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PubMed2003

Variant alleles on the penta E locus in the PowerPlex 16 kit.

Penta E in the PowerPlex 16 kit is a pentanucleotide tandem repeat marker located on Chromosome 15, containing an AAAGA repeat motif. Variant alleles (18.4 and 19.4) were found in the Japanese population. A sequence analysis revealed that both the variant alleles had a partial repeat motif of AAAA, resulting in one-base-shorter alleles compared to known alleles. Despite the relatively large amplicon sizes (379 to 474 bp) of Penta E, an accurate allele assignment can be reliably made by capillary electrophoresis. However, alleles differing in size by only one base (e.g., 18.4 and 19) were not separated and appeared as a single broad peak. The Genotyper software assigned one of the component alleles to this peak. Therefore, such broad peaks require careful interpretation so as to not overlook the other component allele contained by the peak. As an index to recognize a peak containing two alleles, the ratio of peak area to peak height was found to be useful.

Alleles↗
PubMed2003

Isolation of DNA from saliva of betel quid chewers using treated cards.

Betel quid (BQ) chewing, a common tradition in tropical areas, often poses a problem during collection and DNA analysis of buccal samples from many indigenous communities for population genetic studies and in forensic analysis of chewed BQ residues. This study evaluated the use of FTA card, a chemically treated filter paper, in collecting buccal samples from long-term BQ users and subsequent PCR-based analysis using nine STR markers. A low overall success rate of amplification was observed in the samples extracted using a standard organic extraction procedure (7%) as compared with those prepared using the FTA card (89%). The presence of inhibitors in liquid DNA samples was verified when control DNA failed to amplify in the presence of an equal volume of liquid BQ samples. The use of the FTA card is more practical during field sampling than handling tubes containing buccal swabs.

Areca↗
PubMed1992

Amplification of reproducible allele markers for amplified fragment length polymorphism analysis.

A procedure for amplification by PCR of reproducible allele markers for amplified fragment length polymorphism (Amp-FLP) analysis is presented. We have prepared markers for the allelic products of the VNTR loci D1S80 (MCT118) and D17S30 (YNZ22) and for the hypervariable VNTR locus close to the 3' end of the apolipoprotein B gene (apoB) by re-amplifying a mixture of PCR products from individuals with known alleles. These allele markers allow precise and discrete determination of the VNTR alleles at these loci using the Amp-FLP technique that should prove suitable in forensic analyses, paternity testing and population studies.

Alleles↗
PubMed1992

Restriction fragment length polymorphism analysis of zoo animals using HaeIII and four single-locus probes.

Using HaeIII as the restriction endonuclease, restriction fragment length polymorphism analysis of dried blood samples from various animals was conducted. Single-locus probes D2S44, D10S28, D1S7, and D4S139, as well as monomorphic probe D7Z2, were used to examine for banding patterns. If bands were present, the samples were further examined for heterogeneity (whether single or multiple bands were observed) and polymorphism (whether variation in band location was shown between the animals studied within a species). Blood samples from animals, including primates, were obtained from Miami Metrozoo, Miami, Florida. Some of the animals were non-related individuals while others were related. Banding patterns were observed in colobus' for D2S44, D1S7, and D4S139; owl monkeys for D2S44; gorillas for D2S44 and D4S139; gibbons for D2S44 and D4S139; siamangs for D2S44, talapoins for DiS7; cranes for D1S7; and otters for D1S7. Based upon these, all of the animals for which a conclusion could be drawn appeared to be homozygous and monomorphic (exhibited only an invariant single band) for the loci examined except colobus' for D4S139, gorillas for D4S139, cranes for D1S7, and otters for D1S7.

Animals↗
PubMed2003

The development of reduced size STR amplicons as tools for analysis of degraded DNA.

New multiplex PCR sets of commonly used short tandem repeat (STR) markers have been developed to produce PCR products that are reduced in size when compared to standard commercial STR kits. The reduction in size of these amplicons can facilitate the examination and analysis of degraded DNA evidence by improving amplification efficiency. This "miniSTR" approach will permit current forensic practitioners to use STR markers and instrumentation already present in their laboratories and to generate genotyping data that is directly comparable to reference samples and searchable through the FBI's Combined DNA Index System (CODIS) databases. This paper discusses the development of these new primer sets and presents some initial results in the analysis of degraded and aged DNA samples. A method for removal of problematic fluorescent dye artifacts is also described. Comparison studies in over 100 samples have verified that these miniSTR primers can provide fully concordant results to commercial STR kits and can provide improved signal from degraded DNA specimens. These miniplex sets should prove valuable in the analysis of samples where allele dropout and reduced sensitivity of larger STR alleles occurs.

Blotting, Southern↗
PubMed2003

Pharmacogenomics as an aspect of molecular autopsy for forensic pathology/toxicology: does genotyping CYP 2D6 serve as an adjunct for certifying methadone toxicity?

Pharmacogenomics, applied as an aspect of molecular autopsy, may be used as an adjunct for certifying methadone fatalities. Methadone is metabolized by cytochrome P-450 (CYP) 1A2, 3A4, and 2D6. We hypothesized that methadone toxicity may be partially due to CYP 2D6 *3, *4, and *5 variant alleles, resulting in poor drug metabolism. A retrospective analysis was performed on covariables and risk factors of 21 methadone cases from the Milwaukee County Medical Examiner's Office (1998-2000). PCR genotyping showed: one heterozygous for 2D6*3, two homozygous for 2D6*4, five heterozygous for 2D6*4, and one heterozygous for both 2D6*3 and *4. This limited number of cases showed that the prevalence of poor metabolizer was higher but not significantly different from that of a control group (n = 23) (P > 0.05, Fisher Exact Test). Thus, CYP 2D6 mutations may not yet be directly associated with methadone toxicity. However, pharmacogenomics, complementing other case findings, served as an adjunct in interpreting methadone toxicity of poor and intermediate metabolizers.

Adult↗
PubMed2003

[Y-chromosome analysis].

After initially slow progress in identifying DNA polymorphisms on the non recombining part of the human Y chromosome, a large number of polymorphic markers are now available to define individual or population-specific haplotypes or haplogroups. Among them the Y-chromosomal STRs (Short Tandem Repeats) have been increasingly used over the past few years for the study of human evolution as well as for human identification in forensic case-work and paternity testing. After a brief summary of the features of such markers, this paper deals with some applications of the Y-STR haplotyping.

Chromosomes, Human, Y↗
PubMed2004

Establishing the rDNA IGS structure of Cannabis sativa.

The rDNA intergenic spacer (IGS) structure of Cannabis sativa was established and can be used for classification and identification of this species. In this study, DNA fragments of rDNA IGS were amplified by PCR from Cannabis sativa plant extracts and a 1387 bp fragment was obtained. DNA sequence analysis revealed six different repeat motifs. In the middle of the IGS sequence, there were three sequence motifs, and the same three sections of DNA were then repeated with minor variation in sequence. The terminal region of the IGS was composed of another three different repeat units; multiple copies of these terminal repeat motifs were present in no discernible order. Within six repeat motifs, point variations were observed in five. The DNA sequence of the locus was compared with all the plant sequences registered in GenBank by the Fasta program of GCG software with the result that this DNA fragment was significantly different from any other DNA sequence recorded to date. The most similar sequence was that of Hops (Humulus lupulus), but with a similarity of only 88.9% over 579 bp. These specific and complex variations of IGS may be related to the species and geographic distributions.

Base Sequence↗
PubMed2004

Mitochondrial DNA heteroplasmy among hairs from single individuals.

A denaturing gradient gel electrophoresis (DGGE) assay was used to detect mitochondrial DNA (mtDNA) sequence heteroplasmy in 160 hairs from each of three individuals. The HV1 and HV2 heteroplasmic positions were then identified by sequencing. In several hairs, the heteroplasmic position was not evident by sequencing and dHPLC separation of the homoduplex/heteroduplex species was carried out with subsequent reamplification and sequencing to identify the site. The overall detection frequency of sequence heteroplasmy in these hairs was 5.8% (28/480) with DGGE and 4.4% (21/280) with sequencing. Sequence heteroplasmy of hair was observed even when the reference blood sample of the individual was homoplasmic. The heteroplasmic positions were not necessarily observed at sites where high rates of substitution have been reported. In two hairs, a complete single base change from the reference blood sample was observed with sequencing, while the heteroplasmic condition at that site in the hair was observed using DGGE. The DGGE results in such samples would serve as an aid in considering the possibility of match significance. In a forensic case, this situation would lead to the possibility of a failure to exclude rather than to be inconclusive.

Chromatography, High Pressure Liquid↗
PubMed2004

[Haplotype analysis of single nucleotide polymorphisms of mitochondrial DNA].

Mitochondrial DNA (mtDNA) mutations observed in both non-coding control and coding regions are being used widely to characterize human evolution and for identification. Several methodological approaches have been available for detection of single nucleotide polymorphisms (SNPs). SNPs of the non-coding region were mainly analyzed by means of direct sequencing. Especially, sequence analysis of D-loop is often the final resort in forensic and ancient personal identification. However, sequencing is relatively expensive and time-consuming. Furthermore, because the mtDNA molecule is a single linked unit, the statistical significance in forensic cases requires mtDNA matching in comparison with large sequence data. In this study, we developed a procedure of technique simultaneous typing to 11 SNPs and 2 tandem repeat sites in the non-coding and coding region by use of allele-specific amplification. In an analysis to 631 unrelated Japanese individuals the 180 haplotypes were defined in this study, and the level of haplotypic diversity and random mach probability was similar to that obtained by sequencing of the human hypervariable region 1 in mtDNA. These results show the usefulness of mtDNA haplotype analysis by the presented method for personal identification.

Alleles↗
PubMed2004

[Degradation of biomolecules: a comparative study of diagenesis of DNA and proteins in human bone tissue].

Diagenesis of macromolecules is a not yet fully understood process that can be important for anthropological and forensic research. Trying to elucidate the diagenesis of DNA and proteins we investigated the process of fragmentation of DNA and razemisation of aspartic acid in human bone material. We created an in vitro-model of accelerated aging by incubating bone samples in hot water. A comparison of diagenesis of molecules in those artificially aged samples with altogether 30 historical bones from different regions and of different ages was carried out. The in vitro-model showed the expected positive correlation between the increase of razemisation of aspartic acid and DNA fragmentation, while there was a much lesser correlation when investigating historical bones. The in vitro-model showed the expected correlation between the increase of razemisation of aspartic acid and DNA fragmentation and to a much lesser extent in historical bones. This study shows that diagenesis is probably influenced by additional forces affecting different macromolecules in different ways.

Age Determination by Skeleton↗