Serum is free of cellular components. Because DNA is located in the nuclei or mitochondria of cells, serum could be assumed DNA free. Few previously published case reports to date have used serum for DNA typing. Here, we report on human genotyping via short tandem repeat (STR) analysis using serum as a sample, and discuss problems involved in the process.
DNA Fingerprinting* ; DNA* ; Humans ; Microsatellite Repeats* ; Mitochondria

Recently, studies on mitochondrial DNA (mtDNA) have increased rapidly. Conventional parameters, such as diversity index, pairwise comparison, are used to interpret and validate data on autosomal DNA; however, the use of these parameters to validate data from mitochondrial DNA databases (mtDNA DBs) needs to be verified because of the different transmission patterns of mtDNA. This study was done to verify the use of these conventional parameters and to test the "coverage concept" for a new parameter. The mtDNA DB is not very big; however, it is necessary to check how the change in parameters corresponds to the DB size. For this, we artificially rearranged a Korean DB into several small sub-DBs of variable sizes. The results show that the diversity in nucleotide variations and the different haplotype numbers do not vary as the size of DB increases. However, the "coverage" changed a lot. The coverage increased from 0.113 in a DB of 100 people to 0.260 in a DB of 653 people. Additionally, using the "coverage concept", we predicted how the total number of haplotypes changed with variations in the sub-DB size and compared the predicted result with final result. In conclusion, "coverage", in addition to conventional statistical parameters, can be used to check the usability of an mtDNA DB. Finally, we tried to predict the size of the whole mtDNA number in Korea using "saturation concept".
DNA ; DNA, Mitochondrial* ; Haplotypes ; Korea ; Phylogeny

The declining tendency of signal joint T-cell receptor excision circles (sjTRECs) in peripheral blood is known to be age-dependent, and their quantification in blood or bloodstains has recently been introduced as a tool for age estimation. Lymphoid tissues such as the thymus and spleen represent potential candidates for age estimation because they undergo age-related structural and functional changes. In the present study, the correlation between age and sjTREC levels in human lymphoid tissues, namely the thymus, spleen, and blood, obtained from autopsy cases were investigated, with the goal of establishing a reliable age estimation model. Results showed negative regression curves with coefficient values of r=-0.410, r=-0.611, and r=-0.584 for thymus, spleen, and blood, respectively. In addition, this model was testing using thymus samples from the torsos of dismembered bodies from two real forensic cases, and results showed the predicted ages to be close to the actual ages of the victims. Further study will be required to improve accuracy and reduce estimation error, particularly within the lower age range. Nonetheless, these results suggest that quantification of sjTRECs in not only blood but also in other lymphoid tissues could be a useful tool for age estimation in forensic cases.
Autopsy ; Humans* ; Joints* ; Lymphoid Tissue* ; Receptors, Antigen, T-Cell* ; Spleen ; T-Lymphocytes* ; Thymus Gland ; Torso

BACKGROUND: Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). METHODS: Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. RESULTS: In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF > or =7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF > or =7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. CONCLUSIONS: This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations.
Alleles* ; DNA Fingerprinting* ; Gene Frequency ; Genotype ; Haplotypes* ; Hematopoietic Stem Cells ; Histocompatibility Testing ; HLA Antigens ; HLA-A Antigens ; HLA-B Antigens ; HLA-C Antigens ; HLA-DRB1 Chains ; Humans ; Korea ; Leukocytes* ; Sequence Analysis ; Unrelated Donors

Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.

BACKGROUND AND OBJECTIVES: This study is aimed at elucidating potential temporal associations between the occurrence of Kawasaki disease (KD) and various viral infections. SUBJECTS AND METHODS: We obtained monthly patterns of KD from the seventh nationwide survey and viral detection data from the Korea Centers for Disease Control and Prevention from 2009 to 2011 and evaluated temporal correlations between them for each month. The respiratory viruses detected using a multiplex real-time-polymerase chain reaction kit were influenza virus (A/H1N1, A/H3N2, A/H5N1, and B), adenovirus, parainfluenza virus (type 1, 2, 3), respiratory syncytial virus (type A, B), human rhinovirus, human coronavirus (OC43/229E, NL63), human bocavirus, and enterovirus. RESULTS: We obtained data from a total of 13031 patients who were treated for acute KD from 87 hospitals with pediatric residence programs. During this survey, KD showed highest overall incidence in summer and winter seasons and lowest incidence in February and October. We received viral detection data for a total of 14267 patients. Viral detection was highest during winter and spring seasons. The most commonly detected virus was human rhinovirus (32.6%), followed by influenza virus (26.8%). The monthly incidence of KD showed significant correlation with the monthly overall viral detection (p=0.022, r=0.382). In particular, human bocavirus and enterovirus have significant correlations with monthly patterns of KD occurrence (p=0.032 and p=0.007, respectively) and influenza virus correlated with KD occurrence with borderline significance (p=0.063). CONCLUSION: The temporal association between monthly occurrence of KD and viral detection suggests the etiologic importance of precedent infection in the development of KD.
Adenoviridae ; Centers for Disease Control and Prevention (U.S.) ; Coronavirus ; Enterovirus ; Human bocavirus ; Humans ; Incidence ; Korea ; Mucocutaneous Lymph Node Syndrome* ; Orthomyxoviridae ; Paramyxoviridae Infections ; Respiratory Syncytial Viruses ; Rhinovirus ; Seasons

Serum or plasma is free of cellular components. As DNA is in the nucleus or mitochondria of a cell, it can be presumed that serum/plasma is DNA free. However, there are cases wherein serum/plasma is the only resource available for identification analysis, yet no sufficient data are available regarding whether reliable DNA testing can be applied to such cases, and what the influencing factors are when testing is a valid course of action. The aim of this study is to illustrate the factors that can be used in the genetic testing of serum/plasma when identifying an individual. The results showed that the concentration of serum DNA significantly increased over time in 4℃ storage, and the DNA yields from samples stored in heparin tubes were overall higher than from samples stored in ethylenediaminetetraacetic acid tubes. We observed that the concentration of DNA in serum successfully matched 100% to the short tandem repeat data of blood DNA.
DNA Fingerprinting ; DNA* ; Edetic Acid ; Genetic Testing ; Heparin ; Humans ; Microsatellite Repeats ; Mitochondria ; Plasma*

PURPOSE: The current study was conducted in order to develop the Korean Healthy Eating Index (KHEI) for assessing adherence to national dietary guidelines and comprehensive diet quality of healthy Korean adults using the 5th Korea National Health and Nutrition Examination Survey (KNHANES) data. METHODS: The candidate components of KHEI were selected based on literature reviews, dietary guidelines for Korean adults, 2010 Dietary Reference Intakes for Koreans (2010 KDRI), and objectives of HP 2020. The associations between candidate components and risk of obesity, abdominal obesity, and metabolic syndrome were assessed using the 5th KNHANES data. The expert review process was also performed. RESULTS: Diets that meet the food group recommendations per each energy level receive maximum scores for the 9 adequacy components of the index. Scores for amounts between zero and the standard are prorated linearly. For the three moderation components among the total of five, population probability densities were examined when setting the standards for minimum and maximum scores. Maximum scores for the total of 14 components are 100 points and each component has maximum scores of 5 (fruit intakes excluding juice, fruit intake including juice, vegetable intakes excluding Kimchi and pickles, vegetable intake including Kimchi or pickles, ratio of white meat to read meat, whole grains intake, refined grains intake, and percentages of energy intake from carbohydrate) or 10 points (protein foods intake, milk and dairy food intake, having breakfast, sodium intake, percentages of energy intake from empty calorie foods, and percentages of energy intake from fat). The KHEI is a measure of diet quality as specified by the key diet recommendations of the dietary guidelines and 2010 KDRIs. CONCLUSION: The KHEI will be used as a tool for monitoring diet quality of the Korean population and subpopulations, evaluation of nutrition interventions and research.
Adult* ; Breakfast ; Edible Grain ; Diet ; Eating* ; Energy Intake ; Fruit ; Humans ; Korea* ; Meat ; Milk ; Nutrition Policy ; Nutrition Surveys* ; Obesity ; Obesity, Abdominal ; Recommended Dietary Allowances ; Sodium ; Vegetables

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.
Asia ; Asian Continental Ancestry Group* ; Classification* ; Data Mining* ; Decision Trees ; Ethnic Groups* ; Genes, Mitochondrial ; Health Services Needs and Demand ; Humans ; Microsatellite Repeats ; Models, Statistical

Recently, it has been reported that transfused patients can generate admixture-like genetic profiles. As genetic material of the donor can survive for a reasonable time after transfusion, the recipient's genomic DNA is likely to have a mixture pattern. An autopsy case of a man transfused perimortem generated a mixture patterned short tandem repeat profile. Notably, the patient was transfused mostly with nuclear-deficient cells, limiting the donor genetic material available for the recipient. As a result, mixture-like patterns were observed consistently, regardless of change in input DNA content; the sample DNA content, which was serially diluted, ranged from 1 ng to 0.0625 ng. The distributions of foreign peaks appeared to be irreproducible, showing stochastic behaviors throughout the genotyped results. This study suggests that a cautious approach is required when genotyping of a patient who has undergone recent transfusion. One must consider the possibility of obtaining a mixture patterned profile in such patients, and therefore, choose parenchymal organs or tissues for reliable results.
Autopsy ; Blood Transfusion ; DNA ; DNA Fingerprinting ; Humans ; Microsatellite Repeats* ; Tissue Donors