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Background Pure ovarian choriocarcinoma can be gestational or nongestational in origin. Nongestational pure ovarian choriocarcinoma is extremely rare and the prognosis is thought to be worse than that of the gestational type in patients with metastatic disease. We present a case of metastatic pure ovarian choriocarcinoma with poor prognosis in which the origin was identified as nongestational by DNA short tandem repeat (STR) analysis. Case presentation A nulliparous woman in her thirties with metastatic choriocarcinoma was referred to our hospital after initial treatment proved unsuccessful. Two months earlier, she had undergone brain tumor resection and histological examination confirmed choriocarcinoma. Serum human chorionic gonadotropin (hCG) concentration at initial diagnosis was 5030 IU/L. Two cycles of a combination chemotherapy regimen of methotrexate, etoposide, and actinomycin-D (MEA therapy), which is commonly used for gestational choriocarcinoma, was administered. However, the disease could not be controlled. Imaging modalities at presentation revealed tumor present in the left ovary and left lung, but not in the uterus, which led us think that the choriocarcinoma was nongestational. Bleomycin, etoposide, and cisplatin (BEP therapy) which is commonly used for nongestational choriocarcinoma (malignant germ cell tumor) and surgical resection of the uterus, bilateral ovaries, and an affected part of the left lung led to the nadir level of hCG, but the tumor relapsed and levels of hCG again increased. To investigate the origin of choriocarcinoma, we performed DNA STR analysis of tumor cells and oral mucosal cells. Analysis revealed the origin of the choriocarcinoma as nongestational, as the genotype of tumor cells entirely corresponded with that of oral mucosal cells. BEP therapy and chemotherapy regimens administered for nongestational choriocarcinoma and gestational choriocarcinoma proved ineffective, and the patient died 21 months after diagnosis of metastatic choriocarcinoma. Conclusion Metastaic nongestational pure choriocarcinoma of ovary is an extremely rare and an aggressive disease, frequently resulting in poor outcome.

Population studies of 30 insertion/deletion (INDEL) markers were conducted using the Investigator® DIPplex kit (Qiagen) in 197, 80, and 78 unrelated individuals from Japan, Bangladesh, and Indonesia, respectively. No significant deviations from Hardy–Weinberg equilibrium were observed for all but three INDEL markers: two markers in the Japanese samples and one marker in the Bangladeshi and Indonesian samples. The combined power of discrimination values for the 30 INDEL markers in the Japanese, Bangladeshi, and Indonesian populations were 0.999999999983, 0.999999999999, and 0.999999999937, respectively. These results would be useful in forensic genetic investigations and population genetic studies.

Gestational choriocarcinoma is a gestational trophoblastic neoplasia (GTN) originating from trophoblastic cells with abnormal proliferation. Although chemotherapy is effective for treating this cancer, when patients develop chemoresistance, personalized treatment, such as the use of drugs matching their genomes, is required. The present report describes a case of intractable gestational choriocarcinoma identified using a next-generation sequencing (NGS)-based tumor panel. A 51-year-old woman was diagnosed with gestational choriocarcinoma via pathological and short tandem repeat analyses. The patient did not achieve remission despite many regimens of chemotherapy, including high-dose therapy with autologous peripheral blood stem cell transplantation. To identify drugs tailored to this particular choriocarcinoma, NGS was performed on the tumor of the patient, and the tumor genome was compared with that of the patient's blood sample using the NCC Oncopanel System. Consequently, 245 single nucleotide variants (SNVs) with a mean SNV allele frequency of 63.1% were identified. This high frequency was because the genome of the gestational choriocarcinoma contained part of the genome of the partner. Therefore, our experience of the present intractable case of choriocarcinoma suggested that matched normal-tumor pair analysis is not appropriate for treatment decisions in GTN cases. When using an NGS-based tumor panel to assess choriocarcinoma, researchers must consider whether the genomic DNA of the patient and their partner are involved in the GTN.

Introduction Gestational trophoblastic neoplasia (GTN) include a group of malignant neoplasms that originate from the trophoblasts of placental tissue in molar or nonmolar pregnancy. Currently, it is unclear whether the prognosis of high-risk GTN or gestational choriocarcinoma succeeding molar pregnancy or that following a nonmolar one is better. Comparison of the genetic short tandem repeat (STR) patterns of the DNA extracted from the tumor, patient, and her partner allows the genetic origins of the choriocarcinoma to be distinguished - whether it is gestational or non-gestational and whether it is derived from a molar or nonmolar pregnancy in the event it is gestational. This study aimed to investigate the causative pregnancy of patients with high-risk GTN, especially those with poor outcomes, and assess the impact of the causative pregnancy on patient outcome. Methods We evaluated 24 patients who were diagnosed with high-risk GTN between January 2000 and October 2019, including 15 cases of pathologically proven gestational choriocarcinomas and the causative pregnancy was investigated by STR analysis in which tumor DNA could be extracted. Results In high-risk GTN without history of anteceding molar pregnancies, nonmolar pregnancy was the causative pregnancy, which was confirmed in three cases. Molar pregnancy appeared be the causative pregnancy of high-risk GTN in patients with a history of antecedent molar pregnancies either with or without interruption by subsequent nonmolar pregnancies prior to developing high-risk GTN. High-risk GTN in most of the evaluated deceased cases (three of four) was due to nonmolar pregnancy, while all but one case with molar pregnancy as the causative pregnancy survived. Discussion STR analysis can distinguish the causative pregnancy of high-risk GTN, and nonmolar pregnancy as the causative pregnancy might have negative effects on the outcome of the disease.

Short Tandem Repeats (STRs) are a type of DNA polymorphism. This study considers discriminant analysis to determine the population of test individuals using an STR database containing the lengths of STRs observed at more than one locus. The discriminant method based on the Bayes factor is discussed and an improved method is proposed. The main issues are to develop a method that is relatively robust to sample size imbalance, identify a procedure to select loci, and treat the parameter in the prior distribution. A previous study achieved a classification accuracy of 0.748 for the g-mean (geometric mean of classification accuracies for two populations) and 0.867 for the AUC (area under the receiver operating characteristic curve). We improve the maximum values for the g-mean to 0.830 and the AUC to 0.935. Computer simulations indicate that the previous method is susceptible to sample size imbalance, whereas the proposed method is more robust while achieving almost identical classification accuracy. Furthermore, the results confirm that threshold adjustment is an effective countermeasure to sample size imbalance.

Summary: Compelling evidence in Caucasian populations suggests a role for copy-number variations (CNVs) in autism spectrum disorder (ASD) and schizophrenia (SCZ). We analyzed 1,108 ASD cases, 2,458 SCZ cases, and 2,095 controls in a Japanese population and confirmed an increased burden of rare exonic CNVs in both disorders. Clinically significant (or pathogenic) CNVs, including those at 29 loci common to both disorders, were found in about 8% of ASD and SCZ cases, which was significantly higher than in controls. Phenotypic analysis revealed an association between clinically significant CNVs and intellectual disability. Gene set analysis showed significant overlap of biological pathways in both disorders including oxidative stress response, lipid metabolism/modification, and genomic integrity. Finally, based on bioinformatics analysis, we identified multiple disease-relevant genes in eight well-known ASD/SCZ-associated CNV loci (e.g., 22q11.2, 3q29). Our findings suggest an etiological overlap of ASD and SCZ and provide biological insights into these disorders. : Kushima et al. perform comparative analyses of CNVs in ASD and SCZ in a Japanese population. They identify pathogenic CNVs and biological pathways in each disorder with significant overlap. Patients with pathogenic CNVs have a higher prevalence of intellectual disability. Disease-relevant genes are detected in eight well-known ASD/SCZ-associated CNV loci. Keywords: autism spectrum disorder, schizophrenia, copy-number variation, array comparative genomic hybridization, genetic overlap, Japanese population, oxidative stress response, genome integrity, lipid metabolism, gene ontology

It is sometimes necessary to determine whether a forensic biological sample came from a Japanese person. In this study, we developed a 60-locus SNP assay designed for the differentiation of Japanese people from other East Asians using entirely and nearly Japanese-specific alleles. This multiplex assay consisted of 6 independent PCR reactions followed by single nucleotide extension. The average number and standard deviation of Japanese-specific alleles possessed by an individual were 0.81 ± 0.93 in 108 Koreans from Seoul, 8.87 ± 2.89 in 103 Japanese from Tottori, 17.20 ± 3.80 in 88 Japanese from Okinawa, and 0 in 220 Han Chinese from Wuxi and Changsha. The Koreans had 0–4 Japanese-specific alleles per individual, whereas the Japanese had 4–26 Japanese-specific alleles. Almost all Japanese were distinguished from the Koreans and other people by the factorial correspondence and principal component analyses. The Snipper program was also useful to estimate the degree of Japaneseness. The method described here was successfully applied to the differentiation of Japanese from non-Japanese people in forensic cases. This Japanese-specific SNP assay was named Japaneseplex .

In this sexual assault case, the standard preliminary semen examinations could not confirm physically or biochemically whether the accused's semen had stained the victim's skirt because the skirt had been dry-cleaned for stain removal and had been worn for more than a year after the assault. Fortunately, however, a photograph taken just after the assault was found in the court records that showed white stains on the checkered skirt. The locations of the stains were estimated based on the checkered pattern of the fabric, and microscopic examination using Baecchi's staining revealed the presence of spermatozoa. Further analysis indicated the male DNA profile generated from the sperm cells was consistent with the suspect's DNA using three multiplex STR typing systems for a total of 21 autosomal and 17 Y chromosomal short tandem repeats (STRs). Ultimately, the result of the DNA profile played a very useful role as additional evidence.

Gestational trophoblastic diseases (GTDs) are a group of diseases characterized by abnormal cellular proliferation of atypical trophoblasts. A hydatidiform mole is an abnormal pregnancy caused by genetic fertilization disorders, and it can be classified as a complete hydatidiform mole (CHM) or a partial hydatidiform mole. The aim of this study was to establish cell lines from CHMs and to characterize the cells for future studies concerning GTD. HMol1-2C, HMol1-3B, HMol1-8 and HMol3-1B were established from primary cultures of CHM explants following the introduction of different combinations of genes including human telomerase reverse transcriptase (hTERT), a mutant form of CDK (CDK4R24C), cyclin D1, p53C234, MYC and HRAS. HMol1-2C, HMol1-3B, and HMol3-1B were confirmed to originate from trophoblasts of androgenic, homozygous CHMs. These three cell lines exhibited low human chorionic gonadotropin secretion, low migration and invasion abilities, and the potential to differentiate into syncytiotrophoblastic cells via forskolin treatment. These results suggest that these cells exhibit characteristics of trophoblastic cells, especially cytotrophoblastic cells. HMol1-8 was found to consist of diploid cells and originated from maternal cells, suggesting that they were derived from decidual cells. In conclusion, we successfully established three cell lines from CHMs by introduction of hTERT and other genes. Analysis revealed that the genetic origin of each cell line was identical with that of the original molar tissue, and the cell lines exhibited characteristics of trophoblastic cells, which are similar to undifferentiated cytotrophoblasts.

Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (

We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p

CD109 is a glycosylphosphatidylinositol-anchored cell surface protein that is frequently detected in squamous cell carcinomas. CD109 is a negative regulator of TGF-β1 signaling in human keratinocytes, and the N-terminal fragment of CD109 secreted from cells after cleavage by the furin protease is important for modulating TGF-β1 signaling. Previously, we found that CD109 is expressed in human glioblastoma cells; however, the role of CD109 in glioblastoma cells is not established. Here, we describe the effects of CD109 in human glioblastoma cell lines. Three glioblastoma cell lines, SK-MG-1, U251MG and MG178, were tested and CD109 overexpression attenuated TGF-β1 signaling and enhanced EGF signaling in SK-MG-1, but not in U251MG or MG178. The N-terminal CD109 fragment in SK-MG-1 was hyperglycosylated compared with that in MG178 or U251MG. The conditioned medium of CD109-overexpressing SK-MG-1, containing the secreted N-terminal CD109, had a negative effect on TGF-β1 signaling in wild-type SK-MG-1 and MG178, whereas it did not show any effect on EGF signaling. In addition, cell surface CD109 interacts with EGF receptor in SK-MG-1 overexpressing CD109, and exhibited enhanced cell migration and invasion. These findings suggest that CD109 attenuates TGF-β1 signaling and enhances EGF signaling in SK-MG-1 cells and that the membrane-anchored CD109 may play major roles in the EGF signaling pathway.

Mosquitoes occur almost worldwide, and females of some species feed on blood from humans and other animals to support ovum maturation. In warm and hot seasons, such as the summer in Japan, fed mosquitoes are often observed at crime scenes. The current study attempted to estimate the time that elapsed since feeding from the degree of human DNA digestion in mosquito blood meals and also to identify the individual human sources of the DNA using genotyping in two species of mosquito: Culex pipiens pallens and Aedes albopictus. After stereomicroscopic observation, the extracted DNA samples were quantified using a human DNA quantification and quality control kit and were genotyped for 15 short tandem repeats using a commercial multiplexing kit. It took about 3 days for the complete digestion of a blood meal, and genotyping was possible until 2 days post-feeding. The relative peak heights of the 15 STRs and DNA concentrations were useful for estimating the post-feeding time to approximately half a day between 0 and 2 days. Furthermore, the quantitative ratios derived from STR peak heights and the quality control kit (Q129/Q41, Q305/Q41, and Q305/Q129) were reasonably effective for estimating the approximate post-feeding time after 2-3 days. We suggest that this study may be very useful for estimating the time since a mosquito fed from blood meal DNA, although further refinements are necessary to estimate the times more accurately.

The relationships between DNA degradation ratios and the number of detected loci were explored in extremely old seminal stains evaluated using three short tandem repeat (STR) kits: the AmpFlSTR® Identifiler™ PCR Amplification Kit (Identifiler), the AmpFlSTR® Yfiler™ PCR Amplification Kit (Yfiler), and the AmpFlSTR® MiniFiler™ PCR Amplification Kit (MiniFiler). DNA degradation ratios based on 41, 129, and 305bp DNA fragments were calculated (129:41 and 305:41), and the relationships between the ratios and storage duration were also explored. Using the Identifiler kit, the number of loci detected was strongly correlated with the 129:41 ratio (r=0.887), whereas the correlation with the 305:41 ratio was moderate (r=0.656). Using the Yfiler kit, the DYS385 amplicon was detected in all samples, suggesting that DYS385 may be resistant to degradation. The number of detected loci was strongly correlated with the 129:41 ratio (r=0.768), and moderately so with the 305:41 ratio (r=0.515). MiniFiler detected at least seven loci in all samples. In samples that did not yield full profiles, the undetected loci were D7S820 and D21S11, or D21S11 only, suggesting that these loci might be easily degraded. The number of loci detected using STR kits correlated with the DNA degradation ratios. In particular, the 129:41 ratio was particularly useful for estimating the number of loci detectable by STR kits. On the other hand, we suggest that storage duration cannot be accurately estimated using DNA degradation ratios; these ratios were not strongly correlated with storage duration (129:41; r=-0.698, 305:41; r=-0.550). However, the ratios may allow the identification of samples that have been stored for more than 40years.

The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

The genetic differences of the allele frequency distributions for six STR loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, and D17S1290) among regions in Japan were examined using our recently designed hexaplex amplification and typing system, "Midi-6" newly named, to construct a database in the Japanese population. Genotypes at six loci were analyzed in 198, 200, 175, and 196 individuals from the area of Akita, Nagoya, Oita, and Okinawa, respectively, in Japan. The allele frequency distributions were significantly different (p

To assess species specificities among primates of signals from short tandem repeat (STR) loci included in two commercially available kits, mainly the AmpFlSTR Identifiler kit and additionally the GenePrint PowerPlex 16 system, we analyzed 69 DNA samples from 22 nonhuman primate species representing apes, Old World Monkeys (OWMs), New World Monkeys (NWMs), and prosimians. Each prosimian species and the NWM cotton-top tamarin apparently lacked all STR loci probed. Only one peak, the amelogenin-X peak, was evident in samples from all other NWMs, except the owl monkey. In contrast, several loci, including the amelogenin-X peak, was evident in samples from each OWM species. Notably, for each ape sample, the amelogenin peaks were concordant with morphological gender of the individual. Among the primates, especially in apes, the numbers of alleles for STR loci were increasing according to their phylogenetic order: prosimians < NWMs < OWNs < apes, and so among apes: agile gibbons < white handed gibbons < orangutans < gorillas/common chimpanzees/bonobos. The species specificities among primates for a few commercially released multiplex STR kits examined in this study would contribute to forensic examinations.

In the present study 161 Japanese father/son haplotype transfers in 147 pedigrees were analyzed at 14 Y-STRs with two multiplex PCR-based typing systems. Five isolated single repeat mutations were identified at the DYS389I, DYS439, Y-GATA-H4, DYS389II and DYS391 loci, and a pedigree showing triple alleles at the DYS385 locus (a duplicate locus) without allelic discrepancy between the father and son was also observed. The overall mutation rate estimated across the 14 Y-STRs in the Japanese population was 0.22%/locus/meiosis (95% C.I. 0.09-0.51%). This rate was not significantly different (p>0.05) from those of autosomal STRs and Y-STRs in other populations, including German, Austrian, Polish and Norwegian populations. Furthermore, 138 haplotypes were identified in 147 pedigrees with a haplotype diversity value of 0.9983. Therefore, a combination of the two systems should permit effective analysis with sufficient discriminatory power.

We calculated allele frequencies for 13 Combined DNA Index System (CODIS) core short tandem repeat (STR) loci using each more than 100 DNA samples in two Japanese, six Chinese, one Korean, one Thai and one Burmese populations. We analyzed these allele frequency distributions by genetic distance DA to construct a tree based on the neighbor-joining method, and obtained one that is well coincident with their geographical distributions. We also present a genetic relationship including the published ethnic data in the world.

Genotypes data at 105 autosomal STRs with tetranucleotide repeats for Japanese and Korean were analyzed statistically to differentiate between both populations. As a result, almost all of the individuals in both population were categorized into each own population in a 2-dimentional (2D) plots by a factorial correspondence analysis (FCA). Bayes factors (BFs) based on Dirichlet multi-nominal distribution also showed about 92% of Japanese individuals were strongly suggested as Japanese. Furthermore, as a general tendency, it was shown that it was easier to determine Japanese-origin but somewhat more difficult to determine Korean-origin.

Haplotypes and allele frequencies for the 17 Y-chromosomal short tandem repeat (Y-STR) loci, DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 were determined in a sample of 103 unrelated Egyptian males living in the northern region of Nile delta using the AmpFlSTR ® Yfiler™ PCR Amplification Kit.

Highlights • Gestational trophoblastic neoplasia can arise during the first trimester originating from trophoblasts of concurrent pregnancy. • Intraplacental choriocarcinoma can be developed from trophoblasts of a previous pregnancy.

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 inter-alleles), 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.

Filamin A is encoded by the FLNA gene on chromosome Xq28 and functions in cross-linking actin filaments into orthogonal networks in the cortical cytoplasm. FLNA p.V528M was initially detected in a female autopsy case of X-linked bilateral periventricular nodular heterotopia (BPNH), a neuronal migration disorder characterized by subependymal nodules of gray matter. During our mutation analysis of FLNA in a boy with apparent X-linked thrombocytopenia, we detected the p.V528M variant. The patient, mother and sister, who were heterozygous for the substitution, did not have BPNH. We observed an allele frequency of 4.8% in healthy control Japanese, but did not observe the variant in Caucasian subjects. Hemizygous controls had a normal platelet count and size. We suggest that p.V528M is neither associated with BPNH nor with thrombocytopenia and giant platelets, and represents a functional polymorphism.

Allele frequencies and forensic parameters for twelve miniSTR autosomal loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441, D1S1677, D20S480, D6S2439, D6S1056, D9S1118, D4S2639 and D17S1290) were calculated from a sample of 506 unrelated individuals from the Central-East Region of Argentina. No significant deviations from Hardy–Weinberg expectations were found. Furthermore, comparisons with other previously studied populations were made. These twelve miniSTR markers may help forensic laboratories in solving parentage testing as well as in typing degraded DNA samples.

When two mutations, one dominant pathogenic and the other “confining” nonsense, coexist in the same allele, theoretically, reversion of the latter may elicit a disease, like the opening of Pandora's box. However, cases of this hypothetical pathogenic mechanism have never been reported. We describe a lethal form of keratitis-ichthyosis-deafness (KID) syndrome caused by the reversion of the GJB2 nonsense mutation p.Tyr136X that would otherwise have confined the effect of another dominant lethal mutation, p.Gly45Glu, in the same allele. The patient's mother had the identical misssense mutation which was confined by the nonsense mutation. The biological relationship between the parents and the child was confirmed by genotyping of 15 short tandem repeat loci. Haplotype analysis using 40 SNPs spanning the >39 kbp region surrounding the GJB2 gene and an extended SNP microarray analysis spanning 83,483 SNPs throughout chromosome 13 in the family showed that an allelic recombination event involving the maternal allele carrying the mutations generated the pathogenic allele unique to the patient, although the possibility of coincidental accumulation of spontaneous point mutations cannot be completely excluded. Previous reports and our mutation screening support that p.Gly45Glu is in complete linkage disequilibrium with p.Tyr136X in the Japanese population. Estimated from statisitics in the literature, there may be approximately 11,000 p.Gly45Glu carriers in the Japanese population who have this second-site confining mutation, which acts as natural genetic protection from the lethal disease. The reversion-triggered onset of the disesase shown in this study is a previously unreported genetic pathogenesis based on Mendelian inheritance., Author Summary Loss of gene functions due to nonsense mutations is a typical pathogenic mechanism of hereditary diseases. They may, however, in certain genetic contexts, confine the effects of other dominant pathogenic mutations and suppress disease manifestations. We report the first instance in the literature where the reversion of a “confining” nonsense mutation in GJB2 gene released the dominant pathogenic effect of a coexsisting gain-of-function mutation, eliciting the lethal form of keratitis-ichthyosis-deafness syndrome (KID). We describe this form of KID syndrome caused by the reversion of the GJB2 nonsense mutation p.Tyr136X that would otherwise have confined the effect of another dominant lethal mutation, p.Gly45Glu, in the same allele. The patient's mother had the identical misssense mutation which was confined by the nonsense mutation. An epidemiologic estimation demonstrates that approximately 11,000 individuals in the Japanese population may have the same lethal GJB2 mutation, nonetheless protected from the manifestation of the syndrome because they also inherit the common “confining” nonsense mutation. The reversion-triggered onset of the disease shown in this study is a previously unreported genetic pathogenesis based on Mendelian inheritance.

Microsatellites, which involve a repetitive sequence motif (2-6bp), are evenly interspersed throughout eukaryotic genomes. Because of the variety in the numbers of repeat, they are useful genetic markers in the fields of human genetics, forensic sciences, and so on. Recently, phylogenetic studies using microsatellites have been performed in various species. Microsatellites in intergenic sequences, which evolve faster than coding sequences, are informative in the comparison between closely related species. Many of nonhuman primate species share the same microsatellite loci as human, although repeat numbers or nucleotide sequences vary species to species. We introduce some interesting studies and topics in which the interspecies difference of properties of microsatellites and the birth or death of them has been discussed. We also report the nucleotide sequence analysis of a microsatellite D14S299 locus in primates. The nucleotide sequence analyses of microsatellite alleles in primates provide informative data to study on primate evolution or dynamic processes in microsatellite loci.

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.

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.

Allele frequencies and forensic parameters for six miniSTR autosomal loci (D20S480, D6S2439, D6S1056, D9S1118, D4S2639 and D17S1290) were obtained from a sample of 205 unrelated Basque autochthous individuals using the recently designed hexaplex amplification and typing system, "Midi-6". No significant deviations from Hardy–Weinberg expectations were found. Due to the small PCR products (

We constructed a multiplex PCR and genotyping system selecting four pentanucleotide STR loci (Penta E, Penta D, Penta B and D10S2325) with multi-colored fluorescently labeled primer sets that are newly designed in order to genotype from mixed specimens, especially for degraded DNA samples, of which the amplicon sizes are smaller than about 200 bp. The allele frequencies at these four STR loci were calculated in a Japanese population. Sequence analysis was also performed for all alleles at these all STR loci observed in the Japanese population, and the allele distributions at those four loci did not deviated from HWE. The heterozygosities and the power of discriminations (PD) at all the four loci were more than 0.80 and 0.93, respectively. Furthermore, the present study provides a statistical standard to decide whether a one-repeat small peak from a main peak is the stutter peak or the peak originated from mixed individual sample.

Mucinous tumors of the ovary are frequently associated with mature cystic teratomas, and it has been speculated that the mucinous tumors arise from teratoma components. The cellular origins of mature cystic teratomas are believed to be post-meiotic ovarian germ cells, and the analysis of microsatellite markers such as short tandem repeats is suitable for determining the cellular origin of tumors. In this study, we analyzed 3 ovarian mature cystic teratomas, all of which were associated with simultaneous ovarian mucinous tumors within the same ovary. Two of the 3 mucinous tumors were intestinal-type and the other was endocervical type. A laser capture microdissection technique was used to separate the epithelial component of the mucinous tumor, the components of the mature cystic teratoma, and control ovarian somatic tissue. Using short tandem repeat analysis based on 6 markers (D20S480, D6S2439, D6S1056, D9S1118, D4S2639, and D17S1290), we could distinguish the germ cell (homozygous) or somatic (heterozygous) origin of a given component in each sample. The epithelial components of the intestinal-type mucinous tumors in cases 1 and 2 were homozygous, and the epithelial component in case 3 (endocervical type) was heterozygous. All teratomatous components were homozygous, and the control components were heterozygous. In addition, we analyzed 3 mature cystic teratomas without mucinous tumors, and all 3 were homozygous in the tumor component. Our data suggest that the origin of mucinous tumors in the ovary may differ among histological subtypes, and intestinal-type mucinous tumors may arise from mature cystic teratomas, although endocervical-type mucinous tumors may not.

We encountered a triplet pregnancy case with a mole and two normal fetuses, analyzed their karyotypes, and genotyped 15 STR markers and amelogenin after their termination in early pregnancy. The results of genotypes indicated that the triplets were trizygotic. The molar tissue lacked any of the maternal alleles at seven loci and, at one (D2S1338) of the seven loci, transmissions of the heterozygous paternal alleles to the mole were observed. These findings indicated that the mole resulted from dispermic androgenesis. The diagnosis with STR markers should prove very useful to better understand the zygosity of gestation and the genetic origin of hydatidiform moles.

We examined allele frequency distributions at 15 autosomal short tandem repeat (STR) loci including 13 Combined DNA Index System (CODIS) core STRs in four regional Japanese populations (Akita, Nagoya, Oita and Okinawa). Those distributions were compared pairwise and statistically among them. We also analyzed the distributions with published data on a Korean population by genetic distance DA to construct a tree based on the neighbor-joining method. Consequently, we obtained one that coincides well with their geographical distributions.

We analyzed the genotypes and haplotypes at 14 short tandem repeat (STR) loci on Y-chromosome (Y-STRs) in 10 East and Southeast Asian populations including two regional Japanese populations (Nagoya and Okinawa) using two multiplex typing systems. The allele frequency at each locus was calculated in each population and then compared among the populations. We also estimated the gene diversity at each locus and the haplotype diversity in each population. As a result, Japanese populations seemed to be genetically less diverse than other Asian populations. Furthermore, we constructed a tree based on the neighbor-joining method using a genetic distance DA. The resultant tree was comprised of three clusters (Japanese, Chinese and Southeast Asian) and coincided well with their geographical distributions.

The pathogenesis of placental mesenchymal dysplasia (PMD) remains unclear. This report presents a case of PMD with a female fetus complicated with intrauterine growth restriction (IUGR). The ultrasound findings were similar to molar pregnancies, but PMD was suspected based on the presence of low β-hCG levels and a normal karyotype. After delivery, pathological examination of the placenta showed dilated villi and thick-walled vessels lacking trophoblast proliferation, which thus led to a diagnosis of PMD. The VEGF-D (Xp22.31) mRNA expression was found to have increased in the abnormal villi. Whether this is an incidental or X-linked gene specific event in, IUGR complicated, PMD pathogenesis warrants further investigation of VEGF-D expression in PMD.

One of the HLA class II genes, HLA-DQA1, was typed from 290 unrelated healthy Japanese using the oligonucleotide typing method. The HLA-DQA1 gene was enzymatically amplified and typed by dot-blot hybridizations with 10 sequence-specific oligonucleotide probes labeled nonradioactively. Using this method, the HLA-DQA1 genotype was theoretically classified into 36 genotypes: 8 homozygous and 28 heterozygous ones. Actually, 26 genotypes were observed in the present study, and the gene frequency of each allele was calculated. The observed numbers were in accordance with the numbers expected under the Hardy-Weinberg equilibrium. The HLA-DQA1 genotype was also determined in aged bloodstains. Since the genotype is polymorphic in the Japanese population and a very small amount of blood is required for determination, this typing is particularly useful for forensic analysis.

Lineages of structurally related alleles at minisatellite MS32 in human populations show considerable differentiation at the continental level. However, the regional specificity of these lineages remains unknown. We now describe the comparison of allele structures in Thai, Han Chinese, and Japanese populations with lineages previously established for North Europeans and Africans. The great majority of alignable Asian alleles showed their closest structural relative in Asia, with few instances of preferential alignment of Asian with European alleles and only one isolated incident showing a best match with an African allele. Further, there was a strong tendency, most marked for Japanese, for Asian alleles to align preferentially with other alleles from the same population, indicating strong regional specificity of allele lineages. This rapidly evolving minisatellite can therefore serve as a lineage marker for exploring recent events in human population history and dissecting population structure at the fine-scale level, as well as being an extremely informative DNA marker for personal identification.

Nongestational pure choriocarcinoma of the ovary is a very rare germ cell tumor. Except in women before menarche, determination of the origin is very difficult without genetic analysis. We present a pure nongestational choriocarcinoma arising in the left ovary of a 19-year-old woman. Following surgery, pathologic findings of the tumor demonstrated pure choriocarcinoma without combination of other germ cell tumor elements. We confirmed its nongestational origin by DNA polymorphism analysis at 15 short tandem repeat loci. Multiple courses of chemotherapy with methotrexate, etoposide, and actinomycin-D were effective for this case. DNA polymorphism analysis is useful to determine genetic origin in pure choriocarcinoma of the ovary

We have analyzed 105 autosomal polymorphic short tandem repeat (STR) loci for nine East and South-eastern Asian populations (two Japanese, five Han Chinese, Thai, and Burmese populations) and a Caucasian population using a multiplex PCR typing system. All the STR loci are genomewide tetranucleotide repeat markers of which the total number of observed alleles and the observed heterozygosity were 756 and 0.743, respectively, for Japanese populations. Phylogenetic analysis for these allele frequency data suggested that the Japanese populations are more closely related with southern Chinese populations than central and/or northern ones. STRUCTURE program analysis revealed the almost clearly divided and accountable population structure at K=2-6, that the two Japanese populations always formed one group separated from the other populations and never belong to different groups at Kor =3. Furthermore, our new allele frequency data for 91 loci were analyzed with those for 52 worldwide populations published by previous studies. Phylogenetic and multidimensional scaling (MDS) analyses indicated that Asian populations with large population size (six Han Chinese, three Japanese, two Southeast Asia) formed one distinct cluster and are closer to each other than other ethnic minorities in east and Southeast Asia. This pattern may be the caviar of comparing populations with greatly differing population sizes when STR loci were analyzed.

We analyzed 17 Y-STRs and Y haplogroups (Y-hgs) for about 493 Mongolian male samples from 5 regions in Mongoria, and compared with the results from Japanese male samples. Only 358 Y-STR haplotypes (Y-HTs) were observed in Mongolian males, and the haplotype diversity and discrimination capacity were calculated as 0.9934 and 0.7099 whose values were very low by comparing with tja Japanese males (0.9989 and 0.9565, respectively). About 63% of Mongolian males had C3 groups ranging from 50% in Ulaanbaatar to 69% in Ulaangom. The 96% of C3 was C3*, which is C3 except C3a to C3f, in Dalandzadgad, alternatively the 78% of C3 was C3c in Ulaangom. The network analysis with regional information and Y-hgs revealed that at least 4 major "star" or "star"-like cluster exist although the degrees of influence were variable. These clusters suggested that at least 4 major male ancestors with Y-HG-C3 have affected the gene pool of Mongolian males at the different periods.

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.