• Asian Pacific Journal of Cancer Prevention
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• v.16 no.14
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• pp.5647-5654
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• 2015

Gall bladder cancer (GBC) is a gastro-intestinal cancer with high prevalence among north Indian women. Platelet derived growth factor-B (PDGFB) and human epidermal growth factor receptor-2 (HER2) may play roles in the etiology of GBC through the inflammation-hyperplasia-dysplasia-carcinoma pathway. To study the association of PDGFB and HER2 polymorphisms with risk of GBC, 200 cases and 300 controls were considered. PDGFB +286A>G and +1135A>C polymorphisms were investigated with an amplification refractory mutation system and the HER2 $Ile^{655}Val$ polymorphism by restriction fragment length polymorphism. Significant risk associations for PDGFB +286 GG (OR=5.25) and PDGFB +1135 CC (OR=3.19) genotypes were observed for GBC. Gender wise stratification revealed susceptibility for recessive models of PDGFB +1135A>C (OR=3.00) and HER2 $Ile^{655}Val$ (OR=2.52) polymorphisms among female GBC cases. GBC cases with gall stones were predisposed to homozygous +286 GG and +1135 CC genotypes. Significant risk associations were found for ACIle (OR=1.48), GAVal (OR=1.70), GAIle (OR=2.00) haplotypes with GBC cases and GCIle haplotype with female GBC cases (OR=10.37, P=<0.0001). Pair-wise linkage disequilibrium revealed negative associations among variant alleles. On multi-dimensional reduction analysis, a three factor model revealed significant gene-gene interaction for PDGFB +286A>G, PDGFB +1135A>C and HER2 Ile165Val SNPs with GBC. Protein-protein interaction showed significant association of PDGFB and HER2 with the epidermal growth factor receptor signaling pathway.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.12
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• pp.1675-1681
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• 2016

The aim of this study was to detect positional candidate genes located within the support interval (SI) regions based on the results of red blood cell, mean corpuscular volume (MCV), and mean corpuscular hemoglobin quantitative trait locus (QTL) in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs) located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15-which are reported to be related to the hematological traits and clinical features of Down syndrome-were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an $F_2$ resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the $F_2$ intercross population. Among them, the MCV level was highly significant (nominal $p=9.8{\times}10^{-9}$) in association with the DYRK1A-SNP1 (c.2989 G$F_2$ intercross, our approach has limited power to distinguish one particular positional candidate gene from a QTL region.

• Journal of Pharmaceutical Investigation
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• v.39 no.5
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• pp.345-351
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• 2009

Organic cation transporters (OCTs) are important for absorption, elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is located in a cluster on chromosome 6 and OCTs are in major organs such as intestine, liver, kidney, brain and placenta. Therefore, expression levels and function of OCTs directly affect plasma levels and intracellular concentrations of drugs and thereby determine therapeutic response. The aim of this study was to investigate the frequency of the SNPs on OCT1 (C181T and C1022T) and OCT2 (G808T) to analyze haplotype frequency in healthy Korean population. Human subjects have been genotyped for OCT1 (C181T for 195 subjects and C1022T for 825 subjects), using polymerase chain reaction-based diagnostic tests (RFLP). And for OCT2 (G808T), a total of 861 subjects have been genotyped, using pyrosequencing method. Haplotype was statistically inferred using an algorithm based on the expectation-maximization (EM). OCT1 C181T genotyping showed 100% homozygous wild-type (C/C). OCT1 C1022T genotyping showed wild-type (C/C), heterozygous (C/T) and homozygous mutant-type (T/T) and each accounted for 72.1, 24.5 and 3.4%, respectively. OCT2 G808T genotyping results also showed homozygous wild-type (G/G), heterozygous (G/T) and homozygous mutant-type (T/T) and each took 81.8, 17.9 and 0.3%, respectively. Based on these genotype data, haplotype analysis between OCT1 C181T and OCT1 C1022T has proceeded. The result has revealed that linkage disequilibrium between alleles is not obvious (P=0.0122).

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1127-1133
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• 2018

Objective: Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods: A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following genome-wide rapid association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results: A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively. Genome wide significant variants were located on the same region of swine chromosome 14 (SSC14) that spanned from 120 to 124 Mb. Top SNP ALGA008191 was located at 5 kb near the stearoyl-CoA desaturase (SCD) gene. This gene is directly involved in desaturation of stearic acid into oleic acid. General relationship of significant SNPs showed high linkage disequilibrium thus genome-wide signals was attributed to SCD gene. However, understanding the role of other genes like elongation of very long chain fatty acids-3 (ELOVL3) located on this chromosomal segment might help in further understanding of metabolism and biosynthesis of fatty acids. Conclusion: Overall, this study provides evidence that validates SCD gene as strong candidate gene associated with fatty acid composition in Duroc pigs. Moreover, this study confirms significant SNPs near ELOVL3 gene.

• Animal cells and systems
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• v.16 no.4
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• pp.321-328
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• 2012

The oily bittering Acheilognathus koreensis is a freshwater species that is endemic to Korea and is experiencing severe declines in natural populations as a result of habitat fragmentation and water pollution. For the conservation and restoration of this species, it is necessary to assess its genetic diversity at the population level. We developed 13 polymorphic microsatellite loci that were used to analyze the genetic diversity of two populations collected from the Kum River and the Tamjin River in Korea. All loci exhibited Mendelian inheritance patterns when examined in controlled crosses. Both populations revealed high levels of variability, with the number of alleles ranging from 3 to 20 and observed and expected heterozygosities ranging from 0.500 to 0.969 and from 0.529 to 0.938, respectively. None of the loci showed significant deviation from Hardy-Weinberg equilibrium, and one pair of loci showed significant linkage disequilibrium after Bonferroni correction. Pairwise $F_{ST}$ and genetic distance estimation showed significant differences between two populations. These results suggest that the microsatellites developed herein can be used to study the genetic diversity, population structure and conservation measure of A. koreensis.

• Animal cells and systems
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• v.15 no.1
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• pp.37-43
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• 2011

The Korean freshwater crayfish, Cambaroides similis, has recently suffered from range reduction and habitat degradation caused by environmental changes and water pollution. For the conservation and restoration of this species, it is necessary to understand the current population structures of Korean C. similis using estimation of their genetic variation. In this study, eight micro satellite loci were developed and characterized from 49 individuals collected from four locations: one population from Mt. Bukhan (BH) and three populations from Mt. Gwanak (GA) in Seoul, Korea. As a result, the number of alleles per locus ranged from 2 to 12. The observed heterozygosities and expected heterozygosities ranged from 0.000 to 0.833 and from 0.125 to 0.943, respectively, and the former values were significantly lower than the latter ones expected under the Hardy-Weinberg equilibrium. No significant linkage disequilibrium was revealed between any of the locus pairs after Bonferroni correction. From the pairwise Fst results over all samples, higher differentiation between GA-BH population pairs (mean 0.1789) was observed than between GA population pairs (mean 0.0454). This was also supported by Mantel's test showing that the genetic distances of these crayfish populations were significantly correlated with geographic distances. This result may show the regional differentiation caused by restricted gene flow between northern (BH) and southern (GA) populations within Seoul. These micro satellite markers have the potential for use in analyses of the genetic diversity and population structure of C. similis species, with implications for its conservation and management plans.

• Journal of Preventive Medicine and Public Health
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• v.42 no.1
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• pp.1-4
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• 2009

Objectives : Isolated cleft lip with or without cleft palate(CL/P) is among the most common human birth defects, with a prevalence of approximately 1 in 700 live births. The B-Cell Leukemia/lymphoma 3(BCL3) gene has been suggested as a candidate gene for CL/P based on association and linkage studies in some populations. This study tests for an association between markers in BCL3 and isolated, non-syndromic CL/P using a case-parent trio design, while considering parent-of-origin effects. Methods : Forty case-parent trios were genotyped for two single nucleotide polymorphisms(SNPs) in the BCL3 gene. We performed a transmission disequilibrium test(TDT) on individual SNPs, and the FAMHAP package was used to estimate haplotype frequencies and to test for excess transmission of multi-SNP haplotypes. Results : The odds ratio for transmission of the minor allele, OR(transmission), was significant for SNP rs8100239(OR=3.50, p=0.004) and rs2965169(OR=2.08, p=0.027) when parent-of-origin was not considered. Parentspecific TDT revealed that SNP rs8100239 showed excess maternal transmission. Analysis of haplotypes of rs2965169 and rs8100239 also suggested excess maternal transmission. Conclusions : BCL3 appears to influence risk of CL/P through a parent-of-origin effect with excess maternal transmission.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.3
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• pp.341-349
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• 2019

Objective: Internal organs indirectly affect economic performance and well-being of animals. Study of internal organs during later layer period will allow full utilization of layer hens. Hence, we conducted a genome-wide association study (GWAS) to identify potential quantitative trait loci or genes that potentially contribute to internal organ weight. Methods: A total of 1,512 chickens originating from White Leghorn and Dongxiang Blue-Shelled chickens were genotyped using high-density Affymetrix 600 K single nucleotide polymorphism (SNP) array. We conducted a GWAS, linkage disequilibrium analysis, and heritability estimated based on SNP information by using GEMMA, Haploview and GCTA software. Results: Our results displayed that internal organ weights show moderate to high (0.283 to 0.640) heritability. Variance partitioned across chromosomes and chromosome lengths had a linear relationship for liver weight and gizzard weight ($R^2=0.493$, 0.753). A total of 23 highly significant SNPs that associated with all internal organ weights were mainly located on Gallus gallus autosome (GGA) 1 and GGA4. Six SNPs on GGA2 affected heart weight. After the final analysis, five top SNPs were in or near genes 5-Hydroxytryptamine receptor 2A, general transcription factor IIF polypeptide 2, WD repeat and FYVE domain containing 2, non-SMC condensin I complex subunit G, and sonic hedgehog, which were considered as candidate genes having a pervasive role in internal organ weights. Conclusion: Our findings provide an understanding of the underlying genetic architecture of internal organs and are beneficial in the selection of chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.5
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• pp.607-613
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• 2019

Objective: Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods: We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results: A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion: These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.

• Genomics & Informatics
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• v.19 no.4
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• pp.37.1-37.7
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• 2021

Genome-wide association studies (GWASs) facilitated the discovery of countless disease-associated variants. However, GWASs have mostly been conducted in European ancestry samples. Recent studies have reported that these European-based association results may reduce disease prediction accuracy when applied in non-Europeans. Therefore, previously reported variants should be validated in non-European populations to establish reliable scientific evidence for precision medicine. In this study, we validated known associations with type 2 diabetes (T2D) and related metabolic traits in 125,850 samples from a Korean population genotyped by the Korea Biobank Array (KBA). At the end of December 2020, there were 8,823 variants associated with glycemic traits, lipids, liver enzymes, and T2D in the GWAS catalog. Considering the availability of imputed datasets in the KBA genome data, publicly available East Asian T2D summary statistics, and the linkage disequilibrium among the variants (r² < 0.2), 2,900 independent variants were selected for further analysis. Among these, 1,837 variants (63.3%) were statistically significant (p ≤ 0.05). Most of the non-replicated variants (n = 1,063) showed insufficient statistical power and decreased minor allele frequencies compared with the replicated variants. Moreover, most of known variants showed <10% genetic heritability. These results could provide valuable scientific evidence for future study designs, the current power of GWASs, and future applications in precision medicine in the Korean population.