The Y-chromosome, as with other chromosomes in the cell, is subject to mutations. However, unlike autosomal genes, the Y chromosome does not undergo recombination, and therefore individuals from different geographical regions may have differing distribution patterns with respect to Y-chromosome mutations. More detailed knowledge and information regarding Y-chromosome mutations might therefore provide insights into phylogenetic history and personal identification. Here, we describe a case study involving genotype-phenotype discrepancy in an Indian male individual. We found that the mistyping in sex determination was caused by a deletion in the amelogenin Y (AMEL Y) gene. Furthermore, on examining the short tandem repeat (Y-STR) loci using the PowerPlex(R) Y23 System, we found four more deleted loci on Yp11.2 (DYS576, DYS481, DYS570, and DYS458) in this sample. We performed deletion mapping for this sample, and we propose that the microdeletion on the Yp11.2 locus occurred approximately in the 6.44 Mb to 9.75 Mb region. Previous studies have reported that the AMEL Y deletion is a common mutation in the Indian population. Taking into account regional differences, we also analyzed several area-specific Y-chromosome mutations.
Amelogenin ; DNA* ; Humans ; Male ; Microsatellite Repeats ; Recombination, Genetic ; Y Chromosome*

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

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.

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*

Two quadruplex PCR reactions were designed for 7 tetrameric (D3S2406, D4S2368, D5S818, D7S821, D9S925, D13S317, D19S253) and one trimeric (D6S1043) short tandem repeats loci to study the allele frequency and the applicability of genetic variation in these loci in forensic case works. For 310 unrelated Koreans DNA was isolated from peripheral blood using phenol/chloroform method. Quadruplex I was consisted of D4S2368, D6S1043, D7S821, D9S925 and quadruplex II D3S2406, D5S818, D13S317, D19S253. The amplified products were analyzed by 5%polyacrylamide gel electrophoresis followed by silver staining. The heterozygosity in each loci ranged 92.91-66.13%, and PD(Power of Discrimination) was above 0.85 in each loci. Every loci except D6S1043 followed hardy-Weinberg expectation. The cumulative PI was low as 1.65x10-10. Two mutations were noted, one in D19S253 and the other in D9S925 among 234 gametes. With these results above eight STR loci studied here proved to be highly polymorphic enough to be used in forensic field. This study provides valuable population data in these loci for Korean.
DNA ; Electrophoresis ; Gene Frequency ; Genetic Variation ; Germ Cells ; Microsatellite Repeats ; Polymerase Chain Reaction* ; Silver Staining

Two quadruplex PCR reactions were designed for 7 tetrameric (D3S2406, D4S2368, D5S818, D7S821, D9S925, D13S317, D19S253) and one trimeric (D6S1043) short tandem repeats loci to study the allele frequency and the applicability of genetic variation in these loci in forensic case works. For 310 unrelated Koreans DNA was isolated from peripheral blood using phenol/chloroform method. Quadruplex I was consisted of D4S2368, D6S1043, D7S821, D9S925 and quadruplex II D3S2406, D5S818, D13S317, D19S253. The amplified products were analyzed by 5%polyacrylamide gel electrophoresis followed by silver staining. The heterozygosity in each loci ranged 92.91-66.13%, and PD(Power of Discrimination) was above 0.85 in each loci. Every loci except D6S1043 followed hardy-Weinberg expectation. The cumulative PI was low as 1.65x10-10. Two mutations were noted, one in D19S253 and the other in D9S925 among 234 gametes. With these results above eight STR loci studied here proved to be highly polymorphic enough to be used in forensic field. This study provides valuable population data in these loci for Korean.
DNA ; Electrophoresis ; Gene Frequency ; Genetic Variation ; Germ Cells ; Microsatellite Repeats ; Polymerase Chain Reaction* ; Silver Staining

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.
Computational Biology ; DNA, Mitochondrial* ; Gene Frequency ; High-Throughput Nucleotide Sequencing* ; Methods ; Sequence Analysis, DNA

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.
Alcohols ; Aldehyde Dehydrogenase ; Asian Continental Ancestry Group ; Chromosomes, Human, Pair 12 ; DNA ; Flushing ; Humans ; Hypersensitivity ; Microfluidics ; Polymorphism, Single Nucleotide ; Sensitivity and Specificity

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.

Stent thrombosis (ST) is a rare but catastrophic complication of a drug-eluting stent. Although dual antiplatelet therapy with aspirin and clopidogrel significantly reduces the occurrence of ST, it continues to occur and is occasionally associated with clopidogrel resistance. Here, we describe a 71-yr-old man with subacute stent thrombosis and clopidogrel resistance following drug-eluting stent implantation who underwent successful ticagrelor rescue therapy.
Aspirin ; Drug-Eluting Stents ; Humans ; Stents* ; Thrombosis*