• 대한의생명과학회지
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• 제28권3호
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• pp.157-169
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• 2022

DNA typing is the typical technology in the forensic science and plays a significant role in the personal identification of victims and suspects. Short tandem repeat (STR) is the short tandemly repeated DNA sequence consisting of 2~7 bp DNA units in specific loci. It is disseminated across the human genome and represents polymorphism among individuals. Because polymorphism is a key feature of the application of DNA typing STR analysis, STR analysis becomes the standard technology in forensics. Therefore, the DNA database (DNA-DB) was first introduced with 4 essential STR markers for the application of forensic science; however, the number of STR markers was expanded from 4 to 13 and 13 to 20 later to counteract the continuously increased DNA profile and other needed situations. After applying expanded STR markers to the South Korean DNA-DB system, it positively affected to low copy number analysis that had a high possibility of partial DNA profiles, and especially contributed to the theft cases due to the high portion of touch DNA evidence in the theft case. Furthermore, STR marker expansion not only contributed to the resolution of cold cases but also increased kinship index indicating the potential for improved kinship test accuracy using extended STR markers. Collectively, the expansion of the STR locus was considered to be necessary to keep pace with the continuously increasing DNA profile, and to improve the data integrity of the DNA-DB.

• 대한의생명과학회지
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• 제26권4호
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• pp.275-287
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• 2020

Since its introduction in the forensic field, quantitative PCR (qPCR) has played an essential role in DNA analysis. Quality of DNA should be evaluated before short tandem repeat (STR) profiling to obtain reliable results and reduce unnecessary costs. To this end, various human DNA quantification kits have been developed. Among these kits, the PowerQunat® System was designed not only to determine the total amount of human DNA and human male DNA from a forensic evidence item, but also to offer data about degradation of DNA samples. However, a crucial limitation of the PowerQunat® System is its high cost. Therefore, to minimize the cost of DNA quantification, we evaluated kit performance using a reduced volume of reagents (1/2-volume) using DNA samples of varying types and concentrations. Our results demonstrated that the low-volume method has almost comparable performance to the manufacturer's method for human DNA quantification, human male DNA quantification, and DNA degradation index. Furthermore, using a reduced volume of regents, it is possible to run 2 times more reactions per kit. We expect the proposed low-volume method to cut costs in half for laboratories dealing with large numbers of DNA samples.

• 대한의생명과학회지
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• 제27권2호
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• pp.105-110
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• 2021

Short Tandem Repeats (STR) analysis which characterized by genetic polymorphism has been widely used in the forensic genetic fields. Unfortunately, mutation occurred in various STR loci could make it difficult to interpret STR data. Thus, the mutation rate of STR loci plays an important role for the data interpretation in human identification and paternity test. To verify the mutation of the STR loci in the Korean population, 545 trio sets (father, mother, and child) were analyzed with two commercial STR kits that include the 23 autosomal STR loci (D1S1656, TPOX, D2S441, D2S1338, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, D10S1248, TH01, D12S391, VWA D13S317, D16S539, D18S51, D19S433, D21S11, D22S1045, SE33, Penta E and Penta D). As a result, 36 mutations were observed in 14 STR loci. The types of mutation were also classified by the increase or decrease of the alleles. The overall mutation rate was 1.4×10^-3, and the paternal mutation rate was four times higher than that of the maternal. This study will provide more detailed criterion for human identification by the mutation rate of STR loci in the Korean population.

• 분석과학
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• 제29권2호
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• pp.79-84
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• 2016

최근 손안에 들어올 정도로 크기가 작아 범죄현장 등에서 사용이 가능하며, 다른 일반적인 장비들에 비해 가격이 1/10이하로 저렴하여 누구나 사용할 수 있는 MiniPCR^TM mini8 Thermal Cycler (Amplyus, Cambridge, MA, USA)가 개발되었다. 본 연구에서는 DNA감식에 일반적으로 사용되고 네 가지 종류의 상염색체 STR 다중증폭 키트들과 한 종류의 Y 염색체 STR 증폭키트, 그리고 미토콘드리아 DNA HV1/HV2의 염기서열 분석법을 사용하여 MiniPCR^TM mini8 Thermal Cycler의 성능을 Applied Biosystems사의 GeneAmp^® PCR system 9700와 비교하였다. STR 다중증폭키트 키트들의 민감도와 증폭 불균형 정도를 비교한 결과 두 PCR 장비에서 큰 차이가 없었으며, 미토콘드리아 DNA HV1/HV2의 염기서열 분석 결과도 동등하였다. MiniPCR^TM mini8 Thermal Cycler는 DNA 감식 실험실은 물론이고, 가격이 저렴해 학교와 개인이 간편하게 사용할 수 있으며, 휴대가 간편해 차량이나 야외에서 활용 될 수 있을 것으로 기대된다.

• 분석과학
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• 제32권4호
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• pp.155-162
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• 2019

Analysis techniques using DNA profiling are widely used in various fields including forensic science and new technologies such as the Direct PCR amplification method are being developed continuously in order to acquire the DNA profiles efficiently. However, it has a limits such as non-specific amplification according to the quality of crime scene evidence samples. Especially, split peaks caused by excessive DNA samples are one of the important factors that could cause the debate to allow researchers to interpret the DNA profile results. In this study, we confirmed the occurrence rate of split peaks in each STR (short tandem repeats) locus of the $GlobalFiler^{TM}$ kit and investigated the possibility of improving the split peaks using several PCR additives such as DMSO (dimethylsulfoxide), $MgCl_2$, Betaine and Tween-20. As a result, we could make three groups according to the occurrence rate of split peaks in Direct PCR and it was confirmed that the ratio of split peaks could be reduced by DMSO (87.4 %), $MgCl_2$ (84.5 %) and Betaine (86.1 %), respectively. These results indicate that PCR additives such as DMSO, $MgCl_2$ and Betaine can be improve the split peaks in Direct PCR and thereby facilitate subsequently a successful DNA profile results.

• 분석과학
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• 제29권1호
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• pp.43-48
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• 2016

법과학 분야에서 다양한 Y-STR 분석 키트가 개발되어 사용되고 있고, 새로운 키트의 법과학적 적용에 앞서 DNA 감정에 적절한 분석 키트들의 선정과 표준작업절차서의 작성을 위해 실험실 내의 내부적 유효성 검증 및 민감도 시험은 필수적인 과정이다. 본 논문에서는 새로운 상업용 키트인 Yfiler^® PLUS PCR Amplification Kit (Yfiler plus 키트, 2014년 출시)를 AmpF/STR^® Yfiler^TM PCR Amplification Kit (Yfiler 키트, 2004년 출시)와 비교함으로써 민감도에 대한 연구를 수행하였다. Yfiler plus 키트는 Yfiler 키트의 17 개 Y-STR 좌위를 포함하면서 새로운 10 개의 Y-STR 좌위가 추가되었다. 먼저, 표준 DNA 시료인 2800M, 007을 이용하여 두 키트 간의 민감도 차이를 분석하였고, 선별된 0.5 ng 미만의 법과학 현장시료 16 개로부터 검출률을 비교하였다. 그 결과, Yfiler 키트보다 Yfiler plus 키트가 높은 민감도와 검출률을 보였고, 더 많은 좌위에서 Y-STR 프로필을 얻을 수 있었다. 이러한 결과들로부터 낮은 농도의 법과학 현장시료에서 Yfiler plus 키트가 Y-STR 프로필을 검출하는데 더욱 효과적인 분석키트임이 확인되었다.

• 대한의생명과학회지
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• 제28권4호
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• pp.327-333
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• 2022

The DNA profiling of short tandem repeat (STR) markers is a powerful tool for forensic identification and forensic paternity testing. However, STR loci are susceptible to mutation that cause mismatches between parents and children when paternity is tested. Herein, we examined paternity disputes with 23 autosomal STR loci using two commercial human identification kits and revealed successive mismatches at the D13S317 locus across three generations of a Korean family. Additionally, we investigated 12 X-chromosomal STRs and discovered an inconsistency at the DXS10148 locus between the father and daughter of the same Korean family. Furthermore, we confirmed STR genotypes at the D13S317 and DXS10148 loci of the family using sequencing analysis. Consequently, we identified a successive single-step mutation at the D13S317 locus and one single-step mutation at the DXS10148 locus in three generations of the Korean family. Therefore, this case study may be useful for interpreting and understanding forensic paternity tests.

• The Korean Journal of Legal Medicine
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• 제41권2호
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• pp.41-45
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• 2017

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 $AmpliSeq^{TM}$ 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.

• Journal of Korean Medical Science
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• 제33권52호
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• pp.337.1-337.14
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• 2018

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.

• 대한의생명과학회지
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• 제15권3호
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• pp.229-232
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• 2009

DNA isolation for PCR-based short tandem repeat (STR) analysis is essential to recover high yields of amplifiable DNA from low copy number (LCN) DNA samples. There are different methods developed for DNA extraction from the small bloodstain and gloves, commonly found at crime scenes. In order to obtain STR profiles from LCN DNA samples, DNA extraction protocols, namely the automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ method, the automated $QIAcube^{TM}$ method, the automated $Maxwell^{(R)}$ 16 DNA $IQ^{TM}$ Resin method, and the manual $QIAamp^{(R)}$ DNA Micro Kit method, were evaluated. Extracted DNA was quantified by the $Quantifiler^{TM}$ Human DNA Quantification Kit and DNA profiled by $AmpFISTR^{(R)}$ $Identifiler^{(R)}$ Kit. Results were compared based on the amount of DNA obtained and the completeness of the STR profiles produced. The automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ and $QIAcube^{TM}$ methoas produced reproducible DNA of sufficient quantity and quality trom the dried blood spot. This two automated methods showed a quantity and quality comparable to those of the forensic manual standard protocols normally used in our laboratory. In our hands, the automated DNA extraction method is another obvious choice when the forensic case sample available is bloodstain. The findings of this study indicate that the manual simple modified $QIAamp^{(R)}$ DNA Micro Kit method is best method to recover high yields of amplifiable DNA from the numerous potential sources of LCN DNA samples.