• Journal of Animal Science and Technology
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• 제63권1호
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• pp.25-35
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• 2021

The purpose of this study is to estimate the single nucleotide polymorphism (SNP) effect for pH values affecting Berkshire meat quality. A total of 39,603 SNPs from 1,978 heads after quality control and 882 pH values were used estimate SNP effect by single step genomic best linear unbiased prediction (ssGBLUP) method. The average physical distance between adjacent SNP pairs was 61.7kbp and the number and proportion of SNPs whose minor allele frequency was below 10% were 9,573 and 24.2%, respectively. The average of observed heterozygosity and polymorphic information content was 0.32 ± 0.16 and 0.26 ± 0.11, respectively and the estimate for average linkage disequilibrium was 0.40. The heritability of pH45m and pH24h were 0.10 and 0.15 respectively. SNPs with an absolute value more than 4 standard deviations from the mean were selected as threshold markers, among the selected SNPs, protein-coding genes of pH45m and pH24h were detected in 6 and 4 SNPs, respectively. The distribution of coding genes were detected at pH45m and were detected at pH24h.

• Childhood Kidney Diseases
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• 제25권2호
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• pp.92-111
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• 2021

Purpose: Nephrotic syndrome (NS) is the most common form of glomerulopathy in children. Most pediatric patients respond to glucocorticosteroid treatment (steroid-sensitive NS, SSNS), while approximately 10-15% will remain unresponsive or later become steroid-resistant. There has been a long-standing effort to find biomarkers that may predict steroid responsiveness. Methods: We systematically reviewed current studies which investigated clinically relevant biomarkers for predicting steroid responsiveness in pediatric NS. We performed a PubMed and EMBASE search to identify eligible articles. We collected data on urinary markers, blood/serum markers (including cellular phenotypes and mRNA expression), genotypes and HLA allele frequency. Results: A total of 659 articles were identified following electronic and manual searches. After reviewing the titles, abstracts, and full texts, 72 eligible articles were finally included. Vitamin D-binding protein (VDBP) seemed to be significantly elevated in SRNS than in SSNS, in both serum and urine specimen, although further validation is required. Conclusions: The present paper narratively illustrates current understandings of potential biomarkers that may help predict steroid responsiveness. Further investigation and collaboration involving a larger number of patients are necessary.

• Genomics & Informatics
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• 제20권3호
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• pp.28.1-28.7
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• 2022

We described a clinical, laboratory, and genetic presentation of a pathogenic variant of the CYP1B1 gene through a report of a case of primary congenital glaucoma and a trio analysis of this candidate variant in the family with the Sanger sequencing method and eventually completed our study with the secondary/incidental findings. This study reports a rare case of primary congenital glaucoma, an 8-year-old female child with a negative family history of glaucoma and uncontrolled intraocular pressure. This case's whole-exome sequencing data analysis presents a homozygous pathogenic single nucleotide variant in the CYP1B1 gene (NM_000104:exon3:c.G1103A:p.R368H). At the same time, this pathogenic variant was obtained as a heterozygous state in her unaffected father but not her mother. The diagnosis was made based on molecular findings of whole-exome sequencing data analysis. Therefore, the clinical reports and bioinformatics findings supported the relation between the candidate pathogenic variant and the disease. However, it should not be forgotten that primary congenital glaucoma is not peculiar to the CYP1B1 gene. Since the chance of developing autosomal recessive disorders with low allele frequency and unrelated parents is extraordinary in offspring. However, further data analysis of whole-exome sequencing and Sanger sequencing method were applied to obtain the type of mutation and how it was carried to the offspring.

• Korean Journal of Mathematics
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• 제30권1호
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• pp.67-72
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• 2022

For a locus with two alleles (I^A and I^B), the frequencies of the alleles are represented by $$p=f(I^A)={\frac{2N_{AA}+N_{AB}}{2N},\;q=f(I^B)={\frac{2N_{BB}+N_{AB}}{2N}$$ where N_AA, N_AB and N_BB are the numbers of I^AI^A, I^AI^B and I^BI^B respectively and N is the total number of populations. The frequencies of the genotypes expected are calculated by using p², 2pq and q². Choi showed the method of whether some genotypes is in these probabalities. Also he calculate the probability generating function for offspring number of genotype under a diploid model( [1]). In this paper, let x(t, p) be the probability that I^A become fixed in the population by time t-th generation, given that its initial frequency at time t = 0 is p. We find adapted equations for x using the mean change of frequence of alleles and fitness of genotype. Also we apply this adapted equations to several diploid model and it also will apply to actual examples.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.17-17
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• 2022

Leaves are an important organism for photosynthesis and transpiration. The shape of leaf is crucial factor affecting plant architecture. V-shape leaf rolling is enhancing canopy photosynthesis by increasing the CO₂ penetration and the light capture by reducing the shadow between the leaves. Therefore, moderate leaf rolling is thought to more high grain yield per area than flat leaf. We investigated 278 KRICE_CORE accession's Adaxial Leaf Rolling Index (LRI) in first heading using the following equation. For each accession, genomic DNA was used for sequencing. We sequenced the genomics with ~8 X coverage to detect SNPS. Raw reads were aligned against the rice reference (IRGSP 1.0) for SNP identification and genotype calling. To generate genotype data for GWAS, SNPs were filtered with minor allele frequency 0.05. Finally, 841,134 high-quality SNPs were used for our GWAS. The significant threshold was -log10(P)>7.23. From the results, 2 significance SNP were detected. Considering the LD block of 250kbp, 60 candidate gene were selected including Hypothetical gene and Conserved gene. In this poster, we analyzed candidate gene affecting adaxial Leaf Rolling through single-trait GWAS.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.243-243
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• 2022

Leaves are an important organism for photosynthesis and transpiration. The shape of leaf is crucial factor affecting plant architecture. V-shape leaf rolling is enhancing canopy photosynthesis by increasing the CO₂ penetration and the light capture by reducing the shadow between the leaves. Therefore, moderate leaf rolling is thought to more high grain yield per area than flat leaf. We investigated 278 KRICE CORE accession's Adaxial Leaf Rolling Index (LRI) in first heading using the following equation. For each accession, genomic DNA was used for sequencing. We sequenced the genomics with ~8 X coverage to detect SNPS. Raw reads were aligned against the rice reference (IRGSP 1.0) for SNP identification and genotype calling. To generate genotype data for GWAS, SNPs were filtered with minor allele frequency 0.05. Finally, 841,134 high-quality SNPs were used for our GWAS. The significant threshold was -log10(P) >7.23. From the results, 2 significance SNP were detected. Considering the LD block of 250kbp, 60 candidate gene were selected including Hypothetical gene and Conserved gene. In this poster, we analyzed candidate gene affecting adaxial Leaf Rolling through single-trait GWAS.

• 한국작물학회지
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• 제43권4호
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• pp.259-263
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• 1998

High molecular weight glutenin (HMW-Glu) subunit compositions of 73 Korean wheat cultivars and experimental lines were evaluated by using one dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This method is suitable for obtaining a good resolution of 1Dx2 and 1Ax2$^*$ without adverse effects on separation of other HMW-Glu subunits. Korean wheats examined in this study could be divided into 15 different groups on the basis of HMW-Glu subunit compositions. From the wheat lines tested, it was identified that there were three alleles at the Glu-Al, five at the Glu-Bl and three at the Glu-D1 loci. The null allele of the Glu-Al was occurred in high frequency (79.4%), while low frequencies for 1Ax1 (12.3%) and 1Ax2$^*$(8.2%) were found. High frequency (75.3%) of the subunit pairs of 1Bx7+1By8 at the Glu-Bl loci compared with other subunits was found. The frequencies of subunits 1Dx2. 2+1Dy12 and 1Dx2+1Dy12 from the Glu-D1 loci were 54. 8% and 37.0%, respectively. However, a few Korean wheat lines (8.2%) carried 1Dx5 + 1Dy10 subunit pair which are responsible for good breadmaking quality. The information of HMW-Glu subunit compositions provide a useful tool to characterize wheat lines, and can be directly used in selection of breeding lines of different end-use properties.

• IMMUNE NETWORK
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• 제2권4호
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• pp.248-255
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• 2002

Background: TAP1 and TAP2 are two ABC transporter genes located within the class II region of the human MHC. Their protein products form a heterodimer whose function is to transport peptides from the cytoplasm into the endoplasmic reticulum. This study was performed to examine the polymorphism of TAP genes and the distribution of HLA-TAP haplotypes in the Korean population through family analysis. Methods: The subjects used in this study were 50 healthy Korean families consisting of 233 individuals. TAP1 (codons 333 and 637) and TAP2 (codons 379, 565, 577, 651, 665, and 687) typings were carried out by the PCR-restriction fragment length polymorphism (RFLP) method. HLA-DRB1 and DQB1 genotyping results from a previous study were used for HLA-TAP haplotype analysis. Results: The number (gene frequency) of TAP1 and TAP2 alleles detected were 3 for TAP1 (A 81.5%, B 17.0%, and C 1.5%) and 8 for TAP2 (A1 32.0%, A2 12.5%, B 34.0%, Bky2 6.5%, C 7.0%, D 3.0%, E 4.5%, and G 0.5%). Eleven TAP1-TAP2 haplotypes were observed with $frequency{\geq}1%$, among which 4 haplotypes (A-B, B-A1, A-Bky2, and C-E) showed weak but significant positive linkage disequilibrium (P<0.05). When DRB1-DQB1 haplotypes were extended to TAP1 and TAP2 loci, much diversification of haplotypes was observed: 19 different DRB1-DQB1 haplotypes formed 58 different haplotypes extended to TAP1 and TAP2 loci. These results add more evidence to the view that recombination hotspot is present within and around TAP gene region. Conclusion: The allele frequencies of TAP1 and TAP2 genes and the distribution of TAP1-TAP2 and HLA-TAP haplotypes were studied in Koreans based on a family study.

• Asian Pacific Journal of Cancer Prevention
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• 제17권3호
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• pp.1053-1055
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• 2016

Background: Polycythemia rubra vera (PV), being a primary polycythemia, is caused by neoplastic proliferation of erythroid, megakaryocytic and granulocytic lineages which result in panmyelosis. PV patients have a somatic acquired mutation in the Janus kinase (JAK2) pathway, rendering cell proliferation independent of the normal regulatory mechanisms that regulate erythropoiesis. The rational of this study was to determine the prevalence of the JAK-2 V617F mutation in Pakistani patients with PV. Materials and Methods: In this cross sectional study, 26 patients with PV were enrolled from January 2010 to December 2014. Patients were diagnosed based on WHO criteria for PV. All were screened for G-T point mutation (V617F) in the JAK2 gene on chromosome 9 by an allele specific PCR. Results: The mean age was $53.4{\pm}9.31years$ (range 36-72) and the male to female ratio was 2:1. The frequency of JAK2 V617F positivity in our PV patients was found to be 92.3%. Overall 30.7% of patients were asymptomatic and remaining 69.3% presented with symptomatic disease. The mean hemoglobin was $18.1{\pm}1.9g/dl$ with the mean hematocrit of $55.6{\pm}8.3%$. The mean total leukocyte count was $12.8{\pm}7.1{\times}10^9/l$ and the platelet count was $511{\pm}341.9{\times}10^9/l$. A positive correlation of JAK2 V617F mutation was established with high TLC count (P=0.01). No correlation of JAK2 V617F could be established with age or gender (P>0.05). Conclusions: The JAK2 V617F mutation frequency in our PV patients was similar to those reported internationally. Screening for the mutation in all suspected PV cases could be beneficial in differentiating patients with reactive and clonal erythrocytosis.

• Asian Pacific Journal of Cancer Prevention
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• 제16권17호
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• pp.7889-7892
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• 2015

Background: Primary idiopathic myelofibrosis (PMF) is a clonal Ph-chromosome negative myeloproliferative neoplasm characterized by dysregulated kinase signaling and release of abnormal cytokines. In the recent past, following JAK2 V617F mutation invention, important revolution has been made in the molecular diagnostic biology of this disease. The rational of this study was to determine the mutational status of JAK2 V617F in Pakistan patients with PMF. Materials and Methods: In this cross sectional study, 20 patients with PMF were enrolled from January 2011 to December 2014. Diagnosis was based on WHO criteria for PMF. All patients were screened for G-T point mutation (V617F) in the JAK2 gene on chromosome 9 by allele specific PCR. Results: The mean age was $57.9{\pm}16.5years$. The male to female ratio was 3:1. The frequency of JAK2 V617F positivity in our PMF patients was found to be 55%. Positive correlations of JAK2 V617F mutation were established with high TLC count, raised LDH and marked splenomegaly (P<0.05). No correlation of JAK2 V617F could be established with age and gender (P>0.05). Conclusions: The JAK2 V617F mutation frequency in our PMF patients was similar to those reported previously. In our hands JAK2 V617F mutated patients expressed an aggressive disease phenotype. Screening for the mutation in all suspected PMF cases could be beneficial in differentiating patients with reactive and clonal marrow fibrosis.