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PubMed2001

Analysis of 168 short tandem repeat loci in the Japanese population, using a screening set for human genetic mapping.

We devised a multiplex polymerase chain reaction (PCR) amplification and loading system for the convenient typing of 168 short tandem repeat (STR) polymorphic markers in a commercially available screening primer set for human linkage analysis. We genotyped all these 168 STR loci with 32 healthy unrelated Japanese, calculated allele frequencies at each STR locus, and performed three kinds of tests for Hardy-Weinberg equilibrium (HWE). Significant deviations from HWE in all three tests were observed at only three loci, and the average heterozygosity in the Japanese (0.733) was slightly lower than that in Caucasians (0.773). We also examined 32 Caucasians at some selected loci, to be compared with Japanese. Some markers showed greatly different heterozygosities or allelic distributions in Japanese and Caucasian populations. In two groups of STRs, those with and without irregular alleles (or interalleles), the former had a higher proportion of bimodal allelic distribution and possessed more alleles per locus than the latter. However, no significant differences in the observed and expected heterozygosities, or in the powers of discrimination, were found between the two groups. The present basic study of allele frequency databases of these STRs will contribute to further applications in forensic science and human genetics.

Gene Frequency↗

PubMed2002

[Genetic polymorphism of D16S539, D7S820 and D13S317 loci in the Kazak ethnic population].

OBJECTIVE: To analyze the genetic polymorphism of D16S539, D7S820 and D13S317 in Chinese Kazak ethnic population from Xinjiang. METHODS: One hundred and two unrelated individuals and a sample of families (n=42) were investigated by multiplex amplification, 6% denaturing PAGE and silver staining. And, the obtained allele frequencies were compared with those of other populations. RESULTS: Eight, seven, eight alleles were observed at the 3 STR loci respectively and the genotypes distributions were in accordance with Hardy-Weinberg equilibrium. The expected heterozygosities for these loci were 0.9439, 0.9356 and 0.9304; the calculated polymorphism formation content (PIC) was 0.9905; the discrimination power (DP), 0.9998; the paternity exclusion (PE), 0.9572. In addition, significant difference was found in comparison with other populations, and in the sample of families (n=42) no new mutations could be found. CONCLUSION: The multiplex examination of 3 STR loci can be used in forensic identification and population genetics research.

China↗

PubMed2003

Validation of the X-chromosomal STR DXS6809.

This paper presents sequence and population genetic data of the microsatellite marker DXS6809 (GDB 365492) obtained from a German population sample ( n=725 chromosomes). DXS6809 is a highly polymorphic X-linked tetranucleotide polymorphism presenting 12 alleles in our population. Sequencing of 77 PCR products covering 12 alleles (by length), characterised DXS6809 as a marker with a complex repeat sequence structure. A polymorphism information content (PIC) of 0.825 and a mean exclusion chance (MEC) of 0.815 were obtained. A deviation from the Hardy-Weinberg equilibrium (HWE) could not be detected and male and female samples exhibited a similar allele distribution. Kinship testing revealed a typical X-linked inheritance and 2 mutations were found in 394 meioses. DXS6809 is located 90.18 Mb, i.e. 102.3 cM, from the Xp-telomere (Xp-tel), corresponding to Xq21.33. The presented data qualify DXS6809 as a useful supplement to the known forensic ChrX marker panel.

Adolescent↗

PubMed2004

Population genetics of 10 short tandem repeat (STR) loci in a population sample of the ethnic group of Polish Tatars living in the Podlasie area (Northeastern Poland).

Laboratories worldwide are contributing to a large and growing database for different populations. This study provides a 10 STR database for a population sample of Polish Tatars living in the area of Podlasie for the use as a highly discriminatory system of genetic markers in the forensic community. The genotype frequency distributions showed no deviations from the Hardy-Weinberg equilibrium (HWE) except for D3S1358, FGA, D18S51 and D16S539, based on the Fisher Exact Test. Significant differences between the Polish Tatars and the native population of Podlasie were found in loci D3S1358, FGA, D2S1338, D21S11 and D19S433. The combined values of the Matching Probability and of the Power of Exclusion are 1 in 2.83 x 10(-12) and 0.998, respectively.

DNA↗

PubMed2002

A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals.

A database of mitochondrial DNA (mtDNA) hypervariable region 1 (HV1) and region 2 (HV2) sequences of the mtDNA control region was established from 162 unrelated Japanese individuals. The random match probability and the genetic diversity for this database were 0.96% and 0.997, respectively. Length heteroplasmy in the C-stretch regions located around position 16189 in HVI and 310 in HV2 was observed in 37% and 38% of the samples, respectively. A strategy using internal sequencing primers was devised to obtain confirmed sequences in these length heteroplasmic individuals. This database, combined with other mtDNA sequence databases from the Japanese population, will permit the significance of mtDNA match results to be properly reported in mtDNA typing casework in Japan.

Base Sequence↗

PubMed2000

Ancient DNA-typing approaches for the determination of kinship in a disturbed collective burial site.

Several DNA-typing approaches are applied for identification and kinship analysis. Autosomal Short Tandem Repeat (STR) typing produces the genetic fingerprint that is unique to an individual. Y-chromosomal STR typing identifies individuals of the same paternal lineage, and sequence analysis of the hypervariable region of the mitochondrion can identify maternally related individuals. The combined approach of these DNA-typing methods allows the determination of kinship even in complex collective burial situations. In a bronze age collective site, the typing methods were tested for applicability to ancient DNA. For each approach, results were obtained, leading to the conclusion that the determination of kinship is achievable.

Bone and Bones↗

PubMed2000

The analysis of three short tandem repeat (STR) loci in the Slovene population by multiplex PCR.

Allele frequencies for three tetrameric short tandem repeat (STR) loci D3S1358, HUMVWA, and HUMFGA were determined in a Slovene Caucasian population sample. DNA samples from a total of 221 Slovenes were amplified by multiplex PCR using the commercial kit AmpFISTR Blue (Perkin-Elmer). Separation and detection of the amplified STR fragments were carried out using a 377 automated genetic analyzer (Applied Biosystem Division/Perkin Elmer). Seven alleles at the D3S1358 locus, 8 alleles at the HUMVWA31A locus, and 13 alleles at the HUMFGA locus were observed. A deviation from Hardy-Weinberg equilibrium was observed, only at the HUMVWA31A locus (p = 0.045, exact test). The departure at this locus was not significant after Bonferroni correction. There were no detectable departures between pairwise comparisons of the loci. The combined power of discrimination for all three loci is 0.9998, and the power of exclusion is 0.9526. The observed allele frequencies for the loci D3S1358, HUMVWA31A, and HUMFGA are similar to those in European and U.S. Caucasian populations.

Alleles↗

PubMed2003

Likelihood-based inference for genetic correlation coefficients.

We review Wright's original definitions of the genetic correlation coefficients F(ST), F(IT), and F(IS), pointing out ambiguities and the difficulties that these have generated. We also briefly survey some subsequent approaches to defining and estimating the coefficients. We then propose a general framework in which the coefficients are defined, their properties established, and likelihood-based inference implemented. Likelihood methods of inference are proposed both for bi-allelic and multi-allelic loci, within a hierarchical model which allows sharing of information both across subpopulations and across loci, but without assuming constancy in either case. This framework can be used, for example, to detect environment-related diversifying selection.

Alleles↗

PubMed1990

Applying highly polymorphic variable number of tandem repeats loci genetic markers to identity testing.

The detection of alleles of variable number of tandem repeats (VNTR) loci by restriction fragment length polymorphism analysis has become an important aspect of genetic characterization for identity testing. Some VNTR loci are so polymorphic that the analysis of three to five genetic markers could potentially provide unique identity. However, the more informative a genetic marker is (i.e., high degree of polymorphisms), the better it is as an exculpatory tool. This approach currently provides the best avenue for excluding a falsely associated individual with a particular sample. When an analysis fails to exclude an individual as the source of the questioned material, a value (frequency of occurrence) should be placed on the VNTR profiles to assess weight to the inclusion in identity testing. Arbitrarily defined fixed bins were designed to accommodate quasi-continuous data and to provide a result that would not place an underestimation of the frequency of occurrence of a set of alleles attributed to an individual.

Alleles↗

PubMed2000

Detection of sequence variation in the HVII region of the human mitochondrial genome in 689 individuals using immobilized sequence-specific oligonucleotide probes.

We have developed a rapid, immobilized probe-based assay for the detection of sequence variation in the hypervariable segment II (HVII) of the mitochondrial DNA (mtDNA) control region. Using a panel of 17 sequence-specific oligonucleotide (SSO) probes immobilized on nylon membrane strips, we typed 689 individuals from four population groups. The genetic diversity value for each population was calculated from the frequency data, and the frequencies of distinct "mitotypes" in each group were determined. We performed DNA sequence analysis of 129 samples to characterize the sequences associated with "blanks" (absence of probe signals) and weak probe signals. Out of 689 samples, we observed five heteroplasmic samples (excluding the variable C-stretch beginning at position 303) using the immobilized SSO probe panel. The SSO probe strips were used for the analysis of shed hairs and bloodstains from several criminal cases in Sweden, one of which is described here. We conclude that this mtDNA typing system is useful for human identification and significantly decreases casework turnaround time.

Base Sequence↗

PubMed2003

Mitochondrial DNA D-loop hypervariable regions: Czech population data.

In order to identify polymorphic sites and to find out their frequencies and the frequency of haplotypes, the complete D-loop of mitochondrial DNA (mtDNA) from 93 unrelated Czech Caucasians was sequenced. Sequence comparison showed that 85 haplotypes were found and of these 78 were unique, 6 were observed twice and 1 was observed three times. Genetic diversity (GD) was estimated at 0.999 and the probability of two randomly selected sequences matching (random match probability, RMP) at 1.2%. Additionally these calculations were carried out for hypervariable regions 1, 2 (HV1, HV2), for the area between HV1 and HV2 and for the area of the hypervariable region HV3. The average number of nucleotide differences (ANND) was established to be 10.2 for the complete D-loop. The majority of sequence variations were substitutions, particularly transitions. Deletions were found only in the region where HV3 is situated and insertions in the same place and in poly-C tracts between positions 303 and 315 in HV2. A high degree of length heteroplasmy was found especially in the regions of poly-C tracts between positions 16184 and 16193 in HV1 and between positions 303 and 315 in HV2. Position heteroplasmies were found in two cases.

Complementarity Determining Regions↗

PubMed1988

The examination of vaginally inserted plastic tampon applicators for genetic markers and evidence of prior sexual intercourse.

Vaginally inserted plastic tampon applicators were obtained from 42 female volunteers. The applicators were examined for the presence of ABH blood group substances, phosphoglucomutase (PGM), amylase, acid phosphatase, P30, and intact spermatozoa. Each applicator was accompanied by a control blood sample, a saliva specimen, a brief sexual and menstrual history, and method of birth control of the donor. Eight of the male sexual partners of the donors submitted blood and saliva samples. One male sexual partner submitted only a saliva sample. ABH blood group substances corresponding to the donor were recovered from 36 of the 42 applicators. The remaining 6 applicators revealed a combination of the donor's and sexual partner's ABH substances. The female's PGM type was recovered from 34 of the applicators. The remaining 8 applicators failed to show PGM activity. Of the applicators, 15 indicated evidence of prior sexual intercourse by the detection of ABH substances not consistent with the applicator donor (6 samples), high levels of acid phosphatase (11 samples), or recovery of spermatozoa (8 samples) or some combination of these. All applicator samples failed to show the presence of either P30 activity or PGM factors foreign to the female.

Acid Phosphatase↗

PubMed2002

Estimating F-statistics.

A moment estimator of, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 (100) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of theta between pairs of populations. Moment estimates for within- and between-population theta values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir & Cockerham by employing maximum likelihood methods under the assumption that allele frequencies follow the normal distribution over populations. For the case of equal theta values within populations and zero theta values between populations, the maximum likelihood estimate is the same as that given by Robertson & Hill in 1984 (70). The review concludes by relating functions of theta values to times of population divergence under a pure drift model.

Genetics, Population↗

PubMed1999

[Blood-group genotyping by constant denaturing gel electrophoresis (CDGE)].

Constant Denaturing Gel Electrophoresis (CDGE) was used as an analytical method of the genetic markers. Even a single base change in a fragment amplified by PCR was detected exactly by CDGE. The computational simulation of CDGE gave the calculation whether a single base change in a fragment amplified by PCR could be detected by CDGE or not. In this report, genotyping of three blood groups, MN, Duffy and Kidd, and Gc system is described. The regions reflecting allelic differences of each system were amplified from genomic DNAs. The concentration of denaturants (urea and formamide) in CDGE gels was decided with the computational simulation as follows: 15% for MN, 27% for Duffy, 24% for Kidd, 30% for Gc. CDGE was run in TBE buffer at 60 degrees C, 100 V constant voltage. PCR amplified fragments with 1-3 base changes were separated clearly in each gel. By staining the gels with ethidium bromide, the genotype of each system was determined. The genotyping of system by CDGE can avoid mistakes in the conventional method, which requires complicated and multiple troublesome operations. Analysis of PCR amplified fragments by CDGE will make a beneficial contribution to medico-legal practice.

Blood Group Antigens↗

PubMed1995

Social and related implications of DNA fingerprinting and other new DNA technologies.

The discovery of the structure DNA at the beginning of this half of the century, and the recognition that it is virtually the universal genetic material, made it imperative for man, sooner or later, to apply this knowledge for unexpected ends. Genetic engineering, DNA fingerprinting, sequencing of whole genomes (be they of man, plants or microorganisms), or exploitation of the differences between the DNA of the male and the female (for example, of the X and the Y sperm) have thus all been historical imperatives. Today, many such predicted technologies are a reality or have come close to being so. Such DNA-based technologies have enormous social implications, discussed in this article. The impact of these technologies on different societies is likely to be different, in view of the different social conditions that prevail, and the different historical background and cultural traditions. In India, for example, the use of DNA fingerprinting could prevent the large-scale exploitation of women, and several kinds of litigation. On a global scale, the availability of this technique and its refinement to a stage where it would become virtually foolproof could act as a deterrent to certain kinds of crime. There will also be unprecedented benefits to agriculture but also new problems that will need to be faced and resolved. Wisdom demands that we prepare ourselves for a large-scale application of the new DNA technologies that are a historical imperative, understand the problems that are likely to arise, and plan to cope with them before they descend on us in full force.

Agriculture↗

PubMed2003

Haplotype analysis with 14 Y-STR loci using 2 multiplex amplification and typing systems in 2 regional populations in Japan.

In this study 14 Y-STR loci (DYS393, DYS19, DYS391, DYS437, DYS435, DYS439, DYS389II, DYS438, DYS436, DYS390, Y-GATA-H4, DYS385, Y-GATA-A7.1 and DYS392) were analysed in 207 Japanese males from Honshu (main island of Japan, Nagoya City) and 87 Japanese males from Okinawa (southernmost islands of Japan) using two multiplex PCR typing systems, a novel 10-plex amplification system and a new commercially available 6-plex typing kit which had two loci in common. The allele frequency distributions were similar at almost all of the 14 loci. Of the haplotypes observed, 244 were unique in both Japanese populations and 17 haplotypes were observed more than once but the 2 populations shared only 7 haplotypes. The haplotype diversities for the 14 loci were 0.9987 and 0.9976 in Honshu and Okinawa Japanese, respectively. The haplotype analysis at 14 Y-STR loci would be useful for personal identification in forensic fields and for population genetics because of the high divergence of these haplotypes.

Chromosomes, Human, Y↗

PubMed1999

Y chromosome specific polymorphisms in forensic analysis.

Human Y chromosome polymorphisms are increasingly interesting, not only for population genetics or evolutionary studies but also for forensics. The state of the art on this subject is reviewed in this paper and the types of Y polymorphisms and their forensic applications described.

Journal Article↗

PubMed2003

Validation and uses of a Y-chromosome STR 10-plex for forensic and paternity laboratories.

Y-chromosome short tandem repeats (Y-STRs) provide valuable information in cases of rape and questioned paternity, and they allow for the genetic identification of male lineages. The present study validated a Y-STR 10-plex on the ABI PRISM 3100 Genetic Analyzer for use in forensic and paternity laboratories at Orchid Cellmark. Following optimization of the polymerase chain reaction, father-son pairs were analyzed to ensure that each pair generated identical haplotypes. This study demonstrated that the 10-plex is sensitive to 0.125 ng of input DNA and that female samples mixed with male samples did not interfere with Y-STR haplotyping. In a sample of 525 males, there were three instances of locus multiplication, two at DYS19 and one at DYS435. Overall, haplotype diversity was 0.996, suggesting that the 10-plex can effectively distinguish among male lineages.

Chromosomes, Human, Y↗