Identification of genetic polymorphisms in FABP3 and FABP4 and putative association with back fat thickness in Korean native cattle

Seoae Cho,Toe Sung Park,Du Hak Yoon,Hyun Sub Cheong,Sohg Namgoong,Byung Lae Park,Hye Won Lee,Chang Soo Han,Eun Mi Kim,Il Cheong Cheong,Hee Bal Kim,Hyoung Doo Shin 한국생화학분자생물학회 2008 BMB Reports Vol.41 No.1

Analysis of copy number variation in 8,842 Korean individuals reveals 39 genes associated with hepatic biomarkers AST and ALT

( Hyo Young Kim ),( Seoae Cho ),( Jeongmi Yu ),( Samsun Sung ),( Heebal Kim ) 생화학분자생물학회 (구 한국생화학분자생물학회) 2010 BMB Reports Vol.43 No.8

Biochemical tests such as aspartate aminotransferase (AST) and alanine aminotransferase (ALT) are useful for diagnosing patients with liver disease. In this study, we tested the association between copy number variation and the hepatic biomarkers AST and ALT based on 8,842 samples from population-based cohorts in Korea. We used Affymetrix Genome-Wide Human 5.0 arrays and identified 10,534 CNVs using HelixTree software. Of the CNVs tested using univariate linear regression, 100 CNVs were significant for AST and 16 were significant for ALT (P < 0.05). We identified 39 genes located within the CNV regions. DKK1 and HS3ST3B1 were shown to play roles in heparan sulfate biosynthesis and the Wnt signaling pathway, respectively. NAF1 and NPY1R were associated with glycoprotein processes and neuropeptide Y receptor activity based on GO categories. PTER, SOX14 and TM7SF4 were expressed in liver. DPYS and CTSC were found to be associated with dihydropyrimidinuria and Papillon-Lef?vre syndrome phenotypes using OMIM. NPY5R was found to be associated with dyslipidemia using the Genetic Association Database. [BMB reports 2010; 43(8): 547-553]

Genetic variants and signatures of selective sweep of Hanwoo population Korean native cattle

Tae Heon Lee,Seoae Cho,Seok Seo Kang,Jong Soo Chang,Hee Bal Kim,Du Hak Yoon 생화학분자생물학회(구 한국생화학분자생물학회) 2013 BMB Reports Vol.46 No.7

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

Kim, HyoYoung,Sung, Samsun,Cho, Seoae,Kim, Tae-Hun,Seo, Kangseok,Kim, Heebal Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.12

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

A novel genetic variant database for Korean native cattle (Hanwoo): HanwooGDB

Kim, Kwondo,Kwak, Woori,Sung, Sam-Sun,Cho, Seoae,Kim, Heebal,Yoon, Duhak,Lee, Hyun-Jeong Springer-Verlag 2015 Genes & Genomics Vol.37 No.1

African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

Mwai, Okeyo,Hanotte, Olivier,Kwon, Young-Jun,Cho, Seoae Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.7

At least 150 indigenous African cattle breeds have been named, but the majority of African cattle populations remain largely uncharacterized. As cattle breeds and populations in Africa adapted to various local environmental conditions, they acquired unique features. We know now that the history of African cattle was particularly complex and while several of its episodes remain debated, there is no doubt that African cattle population evolved dramatically over time. Today, we find a mosaic of genetically diverse population from the purest Bos taurus to the nearly pure Bos indicus. African cattle are now found all across the continent, with the exception of the Sahara and the river Congo basin. They are found on the rift valley highlands as well as below sea level in the Afar depression. These unique livestock genetic resources are in danger to disappear rapidly following uncontrolled crossbreeding and breed replacements with exotic breeds. Breeding improvement programs of African indigenous livestock remain too few while paradoxically the demand of livestock products is continually increasing. Many African indigenous breeds are endangered now, and their unique adaptive traits may be lost forever. This paper reviews the unique known characteristics of indigenous African cattle populations while describing the opportunities, the necessity and urgency to understand and utilize these resources to respond to the needs of the people of the continent and to the benefit of African farmers.

Genome-wide Association Study of Integrated Meat Quality-related Traits of the Duroc Pig Breed

Lee, Taeheon,Shin, Dong-Hyun,Cho, Seoae,Kang, Hyun Sung,Kim, Sung Hoon,Lee, Hak-Kyo,Kim, Heebal,Seo, Kang-Seok Asian Australasian Association of Animal Productio 2014 Animal Bioscience Vol.27 No.3

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

Ubiquitous Polygenicity of Human Complex Traits: Genome-Wide Analysis of 49 Traits in Koreans

Yang, Jian,Lee, Taeheon,Kim, Jaemin,Cho, Myeong-Chan,Han, Bok-Ghee,Lee, Jong-Young,Lee, Hyun-Jeong,Cho, Seoae,Kim, Heebal Public Library of Science 2013 PLoS genetics Vol.9 No.3

<▼1><P>Recent studies in population of European ancestry have shown that 30%∼50% of heritability for human complex traits such as height and body mass index, and common diseases such as schizophrenia and rheumatoid arthritis, can be captured by common SNPs and that genetic variation attributed to chromosomes are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analysed 49 human quantitative traits, many of which are relevant to human diseases, in 7,170 unrelated Korean individuals genotyped on 326,262 SNPs. For 43 of the 49 traits, we estimated a nominally significant (<I>P</I><0.05) proportion of variance explained by all SNPs on the Affymetrix 5.0 genotyping array ([FORMULA OMISSION]). On average across 47 of the 49 traits for which the estimate of [FORMULA OMISSION] is non-zero, common SNPs explain approximately one-third (range of 7.8% to 76.8%) of narrow sense heritability.</P><P>The estimate of [FORMULA OMISSION] is highly correlated with the proportion of SNPs with association <I>P</I><0.031 (<I>r</I><SUP>2</SUP> = 0.92). Longer genomic segments tend to explain more phenotypic variation, with a correlation of 0.78 between the estimate of variance explained by individual chromosomes and their physical length, and 1% of the genome explains approximately 1% of the genetic variance. Despite the fact that there are a few SNPs with large effects for some traits, these results suggest that polygenicity is ubiquitous for most human complex traits and that a substantial proportion of the “missing heritability” is captured by common SNPs.</P></▼1><▼2><P><B>Author Summary</B></P><P>The “missing heritability” problem has been intensely debated for the last few years. Possible explanations include the existence of many genetic variants each with a small effect, rare variants with large effects, and heritability being over-estimated. Previous studies using whole-genome estimation have demonstrated that for human complex traits such as height, body mass index, and intelligence, a large portion of the heritability can be captured by all the common SNPs on the current genotyping arrays. These studies, however, were all concentrated only on a few traits. In this study, we analysed 49 quantitative traits in a sample of ∼7,000 unrelated Korean individuals. We found that, on average over all the traits, common SNPs on the Affymetrix 5.0 genotyping array explain approximately a third of the heritability, that genetic variants are widely distributed across the whole genome with longer chromosomes explaining more phenotypic variation, and that approximately any 1% of the genome explains 1% of the heritability. Despite examples where a few variants explain a substantial amount of variation, all these results are consistent with polygenicity being ubiquitous for most complex traits.</P></▼2>

The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

Lee, Young-Sup,Kim, Hyeon-Jeong,Cho, Seoae,Kim, Heebal Korea Genome Organization 2014 Genomics & informatics Vol.12 No.4

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

In silico SARS-CoV-2 vaccine development for Omicron strain using reverse vaccinology

Li Vladimir,Lee Chul,Yoo DongAhn,Cho Seoae,Kim Heebal 한국유전학회 2022 Genes & Genomics Vol.44 No.8

Background: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic began in 2019 but it remains as a serious threat today. To reduce and prevent spread of the virus, multiple vaccines have been developed. Despite the efforts in developing vaccines, Omicron strain of the virus has recently been designated as a variant of concern (VOC) by the World Health Organization (WHO). Objective: To develop a vaccine candidate against Omicron strain (B.1.1.529, BA.1) of the SARS-CoV-19. Methods: We applied reverse vaccinology methods for BA.1 and BA.2 as the vaccine target and a control, respectively. First, we predicted MHC I, MHC II and B cell epitopes based on their viral genome sequences. Second, after estimation of antigenicity, allergenicity and toxicity, a vaccine construct was assembled and tested for physicochemical properties and solubility. Third, AlphaFold2, RaptorX and RoseTTAfold servers were used to predict secondary structures and 3D structures of the vaccine construct. Fourth, molecular docking analysis was performed to test binding of our construct with angiotensin converting enzyme 2 (ACE2). Lastly, we compared mutation profiles on the epitopes between BA.1, BA.2, and wild type to estimate the efficacy of the vaccine. Results: We collected a total of 10 MHC I, 9 MHC II and 5 B cell epitopes for the final vaccine construct for Omicron strain. All epitopes were predicted to be antigenic, non-allergenic and non-toxic. The construct was estimated to have proper stability and solubility. The best modelled tertiary structures were selected for molecular docking analysis with ACE2 receptor. Conclusions: These results suggest the potential efficacy of our newly developed vaccine construct as a novel vaccine candidate against Omicron strain of the coronavirus.