Publications by authors named "Sohee Cho"

Inferring the ancestral origin of DNA evidence recovered from crime scenes is crucial in forensic investigations, especially in the absence of a direct suspect match. Ancestry informative markers (AIMs) have been widely researched and commercially developed into panels targeting multiple continental regions. However, existing forensic ancestry inference panels typically group East Asian individuals into a homogenous category without further differentiation.

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Background: Relatives share more genomic regions than unrelated individuals, with closer relatives sharing more regions. This concept, paired with the increased availability of high-throughput single nucleotide polymorphism (SNP) genotyping technologies, has made it feasible to measure the shared chromosomal regions between individuals to assess their level of relation to each other. However, such techniques have remained in the conceptual rather than practical stages in terms of applying measures or indices.

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Background: Determination of genetic relatedness between individuals plays a crucial role in resolving numerous civil cases involving familial relationships and in forensic investigation concerning missing persons. Short tandem repeats (STRs), known for their high degree of DNA polymorphism, have traditionally been the primary choice of DNA markers in genetic testing, but their application for kinships testing is limited to cases involving close kinship. SNPs have emerged as promising supplementary markers for kinship determination.

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Background: Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background.

Objective: To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers.

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Context.—: Mitochondria and mitochondrial DNA have been suggested to play a role in cancer initiation and progression. Knowledge of mitochondrial DNA could provide a breakthrough to advance cancer management.

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The determination of tissue type is important when reconstructing a crime scene as skin cells may indicate innocent contact, whereas other types of cells, such as blood and semen, may indicate foul play. Up to now, there has been no specific DNA methylation-based marker to distinguish skin cell DNA from other body fluids. The goal of this study is to develop a DNA methylation-based assay to detect and identify skin cells collected at forensic crime scenes for use in DNA typing.

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When DNA profiles obtained from biological evidence at a crime scene fail to match suspects or anyone in the database, forensic DNA phenotyping, which is the prediction of externally visible characteristics, can facilitate a traced search for an unknown suspect by limiting the search range. Therefore, age, trait, or lifestyle predictors, as well as the predictor for colorations, have been researched in the forensic field. In the present study, for the development of a prediction model for BMI or obesity, we investigated several previously reported BMI- or obesity-associated genetic and epigenetic markers that included four CpGs (cg06500161, cg00574958, cg12593793, and cg10505902 of the ABCG1, CPT1A, LMNA, and PDE4DIP genes, respectively), and eight SNPs (rs12463617, rs1558902, rs591166, rs11030104, rs11671664, rs6545814, rs16858082, and rs574367 near the TMEM18, FTO, MC4R, BDNF, GIPR/QPCTL, ADCY3/RBJ, GNPDA2, and SEC16B genes, respectively) in 700 Koreans within the BMI ranging from 16.

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DNA analysis of degraded samples and low-copy number DNA derived from skeletal remains, one of the most challenging forensic tasks, is common in disaster victim identification and genetic analysis of historical materials. Massively parallel sequencing (MPS) is a useful technique for STR analysis that enables the sequencing of smaller amplicons compared with conventional capillary electrophoresis (CE), which is valuable for the analysis of degraded DNA. In this study, 92 samples of human skeletal remains (70+ years postmortem) were tested using an in-house MPS-STR system designed for the analysis of degraded DNA.

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Chimerism is the presence of two genetically different cell lines within a single organism, which is rarely observed in humans. Usually, chimerism in the human body is revealed by the finding of an abnormal phenotype during a medical examination or is unexpectedly detected in routine genetic analysis. However, the incidence or underlying mechanism of chimerism remains unclear due to the lack of information on this infrequent biological event.

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Single nucleotide polymorphisms (SNPs) are valuable markers complementary to conventional forensic short tandem repeat (STR) markers in genetic typing, with potential advantages in challenging forensic casework. With the advent of high-throughput technologies, such as microarrays and massively parallel sequencing, the use of SNP typing has now expanded to large-scale forensic applications. Herein, a forensic case is presented to demonstrate the usefulness of SNP typing in identifying large-scale human bone remains with reference database construction.

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Article Synopsis
  • The study aims to create a method for identifying body fluids (like saliva, blood, and semen) using specific DNA methylation patterns.
  • Researchers focused on amplifying and sequencing genetic markers to measure methylation at various sites and analyzed 124 modified DNA samples.
  • Ultimately, they developed a streamlined process that can efficiently identify fluid types using just five key CpG sites, making it practical for forensic labs.
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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.

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Article Synopsis
  • Massively parallel sequencing (MPS) can provide valuable ancestry information even when there are no reference samples to compare against.
  • The HID-Ion AmpliSeq Ancestry Panel analyzed 750 unrelated individuals from various Asian populations to evaluate its accuracy in determining biogeographic ancestry.
  • The results identified Northeast Asians and Vietnamese primarily as East Asians, while some individuals from Nepal, India, and Pakistan were misclassified as Europeans, highlighting the need for larger sample sizes for more comprehensive population analysis.
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Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems.

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Mutations occur in Y chromosome genes similar to autosomal genes. However, unlike autosomal genes, Y chromosome genes do not undergo recombination, which produce distinctive characteristics and distribution patterns in different geographic regions. Therefore, detailed analysis of mutations of Y chromosome genes might provide information for personal identification or analysis of phylogenetic history.

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Numerous molecular biomarkers have been proposed as predictors of chronological age. Among them, T-cell specific DNA rearrangement and DNA methylation markers have been introduced as forensic age predictors in blood because of their high prediction accuracy. These markers appear highly promising, but for better application to forensic casework sample analysis the proposed markers and genotyping methods must be tested further.

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The usefulness of single nucleotide polymorphism (SNP) loci for kinship testing has been demonstrated in many case works, and suggested as a promising marker for relationship identification. For interpreting results based on the calculation of the likelihood ratio (LR) in kinship testing, it is important to prepare cutoffs for respective relatives which are dependent on genetic relatedness. For this, analysis using true pedigree data is significant and reliable as it reflects the actual frequencies of markers in the population.

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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.

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Age estimation based on quantifying signal joint T cell receptor excision circle (sjTREC) in T cells has been established to be a promising approach in forensic practice and demonstrated in different ethnic groups. Considering that the homeostasis of T cells carrying sjTRECs is closely related to the immunologic status of a person, it is important to investigate the influence of various immunologic statuses on the age estimation model. In this study, quantification of sjTREC contents was performed for groups of people with various immune system statuses, and the result showed less correlation with chronological age (r  = 0.

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Background: Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population.

Case Report: 169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members.

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A collaborative exercise on DNA methylation based body fluid identification was conducted by seven laboratories. For this project, a multiplex methylation SNaPshot reaction composed of seven CpG markers was used for the identification of four body fluids, including blood, saliva, semen, and vaginal fluid. A total of 30 specimens were prepared and distributed to participating laboratories after thorough testing.

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In forensic field investigations using single nucleotide polymorphism (SNP) have been performed for various purposes. Based on the characteristics of SNP, it is essential to have a multi-amplification technology and a platform to analyze the amplified SNP markers accurately. Here, we have developed a platform based on the resequencing array of Affymetrix analyzing 169 SNP markers amplified via multiplex PCR and verified its forensic application.

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The estimation of age from biological samples (i.e., remains) at crime scenes could provide useful information about both victims and other persons related to criminal activities.

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SA β-Gal activity is a key marker of cellular senescence. The origin of this activity is the lysosomal β-galactosidase, whose activity has increased high enough to be detected at suboptimal pH. SA β-Gal is also expressed in the cells in quiescence driven by serum-starvation or a high confluency, and it has been hypothesized that SA β-Gal positivity is rather a surrogate marker of high lysosome content or activity.

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