Age-related DNA methylation analysis for forensic age estimation using post-mortem blood samples from Japanese individuals.

As one of external visible characteristics (EVCs) in forensic phenotyping, age estimation is essential to providing additional information about a sample donor. With the development of epigenetics, age-related DNA methylation may be used as a reliable predictor of age estimation. With the aim of building a feasible age estimation model for Japanese individuals, 53 CpG sites distributed between 11 candidate genes were selected from previous studies. The DNA methylation level of each target CpG site was identified and measured on a massive parallel platform (synthesis by sequencing, Illumina, California, United States) from 60 forensic blood samples during the initial training phase. Multiple linear regression and quantile regression analyses were later performed to build linear and quantile age estimation models, respectively. Four CpG sites on four genes- ASPA, ELOVL2, ITGA2B, and PDE4C -, were found to be highly correlated with chronological age in DNA samples from Japanese individuals (|R| > 0.75). Subsequently, an independent validation dataset (n = 30) was used to verify and evaluate the performance of the two models. Comparison of mean absolute deviation (MAD) with other indicators showed that both models provide accurate age predictions (MAD: linear = 6.493 years; quantile = 6.243 years). The quantile model, however, can provide the changeable prediction intervals that grow wider with increasing age, and this tendency is consistent with the natural aging process in humans. Hence, the quantile model is recommended in this study.

MAPlex - A massively parallel sequencing ancestry analysis multiplex for Asia-Pacific populations.

Current forensic ancestry-informative panels are limited in their ability to differentiate populations in the Asia-Pacific region. MAPlex (Multiplex for the Asia-Pacific), a massively parallel sequencing (MPS) assay, was developed to improve differentiation of East Asian, South Asian and Near Oceanian populations found in the extensive cross-continental Asian region that shows complex patterns of admixture at its margins. This study reports the development of MAPlex; the selection of SNPs in combination with microhaplotype markers; assay design considerations for reducing the lengths of microhaplotypes while preserving their ancestry-informativeness; adoption of new population-informative multiple-allele SNPs; compilation of South Asian-informative SNPs suitable for forensic AIMs panels; and the compilation of extensive reference and test population genotypes from online whole-genome-sequence data for MAPlex markers. STRUCTURE genetic clustering software was used to gauge the ability of MAPlex to differentiate a broad set of populations from South and East Asia, the West Pacific regions of Near Oceania, as well as the other globally distributed population groups. Preliminary assessment of MAPlex indicates enhanced South Asian differentiation with increased divergence between West Eurasian, South Asian and East Asian populations, compared to previous forensic SNP panels of comparable scale. In addition, MAPlex shows efficient differentiation of Middle Eastern individuals from Europeans. MAPlex is the first forensic AIM assay to combine binary and multiple-allele SNPs with microhaplotypes, adding the potential to detect and analyze mixed source forensic DNA.

Complete androgen insensitivity in a 47,XXY patient with uniparental disomy for the X chromosome.

We describe a unique patient with complete androgen insensitivity syndrome and a 47,XXY karyotype. Androgen receptor assay using cultured pubic skin fibroblasts showed no androgen-binding capacity. Sequence analysis of the androgen receptor gene demonstrated two nonsense mutations, one in exon D and one in exon E. Microsatellite marker analysis showed that the patient is homozygous for all five Xq loci examined. The results suggest that the long-arms of the two X chromosomes are identical, i.e., uniparental isodisomy at least for Xq, and carry the same mutations in the androgen receptor gene. This explains how complete androgen insensitivity syndrome occurred in this 47,XXY individual.

Preferential X-chromosome inactivation in women with idiopathic recurrent pregnancy loss.

OBJECTIVE: To determine whether preferential X-chromosome inactivation (P-XCI) relates to idiopathic recurrent pregnancy loss. DESIGN: A retrospective study. SETTING: Infertility clinics and laboratory. PATIENT(S): Women with idiopathic recurrent pregnancy loss (group I), women who had given birth to children but with no history of spontaneous abortion (group II), and women without a history of pregnancy (group III). INTERVENTION(S): DNA samples from the heterozygotes for the (CAG)n polymorphism within the androgen receptor gene were modified with sodium bisulfite, PCR-amplified with primer pairs for methylated androgen receptor alleles (M-PCR) and unmethylated alleles (U-PCR), and subjected to electrophoresis. MAIN OUTCOME MEASURE(S): Band peak patterns and peak area sizes. RESULT(S): In group I, 7 (16.7%) of 42 heterozygotes exhibited P-XCI; four possessed single-peak patterns in the M-PCR and U-PCR products, and three had two-peak patterns in which the peak sizes differed considerably. In group II, 2 (5.6%) of 36 heterozygotes exhibited P-XCI as determined by the two-peak patterns. In group III, none of the 47 heterozygotes exhibited P-XCI. CONCLUSION(S): The incidence of P-XCI was statistically higher in group I than in the other groups. As P-XCI characterized by single-peak patterns was observed only in group I, such patterns, which may result from undiscovered cytogenetic or molecular abnormalities of the X-chromosome, likely correlate with pregnancy loss.

Polymorphism of 17 STRs by multiplex analysis in Japanese population.

Genotype and distribution of allele frequencies at 17 STRs were studied in 526 unrelated Japanese individuals using the PowerPlex 16 system and the AmpFlSTR Identifiler.

Intracerebral haematoma: traumatic or non-traumatic.

A 35-year-old woman, a chronic alcoholic, died from an intracerebral haematoma 10 hr after she fell downstairs. Some subcutaneous bleeding was seen on the head and face, but there were no new skull fractures and surface contusions of the brain. She appeared to have few predisposing conditions for non-traumatic cerebral haemorrhage. In addition, the haematoma was mainly located "lateral" to the basal ganglia, not where hypertensive bleeding most commonly occurs, and subdural and haemorrhage in the corpus callosum was found with subdural/and subarachnoid haemorrhage. We concluded that on falling a shearing strain from a rotating force produced the intracerebral haemorrhage, but without skull fractures and surface contusions of the brain. She had been admitted to a neurosurgical hospital just 11 months before this incident because of an epidural haemorrhage with left temporal bone fracture. Mild thrombocytopenia was found during that hospitalization. In this report, this abnormality was thought to have some relation to the formation of the huge haematoma occurring after the intracerebral bleeding started.

Laceration of the liver with delayed massive intra-abdominal hemorrhage: a case report of child abuse.

A 3-year-old girl was found unresponsive in the bedroom and expired at a hospital. Autopsy revealed massive intra-abdominal bleeding due to laceration of the liver and mesenterium with multiple rib fractures and multiple fresh and old bruises. The time of the assault causing the liver trauma was questioned because the perpetrator, her mother's boyfriend, denied any outrages on that particular day although he confessed that he had physically abused her for several months. Microscopically, numerous polymorph leucocytes infiltrated exclusively surrounding the lacerated area of the liver. Many hepatocytes were necrotic and cord arrangement of the parenchymal cells was destroyed. There should be a certain time lag between the major assault and massive intra-abdominal hemorrhage, which was not inconsistent with the statement of the perpetrator.

[Simple and rapid detection of HLA-DRB polymorphism from forensic samples].

Simple and rapid detection of HLA-DRB polymorphism has been performed using AMPLICOR HLA-DRB Typing Kit. We tried to apply this kit to various forensic samples. When DNA was extracted from the forensic samples using conventional phenol-chloroform method, addition of 7.5 mM MgCl2 was required to PCR amplification. HLA-DRB types were detected from DNA more than 0.1 ng by PCR amplification. Typing of unrelated 50 Japanese showed 38 different patterns, of which 30 patterns occurred once in the group. A total of 16 serotypes were deduced from the HLA-DRB DNA types. Out of them, high frequency serotypes were DR4 (24%), DR9 (18%) and DR15/16 (14%). This kit was very useful in forensic cases such as rape and in paternity cases. When we tried to detect HLA-DRB types from a single hair shaft of 3 cm in length, we were successful in detection from only one of five persons.

[Spreadsheets of a conventional application software for calculation of plausibility of paternity: application to parentage testing with highly polymorphic markers in deceased party].

We designed a spreadsheet package for the computation of plausibility of paternity, that can cope with highly polymorphic genetic markers and cases of deceased parties. The application program is Microsoft EXCEL, which is one of the best-selling spreadsheet software running on both Microsoft Windows and Macintosh OS. Komatsu's formula for paternity testing was mainly employed in the spreadsheet package. Probability of the mother-child-alleged father combination was calculated using "IF" function to compare the members' genotypes, whereas "VLOOKUP (or HLOOKUP)" function was employed to refer to a list of genes and their frequencies. In case of a phenotype consisting of several genotypes, the list of phenotypes versus genotypes was also given, to which the function referred. To extend these spreadsheets available for the test of deceased party, additional sheets were also created to estimate frequencies of alleged father's possible genotypes. These probabilities were calculated on the basis of types of his parents and siblings, those of his wife and their biological children, and those of both. This package would be cut out to compute the probability of paternity with extremely polymorphic loci with gentle user interface. Calculation time is satisfactorily short, although it requires considerably large disk space in some extremely complicated cases. Japanese version of this package is freely available at anonymous FTP site of the Department of Forensic Medicine, Tohoku University School of Medicine.

[Effect of postmortem change on detection of apoptosis in rats].

Terminal deoxynucleotidyl transferase(TdT)-mediated dUTP-digoxigenin nick end labeling (TUNEL) assay is useful to detect apoptotic cells in situ. We examined by hematoxylin-eosin (H-E) and TUNEL assay whether or not postmortem delay affects the development of apoptotic signals of cells in various organs. Wistar Imamichi rats were radiated by X-ray and sacrificed six hours after radiation. The spleen, thymus, adrenal and testis were excised and kept in a moist chamber at room temperature. Each tissue was fixed after different time intervals 0, 6, 12, 24 hours and paraffin-embedded sections were made. In the no-radiation group, a few of TUNEL positive cells were observed in the spleen, thymus and testis sections, but not in the adrenal. No increase in the number of apoptotic cells was observed with postmortem delay. In the radiation group, we observed in the spleen and thymus, much increase in the number of TUNEL positive cells, of which nuclei were clearly and deeply stained, corresponding to the area where shrinking nuclei were observed in H-E section. In testis sections, there was a little increase in the number of positively stained cells, and no change was observed in H-E section. With postmortem delay, the margin of the TUNEL positive cells changed from clear to indistinct, and the positive area was spread around. Our results show that it is difficult to distinguish apoptotic cells from postmortem change. It is possible, however, to detect TUNEL positive cell together with postmortem changes as the spread of the TUNEL positive area after 24 hours postmortem delay. It is important to consider the effect of the postmortem change when we adapt TUNEL assay to autopsy cases.

ABO genotyping by PCR-direct sequencing.

The PCR-direct sequence method was applied to ABO genotyping. At the 261st nucleotide of the genes of A and B glycosyltrasferase, it was easily detected that the nucleotide was guanine in AA, AB and BB genotypes and that the nucleotide was ademine in only OO. In AO and BO, substitution of A to G was confirmed by the dye primer method, but it was difficult to detect correctly by the dye terminator method. At the 297th, nucleotide substitution between A and B alleles was confirmed by the both methods. As this position, O allele was subdivided into three types, OAOA, OGOG and OAOG. At the 703rd, nucleotide substitution between A and B alleles was easily detected by the both methods. The PCR-direct sequence method was suitable to confirm the nucleotide substitution or deletion directly and to prevent the mistyping by other methods.

[Application of stochastical analysis to maternity testing without putative mother].

In a maternity test in which the putative mother was deceased, the cumulative probability of maternity (PM) was calculated at 0.822 from 24 genetic markers by the stochastical method. This PM may not be evaluated in the same way as that of usual paternity cases. We applied the same method to two families whose blood relationships were undoubted. We compared the PMs in the cases in which maternal genotypes were estimated and were defined. Also, we calculated the PMs in the case of real maternal relationship and false maternal one. The estimated PM from real maternity relationship was significantly higher than that from false maternal one.

Significance of levels of IL-6 and IL-8 after trauma: a study of 11 cytokines post-mortem using multiplex immunoassay.

PURPOSE: To identify cytokines useful for diagnosis of traumatic death. METHODS: Post-mortem serum levels of 11 cytokines were assayed for 43 people who died of traumatic injury or from non-traumatic causes. Levels of granulocyte-macrophage colony stimulating factor, gamma interferon, interleukin IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-13, and tumour necrosis factor-alpha were measured using multiplex immunoassay. RESULTS: Levels of granulocyte-macrophage colony stimulating factor (p<0.01), IL-6 (p<0.001), and IL-8 (p<0.01) among the traumatic group were significantly higher than those among the non-traumatic group. Anatomical trauma severity was also estimated using the total abbreviated injury scale and injury severity score, revealing significant positive correlations between the former and IL-6 (rs=0.6523, p<0.01) and IL-8 levels (rs=0.6584, p<0.01). CONCLUSIONS: Levels of IL-6 and IL-8 assist differentiation between traumatic and non-traumatic death, are useful objective indices of trauma severity and can support a diagnosis of traumatic death.

Short tandem repeat analysis in Japanese population.

Short tandem repeats (STRs), known as microsatellites, are one of the most informative genetic markers for characterizing biological materials. Because of the relatively small size of STR alleles (generally 100-350 nucleotides), amplification by polymerase chain reaction (PCR) is relatively easy, affording a high sensitivity of detection. In addition, STR loci can be amplified simultaneously in a multiplex PCR. Thus, substantial information can be obtained in a single analysis with the benefits of using less template DNA, reducing labor, and reducing the contamination. We investigated 14 STR loci in a Japanese population living in Sendai by three multiplex PCR kits, GenePrint PowerPlex 1.1 and 2.2. Fluorescent STR System (Promega, Madison, WI, USA) and AmpF/STR Profiler (Perkin-Elmer, Norwalk, CT, USA). Genomic DNA was extracted using sodium dodecyl sulfate (SDS) proteinase K or Chelex 100 treatment followed by the phenol/chloroform extraction. PCR was performed according to the manufacturer's protocols. Electrophoresis was carried out on an ABI 377 sequencer and the alleles were determined by GeneScan 2.0.2 software (Perkin-Elmer). In 14 STRs loci, statistical parameters indicated a relatively high rate, and no significant deviation from Hardy-Weinberg equilibrium was detected. We apply this STR system to paternity testing and forensic casework, e.g., personal identification in rape cases. This system is an effective tool in the forensic sciences to obtain information on individual identification.

Sudden unexpected death in childhood due to eosinophilic myocarditis.

A 12-year-old boy with no previous serious medical history experienced abdominal discomfort and chest pains for 5 days and suddenly died. The autopsy revealed diffuse and extensive infiltration of eosinophils into the myocardium, with poorly formed granulomas and few fibrotic changes. The necrotic changes was so extensive that Charcot-Leyden crystals formed. The other visceral organs had no specific pathologic changes except for mild lymphocytic infiltration with an increase in goblet cells in the bronchial areas and eosinocytosis in the blood vessels. An initial viral infection seemed to have caused subsequent eosinophil activation due to an allergic condition. Eosinophilic myocarditis is a rare cause of sudden death in apparently healthy children. Cardiac toxicity of eosinophils is, however, well established and dominates the ultimate prognosis of patients with complicated eosinophilia.

Correlation between serum IL-6 levels and death: usefulness in diagnosis of "traumatic shock"?

Interleukin-6 (IL-6) has been considered as an important mediator of inflammation. Clinically it is a well-known marker of the severity of injury following major trauma. In this study, the levels of IL-6 in body serum were applied to a traumatic death index. Of ninety victims 55 were men and 35 women, with a mean age of 53.4+/- 19 (S.D.) years. The cases were classified as traumatic deaths (38 cases), non-traumatic deaths other than natural causes of deaths (36 cases), and deaths due to natural causes (16 cases). All samples were collected within 2 days after death. The mean values of IL-6 levels of the traumatic, non-traumatic and disease groups were 8608.97, 2205.65, and 3266.64 pg/ml, respectively. Some cases in non-traumatic and disease cases were beyond 10 000 pg/ml, however, the mean value of the traumatic group was statistically higher than that of the other two groups. Even though several cases had high levels of IL-6 in spite of instantaneous death, the results showed that IL-6 levels are helpful in the diagnosis of traumatic shock.

Monoclonal antibody against an amniotic protein carrying ABH blood group epitopes and its forensic application.

A mouse monoclonal antibody against an amniotic protein carrying ABH antigenic epitopes was established. BALB/c mice were immunized by an amniotic protein of molecular weight over 200 kDa, which had proved to be the carrier protein of ABH blood group epitopes by analysis with SDS-PAGE and immunoblotting. The antibody, ASP-1, was directed to the amniotic carrier protein without affecting the ABH blood group antigenicity, and did not cross-react with other body fluids which included blood, saliva, semen, urine or vaginal secretion. The immunoglobulin class of ASP-1 was IgG1 with a titer of 1 : 1,600. ASP-1 was used to detect the ABH blood group of amniotic fluid by the sandwich ELISA in which wells of plates were coated with ASP-1, and the ABH blood group of the captured protein was detected with mouse IgM anti-A and -B antibodies and enzyme conjugated anti-mouse IgM. The sandwich ELISA could successfully detect the blood group of amniotic fluid in mixed body fluids.

Comparison of the likelihood ratio and identity-by-state scoring methods for analyzing sib-pair test cases: a study using computer simulation.

To assess the power and significance of the likelihood ratio (LR) and the identity-by-state scoring (IBS) methods for a pair of siblings, we performed computer simulations by use of 10 DNA markers (HLA-DQalpha, D1S80, and 8 short tandem repeat loci) that were frequently analyzed in paternity tests in Japan. The combined power of discrimination of these 10 markers in the Japanese population is 0.999 999 999 98. Pedigrees each consisting of 10,000 pair of full-siblings, half-siblings and unrelated individuals were generated and typed on all markers as random samples. Both the summation of log10 LR and IBS of each group had approximate standard normal distribution with significant differences between the means. Statistical studies showed that the LR method has 91% power to detect unrelated individuals and 38% power to detect half-siblings as not full-siblings with a 5% false-positive rate, whereas the IBS method does 87% and 42% powers, respectively. In 62% of full-siblings, in contrast with only 0.2% of unrelated individuals, the values of LR exceeded 100 which was equivalent to 0.99 of probability of full-sibship at 50% prior probability. The advantage of the LR method over IBS method was convincing especially for the detection of unrelated individuals as not half-siblings, however, the latter would be also informative for sib-pair tests if sufficient number of polymorphic markers are available.

Diatom numbers around the continental shelf break.

Diatom concentrations in seawater were examined monthly at four aquatic areas. Diatom concentrations inside a bay showed a monthly variation, but these were detectable. On the other hand, in the open sea around the continental shelf break, there were few diatoms in any season. When a person drowns in the open sea, the diatom test cannot be expected to function reliably.

X chromosome inactivation patterns in 45,X/46,XX mosaics.

To investigate X chromosome inactivation (XCI) patterns in 45,X/46.XX mosaics, genomic DNA was extracted from peripheral blood samples of 15 female subjects who showed different proportions of 45,X cell clones. XCI patterns were analyzed using two assays. The first assay was the BstXI restriction endonuclease detection of an X-linked phosphoglycerate kinase (PGK) gene polymorphism following digestion of the DNA with methylation-sensitive HpaII, or with methylation-insensitive AfaI as a control. The second assay was the detection of a CAG triplet repeat polymorphism in the X-linked androgen receptor (AR) gene after sodium bisulfite treatment. Of the 15 subjects, 11 were informative due to heterozygosity for at least one of the polymorphisms (6 were heterozygous for the PGK polymorphism and 9 were heterozygous for the AR polymorphism). Four of the 11 informative subjects (36%) showed extremely skewed XCI for at least one of the polymorphisms, which was a much higher incidence than previously reported for normal females. Moreover, 3 of these 4 women had proportions of 45,X cell clones greater than 20%. Although our results may be due to several possible cytogenetic or molecular mechanisms, the most likely explanation is that cases of 45,X/46,XX that contain relatively high levels of 45,X cell clones probably arose due to structural aberrations of the X chromosome undetectable by conventional karyotyping.