groups. The calculated parameters a priori probability of exclusion (Pex) and "power of discrimination" (PD) show how informative these loci are for the determination of identity and relatedness of individuals.

Ethnicity↗
PubMed2001

Introduction to DNA analysis.

This article discusses the specific use of DNA analysis as one scientific method used in solving crime. Case studies presented here provide examples of crime investigations where the use of DNA analysis can prove beneficial.

DNA↗