Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs

Oh, Y.N.,Lee, H.Y.,Lee, E.Y.,Kim, E.H.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.15 No.-

In this study, 363 Korean father-son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93x10<SUP>-2</SUP>, with an average estimated mutation rate of 6.66x10<SUP>-3</SUP>. Two father-son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father-son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.

Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing

Kwon, S.Y.,Lee, H.Y.,Kim, E.H.,Lee, E.Y.,Shin, K.J. Elsevier Science 2016 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.25 No.-

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex<SUP>®</SUP> Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq<SUP>®</SUP> System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories.

Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan

Lee, E.Y.,Shin, K.J.,Rakha, A.,Sim, J.E.,Park, M.J.,Kim, N.Y.,Yang, W.I.,Lee, H.Y. Elsevier Science 2014 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.11 No.-

We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.

Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

Kwon, S.Y.,Lee, H.Y.,Lee, E.Y.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.19 No.-

Y chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, and are thereby widely used in the fields such as human evolution, anthropology and forensic genetics. The Y haplogroup tree was recently revised with newly suggested Y-SNP markers for designation of several subgroups of haplogroups C2, O2b and O3a, which are predominant in Koreans. Therefore, herein we analyzed these newly suggested Y-SNPs in 545 unrelated Korean males who belong to the haplogroups C2, O2b or O3a, and investigated the reconstructed topology of the Y haplogroup tree. We were able to confirm that markers L1373, Z1338/JST002613-27, Z1300, CTS2657, Z8440 and F845 define the C2 subhaplogroups, C2b, C2e, C2e1, C2e1a, C2e1b and C2e2, respectively, and that markers F3356, L682, F11, F238/F449 and F444 define the O subhaplogroups O2b1, O2b1b, O3a1c1, O3a1c2 and O3a2c1c, respectively. Among six C2 subhaplogroups (C2b, C2e, C2e1*, C2e1a, C2e1b and C2e2), the C2e haplogroup and its subhaplogroups were found to be predominant, and among the four O2b subhaplogroups (O2b*, O2b1*, O2b1a and O2b1b), O2b1b was most frequently observed. Among the O3a subhaplogroups, O3a2c1 was predominant and it was further divided into the subhaplogroups O3a2c1a and O3a2c1c with a newly suggested marker. However, the JST002613-27 marker, which had been known to define the haplogroup C2f, was found to be an ancestral marker of the C2e haplogroup, as is the Z1338 marker. Also, the M312 marker for the O2b1 haplogroup designation was replaced by F3356, because all of the O2b1 haplotypes showed a nucleotide change at F3356, but not at M312. In addition, the F238 marker was always observed to be phylogenetically equivalent to F449, while both of the markers were assigned to the O3a1c2 haplogroup. The confirmed phylogenetic tree of this study with the newly suggested Y-SNPs could be valuable for anthropological and forensic investigations of East Asians including Koreans.

A multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a

Lee, E.Y.,Lee, H.Y.,Kwon, S.Y.,Oh, Y.N.,Yang, W.I.,Shin, K.J. ELSEVIER SCIENCE B V AMSTERDAM 2017 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.26 No.-

<P>In forensic science and human genetics, Y-chromosomal short tandem repeats (Y-STRs) have been used as very useful markers. Recently, more Y-STR markers have been analyzed to enhance the resolution power in haplotype analysis, and 13 rapidly mutating (RM) Y-STRs have been suggested as revolutionary tools that can widen Y-chromosomal application from paternal lineage differentiation to male individualization. We have constructed two multiplex PCR sets for the amplification of 13 RM Y-STRs, which yield small-sized amplicons (<400 bp) and a more balanced PCR efficiency with minimum PCR cycling. In particular, with the developed multiplex PCR system, we could separate three copies of DYF403S1a into two copies of DYF403S1a and one of DYF403S1b1. This is because DYF403S1b1 possesses distinguishable sequences from DYF403S1a at both the front and rear flanking regions of the repeat motif; therefore, the locus could be separately amplified using sequence-specific primers. In addition, the other copy, defined as DYF403S1b by Ballantyne et al., was renamed DYF403S1b2 because of its similar flanking region sequence to DYF403S1b1. By redefining DYF403S1 with the developed multiplex system, all genotypes of four copies could be successfully typed and more diverse haplotypes were obtained. We analyzed haplotype distributions in 705 Korean males based on four different Y-STR subsets: Yfiler, PowerPlex Y23, Yfiler Plus, and RM Y-STRs. All haplotypes obtained from RM Y-STRs were the most diverse and showed strong discriminatory power in Korean population. (C) 2016 Elsevier Ireland Ltd. All rights reserved.</P>

발화합성용액의 pH가 Y₁Ba₂Cu₃O_7-x 초전도상 생성 속도에 미치는 영향

박정식,김영순,양석우,김춘영,신형식,Park, J.S.,Kim, Y.S.,Yang, S.W.,Kim, C.Y.,Shin, H.S. 한국공업화학회 1998 공업화학 Vol.9 No.2

$Y_2O_3$(99.9%)와 $BaCO_3$(99.9%) 및 CuO(99.9%)를 사용하여 $Y_1Ba_2Cu_3O_{7-x}$(123) 분말을 발화합성법에 의해 제조하였다. 발화전 용액을 여러 가지 pH로 변화시켜 제조하였으며, 이 분말을 성형하여 열처리 온도와 시간 변화에 따른 상형성과 반응특성을 조사하였다. 시료의 조성과 조직의 특성은 ICP와 SEM을 이용하여 측정하였고, Y-Ba-Cu-O계의 상형성과 전화율을 결정하기 위해 X선 회절분석을 하였다. 발화합성법을 이용하여 pH 7(${\pm}0.3$)에서 제조된 123 분말이 순도와 균일성 및 반응특성에서 가장 좋은 결과를 보였다. pH 7(${\pm}0.3$)에서 제조된 분말을 이용한 123 상생성에 따른 활성화에너지(${\Delta}E_a$)는 191kJ/mol으로서 고상반응법의 230kJ/mol에 약 13% 정도 더 낮았다. The $Y_1Ba_2Cu_3O_{7-x}$(123) superconductor powders were prepared by pyrophoric synthesis method(PSM) using $Y_2O_3$(99.9%), $BaCO_3$(99.9%), and CuO(99.9%) powders. The phase formation and reaction kinetics of 123 superconductor manufactured with powders prepared in various pHs of pyrophoric synthetic solution have been studied through the experiments at various heat treatment temperatures and times. Inductively coupled plasma(ICP) spectroscopy and scanning electron microscopy(SEM) measurements were performed to examine the composition and morphology of the sample. X-ray diffraction(XRD) analysis was done to determine phase formation and conversion ratio of Y-Ba-Cu-O systems. The 123 powder prepared at pH 7(${\pm}0.3$) yields the best result in terms of purity, homogeneity, and reactivity. The activation energies(${\Delta}E_a$) of 123 phase formation were found to be 191 kJ/mol and 230kJ/mol in solid state reaction method and pyrophoric synthesis method, respectively.

발화합성용액의 pH 가 Y1Ba2Cu3O7-x 초전도상 생성 속도에 미치는 영향

박정식,김영순,양석우,김춘영,신형식 ( J . S . Park,Y . S . Kim,S . W . Yang,C . Y . Kim,H . S,Shin ) 한국공업화학회 1998 공업화학 Vol.9 No.2

Y₂O₃(99.9%)와 BaCO₃(99.9%) 및 CuO(99.9%)를 사용하여 Y₁Ba₂Cu₃O_(7-x)(123) 분말을 발화합성법에 의해 제조하였다. 발화전 용액을 여러 가지 pH로 변화시켜 제조하였으며, 이 분말을 성형하여 열처리 온도와 시간 변화에 따른 상형성과 반응특성을 조사하였다. 시료의 조성과 조직의 특성은 ICP와 SEM을 이용하여 측정하였고, Y-Ba-Cu-O계의 상형성과 전화율을 결정하기 위해 X선 회절분석을 하였다. 발화합성법을 이용하여 pH 7(±0.3)에서 제조된 123 분말이 순도와 균일성 및 반응특성에서 가장 좋은 결과를 보였다. pH 7(±0.3)에서 제조된 분말을 이용한 123 상생성에 따른 활성화에너지(ΔE_n)는 191 kJ/mol으로서 고상반응법의 230 kJ/mol에 약 13% 정도 더 낮았다. The Y₁Ba₂Cu₃O_(7-x)(123) superconductor powders were prepared by pyrophoric synthesis method(PSM) using Y₂O₃(99.9%), BaCO₃(99.9%), and CuO(99.9%) powders. The phase formation and reaction kinetics of 123 superconductor manufactured with powders prepared in various pHs of pyrophoric synthetic solution have been studied through the experiments at various heat treatment temperatures and times. Inductively coupled plasma(ICP) spectroscopy and scanning electron microscopy(SEM) measurements were performed to examine the composition and morphology of the sample. X-ray diffraction(XRD) analysis was done to determine phase formation and conversion ratio of Y-Ba-Cu-O systems. The 123 powder prepared at pH 7(±0.3) yields the best result in terms of purity, homogeneity, and reactivity. The activation energies(ΔE_n) of 123 phase formation were found to be 191 kJ/mol and 230 kJ/mol in solid state reaction method and pyrophoric synthesis method, respectively.

대학생의 인터넷중독 및 스마트폰 중독 정도와 미술 치료 인식에 대한 조사 연구

박혜원,송승윤,윤하영,이경현,이소영,이지원,진예은,최시온,허은서,황다빈,신주현,이인영 이화여자대학교 간호학회 2018 이화간호학회지 Vol.- No.52

Purpose: Investigate the level of Internet and smart phone addiction of college students and difference of their perception on the art therapy. Method: Data was collected using 4 categories of questionnaires. Participants of this study were 383 college students who are currently attending universities located in seoul, Kyung-Ki and Incheon. The Chi-square test, One-way Analysis of Variance, Scheffé test were performed using IBM SPSS Statistics 23.0 Result: First, the study has established that the status of attending universities, grade, people who living with, age affected the level of Internet addiction of college students. In terms of the level of smart phone addiction of college students, the status of attending universities, gender, age were the affective factors. Second, there was a significant difference on the perception of the advantages of the art therapy and the level of acknowledging it, depending on the level of Internet addiction. Finally, depending on the level of smartphone addiction, there was a significant difference in the level of perception of the art therapy, expectation toward the art therapy and the helpfulness of art therapy. The more the participants are close to the addicted level, the more they want to experience the art therapy. Conclusion: These results suggest. First, it is necessary to use bigger group of participants. Second, it is necessary to improve the research methods for college students. Third, nurse should offer holistic care toward the patients regarding their general characteristics by adapting this study. Finally, it is necessary to improve the art therapy programs for the college students who are addicted to the Internet and smartphone and to develop researches proving the effectiveness of these programs.

수험생활 중 경주 및 포항 지진 경험

김선주,김유영,김은주,박솔민,배지윤,이민영,이유진,정재원,Li Keying,Wuyingjinzhu,신수진,도지영 이화여자대학교 간호과학대학 2019 이화간호학회지 Vol.- No.53

Purpose: The purpose of this study was to understand the experiences of Gyeongju and Pohang earthquakes during the examinees’ life. Methods: This study applied Colaizzis’s Phenomenological method. The Data was collected through in-depth interviews with a total 8 students of university in Seoul. Results: On the analysis of the interviews, their experience can be expressed as ‘Feeling embarrassed and frightened by earthquakes’, ‘Reduced susceptibility to earthquake hazards due to heavy exam pressure’, ‘Increased exam stress due to earthquake’, ‘Feeling the inadequacy of examinees' earthquake related safety measures in retrospect’. Conclusion: This study was meaningful in deeply understanding of their experiences and revealing that the examinees were more focused on studying rather than actively coping with the disaster. Furthermore, it reconsider the social climate surrounding college admission exams. This study meaningfully discovered that examinees could not stably prepare for both the exam and the earthquake evacuation procedures due to the timing of the earthquake in relation to their upcoming college admission test. Therefore, this study highlighted the examinees’ difficulties due to the earthquakes and increased the necessity of acute phase nursing intervention in relation to the seismic safety education system.

Serum lactoferrin level as a serologic biomarker for allergic rhinitis

Choi, G. -S.,Shin, S. -Y.,Kim, J. -H.,Lee, H. -Y.,Palikhe, N. S.,Ye, Y. -M.,Kim, S. -H.,Park, H. -S. Blackwell Publishing Ltd 2010 Clinical and experimental allergy Vol.40 No.3

<P>Summary</P><P>Background</P><P>Allergic rhinitis (AR) is a very common disease and a risk factor for allergic asthma. The discovery of new biomarkers for the early detection of AR would improve the clinical outcomes and reduce socio-economic burden. We sought to identify a novel serologic marker for detection of AR using a proteomic approach.</P><P>Methods</P><P>To identify the proteins involved in AR, comparative proteomics was applied using nasal lavage fluids (NLFs) taken before and after a nasal provocation test (NPT) with <I>Dermatophagoides pteronyssinus</I> (<I>Dpt</I>) in a subject with AR sensitized to <I>Dpt</I>. The clinical relevance of the identified proteins was evaluated by ELISA using NLFs and sera from the three study groups: <I>Dpt</I>-sensitive AR; asymptomatic <I>Dpt</I>-sensitive controls; and non-atopic healthy controls. The sensitivities and specificities of the candidate proteins for predicting AR were determined using receiver operating characteristic (ROC) curves.</P><P>Results</P><P>In proteomic analysis, lactoferrin expression was up-regulated after NPT. The validation study using ELISA showed a significantly lower serum lactoferrin level in the AR group than those of the other two groups (<I>P</I><0.05, respectively). To discriminate between subjects with or without AR, the optimal serum cut-off level of lactoferrin was set at <307 ng/mL using the ROC curve. The sensitivity and specificity for predicting AR were 81.4% and 58%. When combined with serum <I>Dpt</I>-specific IgE level, the sensitivity and specificity for predicting AR were 76.7% and 79.2%.</P><P>Conclusion</P><P>These results suggest that the serum lactoferrin level is associated with the phenotype of <I>Dpt</I>-sensitive AR, and in combination with the serum <I>Dpt</I>-specific IgE level, may be a potential serologic marker for early detection of AR.</P><P><I>Cite this as</I>: G.-S. Choi, S.-Y. Shin, J.-H. Kim, H.-Y. Lee, N. S. Palikhe, Y.-M. Ye, S.-H. Kim and H.-S. Park, <I>Clinical & Experimental Allergy</I>, 2010 (40) 403–410.</P>