Construction of 13-locus X-STR multiplex PCR system that reinforces Argus X-12 kit discrimination capacity: Application to the Malay population.

Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a unique commercially available kit, can obtain haplotypes of 4 linkage groups (LGs) consisting of 3 markers. Although many population data have been reported for forensic purposes, differences in discrimination ability exist between LG1 and LG2, 3, and 4 in East Asian populations, and the data of this kit would become more useful if the discrimination ability of the latter groups were increased. Therefore, for matches found using this kit for some linkage group data, then to increase the identification ability, we additionally introduced 13 X-STR loci and established a method allowing comparison using data from 25 loci. The 13X-STRs add two locus data to each of LG2, 3, and 4, and also add two closely linked group (CLG) data between LG2 and 3 and LG3 and 4 in one multiplex PCR. Assessment of this method for a Malay population for which data by Argus X-12 had already been reported showed that the frequencies of distinct haplotypes in LG2, 3, and 4 were increased by 33.0-42.6 %, and frequencies of unique haplotypes increased by 45.4-59.2 %. The respective haplotype diversity values of the additional 3-locus and 4-locus CLGs were 0.9838 and 0.9939, which helps to improve discriminatory power and to predict recombination locations on the X chromosome. Although we have been testing these loci with Japanese subjects, this system would also be useful for the Malay population.

Double suicide in Japan in the post-war reconstruction period, with reference to contemporary Japan.

After Japan's post-war reconstruction, in the early 1950s, cases of double suicide, in which two people (particularly young lovers) leave a suicide note and die together, were a relatively frequent occurrence. During the three-year period between 1954 and 1956, 5466 suicides were recorded in the special wards of Tokyo, including 79 cases of double suicides, accounting for 158 deaths. In these double suicide cases (2.89% of all deaths by suicide), the evidence revealed that 65.8% involved lovers and 29.1% involved married couples. By contrast, contemporary data indicate a large drop in suicide pacts between lovers to 15.9% and an increase between spouses to 48.8%. Conceivably, the relatively high double-suicide rate after post-war reconstruction reflected difficulties for the younger generation in reconciling 'marriage based primarily on love' and the traditional family system, specifically marriage problems and stress caused by rapidly changing post-war values. One notable difference between victims of double suicide in 1954-1956 and the contemporary period is the younger average age of the former. Another important shift was found in the most common causes of death among victims of double suicide: in 1954-1956 these were poisoning by cyanide or hypnotic drugs, compared to carbon monoxide poisoning and hanging in modern times. We discuss similarities and differences concerning double suicides in relation to social and economic conditions in Japan in the 1950s and today.

Non-polyalanine repeat mutation in PHOX2B is detected in autopsy cases of sudden unexpected infant death.

BACKGROUND: Congenital central hypoventilation syndrome (CCHS), which is caused by PHOX2B with phenotypic variations, has a point of controversy: CCHS is putatively involved in autopsy cases of sudden unexpected infant death (SUID) including sudden infant death syndrome. OBJECTIVE: The relation of CCHS to SUID cases was investigated by extensive genotyping of PHOX2B. METHODS: We analyzed 93 DNA samples of less than one-year-old SUID cases that were autopsied in our department. Unrelated adult volunteers (n = 942) were used as the control. RESULTS: No polyalanine tract expansion was detected in the SUID cases. The allelic frequencies of repeat contractions and SNP (rs28647582) in intron 2 were not significantly different from that in those control group. Further extensive sequencing revealed a non-polyalanine repeat mutation (NPARM) of c.905A>C in a sudden death case of a one-month-old male infant. This missense mutation (p.Asn302Thr), registered as rs779068107, was annotated to 'Affected status is unknown', but it might be associated with the sudden death. CONCLUSION: NPARM was more plausibly related to sudden unexpected death than expansions because of severe clinical complications. This finding indicates possible CCHS involvement in forensic autopsy cases without ante-mortem diagnosis.

Y chromosome analysis for common surnames in the Japanese male population.

For many years of Japan's long history, Japanese surnames have been handed down patrilineally. This study investigated relations between major surnames and Y chromosomal polymorphism among the Japanese male population. To analyze genetic phylogeny in namesakes, the Y-single nucleotide polymorphism (SNP) plus Y-short tandem repeat (STR) approach was employed. A haplogroup based on SNPs and haplotypes at 17 STR loci were typed in 567 unrelated volunteers recruited in Kanagawa, Japan. Samples covered 27 common surnames such as Satoh and Suzuki, each name having 10-55 bearers. Significant difference was found for SNP haplogroup compositions and a multidimensional scaling plot using STR haplotypes in several surname groups. By contrast, these common surnames displayed wide diversity with phylogenetic networks, suggesting that no genetic drift event has occurred in their history. In all, 22 descent clusters were found, as judgcriteria ed by ad hoc of groups within five mutational steps in the 15 STR loci with the same haplogroup. The times of the most recent common ancestor ranged from 279 to over 2577 years. According to the approximate millennium span of Japanese surname history, descent criteria are expected to be reasonable for grouping within four step-neighbors. High heterogeneity of common surnames resembles that observed for England and Spain, but not for Ireland. Our results highlight that common Japanese surnames consist of descent clusters and many singletons, reflecting a mixture of long-term bearers and short-term bearers among the population. The genetic study of this population revealed characteristic features of Japanese surnames.

Jervell and Lange-Nielsen syndrome with novel KCNQ1 and additional gene mutations.

We encountered a boy with Jervell and Lange-Nielsen syndrome (JLNS) with compound heterozygous KCNQ1 mutations, maternal Trp248Phe and a novel paternal mutation, Leu347Arg. His father showed long QT (LQT) and arrhythmia. His mother was asymptomatic with no ECG abnormalities. The proband and his father had an additional mutation (SNTA1 Thr372Met), which is reportedly related to SIDS. These results suggest that multiple gene mutations influence the phenotype of KCNQ1 mutation-related arrhythmia.

MicroRNA profiling of gastric content from breast-fed and formula-fed infants to estimate last feeding: a pilot study.

Recently, we were consulted about a challenging case, where an infant died by poisoning and the drug-dependent mother insisted that she unintentionally gave the toxic drug through breast milk. Accordingly, we investigated the utility of immunoblotting and microRNA (miRNA) profiling of the infant's gastric content (GC) to differentiate between breast-feeding and formula-feeding. As a pilot study, we sampled the GC from breast-fed (GCB) and formula-fed (GCF) infants, as well as gastric juice (GJ) from fasted adults at autopsy. Breast milk (BM) samples were collected from volunteers within 1 year post-delivery. By immunoblotting, lactoferrin and gross cystic disease fluid protein (GCDEP) were clearly detected in BM, but could not be detected in GCB. Similarly, ß-lactoglobulin was detected in formula milk, but could not be detected in GCF. Meanwhile, miRNA sequencing revealed that the miRNA expression profile of GCB was closer to BM than GCF and GJ. Especially, miR-151a and miR-186 were more abundant in BM and GCB than in GCF and GJ. Our study is the first to elucidate the human GJ miRNA profile and demonstrate the possibility that miR-151a and miR-186 in GC may be the biomarker of breast-feeding.

The Impact of Discontinuation of the Medical Examiner System: Cases of Drowning in the Bathtub at Home.

The incidence of death by drowning greatly varies among different prefectures in Japan, mainly due to climate difference. However, there could be other factors affecting the incidence of deaths besides climate, for example, differences in regional death investigation systems. Here, we aimed to elucidate other such factors affecting the mortality data of drowning in the bathtub, especially the effects of discontinuing the medical examiner system. Police data in Kyoto and ambulatory care information in Yokohama were used. Data on cases of elderly individuals found dying or dead in the bathtub at home in winter 2014-2015 were obtained. The following data were collected for each case: age, gender, presence/absence of ambulatory transport, performance of autopsy, and cause of death. The autopsy and drowning rates in Kyoto were 0%, whereas both values in Yokohama were significantly higher at 93.1% and 89.4%, respectively (the denominator of each of the rates is the total number of elderly (aged 65 or over) individuals found dying or dead in the bathtub at home in each city during each winter). Despite no significant difference of incidence of total bath-related death, the proportion of drowning-related deaths was overwhelmingly higher in Yokohama than in Kyoto. The difference can be attributed to the difference in autopsy rates between the two cities, mainly caused by the presence/absence of a medical examiner system. Therefore, we should pay careful attention to future changes in autopsy/drowning rates in Yokohama, and ascertain whether the change might be continuously influenced by the abolishment of this system.

Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study.

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21-45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.

The importance of the rate of pure "attended deaths at home" for objective outcome indicator for assessing the prevalence of home care in Japan.

BACKGROUND: No study has yet been performed on the importance of the rate of pure "attended deaths at home," excluding examined deaths subjected to a postmortem examination. Therefore, in the present study, we investigated actual state of pure "attended deaths at home," in order to provide reference data for the future development of end-of-life care at home. METHODS: We performed a detailed survey in Yokohama City according to the type of death, age, and underlying cause of death in cases of home deaths, based on the detailed version of the Vital Statistics Survey Death Forms. Then, we divided deaths occurring in each municipality in Kanagawa Prefecture into two categories: "examined deaths" or "attended deaths," which were also stratified by the place of death, based on the Vital Statistics, and data on number of death cases subjected to postmortem examination from the Kanagawa Prefectural Police Headquarters. RESULTS: In 2013, the survey in Yokohama City showed large differences in age distribution and cause of death between examined and attended deaths. In 2014, home deaths accounted for 15.7% of all deaths in the prefecture, whereas the overall proportion of attended deaths at home was 6.9%. CONCLUSIONS: We should utilize the rate of pure "attended deaths at home" for objective outcome indicator.

A descriptive study of solitary death in Yokohama City.

BACKGROUND: The solitary death rate in Japan is expected to continue increasing because of its growing super-aged society and the rapid growth of home care in the country. To accurately determine the actual status of solitary deaths, we used a novel analysis method of combining vital statistics and ambulatory care information in Yokohama City. METHODS: Data of persons who died at home in 2013 were obtained from death certificate notifications. We also obtained the emergency transportation records that matched the cases of these death certificate notifications. Then, we gathered information regarding age, gender, marital status, and cause of death for the matched cases. RESULTS: There were 1890 "suspected unnatural deaths," in which most solitary deaths could be included, among all citizens who died at home (n = 4847). We were able to match 1503 of these cases with emergency transportation records. These 1503 cases were divided into two groups, "solitary death" (n = 349) and "un-solitary death" (n = 1154) according to the postmortem interval until finding (PMI-f). Pearson's χ2 tests conducted for the two groups revealed that there were significant differences regarding the proportion of persons who were elderly, unmarried, male, and had a hepatic disease and senility. A logistic regression analysis also showed that an increased likelihood of a prolonged PMI-f was associated with males and an unmarried status with hepatic diseases. CONCLUSIONS: Unmarried, male sex, and liver diseases are independent risks for solitary death in Yokohama City.

Pyogenic granuloma associated with Actinomyces israelii.

Peculiar findings of orofacial actinomycosis mimicking the clinical appearance of a tumor of the upper gingiva are reported. An 83-year-old man with bleeding of the gingiva visited our hospital. The clinical diagnosis was a benign gingival tumor, and the lesion was surgically removed. Histologically, the excised specimens showed an ulcerative granuloma lesion covered by bacterial colonies consisting of club-shaped filaments. DNA samples were extracted from paraffin sections and examined by polymerase chain reaction (PCR) for Actinomyces species. The PCR products examined by direct DNA sequencing demonstrated the presence of Actinomyces israelii. Finally, a pathological diagnosis was made of a pyogenic granuloma associated with actinomycosis. The PCR method aided the early and exact diagnosis of the paraffin-embedded sample of oral mucosal infectious diseases including actinomycosis.

Combined effects of multiple linked loci on pairwise sibling tests.

The advanced multiplex STR system, PowerPlex Fusion, includes four linked locus pairs. The conventional Identifiler system has one pair of linked loci. Therefore, sibling tests conducted using the advanced system might be more affected by linkage than those conducted using the conventional system. This study simulated single and combined effects of the four linked locus pairs on pairwise sibling tests. Simulated genotypes of 100,000 pairs of full siblings and nonrelatives were constructed according to allele frequencies of the Japanese population. The single linkage effect was evaluated for simulated genotype data by calculating both the likelihood ratio accounting for the linkage between two loci and the likelihood ratio ignoring the linkage. The combined effect was obtained by multiplication of the respective single effects. Furthermore, we investigated the possibility that ignoring the linkage affects subject classification by introducing a scale of the likelihood ratio into sibling tests. The single effect in the Identifiler analysis was 0.645-1.746 times if the linkage was ignored. Overestimations and underestimations were predictable from the identical-by-state status at two linked loci. The combined effect in the PowerPlex Fusion analysis was 0.217-7.390 times. Ignoring the linkage rarely caused a false conclusive or inconclusive result, even from PowerPlex Fusion analysis. Application of the advanced system improved sibling tests considerably. The additional examined loci were more beneficial than the adverse effect of the linkage derived from the four linked locus pairs.

Cytokine Elevation in Sudden Death With Respiratory Syncytial Virus: A Case Report of 2 Children.

Respiratory syncytial virus (RSV) is the most common viral cause of bronchiolitis and pneumonia in young children worldwide. Premature birth, bronchopulmonary dysplasia, congenital heart disease, and Down syndrome are risk factors for high mortality and prolonged morbidity after RSV infection. Conversely, many previously healthy, full-term children are also admitted to the hospital because of RSV, and some of them experience severe sequelae or die due to the virus. Various complications of RSV infection have been reported, such as encephalopathy, encephalitis, and cardiomyopathy. However, the pathogenesis of serious cases in children without an underlying disease has not been elucidated. In this report, we present 2 RSV-related deaths of children who were born at full-term and developed normally up to the age of 19 months. Their cardiopulmonary arrests occurred within half a day after the onset of symptoms, such as cough and high fever. Many postmortem examinations were performed to investigate their unexpected deaths. Histopathological examinations revealed extensive bronchiolitis and mild pneumonia accompanying airway obstruction. Immunostaining revealed the presence of the virus mainly in bronchial epithelia, but not in alveoli. Complete brain edema was prominent, and encephalopathy was developing. Blood tests revealed that the IL-6 level was elevated more than >200-fold above normal, despite a normal C-reactive protein level. Because IL-6 may reflect the severity of bronchial epithelial damage and contribute to brain edema, an extreme elevation of IL-6 may predict the risk for sudden death in children with RSV infection.

Evaluation of Y chromosomal SNP haplogrouping in the HID-Ion AmpliSeq™ Identity Panel.

The Y chromosomal haplogroup determined from single nucleotide polymorphism (SNP) combinations is a valuable genetic marker to study ancestral male lineage and ethical distribution. Next-generation sequencing has been developed for widely diverse genetics fields. For this study, we demonstrate 34 Y-SNP typing employing the Ion PGM™ system to perform haplogrouping. DNA libraries were constructed using the HID-Ion AmpliSeq™ Identity Panel. Emulsion PCR was performed, then DNA sequences were analyzed on the Ion 314 and 316 Chip Kit v2. Some difficulties became apparent during the analytic processes. No-call was reported at rs2032599 and M479 in six samples, in which the least coverage was observed at M479. A minor misreading occurred at rs2032631 and M479. A real time PCR experiment using other pairs of oligonucleotide primers showed that these events might result from the flanking sequence. Finally, Y haplogroup was determined completely for 81 unrelated males including Japanese (n=59) and Malay (n=22) subjects. The allelic divergence differed between the two populations. In comparison with the conventional Sanger method, next-generation sequencing provides a comprehensive SNP analysis with convenient procedures, but further system improvement is necessary.

MicroRNA Stability in FFPE Tissue Samples: Dependence on GC Content.

MicroRNAs (miRNAs) are small non-coding RNAs responsible for fine-tuning of gene expression at post-transcriptional level. The alterations in miRNA expression levels profoundly affect human health and often lead to the development of severe diseases. Currently, high throughput analyses, such as microarray and deep sequencing, are performed in order to identify miRNA biomarkers, using archival patient tissue samples. MiRNAs are more robust than longer RNAs, and resistant to extreme temperatures, pH, and formalin-fixed paraffin-embedding (FFPE) process. Here, we have compared the stability of miRNAs in FFPE cardiac tissues using next-generation sequencing. The mode read length in FFPE samples was 11 nucleotides (nt), while that in the matched frozen samples was 22 nt. Although the read counts were increased 1.7-fold in FFPE samples, compared with those in the frozen samples, the average miRNA mapping rate decreased from 32.0% to 9.4%. These results indicate that, in addition to the fragmentation of longer RNAs, miRNAs are to some extent degraded in FFPE tissues as well. The expression profiles of total miRNAs in two groups were highly correlated (0.88

MicroRNA deep sequencing reveals chamber-specific miR-208 family expression patterns in the human heart.

BACKGROUND: Heart chamber-specific mRNA expression patterns have been extensively studied, and dynamic changes have been reported in many cardiovascular diseases. MicroRNAs (miRNAs) are also important regulators of normal cardiac development and functions that generally suppress gene expression at the posttranscriptional level. Recent focus has been placed on circulating miRNAs as potential biomarkers for cardiac disorders. However, miRNA expression levels in human normal hearts have not been thoroughly studied, and chamber-specific miRNA expression signatures in particular remain unclear. METHODS AND RESULTS: We performed miRNA deep sequencing on human paired left atria (LA) and ventricles (LV) under normal physiologic conditions. Among 438 miRNAs, miR-1 was the most abundant in both chambers, representing 21% of the miRNAs in LA and 26% in LV. A total of 25 miRNAs were differentially expressed between LA and LV; 14 were upregulated in LA, and 11 were highly expressed in LV. Notably, the miR-208 family in particular showed prominent chamber specificity; miR-208a-3p and miR-208a-5p were abundant in LA, whereas miR-208b-3p and miR-208b-5p were preferentially expressed in LV. Subsequent real-time polymerase chain reaction analysis validated the predominant expression of miR-208a in LA and miR-208b in LV. CONCLUSIONS: Human atrial and ventricular tissues display characteristic miRNA expression signatures under physiological conditions. Notably, miR-208a and miR-208b show significant chamber-specificity as do their host genes, α-MHC and ß-MHC, which are mainly expressed in the atria and ventricles, respectively. These findings might also serve to enhance our understanding of cardiac miRNAs and various heart diseases.

Effects of using the GlobalFiler™ multiplex system on parent-child analyses of cases with single locus inconsistency.

Parent-child analyses sometimes reveal inconsistency of shared alleles at only one locus. This is conventionally called "single locus exclusion", which results from mutational events and the presence of null alleles. Here, in parent-child analyses of the Japanese population, we detected exclusions by using the GlobalFiler™ system comprising 21 short tandem repeat loci. One- or two-step mutations resulting from strand slippage causing gain or loss were observed in seven of 221 parent-child transmissions. The incidences of single locus inconsistency of alleles were 5.88×10(-2) and 8.40×10(-3) for paternal and maternal relationships, respectively. With calculation using a set of 15 loci in the Identifiler® multiplex system, the combined likelihood ratio (CLR) values were limited to less than 100 in all five cases accompanied by single inconsistency. The addition of six loci recovered the CLR values to over 10,000 in three cases. Application of this advanced system may increase the detected occurrence of mutational events, but it should be beneficial for inference in parent-child analyses, particularly in cases accompanied by genetic inconsistency.

MicroRNA Stability in Postmortem FFPE Tissues: Quantitative Analysis Using Autoptic Samples from Acute Myocardial Infarction Patients.

MicroRNAs (miRNAs) are very short (18-24 nucleotides) nucleic acids that are expressed in a number of biological tissues and have been shown to be more resistant to extreme temperatures and pH compared to longer RNA molecules, like mRNAs. As miRNAs contribute to diverse biological process and respond to various kinds of cellular stress, their utility as diagnostic biomarkers and/or therapeutic targets has recently been explored. Here, we have evaluated the usefulness of miRNA quantification during postmortem examination of cardiac tissue from acute myocardial infarction (AMI) patients. Cardiac tissue was collected within one week of the patient's death and either frozen (19 samples) or fixed in formalin for up to three years (36 samples). RNA integrity was evaluated with an electropherogram, and it appears that longer RNAs are fragmented after death in the long-term fixed samples. Quantitative PCR was also performed for seven miRNAs and three other small RNAs in order to determine the appropriate controls for our postmortem analysis. Our data indicate that miR-191 and miR-26b are more suitable than the other types of small RNA molecules as they are stably detected after death and long-term fixation. Further, we also applied our quantitation method, using these endogenous controls, to evaluate the expression of three previously identified miRNA biomarkers, miR-1, miR-208b, and miR-499a, in formalin-fixed tissues from AMI patients. Although miR-1 and miR-208b decreased (1.4-fold) and increased (1.2-fold), respectively, in the AMI samples compared to the controls, the significance of these changes was limited by our sample size. In contrast, the relative level of miR-499a was significantly decreased in the AMI samples (2.1-fold). This study highlights the stability of miRNAs after death and long-term fixation, validating their use as reliable biomarkers for AMI during postmortem examination.

Evaluation of advanced multiplex short tandem repeat systems in pairwise kinship analysis.

The AmpFLSTR Identifiler Kit, comprising 15 autosomal short tandem repeat (STR) loci, is commonly employed in forensic practice for calculating match probabilities and parentage testing. The conventional system exhibits insufficient estimation for kinship analysis such as sibship testing because of shortness of examined loci. This study evaluated the power of the PowerPlex Fusion System, GlobalFiler Kit, and PowerPlex 21 System, which comprise more than 20 autosomal STR loci, to estimate pairwise blood relatedness (i.e., parent-child, full siblings, second-degree relatives, and first cousins). The genotypes of all 24 STR loci in 10,000 putative pedigrees were constructed by simulation. The likelihood ratio for each locus was calculated from joint probabilities for relatives and non-relatives. The combined likelihood ratio was calculated according to the product rule. The addition of STR loci improved separation between relatives and non-relatives. However, these systems were less effectively extended to the inference for first cousins. In conclusion, these advanced systems will be useful in forensic personal identification, especially in the evaluation of full siblings and second-degree relatives. Moreover, the additional loci may give rise to two major issues of more frequent mutational events and several pairs of linked loci on the same chromosome.

Identification of the actinomycete 16S ribosomal RNA gene by polymerase chain reaction in oral inflammatory lesions.

OBJECTIVES: To examine the histopathological characteristics of inflammatory lesions containing Actinomyces based on DNA sequencing. Furthermore, case reports of actinomycosis in the maxillofacial region are summarized by a review of the literature. STUDY DESIGN: The study comprised 12 cases of inflammatory lesions containing Actinomyces as diagnosed by DNA analysis. The average age of the subjects was 59 ± 15 years (6 males; 6 females). RESULTS: The distribution of causative bacteria was: Actinomyces israelii in 9 cases, Actinomyces gerencseriae in 2 cases, and Actinomyces naeslundii in 1 case. Four cases diagnosed by DNA sequencing were positive for "Druse," a known morphological diagnostic characteristic of actinomycosis, and 8 cases lacked typical colony formation. CONCLUSIONS: DNA analysis using paraffin-embedded samples is effective for both early and accurate diagnosis of oral lesions containing Actinomyces.