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.

A new triplex STR system without irregular alleles by silver staining and its potential application to forensic analysis.

In order to increase the discriminating power of DNA analysis in forensic science, we devised a new triplex STR system using three novel STR loci we previously reported, D14S299 (wglc5), D15S233 (wgldl), and 9q2h2. We designated this system a CDH triplex system. The CDH triplex system showed a high discriminating power, especially in Caucasians. This system is composed of three STR loci showing only regular tetranucleotide repeat alleles. We easily enlarged the databases mainly of Japanese, using this system, and compared them with those of Caucasian and Chinese. This CDH triplex system therefore appears to be useful for forensic practice.

The application of minisatellite variant repeat mapping by PCR (MVR-PCR) in a paternity case showing false exclusion due to STR mutation.

A boy and a girl with their mother brought a paternity suit against an alleged but deceased father. We tested six conventional genetic markers, the AmpliType PM+ DQA1 and twelve STR loci the children and mother together with the alleged paternal grandparents. We also DNA typed the bloodstain found later in the alleged father's medical record. Only the result at D3S1358 in a nineplex STR system excluded the alleged father from parentage of the boy, whereas all markers were inclusive for the girl. Accordingly, we performed sequence analysis at D3S1358 to confirm the presence of a paternal exclusion or mutation. The sequence analysis indicated that the boy's allele 17 could have originated from either of the alleged father's allele 16 or 18 by a single-step mutation associated with slippage mutation in STR loci. We carried out minisatellite variant repeat mapping by PCR (MVR-PCR) at loci D1S8 (MS32) and D7S21 (MS31A) and mapped allele haplotypes of all individuals except the deceased alleged father. The MVR-PCR analysis showed that the boy has no inconsistency with the relationship between the alleged grandparents, and was very effective at increasing the paternity index (PI) value. We conclude that there is biological relationship between not only the girl but also the boy and the alleged father.

[Tests for Hardy-Weinberg equilibrium in Japanese population].

In population genetics, the absence of the departure from Hardy-Weinberg equilibrium (HWE) is usually tested when a population study of a certain DNA marker is performed to show the observed allele frequencies represent those of the whole population. The goodness-of-fit test (chi 2 test) assuming chi 2 approximation has frequently been used with classical blood type markers having a few alleles. However, new tests suitable for DNA markers having many alleles, such as homozygosity test, likelihood ratio test and Guo-Thompson's (G-T') exact test, have recently been devised. In the present study, appropriate tests for HWE was studied using population data of 206 Japanese individuals with 9 different short tandem repeat loci. Firstly, we found that the recommendation of NRC II for the treatment of rare allele frequencies (If a bin in the database contains fewer than five entries, it is pooled with adjacent bins so that no bin has fewer than five) is quite reasonable for personal identification in forensic sciences. Secondly, we proposed that homozygosity test, likelihood ratio test and G-T's exact test should be applied altogether and HWE of the sample population should be valid only when all of the three tests were cleared.

The potential contribution of MVR-PCR to paternity probabilities in a case lacking a mother.

Minisatellite variant repeat (MVR) mapping using the polymerase chain reaction (PCR) was applied to a paternity case lacking a mother to evaluate the paternity probability. After three flanking polymorphic sites at each of MS31A and MS32 loci were investigated from the child and alleged father, allele-specific MVR-PCR was performed using genomic DNA. It was confirmed that one allele in the child was identical to that in the alleged father at both loci. Mapped allele codes were compared with allele structures established from population surveys. No perfect matches were found although some motifs were shared with other Japanese alleles. The paternity index and probability of paternity exclusion at these two MVR loci were then estimated, establishing the power of MVR-PCR even in paternity cases lacking a mother.

Allele distribution at nine STR loci--D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820--in the Japanese population by multiplex PCR and capillary electrophoresis.

Nine tetranucleotide short tandem repeat (STR) loci, D3S1358, vWA, FGA TH01, TPOX, CSF1PO, D5S818, D13S317 and D7S820, were analyzed in the Japanese population with a newly released kit for personal identification using multiplex PCR with fluorescent-labeled primers following capillary electrophoresis. The observed heterozygosities were 0.67, 0.77, 0.82, 0.61, 0.62, 0.73, 0.78, 0.81 and 0.74, respectively, and the combined discrimination power of the nineplex was 0.9999999991. None of the nine loci deviated from Hardy-Weinberg equilibrium expectations using the chi-square test, homozygosity test, likelihood ratio test and exact test after the grouping of the alleles. The nine STR loci allele frequencies were significantly different from those of other ethnic populations.

DNA typing of primate major histocompatibility complex (Mhc)-DQA1 locus by PCR and dot blot hybridization.

Non-human primates (NHPs) are increasingly utilized as models to investigate different aspects of immune responses against self (autoimmunity) and foreign antigens. These animals provide valuable models for testing the efficacy of candidate vaccines against pathogens such as human immunodeficiency virus (HIV) and also fertility regulating agents (immunocontraceptives). In order to fully understand the effects of vaccination, it may be necessary to elucidate the immunogenetic background of these animals. The major histocompatibility complex (Mhc) molecules play an important role in the generation of effective immune responses. Serological techniques have been used in the identification of human leukocyte antigens (HLA) necessary for cross-matching organs and tissues for transplantation. However, the application of this technique for typing monkey Mhc alleles has been hampered by unavailability of well characterized immunological reagents. Polymerase chain reaction (PCR)-based techniques such as restriction fragment length polymorphism (RFLP) and sequence-specific oligonucleotide probe hybridization (SSOP) have been extensively used for typing HLA-DP, DQ and DR alleles. A commercially available Kit (AmpliTypeR) designed for amplification and typing of HLA DQalpha alleles is routinely used in typing DNA samples for forensic casework. In the present study, we have evaluated this kit for possible application in routine typing of primate DQA1 alleles. Genomic DNA from ten African primate species (23 individuals) was isolated from peripheral blood lymphocytes and polymorphic second exon of DQA1 locus amplified using GH26 and GH27 PCR primers. The PCR products were hybridized on a nylon membrane containing immobilized sequence-specific oligonucleotide probes. Our results show seven of the nine probes hybridizing with primate DQA1 alleles, indicating that typing of equivalent primate alleles can be accomplished at lower stringency conditions. However, it may be necessary to design additional oligonucleotides probes (based on available primate DQA1 sequences) to improve the discriminating power of this kit for use in routine typing of Old World monkey DQA1 alleles.

Sequence analysis of alleles at a microsatellite locus D14S299 (wg1c5) and population genetic comparisons.

In order to increase the discriminating power of DNA analysis in personal identification, we evaluated the forensic utility of the microsatellite locus D14S299 (wg1c5) in the Japanese population and also in the Chinese and Caucasian populations. Twelve different alleles were identified in length by gel electrophoresis with silver staining. The major alleles in Japanese were sequenced and designated as the numbers of the variable repeats (GGAT or GGAA). There were five variable regions and extensive homoplasy was found. However, the allele fragment lengths were in 4 bp increments and no "interalleles" were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.726 and 0.689, respectively in Japanese. Those in Chinese (0.743 and 0.704) were similar to those in Japanese, while those in Caucasians (0.812 and 0.781) were much higher. After adjacent alleles were combined to yield at least five entries, statistical analysis was performed. The power of discrimination (PD) was 0.887 in Japanese, 0.895 in Chinese and 0.935 in Caucasians and no significant deviations from the Hardy-Weinberg equilibrium were found in the three populations. We retyped all apparently homozygous samples using an alternative pair of flanking primers and found them to be true homozygotes. D14S299 appears to be a useful STR locus for forensic practice.

Tetrameric short tandem repeat (STR) system D15S233 (wg1d1): sequencing and frequency data in the japanese and Chinese populations.

We evaluated the forensic usefulness of D15S233 (wg1d1), a tetrameric short tandem repeat (STR) locus, in the Japanese and Chinese populations. Typing was performed by denaturing polyacrylamide gel electrophoresis followed by silver staining. Nine different alleles were found in 472 Japanese chromosomes and seven in 186 Chinese chromosomes. 102 alleles sequenced were composed of two kinds of repeats (AGGA and GGGA). All alleles differed in size by one tetranucleotide repeat unit, and no insertion or deletion was found. The expected unbiased heterozygosities in Japanese and Chinese were 0.766 and 0.785, respectively. No significant deviations from the Hardy-Weinberg equilibrium were found in either population. We retyped all samples using an alternative pair of flanking primers in order to detect any spurious appearances of homozygotes due to sequence variation at the primer annealing site. One heterozygous sample had unbalanced density bands when the original primer set was used, but equal density bands when our newly designed primer set was used. Sequencing analysis revealed that the sparser allele had one nucleotide substitution near the 5' end of the annealing site of the original primer region. Thus, all apparently homo/heterozygous samples were thought to be truly homo/heterozygous. We also applied the D15S233 locus to paternity testing and forensic identification. Our results suggest that this locus should be a very useful STR locus for forensic practice in Japanese and Chinese.

Purification of nuclear DNA from single hair shafts for DNA analysis in forensic sciences.

The typing of nuclear DNA from hair shafts has often been unsuccessful to date. We tried to type one of the nuclear DNA loci, HLA-DQA1, from hair shafts, using an efficient cetyl-trimethyl ammonium bromide (CTAB) precipitation for DNA purification and a sensitive semi-nested PCR. After thorough washing with ethanol and water, hair shafts were digested by proteinase K in the presence of dithiothreitol, followed by a purification step including CTAB-DNA precipitation. The specific region of HLA-DQA1 gene was amplified by the semi-nested PCR, and the amplified products were cloned and sequenced. The HLA-DQA1 genotype was determined by comparing the sequence to the known sequence of each allele. All genotypes of HLA-DQA1 were successfully typed with hair shafts from six known heterozygotes, although one of them showed the predominant appearance of one allele. For correct typing, a template DNA equivalent to a hair shaft of 5 or 10 cm in length was necessary. Without the CTAB-DNA precipitation step, DNA extract from such hair shafts inevitably contains enough melanin to inhibit PCR. The present results suggest that hair shafts can be used for the typing of nuclear DNA loci.

Evaluation of two new STR loci 9q2h2 and wg3f12 in a Japanese population.

Two short tandem repeat (STR) loci (9q2h2 and wg3f12) have been evaluated in a Japanese population. Ten and seven different alleles were observed in 9q2h2 and wg3f12 respectively. 9q2h2 displayed simple polymorphism in tetrameric repeat structure; by contrast, wg3f12 contained variable numbers of tetrameric repeats and a 30-bp deletion/insertion polymorphism. No "interalleles" were found. The expected heterozygosities of 9q2h2 and wg3fl2 were 0.749 and 0.574, respectively. No deviation from Hardy-Weinberg equilibrium was found.

Evaluation of the paternity probability on an application of minisatellite variant repeat mapping using polymerase chain reaction (MVR-PCR) to paternity testing.

Minisatellite variant repeat (MVR) mapping using polymerase chain reaction (PCR) was applied to a practical case of paternity testing to evaluate the paternity probability. In order to obtain single allele mapping by allele-specific MVR-PCR, three flanking polymorphic sites for each of the MS31A and MS32 loci were investigated and all three individuals were typed as heterozygous for at least one flanking polymorphic site at each locus. Allele-specific MVR-PCR was then performed using genomic DNA. It was confirmed that one allele in the child was identical to that from the mother and the other one in the child was identical to that from the alleged father. Mapped allele codes were also compared with those in the database by dot-matrix analysis, and no identical allele was found although some motifs were shared with Japanese alleles. The paternity index and the probability of paternity exclusion in the case at these two MVR loci were calculated using the presumed values of the allele frequencies. These studies seem to illustrate the practical value of MVR mapping of MS31A and MS32 loci in paternity testing.

DNA analysis of a grandfather-father-son relationship from 300-year-old remains of the Date clan in Japan.

The grandfather-father-son relationship of the first three lords of the Date clan in Japan was ascertained by HLA-DNA sequencing analysis. From their hairs and dried lung tissue found in ca. 300-year-old remains, DNA was extracted with usual phenol-chloroform method followed by purification with cetyltrimethylammonium bromide (CTAB). Two HLA class II genes, HLA-DQA1 and -DPB1, were amplified by seminested, or dual/triple PCR. The PCR products were cloned and analyzed by automated sequencing. Since the three lords shared a haplotype of DQA1*0301-DPB1*0402, we concluded that there is no inconsistency in their lineage. This is the first case of biological evidence for a historical Samurai family relationship in the 17-18th centuries.

Maternal identification from skeletal remains of an infant kept by the alleged mother for 16 years with DNA typing.

This is a case study concerning maternal identification by DNA typing at various loci. An infant skeleton was found in the alleged mother's apartment after it was kept for 16 years. We obtained the skeletal remains as well as saliva stains from the alleged mother. DNA typing was conducted for three loci in the HLA class II region (HLA-DQA1, -DPB1, and DRB1), five loci with the AmpliType PM kit (LDLR, GYPA, HBGG, D7S8, and GC), five STR loci (LPL, vWA, F13B, TH01, and TPOX) and D-loop region in mtDNA for maternal identification. Sex determination was accomplished using fluorescent DNA capillary electrophoresis typing. Approximately 5 ng of human DNA was recovered from 1 g of femur bone retrieved from the infant skeletal remains. The probability of two unrelated Japanese sharing the same genotypes was estimated as 7.2 x 10(-11). The combined probability of exclusion that an individual is not the mother was also calculated at 0.998. We therefore conclude that the skeleton is from a female infant, and that there is no inconsistency in the claim that the infant was a daughter of the alleged mother.

A rapid typing system at three STR loci from bloodstains using a simple DNA extraction kit and capillary electrophoresis.

A rapid typing method for STR analysis from bloodstains was devised. DNA from three-year-old bloodstains of six individuals was extracted with a cationic detergent in a newly-released kit. Amounts of DNA extracted by the kit were 16.2 +/- 1.8 ng from 10 microliters of fresh blood samples. DNA was also extracted from bloodstains of three months and three years left at room temperature, and amounts of extracted DNA were estimated at 2.2 +/- 1.0 ng and 0.1 +/- 0.1 ng, respectively. The PCR mixture supplied with the kit, plus three sets of fluorescently labeled primers, were directly added to the tube used for DNA extraction. The amplified products were then analyzed by capillary electrophoresis, and the obtained data were automatically sized and typed using computer software. Three genotypes of all bloodstains except one sample at a single locus were determined correctly as those of freshly collected blood from the same individuals although some stains contained no more than 0.1 ng. Using this typing system, we were able to type three STR loci, HUMTH01, HUMF13A1 and HUMFES/FPS, from a single bloodstain within five hours. This typing is particularly useful for forensic practice.

Evaluation of tetranucleotide repeat locus D7S809 (wg1g9) in the Japanese population.

The tetrameric short tandem repeat (STR) locus (D7S809) has been evaluated in the Japanese population. In order to detect the alleles, PCR was carried out using primers, one of which was end labelled with 32P, and PCR products were separated by electrophoresis on a denaturing polyacrylamide gel. Using this method, accurate genotypes could be determined from as little as 0.5 ng of genomic DNA. Thirteen different alleles were identified on 256 chromosomes tested. All alleles differed in size by one (4 bp) repeat unit, and no "interalleles' were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.86 and 0.83, respectively. We observed 42 of the 91 possible different genotypes. The power of discrimination (PD) was 0.96, and no significant deviations from the Hardy-Weinberg equilibrium were found. We retyped all apparently homozygous samples using an alternative pair of flanking primers in order to confirm homozygosity. We also demonstrated a typing result involving sexual assault. D7S809 appears to be a very useful STR locus for forensic practice in Japanese.

Analysis of allelic structures at the D7S21 (MS31A) locus in the Japanese, using minisatellite variant repeat mapping by PCR (MVR-PCR).

To sample the diversity of allelic structures at the D7821 (MS31 A) locus in the Japanese, allele-specific minisatellite variant repeat mapping using polymerase chain reaction (MVR-PCR) was performed on genomic DNA from a number of Japanese individuals. Three polymorphic positions in the MS31A 5' flanking DNA were typed from 214 un related Japanese, and the distribution of haplotypes was analysed. Allele-specific MVR-PCR using primers that discriminate between different alleles at these polymorphic positions in heterozygous individuals, allows single alleles to be mapped from genomic DNA in approximately 80% of Japanese. 149 Japanese alleles have been mapped to date and all of them, except for two pairs of indistinguishable alleles, have different internal structures. More than half of the mapped alleles showed similar regions of internal structure to other alleles and were classified into groups on this basis.

Applications of minisatellite variant repeat (MVR) mapping for maternal identification from remains of an infant and placenta.

Minisatellite variant repeat (MVR) mapping using the polymerase chain reaction (PCR) at D1S8 (MS32) was applied to a practical forensic case of an infant and placenta found in an incinerator. They were thought to be left for a few days postmortem, and the infant was severely burnt when found. DNA was extracted from the infantile muscle and maternal placental hematoma. MVR-PCR analysis as well as other common DNA typing (D1S80, HLA-DQA1) were performed on both DNA samples. Both MVR diploid codes were matched although some extra faint bands in the ladder were observed from the maternal placental sample, which probably indicated superimposing of an allele derived only from the mother, and not the infant. In order to detect the original maternal alleles, three flanking polymorphic sites were typed and allele-specific MVR-PCR was performed. Finally, one maternal allele not inherited by the infant and two alleles from the infant were typed. Two alleles suggested the infant and/or mother was Japanese. The two diploid codes including one possibly from the mother were deduced and compared with other codes in the databases for evaluating the discriminating power.