Revealing Joseon period People’s single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea / 대한해부학회지

Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.

Comparison of Two Variant Analysis Programs for Next-Generation Sequencing Data of Whole Mitochondrial Genome

Background@#With advance of next-generation sequencing (NGS) techniques, the need for mitochondrial DNA analysis is increasing not only in the forensic area, but also in medical fields. @*Methods@#Two commercial programs, Converge Software (CS) and Torrent Variant Caller for variant calling of NGS data, were compared with a considerable amount of sequence data of 50 samples with a homogeneous ethnicity. @*Results@#About 2,300 variants were identified and the two programs showed about 90% of consistency. CS, a dedicated analysis program for mitochondrial DNA, showed some advantages for forensic use. By additional visual inspection, several causes of discrepancy in variant calling results were identified. Application of different notation rules for mitochondrial sequence and the minor allele frequency close to detection threshold were the two most significant reasons. @*Conclusion@#With prospective improvement of each program, researchers and practitioners should be aware of characteristics of the analysis program they use and prepare their own strategies to determine variants.

Therapy-Related Acute Myeloid Leukemia Diagnosed at Postmortem in a Long-term Survivor of Advanced Hepatocellular Carcinoma / 대한법의학회지

Acute myeloid leukemia (AML) is a common hematologic malignancy with high mortality and a short survival period in adults. About 10% of these cases, called therapy-related AML, are reported to be the consequence of chemotherapy or radiotherapy of previous malignancy. In a clinical setting, this is usually diagnosed by peripheral blood smear or bone marrow biopsy by assessing the proportion of blasts. However, postmortem blood samples are not suitable for smear analysis because of hemolysis. Therefore, ancillary tests for identifying leukemic infiltration or related molecular change can provide an alternative diagnostic clue for AML. The deceased had been treated for 3 years for a combined type of hepatocellular carcinoma with multiple pulmonary metastases. Treatments included the resections of primary and metastatic tumors, chemotherapy, and radiotherapy, which prevented further progression of his cancer. One year after the last treatment, he suddenly collapsed without any specific symptoms and shortly died. The microscopic examination of the autopsy samples revealed extensive extramedullary infiltration of leukemia, which was confirmed as an AML by a series of ancillary immunohistochemical staining. This case illustrates both the importance of careful hematologic observation in cancer survivors and the necessity of a detailed medical diagnosis in a medicolegal autopsy.

Investigation of Mosaicism Detected in STR Typing / 대한법의학회지

Short tandem repeats (STRs) are the most popular markers for human identification in forensics. These markers can be easily analyzed through a multiplex polymerase chain reaction and electrophoresis and provide high discrimination power. However, in STR analysis, several atypical phenomena can be observed such as allelic dropouts, drop-ins, or imbalance, which may be due to DNA polymerase slippage or DNA degradation effects. The observed atypical STR profiles can also provide information for mixed DNA samples or chromosomal abnormalities. In this study, we report a case of mosaicism detected in routine casework of paternity testing. Hair samples from a phenotypically normal male were tested, and the result presented a typical STR profile of a female for the amelogenin gene (XX). Through chromosome analysis using peripheral blood, it was found that 45,X/46,XY mosaicism resulted in the discrepancy between the genotype and the phenotype. In addition, the amount of Y chromosome detected was particularly low in hair compared to that in blood. This study shows that mosaicism can make interpretation difficult during STR analysis and suggests that sample types and repeated analysis should be considered even for routine STR testing.

Concern about the Diagnosis of Sudden Infant Death Syndrome in Current Death Investigation System / 대한법의학회지

Because their contents would be utilized in many parts of society, medical diagnosis should be accurate and veracious especially for dead body. Autopsy records are one of the representative form of medical diagnosis determined by forensic pathologists, which are superior to the certificates for postmortem inspection in their completeness. But autopsy has its own limitation because of morphologic and biochemical changes in postmortem status and diagnostic criteria mainly based on clinical situations. Also, various diseases with only functional impairments or borderline/ambiguous changes make the forensic diagnosis difficult, for example, sudden infant death syndrome (SIDS). Even though numerous researchers with various backgrounds have been dedicated to clarifying the nature of SIDS, it seems too early to use this term in autopsy diagnosis in general. A thorough investigation of the death scene, the family dynamics, and the medical history should be guaranteed and the forensic pathologists should agree for the definition and diagnostic criteria of SIDS based on scientific knowledge.

Intentional Death Caused by the Overdose of Nonprescription Drugs: An Autopsy Case of Acetaminophen Poisoning / 대한법의학회지

Acetaminophen or paracetamol (N-acetyl-para-aminophenol [APAP]) is a safe and effective antipyretic and analgesic drug and is a representative nonprescription drug. However, APAP is one of the most common nonprescription drugs used for intentional overdose or suicide, thereby resulting in hundreds of deaths annually in the United States. Moreover, the misuse of nonprescription drugs is a cause of increasing concern in Korea with the revision of the Pharmaceutical Affairs Law in 2012. Generally, the mortality rate of APAP overdose is extremely low due to the well-established treatment guidelines and availability of antidotes. However, it should not be overlooked because of the high number of either accidental or intentional APAP overdose cases recorded every day. To achieve a good prognosis, individuals with APAP overdose must be immediately identified and brought to the hospital. Herein, we report an autopsy case of an individual with APAP overdose who died due to acute liver injury.

Single Nucleotide Polymorphisms Associated with Alcohol-Induced Flushing Syndrome in Korean Population / 대한법의학회지

Alcohol-induced flushing syndrome is one of the alcohol hypersensitivity reactions commonly found among Asian population. This study was designed to find markers that can predict this particular propensity among Korean population and to assess the applicability of this finding to build a prediction model as forensic DNA phenotyping tool to operate in practical forensic cases. Five hundred seventy unrelated Koreans were genotyped using microfluidic technology with 24 possible candidate single nucleotide polymorphism (SNP) markers. Of the 24 candidate SNPs, four markers, rs671, rs2074356, rs4646776, and rs10849915, on chromosome 12 showed statistically significant association with P-values ranging from 1.39×10⁻¹⁴ to 0.004988 among our subjects. All four markers show relatively high specificity values, ranging from 0.804651 to 0.972093, presenting their capabilities as differential SNPs that can distinguish a person with or without alcohol-induced flushing syndrome. Maneuvering these candidate SNPs as well as finding additional potential markers through future studies will help building an appropriate prediction model for Koreans that can be used as supplementary tool for individual identification.

Classification of Common Relationships Based on Short Tandem Repeat Profiles Using Data Mining / 대한법의학회지

We reviewed past studies on the identification of familial relationships using 22 short tandem repeat markers. As a result, we can obtain a high discrimination power and a relatively accurate cut-off value in parent-child and full sibling relationships. However, in the case of pairs of uncle-nephew or cousin, we found a limit of low discrimination power of the likelihood ratio (LR) method. Therefore, we compare the LR ranking method and data mining techniques (e.g., logistic regression, linear discriminant analysis, diagonal linear discriminant analysis, diagonal quadratic discriminant analysis, K-nearest neighbor, classification and regression trees, support vector machines, random forest [RF], and penalized multivariate analysis) that can be applied to identify familial relationships, and provide a guideline for choosing the most appropriate model under a given situation. RF, one of the data mining techniques, was found to be more accurate than other methods. The accuracy of RF is 99.99% for parent-child, 99.44% for full siblings, 90.34% for uncle-nephew, and 79.69% for first cousins.

Classification of Common Relationships Based on Short Tandem Repeat Profiles Using Data Mining / 대한법의학회지

We reviewed past studies on the identification of familial relationships using 22 short tandem repeat markers. As a result, we can obtain a high discrimination power and a relatively accurate cut-off value in parent-child and full sibling relationships. However, in the case of pairs of uncle-nephew or cousin, we found a limit of low discrimination power of the likelihood ratio (LR) method. Therefore, we compare the LR ranking method and data mining techniques (e.g., logistic regression, linear discriminant analysis, diagonal linear discriminant analysis, diagonal quadratic discriminant analysis, K-nearest neighbor, classification and regression trees, support vector machines, random forest [RF], and penalized multivariate analysis) that can be applied to identify familial relationships, and provide a guideline for choosing the most appropriate model under a given situation. RF, one of the data mining techniques, was found to be more accurate than other methods. The accuracy of RF is 99.99% for parent-child, 99.44% for full siblings, 90.34% for uncle-nephew, and 79.69% for first cousins.

Single Nucleotide Polymorphisms Associated with Alcohol-Induced Flushing Syndrome in Korean Population / 대한법의학회지

Alcohol-induced flushing syndrome is one of the alcohol hypersensitivity reactions commonly found among Asian population. This study was designed to find markers that can predict this particular propensity among Korean population and to assess the applicability of this finding to build a prediction model as forensic DNA phenotyping tool to operate in practical forensic cases. Five hundred seventy unrelated Koreans were genotyped using microfluidic technology with 24 possible candidate single nucleotide polymorphism (SNP) markers. Of the 24 candidate SNPs, four markers, rs671, rs2074356, rs4646776, and rs10849915, on chromosome 12 showed statistically significant association with P-values ranging from 1.39×10⁻¹⁴ to 0.004988 among our subjects. All four markers show relatively high specificity values, ranging from 0.804651 to 0.972093, presenting their capabilities as differential SNPs that can distinguish a person with or without alcohol-induced flushing syndrome. Maneuvering these candidate SNPs as well as finding additional potential markers through future studies will help building an appropriate prediction model for Koreans that can be used as supplementary tool for individual identification.

Acute Myocardial Infarction due to Cardiac Allograft Vasculopathy: An Autopsy Report / 대한법의학회지

After the Organ Transplant Act was enforced in 2000, the criteria for the diagnosis of brain death have been legalized, and cardiac transplantation has become a promising treatment choice for patients with chronic heart disease. Even though more than hundreds of cases have been accumulated in the national registry and the survival rates are increasing, the compliance of long-term survivors may decrease paradoxically, which can hinder the efforts to enhance the quality of the registry. The patients who are lost from the doctor's surveillance and die outside hospitals should be appropriately examined to determine the cause of death so that the influence of their medical condition, if any, on their death could be revealed. Here, we report an autopsy case of a patient who died of a complication of chronic rejection after cardiac transplantation.

Sudden Cardiac Death due to Coronary Fibromuscular Dysplasia: Case Report and Literature Review / 대한법의학회지

Fibromuscular dysplasia (FMD) of the coronary artery is a rare cause of sudden cardiac death; however, its prevalence and fatality may have been overlooked so far. A 47-year-old man complained of pain in his back and shoulder and became unconscious. Despite resuscitation, he died 3 hours after symptom onset. The heart weight was in the normal range; however, all three major coronary arteries showed intimal thickening without atherosclerosis or inflammatory cell infiltration. Fragmentations and duplications of the internal elastic lamina which are histologic features of intimal fibroplasia, a focal-type FMD, were observed. The prevalence of coronary FMD remains unknown, although it may be related to spontaneous coronary artery dissection and sudden death. The histopathologic confirmation of coronary FMD and exclusion of other possible coronary diseases through autopsy are essential to reveal the nature of the disease and therefore apply the information in dealing with legal problems after death.

Detection of Innate and Artificial Mitochondrial DNA Heteroplasmy by Massively Parallel Sequencing: Considerations for Analysis

BACKGROUND: Mitochondrial heteroplasmy, the co-existence of different mitochondrial polymorphisms within an individual, has various forensic and clinical implications. But there is still no guideline on the application of massively parallel sequencing (MPS) in heteroplasmy detection. We present here some critical issues that should be considered in heteroplasmy studies using MPS. METHODS: Among five samples with known innate heteroplasmies, two pairs of mixture were generated for artificial heteroplasmies with target minor allele frequencies (MAFs) ranging from 50% to 1%. Each sample was amplified by two-amplicon method and sequenced by Ion Torrent system. The outcomes of two different analysis tools, Torrent Suite Variant Caller (TVC) and mtDNA-Server (mDS), were compared. RESULTS: All the innate heteroplasmies were detected correctly by both analysis tools. Average MAFs of artificial heteroplasmies correlated well to the target values. The detection rates were almost 90% for high-level heteroplasmies, but decreased for low-level heteroplasmies. TVC generally showed lower detection rates than mDS, which seems to be due to their own computation algorithms which drop out some reference-dominant heteroplasmies. Meanwhile, mDS reported several unintended low-level heteroplasmies which were suggested as nuclear mitochondrial DNA sequences. The average coverage depth of each sample placed on the same chip showed considerable variation. The increase of coverage depth had no effect on the detection rates. CONCLUSION: In addition to the general accuracy of the MPS application on detecting heteroplasmy, our study indicates that the understanding of the nature of mitochondrial DNA and analysis algorithm would be crucial for appropriate interpretation of MPS results.

Sudden Cardiac Death due to Coronary Fibromuscular Dysplasia: Case Report and Literature Review / 대한법의학회지

Fibromuscular dysplasia (FMD) of the coronary artery is a rare cause of sudden cardiac death; however, its prevalence and fatality may have been overlooked so far. A 47-year-old man complained of pain in his back and shoulder and became unconscious. Despite resuscitation, he died 3 hours after symptom onset. The heart weight was in the normal range; however, all three major coronary arteries showed intimal thickening without atherosclerosis or inflammatory cell infiltration. Fragmentations and duplications of the internal elastic lamina which are histologic features of intimal fibroplasia, a focal-type FMD, were observed. The prevalence of coronary FMD remains unknown, although it may be related to spontaneous coronary artery dissection and sudden death. The histopathologic confirmation of coronary FMD and exclusion of other possible coronary diseases through autopsy are essential to reveal the nature of the disease and therefore apply the information in dealing with legal problems after death.

Acute Myocardial Infarction due to Cardiac Allograft Vasculopathy: An Autopsy Report / 대한법의학회지

After the Organ Transplant Act was enforced in 2000, the criteria for the diagnosis of brain death have been legalized, and cardiac transplantation has become a promising treatment choice for patients with chronic heart disease. Even though more than hundreds of cases have been accumulated in the national registry and the survival rates are increasing, the compliance of long-term survivors may decrease paradoxically, which can hinder the efforts to enhance the quality of the registry. The patients who are lost from the doctor's surveillance and die outside hospitals should be appropriately examined to determine the cause of death so that the influence of their medical condition, if any, on their death could be revealed. Here, we report an autopsy case of a patient who died of a complication of chronic rejection after cardiac transplantation.

A proposal for writing a better death certificate

Guidelines for writing death certificates have recently been released in various forms. However, the educational efforts of medical doctors do not seem to have led to significant improvements in the accuracy of death certificates. A death certificate can be considered as the process through which an individual's treatment sequence, and even life, is completed and summarized. Additionally, the decision about how to fill out a death certificate affects the amount of death compensation, the necessity of a legal investigation, and has implications for health care planning. However, the death certificate form used in Korea requires background knowledge of not only medicine, but also the legal system, which has placed a considerable burden on physicians in clinical practice. In addition to the continuous educational efforts of the community of physicians, other members of society should show appropriate appreciation and attention for the death investigation system. In the development of the system, the unique characteristics of the healthcare environment in Korea should be considered.

A proposal for writing a better death certificate

Guidelines for writing death certificates have recently been released in various forms. However, the educational efforts of medical doctors do not seem to have led to significant improvements in the accuracy of death certificates. A death certificate can be considered as the process through which an individual's treatment sequence, and even life, is completed and summarized. Additionally, the decision about how to fill out a death certificate affects the amount of death compensation, the necessity of a legal investigation, and has implications for health care planning. However, the death certificate form used in Korea requires background knowledge of not only medicine, but also the legal system, which has placed a considerable burden on physicians in clinical practice. In addition to the continuous educational efforts of the community of physicians, other members of society should show appropriate appreciation and attention for the death investigation system. In the development of the system, the unique characteristics of the healthcare environment in Korea should be considered.

Forensic DNA Phenotyping: A Review in Korean Perspective / 대한법의학회지

Forensic DNA phenotyping (FDP) using human externally visible characteristics (EVCs) is an emerging new technique that allows for the prediction of phenotypic traits of a person of interest using relevant sets of genetic markers. This technique predicts not only physical appearances, but also the behavioral characteristics as well as biogeographical information, serving as a powerful supplementary tool to narrow down the investigative pool in various forensic cases. Over the past few years, many countries, Europe and America being at the forefront, have conducted significant research to identify related markers for predicting pigmentation traits such as eye, hair, and skin color. Furthermore, some commercial platforms are now available for practical use in forensic cases. Korea and other Asian countries have also dedicated remarkable research to identify relevant markers to utilize FDP in forensic investigations. However, a slightly different approach is needed because Asians have limited phenotypic variations than Western populations. Thus, medically irrelevant and simple propensity traits such as smoking and alcohol consumption could be used to compensate for the limited phenotypic variations. This article is intended to inform readers about the progress and worldwide trends in EVC research, as well as the whereabouts and future prospects of FDP-related research in Korea. Although various legal and ethical disputes must be resolved beforehand, employing an FDP system can certainly be a powerful complementary tool for providing additional clues in forensic investigations.

Asian Ethnic Group Classification Model Using Data Mining / 대한법의학회지

In addition to identifying genetic differences between target populations, it is also important to determine the impact of genetic differences with regard to the respective target populations. In recent years, there has been an increasing number of cases where this approach is needed, and thus various statistical methods must be considered. In this study, genetic data from populations of Southeast and Southwest Asia were collected, and several statistical approaches were evaluated on the Y-chromosome short tandem repeat data. In order to develop a more accurate and practical classification model, we applied gradient boosting and ensemble techniques. To infer between the Southeast and Southwest Asian populations, the overall performance of the classification models was better than that of the decision trees and regression models used in the past. In conclusion, this study suggests that additional statistical approaches, such as data mining techniques, could provide more useful interpretations for forensic analyses. These trials are expected to be the basis for further studies extending from target regions to the entire continent of Asia as well as the use of additional genes such as mitochondrial genes.

SNP-Based Fetal DNA Detection in Maternal Serum Using the HID-Ion AmpliSeq™ Identity Panel / 대한법의학회지

Fetal DNA (fDNA) detection in maternal serum is a challenge due to low copy number and the smaller size of fDNA fragments compared to DNA fragments derived from the mother. Massively parallel sequencing (MPS) is a useful technique for fetal genetic analysis that is able to detect and quantify small amounts of DNA. In this study, seven clinical samples of maternal serum potentially containing fDNA were analyzed with a commercial single nucleotide polymorphism (SNP) panel, the HID-Ion AmpliSeq™ Identity Panel, and the results were compared to those from previous studies. Reference profiles for mothers and fetuses were not available, but multiple Y chromosomal SNPs were detected in two samples, indicating that fDNA was present in the serum and thereby validating observations of autosomal SNPs. This suggests that SNP-based MPS can be valuable for fDNA detection, thereby offering an insight into fetal genetic status. This technology could also be used to detect small amounts of DNA in mixed DNA samples for forensic applications.