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PubMed1994

A microsatellite polymorphism in the von Willebrand factor gene: comparison of allele frequencies in different population samples and evaluation for forensic medicine.

The allele frequencies at the tetranucleotide repeat (TCTA) vWA locus in the vWF gene were determined in the general Finnish population, in a population representing an internal isolate of Finland, in the Vologda-Russian population, and in US Black population samples. The allele and genotype frequencies from these population samples were compared with each other and with those reported from Spanish and British population samples. Statistically significant differences were demonstrated between most of the different groups (Finns vs. Vologda-Russians, Finns vs. US Blacks, Finns vs. Spanish, Vologda-Russians vs. US Blacks, Vologda-Russians vs. Spanish, US Blacks vs. Spanish and US Blacks vs. British Caucasians), but not between the two Caucasoid population samples from Finland and Great Britain, nor between or within the subpopulation samples from Finland and those from Vologda-Russia. In addition, the vWA marker was evaluated and demonstrated to be reliable for forensic purposes and paternity testing.

Adult↗

PubMed1992

Application of an allele-specific polymerase chain reaction to the direct determination of ABO blood group genotypes.

The allele-specific polymerase chain reaction (ASPCR) procedure has proven a powerful tool for the detection and analysis of known genetic polymorphisms. Here, we present a novel application of the ASPCR technique to determine the ABO genotypes of individuals without the need of family analysis. The method introduces a new strategy for primer design that permits the identification of the different ABO genotypes according to the molecular size of allele-specific amplification products. Four primer sets, each specific for a different set of ABO alleles, are mixed in one reaction and the amplification products are resolved on a polyacrylamide gel. Forty-one individuals belonging to various families, whose ABO phenotypes were previously determined serologically, were typed with this new variation of the ASPCR technique. A 100% correlation between the serology and the ASPCR data was found. The Mendelian segregation of ABO alleles was also demonstrated in families. The method is rapid, simple, reproducible, and specific. Potential applications include gene mapping, genetic disease diagnosis, HLA typing, paternity testing, and forensic science.

ABO Blood-Group System↗

PubMed2005

The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.

The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.

Chromosomes, Human, Y↗

PubMed2005

Some mathematical problems in the DNA identification of victims in the 2004 tsunami and similar mass fatalities.

DNA is a major and essential identification tool for mass fatality incidents including the hundreds of thousands of victims of the 2004 Indian Ocean tsunami. Mathematical complications characteristic of this sort of mass fatality include prevalence of related victims, the many races represented among the victims, and various identification modalities in tandem with DNA. Four mathematical problems of interest are discussed in this paper. (1) Other quantifiable factors (i.e. geography) can be formally accounted for by including a likelihood ratio that can be thought of as reducing the "effective number of victims." (2) When a victim is found and tentatively identified as V, but then it comes to light that the victim has a relative W who is also missing, confidence in the identity is depressed. To account for the existence of W, increment the effective number of victims by the likelihood ratio supporting W as the identity of the victim. (3) When several apparently related victims are found, their mutual identities should be calculated simultaneously. Compared to one-at-a-time, serial identifications, this is both logical and may lead to much more confidence in the identities. (4) Although there may be many different population groups represented among the missing, it is generally sufficient to consider population statistics for only a few of them in deciding whether to declare an identification.

DNA↗

PubMed2006

Allele frequency distribution based on 17 STR markers in three major Dravidian linguistic populations of Andhra Pradesh, India.

Allele frequencies for 15 tetranucleotides and 2 pentanucleotides repeat loci were determined in 317 unrelated, healthy individuals of Andhra Pradesh, India, belonging to three pre-dominant endogamous populations namely, Kappu Naidu, Kamma Chaudhary and Kapu Reddy. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all loci with few exceptions, which were not significant after applying Bonferroni's correction. Statistical parameters of forensic interest; observed heterozygosity, probability of homozygosity, probability of extact test, power of discrimination, match probability, polymorphism information content, power of exclusion and mean paternity index were determined for all loci. The present study reveals that Penta E and D2S1338 are the most informative loci in all the studied populations. The combined power of discrimination was greater than 0.976, whereas the cumulative power of exclusion gave an expected value of 0.9999 for all the tested microsatellite loci. No difference was observed in the discriminatory power of 15 loci in studied populations on comparison with other populations of India. Population differentiation tests revealed significant differences between the studied and neighboring populations at several loci. Analyzed parameters indicate the utility and efficacy of the studied 17 STR systems as a powerful tool in forensic human identification, paternity testing and human population genetic studies.

DNA Fingerprinting↗

PubMed2004

Analysis of two types of novel alleles in the DXS10011 locus.

A population study of the short tandem repeat locus DXS10011 was carried out in a sample of 104 unrelated Japanese individuals (56 males, 48 females). Thirty-six different alleles were distinguished. The power of discrimination was 0.933 (male) and 0.997 (female). Sequence analysis of alleles was examined for 34 samples. The sequence structures of the alleles were classified into three types: A, B and C. Type A had a regular repeat structure of the repeat region: (GAAA)(n). Types A and B differed in the base sequence of the repeat region. As an A (adenine) insertion in 5' upstream of (GAAA)(n) repeat unit was type C, this type was differentiated from type A.

Chromosomes, Human, X↗

PubMed2002

A new pentaplex system to study short tandem repeat markers of forensic interest on X chromosome.

A new method has been optimised to amplify five X chromosome short tandem repeat (STR) markers of interest in forensic medicine: human phosphoribosyl transferase (HPRTB), DXS101, androgen receptor (ARA), DXS7423 and DXS8377. Markers were conveniently amplified in a single PCR reaction with fluorochrome-labelled primers, which allowed the analysis of fragment sizes after injection into a capillary electrophoresis system. The most common alleles of each locus were sequenced and used in a control ladder to type unknown samples.

Adult↗

PubMed2003

Mitochondrial DNA cytochrome oxidase I gene: potential for distinction between immature stages of some forensically important fly species (Diptera) in western Australia.

Forensic entomology requires the fast and accurate identification of insects collected from a corpse for estimation of the postmortem interval (PMI). Identification of specimens is traditionally performed using morphological features of the insect. Morphological identification may be complicated however by the numerical diversity of species and physical similarity between different species, particularly in immature stages. In this study, sequencing was performed to study the mitochondrial DNA (mtDNA) as the prospective basis of a diagnostic technique. The sequencing focused on a section of the cytochrome oxidase I encoding region of mtDNA. Three species of calliphorid (blow flies) commonly associated with corpses in western Australia, Calliphora dubia, Chrysomya rufifacies and Lucilia sericata, in addition to specimens of Calliphora augur and Chrysomya megacephala were studied. Phylogenetic analysis of data revealed grouping of species according to genus. The DNA region sequenced allowed identification of all species, providing high support for separation on congeneric species. Low levels of variation between some species of the same genus however indicate that further sequencing is required to locate a region for development of a molecular-based technique for identification.

Animals↗

PubMed1997

Distribution of HLA-DQA1 alleles in Arab and Pakistani individuals from Dubai, United Arab Emirates.

PCR-based typing of the HLA-DQA1 locus, using allele specific oligonucleotide (ASO) probes and reverse dot blot methodology was used to determine allelic distributions and construct a database for Arab and Pakistani individuals living in Dubai. Genotype and allelic frequencies were calculated, and the data were tested for departures from Hardy-Weinberg (HWE) equilibrium. The most frequent HLA-DQA1 alleles among Dubaian Arabs are DQA1 4 and 1.2. Among Pakistanis, the most frequent allele is also DQA1 4. No significant deviations from HWE were detected.

Alleles↗

PubMed1997

Spanish population data on seven loci: D1S80, D17S5, HUMTH01, HUMVWA, ACTBP2, D21S11 and HLA-DQA1.

Blood samples from 120 Spanish Caucasian individuals were amplified and typed by electrophoresis at six loci, and by reverse dot-blot hybridization at one locus. Results demonstrate the assumption of independence within and between the seven loci analyzed. Therefore, a Spanish population database has been established and statistical analysis shows that a high degree of discrimination can be obtained when all seven (or fewer) loci are used to characterize forensic biological evidence.

DNA↗

PubMed1998

Allelic frequency distribution for three VNTR markers--D6S132, D7S467, D17S26--in Rio de Janeiro population, Brazil.

A sample population of Rio de Janeiro, Brazil, was tested for D6S132, D7S467, and D17S26 VNTR loci to determine the fixed-bin frequencies of alleles. RFLP analysis was obtained by HaeIII-digested genomic DNA. The three VNTR loci meet Hardy-Weinberg expectations, and there is no evidence for association of alleles between the VNTR loci. The frequency data can be used in forensic analysis, in paternity tests and to estimate the frequency of a DNA profile in the general Brazilian population.

Alleles↗

PubMed2003

Analysis of the polymorphic structure of short tandem repeats locus D18S555.

We analyzed the polymorphic structure of the short tandem repeats (STR) (RRGG) locus D18S555 by DNA sequencing, and examined the distribution of alleles in DNA samples from Japanese and Chinese individuals. DNA sequence analysis showed that the alleles at this locus consisted of deletions or insertions of (gaaagaaagaat), (ggaa), (ggaaggaaggag), (ggaaggagggaaggaaggag), (gggaggaa), and (ggga) 5, with each allele having its own DNA sequence. Analysis of 200 unrelated Japanese and 169 unrelated Chinese subjects identified 11 alleles, of which alleles 4, 6, and 13 occurred with a high frequency. There was no difference in allele frequency between the two ethnic groups. These results indicate that the genotyping of D18S555 alleles requires no sequence analysis, and making the locus applicable to forensic identity.

Asian People↗

PubMed2003

Effects of environmental conditions to which nails are exposed on DNA analysis of them.

To investigate the feasibility of DNA analysis of nails taken from human remains after environmental exposure, we tested the quantity and quality of DNA that could be recovered from nails exposed to various conditions. We first investigated whether there is an inter- or intra-subject difference in the DNA content of nails using nails obtained from 333 volunteers. DNA content did not significantly differ between males and females, or between young and elderly groups. In addition, no statistically significant differences were observed among nail samples obtained from each finger of the same person. Then thumbnails of five volunteers were left in dried soil, wet soil, river water, sea water, distilled water or air for 3 months. Each nail sample was tested monthly for sex chromosome-specific repeats, ABO genotype, STRs (TH01, TPOX, CSF1PO, FES and vWA loci), and D1S80 locus. These markers were correctly detected from nails after 1 month, irrespective of environmental conditions. Thereafter, the detection rates were decreased to various degrees, except for nails left in air. The detection of longer DNA markers tended to be more difficult than the detection of shorter markers. Nails were more fragile in wet soil than in any other condition. However, nonspecific PCR products were not observed in any nail sample. Our results reconfirmed the usefulness of the nail as a specimen for forensic DNA analysis.

Adolescent↗

PubMed2003

Polymorphism profile of nine short tandem repeat Loci in the Han chinese.

Nine short tandem repeat (STR) markers (D3S1358, VWA, FGA, THO1, TPOX, CSFIPO, D5S818, D13S317, and D7S820) and a sex-identification marker (Amelogenin locus) were amplified with multiplex PCR and were genotyped with a four-color fluorescence method in samples from 174 unrelated Han individuals in North China. The allele frequencies, genotype frequencies, heterozygosity, probability of discrimination powers, probability of paternity exclusion and Hardy-Weinberg equilibrium expectations were determined. The results demonstrated that the genotypes at all these STR loci in Han population conform to Hardy-Weinberg equilibrium expectations. The combined discrimination power (DP) was 1.05 x 10(-10) within nine STR loci analyzed and the probability of paternity exclusion (EPP) was 0.9998. The results indicate that these nine STR loci and the Amelogenin locus are useful markers for human identification, paternity and maternity testing and sex determination in forensic sciences.

Amelogenin↗

PubMed1979